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[
    {
        "creation_date": "2019-08-08",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000041-a-1",
        "publish_date": "2019-08-08",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study infers the activity of variants in Src kinases's catalytic domain by measuring their effects on yeast growth, and therefore phosphotransferase activity. The resulting dataset includes variants classified as gain of function, loss of function. or neutral.",
        "method_text": "Variant scores were calculated using Enrich2 weighted least squares regression and wild-type normalization. The `activity_score` is `-1 * score`, because negative scores indicate depletion in the population, which is associated with higher kinase activity.\r\n\r\nVariants were classified as \"gain of function\" \"neutral\" or \"loss of function\" based on whether they were within +/- 2 standard deviations of the mean score of synonymous variants (variants with wild type amino acid sequence). These categories are denoted by 1, 0, or -1 in the table respectively.",
        "short_description": "Amino acid scores for deep mutational scan of the Src kinase catalytic domain.",
        "title": "Amino acid scores for Src CD",
        "keywords": [
            {
                "text": "subassembly"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "kinase"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "Enrich2"
            },
            {
                "text": "NNK mutagenesis"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30956043",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30956043",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Src catalytic domain",
            "reference_sequence": {
                "sequence": "CTGCGGCTGGAGGTCAAGCTGGGCCAGGGCTGCTTTGGCGAGGTGTGGATGGGGACCTGGAACGGTACCACCAGGGTGGCCATCAAAACCCTGAAGCCTGGCACGATGTCTCCAGAGGCCTTCCTGCAGGAGGCCCAGGTCATGAAGAAGCTGAGGCATGAGAAGCTGGTGCAGTTGTATGCTGTGGTTTCAGAGGAGCCCATTTACATCGTCACGGAGTACATGAGCAAGGGGAGTTTGCTGGACTTTCTCAAGGGGGAGACAGGCAAGTACCTGCGGCTGCCTCAGCTGGTGGACATGGCTGCTCAGATCGCCTCAGGCATGGCGTACGTGGAGCGGATGAACTACGTCCACCGGGACCTTCGTGCAGCCAACATCCTGGTGGGAGAGAACCTGGTGTGCAAAGTGGCCGACTTTGGGCTGGCTCGGCTCATTGAAGACAATGAGTACACGGCGCGGCAAGGTGCCAAATTCCCCATCAAGTGGACGGCTCCAGAAGCTGCCCTCTATGGCCGCTTCACCATCAAGTCGGACGTGTGGTCCTTCGGGATCCTGCTGACTGAGCTCACCACAAAGGGACGGGTGCCCTACCCTGGGATGGTGAACCGCGAGGTGCTGGACCAGGTGGAGCGGGGCTACCGGATGCCCTGCCCGCCGGAGTGTCCCGAGTCCCTGCACGACCTCATGTGCCAGTGCTGGCGGAAGGAGCCTGAGGAGCGGCCCACCTTCGAGTACCTGCAGGCCTTCCTG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 269,
                "identifier": "P12931",
                "url": "http://purl.uniprot.org/uniprot/P12931",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000041-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "std",
            "epsilon",
            "activity_score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000041-a-1",
        "variant_count": 3506,
        "experiment": "urn:mavedb:00000041-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-11-11",
        "modification_date": "2020-11-11",
        "urn": "urn:mavedb:00000048-a-1",
        "publish_date": "2020-11-11",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilised site-saturation mutagenesis (SSM) to measure the functional consequences of mutations in the human chemokine receptor, CXCR4 and to map ligand interaction sites. Cells were selected for CXCR4 surface expression.",
        "method_text": "Data obtained from sorting cells for anti-myc staining was analysed using Enrich (version unspecified). Log2 enrichment ratios were calculated and normalised by subtracting the frequency of the WT sequence.  Log2 enrichment ratios for four replicates (two replicates each for two tags) were averaged to obtain variant scores. Note that the scores here were not reported in the manuscript tables, but were calculated from the replicate enrichment ratios that were reported.",
        "short_description": "Deep mutational scan selecting for cell surface expression of CXCR4 in Expi293F cells.",
        "title": "CXCR4 surface expression",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29678950",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29678950",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23827138",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23827138",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-6681-7994"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "CXCR4",
            "reference_sequence": {
                "sequence": "GAGGGGATCAGTATATACACTTCAGATAACTACACCGAGGAAATGGGCTCAGGGGACTATGACTCCATGAAGGAACCCTGTTTCCGTGAAGAAAATGCTAATTTCAATAAAATCTTCCTGCCCACCATCTACTCCATCATCTTCTTAACTGGCATTGTGGGCAATGGATTGGTCATCCTGGTCATGGGTTACCAGAAGAAACTGAGAAGCATGACGGACAAGTACAGGCTGCACCTGTCAGTGGCCGACCTCCTCTTTGTCATCACGCTTCCCTTCTGGGCAGTTGATGCCGTGGCAAACTGGTACTTTGGGAACTTCCTATGCAAGGCAGTCCATGTCATCTACACAGTCAACCTCTACAGCAGTGTCCTCATCCTGGCCTTCATCAGTCTGGACCGCTACCTGGCCATCGTCCACGCCACCAACAGTCAGAGGCCAAGGAAGCTGTTGGCTGAAAAGGTGGTCTATGTTGGCGTCTGGATCCCTGCCCTCCTGCTGACTATTCCCGACTTCATCTTTGCCAACGTCAGTGAGGCAGATGACAGATATATCTGTGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATCATGGTTGGCCTTATCCTGCCTGGTATTGTCATCCTGTCCTGCTATTGCATTATCATCTCCAAGCTGTCACACTCCAAGGGCCACCAGAAGCGCAAGGCCCTCAAGACCACAGTCATCCTCATCCTGGCTTTCTTCGCCTGTTGGCTGCCTTACTACATTGGGATCAGCATCGACTCCTTCATCCTCCTGGAAATCATCAAGCAAGGGTGTGAGTTTGAGAACACTGTGCACAAGTGGATTTCCATCACCGAGGCCCTAGCTTTCTTCCACTGTTGTCTGAACCCCATCCTCTATGCTTTCCTTGGAGCCAAATTTAAAACCTCTGCCCAGCACGCACTCACCTCTGTGAGCAGAGGGTCCAGCCTCAAGATCCTCTCCAAAGGAAAGCGAGGTGGACATTCATCTGTTTCCACTGAGTCTGAGTCTTCAAGTTTTCACTCCAGC",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 1,
                "identifier": "P61073",
                "url": "http://purl.uniprot.org/uniprot/P61073",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000048-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "rep1_anti-myc-FITC",
            "rep2_anti-myc-FITC",
            "rep1_anti-myc-Alexa",
            "rep2_anti-myc-Alexa"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000048-a-1",
        "variant_count": 7021,
        "experiment": "urn:mavedb:00000048-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-09-16",
        "urn": "urn:mavedb:00000068-b-1",
        "publish_date": "2021-09-16",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors leveraged CRISPR-Cas9 technique to construct cell lines without wild type TP53 expression (p53NULL) in A549 human lung carcinoma. These cell lines are later transferred with p53 mutant library in order to study the function of these variants. This study used nutlin-3 which interrupts a negative regulator of p53 during the selection process.",
        "method_text": "Variant counts before and after selection are determined by Hiseq4000 which was further processed by ORFcall software. The logarithm (base 2) ratio of counts after and before selection is first calculated. This values is then normalized by all non-wildtype residues and synonymous variants. The Z scores are calculated by the averaged and standardized values between 2 replicates. This paper was using an older version of TP53 reference sequence, and we are depositing the result according to their published data.",
        "short_description": "TP53 saturation mutagenesis screens with TP53 null cell line using nutlin-3 which interrupts a negative regulator of p53",
        "title": "Mutated p53 with nutlin-3",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.1038/s41588-018-0204-y",
                "url": "https://doi.org/10.1038/s41588-018-0204-y",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "30224644",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30224644",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TP53 (P72R)",
            "reference_sequence": {
                "sequence": "ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCGCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATGGGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACTCCAGTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCGCAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGCACTAAGCGAGCACTGCCCAACAACACCAGCTCCTCTCCCCAGCCAAAGAAGAAACCACTGGATGGAGAATATTTCACCCTTCAGATCCGTGGGCGTGAGCGCTTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGGAAGGAGCCAGGGGGGAGCAGGGCTCACTCCAGCCACCTGAAGTCCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAAACTCATGTTCAAGACAGAAGGGCCTGACTCAGACTAG",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000068-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000068-b-1",
        "variant_count": 8274,
        "experiment": "urn:mavedb:00000068-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-c-1",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\n\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Miconazole",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "alpha-synuclein",
            "reference_sequence": {
                "sequence": "ATGGATGTATTCATGAAAGGACTTTCAAAGGCCAAGGAGGGAGTTGTGGCTGCTGCTGAGAAAACCAAACAGGGTGTGGCAGAAGCAGCAGGAAAGACAAAAGAGGGTGTTCTCTATGTAGGCTCCAAAACCAAGGAGGGAGTGGTGCATGGTGTGGCAACAGTGGCTGAGAAGACCAAAGAGCAAGTGACAAATGTTGGAGGAGCAGTGGTGACGGGTGTGACAGCAGTAGCCCAGAAGACAGTGGAGGGAGCAGGGAGCATTGCAGCAGCCACTGGCTTTGTCAAAAAGGACCAGTTGGGCAAGAATGAAGAAGGAGCCCCACAGGAAGGAATTCTGGAAGATATGCCTGTGGATCCTGACAATGAGGCTTATGAAATGCCTTCTGAGGAAGGGTATCAAGACTACGAACCTGAAGCCTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P37840",
                "url": "http://purl.uniprot.org/uniprot/P37840",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg16",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.10",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000045-c-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000045-c-1",
        "variant_count": 2800,
        "experiment": "urn:mavedb:00000045-c",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000018-a-1",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {
            "chr": "11",
            "end": 5227208,
            "start": 5227022,
            "reference": "hg38"
        },
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "The effect of each variant was calculated using a multiple linear regression model based on the DNA counts and RNA counts. Each variant needed to have 10 unique barcode tags to be included in the downstream analyses.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>\r\n\r\nMetadata contains the genomic coordinates for the target sequence.\r\n\r\nColumn descriptions:\r\n\r\n- 'score' is the Log2 variant expression effect derived from the fit of the linear model (coefficient).\r\n- 'p-value' is the P-value of the coefficient.\r\n- 'unique_tags' is the number of unique tags associated with the variant.\r\n- 'dna_sequences' is the count of DNA sequences that contain the variant (used for fitting the linear model).\r\n- 'rna_sequences' is the count of RNA sequences that contain the variant (used for fitting the linear model).",
        "short_description": "Saturation mutagenesis MPRA of HBB promoter in HEL 92.1.7 cells.",
        "title": "Saturation mutagenesis MPRA of HBB promoter",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "HBB promoter",
            "reference_sequence": {
                "sequence": "GGTGTCTGTTTGAGGTTGCTAGTGAACACAGTTGTGTCAGAAGCAAATGTAAGCAATAGATGGCTCTGCCCTGACTTTTATGCCCAGCCCTGGCTCCTGCCCTCCCTGCTCCTGGGAGTAGATTGGCCAACCCTAGGGTGTGGCTCCACAGGGTGAGGTCTAAGTGATGACAGCCGTACCTGTCCTT",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000018-a-1",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "p-value",
            "unique_tags",
            "dna_sequences",
            "rna_sequences"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000018-a-1",
        "variant_count": 623,
        "experiment": "urn:mavedb:00000018-a",
        "is_meta_analysis": false,
        "data_usage_policy": "We are making our data available prior to publication in line with Fort Lauderdale principle, allowing others to use the data but allowing the data producers to make the first presentations and to publish the first paper with global analyses of the data. In addition, we also reserve the right to publish the first analysis of the differences seen in the TERT knock-down experiments and alternative cell-type experiments. Studies that do not overlap with these intentions may be submitted for publication at any time, but must appropriately cite the data source. After publication of the data, the first publication of the data producers should be cited for any use of these data."
    },
    {
        "creation_date": "2021-09-28",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-c-1",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "Each of the seven libraries was sequenced individually and analyzed separately using in-house Python scripts archived at https://github.com/elifesciences-publications/DMS-FastQ-processing.\r\n\r\nReads that had more than 20 base mismatches between forward and reverse reads were discarded. Merged reads with a posterior Q score of 10 were also discarded. Variants with an unexpectedly high error rate or mutations in more than one codon were also discarded.\r\n\r\nFitness scores were calculated as a ratio of frequency ratios:\r\n\r\n$$s_v = \\log_2\\left(\\frac{\\frac{f_{v, selected}}{f_{v, non-selected}}}{\\frac{f_{wt, selected}}{f_{wt, non-selected}}}\\right)$$\r\n\r\nThe mean fitness score of all synonymous variants in each library was subtracted from all variants in that library to normalize the scores between libraries.\r\n\r\nThe scores are the average of two replicates if the variant was scored in both replicates, otherwise the score given is the score from one replicate. Variants that were scored in both replicates have a standard deviation (SD) calculated from the two replicate scores.",
        "short_description": "Amino acid scores for deep mutational scan of VIM-2 metallo-β-lactamase at 128 µg/mL ampicillin at 37C",
        "title": "VIM-2 128 µg/mL AMP at 37C",
        "keywords": [
            {
                "text": "ampicillin"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "VIM-2 with p.Met1_Phe2insGly",
            "reference_sequence": {
                "sequence": "ATGGGATTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGCCCGCTCGCTTTTTCCGTAGATTCTAGCGGAGAATATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTTGAAGGACTTTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAATTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTTGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000073-c-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "SD"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000073-c-1",
        "variant_count": 5549,
        "experiment": "urn:mavedb:00000073-c",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-08-16",
        "modification_date": "2022-08-16",
        "urn": "urn:mavedb:00000099-a-1",
        "publish_date": "2022-08-16",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study presents a cell-based assay for functional characterization of variants of unknown significance (VUS) in rhodopsin (RHO). 210 previously-observed RHO variants were assayed for cell surface expression using a flow cytometry-based assay.",
        "method_text": "Variants were counted by identifying 20bp “probes” unique to each of the variants tested in the assay. Variants were counted using grep.\r\n\r\nThe score was calculated as: \r\n\r\n$$s_v = \\log_2 \\left( \\frac{\\frac{c_{v,high}}{c_{wt,high}} {\\frac{c_{v,low}}{c_{wt,low}} \\right)$$\r\n\r\nThree biological replicates were performed and used to calculate average scores and confidence intervals for each variant. Note that the confidence level chosen was not reported.\r\n\r\nResults from the single-plex RHO surface assay are also reported, as ‘single_plex_mean’ and ‘single_plex_stderr’.",
        "short_description": "Rhodopsin VUS surface expression",
        "title": "Rhodopsin surface expression",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30977563",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30977563",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "RHO",
            "reference_sequence": {
                "sequence": "ATGAATGGCACAGAAGGCCCTAACTTCTACGTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGATGAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": {
                "offset": 0,
                "identifier": "NM_000539.3",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_000539.3",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000099-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "ci_low",
            "ci_high",
            "single_plex_mean",
            "single_plex_stderr"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000099-a-1",
        "variant_count": 211,
        "experiment": "urn:mavedb:00000099-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2018-06-29",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-c-1",
        "publish_date": "2018-06-29",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957)",
        "method_text": "##Scoring procedure:\r\nDMS-TileSeq reads were processed using the [dmsPipeline](https://bitbucket.org/rothlabto/dmspipeline) software. Briefly, TileSeq read counts were used to establish relative allele frequencies in each condition. Non-mutagenized control counts were subtracted from counts (as estimates of sequencing error). log ratios of selection over non-selection counts were calculated. The resulting TileSeq fitness values were then normalized to 0-1 scale where 0 corresponds to the median nonsense score and 1 corresponds to the median synonymous score. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for more details.",
        "short_description": "A Deep Mutational Scan of human Calmodulin using functional complementation in yeast via DMS-TileSeq.",
        "title": "Human Calmodulin DMS-TileSeq",
        "keywords": [
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29269382",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29269382",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "CALM1",
            "reference_sequence": {
                "sequence": "ATGGCTGATCAGCTGACCGAAGAACAGATTGCTGAATTCAAGGAAGCCTTCTCCCTATTTGATAAAGATGGCGATGGCACCATCACAACAAAGGAACTTGGAACTGTCATGAGGTCACTGGGTCAGAACCCAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGTAATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAATGAAAGATACAGATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTGACAAGGATGGCAATGGTTATATCAGTGCAGCAGAACTACGTCACGTCATGACAAACTTAGGAGAAAAACTAACAGATGAAGAAGTAGATGAAATGATCAGAGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAAGAATTCGTACAGATGATGACTGCAAAATGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P0DP23",
                "url": "http://purl.uniprot.org/uniprot/P0DP23",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000198668",
                "url": "http://www.ensembl.org/id/ENSG00000198668",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 833,
                "identifier": "NM_001363670.1",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_001363670.1",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000001-c-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "se"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000001-c-1",
        "variant_count": 5957,
        "experiment": "urn:mavedb:00000001-c",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-27",
        "modification_date": "2020-11-20",
        "urn": "urn:mavedb:00000049-a-3",
        "publish_date": "2020-11-20",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "A deep mutational scan of human MTHFR via functional complementation in yeast at 100ug/ml folate in A222V background",
        "title": "MTHFR at 100ug/ml folate in A222V background",
        "keywords": [
            {
                "text": "imputation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "homocystinuria"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1628-9390",
            "0000-0002-9219-4310",
            "0000-0002-2550-2141",
            "0000-0001-6465-5776"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MTHFR",
            "reference_sequence": {
                "sequence": "ATGGTGAACGAAGCCAGAGGAAACAGCAGCCTCAACCCCTGCTTGGAGGGCAGTGCCAGCAGTGGCAGTGAGAGCTCCAAAGATAGTTCGAGATGTTCCACCCCGGGCCTGGACCCCGAGCGGCATGAGAGACTCCGGGAGAAGATGAGGCGGCGATTGGAATCTGGTGACAAGTGGTTCTCCCTGGAATTCTTCCCTCCTCGAACTGCTGAGGGAGCTGTCAATCTCATCTCAAGGTTTGACCGGATGGCAGCAGGTGGCCCCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCCTGGCTCAGACAAGGAGACCTCCTCCATGATGATCGCCAGCACCGCCGTGAACTACTGTGGCCTGGAGACCATCCTGCACATGACCTGCTGCCGTCAGCGCCTGGAGGAGATCACGGGCCATCTGCACAAAGCTAAGCAGCTGGGCCTGAAGAACATCATGGCGCTGCGGGGAGACCCAATAGGTGACCAGTGGGAAGAGGAGGAGGGAGGCTTCAACTACGCAGTGGACCTGGTGAAGCACATCCGAAGTGAGTTTGGTGACTACTTTGACATCTGTGTGGCAGGTTACCCCAAAGGCCACCCCGAAGCAGGGAGCTTTGAGGCTGACCTGAAGCACTTGAAGGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGCTTTTCTTTGAGGCTGACACATTCTTCCGCTTTGTGAAGGCATGCACCGACATGGGCATCACTTGCCCCATCGTCCCCGGGATCTTTCCCATCCAGGGCTACCACTCCCTTCGGCAGCTTGTGAAGCTGTCCAAGCTGGAGGTGCCACAGGAGATCAAGGACGTGATTGAGCCAATCAAAGACAACGATGCTGCCATCCGCAACTATGGCATCGAGCTGGCCGTGAGCCTGTGCCAGGAGCTTCTGGCCAGTGGCTTGGTGCCAGGCCTCCACTTCTACACCCTCAACCGCGAGATGGCTACCACAGAGGTGCTGAAGCGCCTGGGGATGTGGACTGAGGACCCCAGGCGTCCCCTACCCTGGGCTCTCAGCGCCCACCCCAAGCGCCGAGAGGAAGATGTACGTCCCATCTTCTGGGCCTCCAGACCAAAGAGTTACATCTACCGTACCCAGGAGTGGGACGAGTTCCCTAACGGCCGCTGGGGCAATTCCTCTTCCCCTGCCTTTGGGGAGCTGAAGGACTACTACCTCTTCTACCTGAAGAGCAAGTCCCCCAAGGAGGAGCTGCTGAAGATGTGGGGGGAGGAGCTGACCAGTGAAGAAAGTGTCTTTGAAGTCTTCGTTCTTTACCTCTCGGGAGAACCAAACCGGAATGGTCACAAAGTGACTTGCCTGCCCTGGAACGATGAGCCCCTGGCGGCTGAGACCAGCCTGCTGAAGGAGGAGCTGCTGCGGGTGAACCGCCAGGGCATCCTCACCATCAACTCACAGCCCAACATCAACGGGAAGCCGTCCTCCGACCCCATCGTGGGCTGGGGCCCCAGCGGGGGCTATGTCTTCCAGAAGGCCTACTTAGAGTTTTTCACTTCCCGCGAGACAGCGGAAGCACTTCTGCAAGTGCTGAAGAAGTACGAGCTCCGGGTTAATTACCACCTTGTCAATGTGAAGGGTGAAAACATCACCAATGCCCCTGAACTGCAGCCGAATGCTGTCACTTGGGGCATCTTCCCTGGGCGAGAGATCATCCAGCCCACCGTAGTGGATCCCGTCAGCTTCATGTTCTGGAAGGACGAGGCCTTTGCCCTGTGGATTGAGCGGTGGGGAAAGCTGTATGAGGAGGAGTCCCCGTCCCGCACCATCATCCAGTACATCCACGACAACTACTTCCTGGTCAACCTGGTGGACAATGACTTCCCACTGGACAACTGCCTCTGGCAGGTGGTGGAAGACACATTGGAGCTTCTCAACAGGCCCACCCAGAATGCGAGAGAAACGGAGGCTCCATGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P42898",
                "url": "http://purl.uniprot.org/uniprot/P42898",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000177000",
                "url": "http://www.ensembl.org/id/ENSG00000177000",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 230,
                "identifier": "NM_005957",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_005957",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000049-a-3",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "se",
            "exp.score",
            "exp.se",
            "df",
            "pred.score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000049-a-3",
        "variant_count": 13690,
        "experiment": "urn:mavedb:00000049-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-08-07",
        "modification_date": "2019-08-07",
        "urn": "urn:mavedb:00000039-a-4",
        "publish_date": "2019-08-07",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effects of yeast HSP90 variants under the control of different promoters to explore the relationship between protein sequence and expression level. The results showed that reduced expression level (compared to wild-type expression) revealed new partial loss of function mutations.",
        "method_text": "Growth rates were calculated for each variant and converted into selection coefficients. The selection coefficient for each variant under control of this promoter/UTR combination is reported as the score. For variants with multiple synonymous codons, the reported coefficient is the average of all synonymous variant's selection coefficients.\r\n\r\nVariants annotated as \"null-like\" have a score of -1.",
        "short_description": "Deep mutational scan of all single mutants in a nine-amino acid region of Hsp90 (Hsp82) in Saccharomyces cerevisiae under the control of the CYC promoter, no 3'UTR added.",
        "title": "Deep mutational scan of HSP90, CYCdter construct",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "promoter"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23825969",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23825969",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "HSP90",
            "reference_sequence": {
                "sequence": "CAATTTGGTTGGTCTGCTAATATGGAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 581,
                "identifier": "P02829",
                "url": "http://purl.uniprot.org/uniprot/P02829",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000039-a-4",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000039-a-4",
        "variant_count": 189,
        "experiment": "urn:mavedb:00000039-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-10-16",
        "modification_date": "2020-11-25",
        "urn": "urn:mavedb:00000050-a-1",
        "publish_date": "2020-11-25",
        "created_by": "0000-0002-6145-882X",
        "modified_by": "0000-0002-6145-882X",
        "extra_metadata": {},
        "abstract_text": "Loss-of-function scores for MSH2 variants in human MSH2- HAP1 cells.",
        "method_text": "Scores represent the log2-scaled enrichment of each MSH2 variant after selection with 6-TG compared with mock selection, averaged over three replicates.  Positive scores correspond to loss-of-function and negative scores correspond to functionally neutral variants.",
        "short_description": "MSH2 loss-of-function (LOF) scores in human HAP1 cells.",
        "title": "MSH2 LOF scores (HAP1)",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6145-882X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MSH2",
            "reference_sequence": {
                "sequence": "ATGGCGGTGCAGCCGAAGGAGACGCTGCAGTTGGAGAGCGCGGCCGAGGTCGGCTTCGTGCGCTTCTTTCAGGGCATGCCGGAGAAGCCGACCACCACAGTGCGCCTTTTCGACCGGGGCGACTTCTATACGGCGCACGGCGAGGACGCGCTGCTGGCCGCCCGGGAGGTGTTCAAGACCCAGGGGGTGATCAAGTACATGGGGCCGGCAGGAGCAAAGAATCTGCAGAGTGTTGTGCTTAGTAAAATGAATTTTGAATCTTTTGTAAAAGATCTTCTTCTGGTTCGTCAGTATAGAGTTGAAGTTTATAAGAATAGAGCTGGAAATAAGGCATCCAAGGAGAATGATTGGTATTTGGCATATAAGGCTTCTCCTGGCAATCTCTCTCAGTTTGAAGACATTCTCTTTGGTAACAATGATATGTCAGCTTCCATTGGTGTTGTGGGTGTTAAAATGTCCGCAGTTGATGGCCAGAGACAGGTTGGAGTTGGGTATGTGGATTCCATACAGAGGAAACTAGGACTGTGTGAATTCCCTGATAATGATCAGTTCTCCAATCTTGAGGCTCTCCTCATCCAGATTGGACCAAAGGAATGTGTTTTACCCGGAGGAGAGACTGCTGGAGACATGGGGAAACTGAGACAGATAATTCAAAGAGGAGGAATTCTGATCACAGAAAGAAAAAAAGCTGACTTTTCCACAAAAGACATTTATCAGGACCTCAACCGGTTGTTGAAAGGCAAAAAGGGAGAGCAGATGAATAGTGCTGTATTGCCAGAAATGGAGAATCAGGTTGCAGTTTCATCACTGTCTGCGGTAATCAAGTTTTTAGAACTCTTATCAGATGATTCCAACTTTGGACAGTTTGAACTGACTACTTTTGACTTCAGCCAGTATATGAAATTGGATATTGCAGCAGTCAGAGCCCTTAACCTTTTTCAGGGTTCTGTTGAAGATACCACTGGCTCTCAGTCTCTGGCTGCCTTGCTGAATAAGTGTAAAACCCCTCAAGGACAAAGACTTGTTAACCAGTGGATTAAGCAGCCTCTCATGGATAAGAACAGAATAGAGGAGAGATTGAATTTAGTGGAAGCTTTTGTAGAAGATGCAGAATTGAGGCAGACTTTACAAGAAGATTTACTTCGTCGATTCCCAGATCTTAACCGACTTGCCAAGAAGTTTCAAAGACAAGCAGCAAACTTACAAGATTGTTACCGACTCTATCAGGGTATAAATCAACTACCTAATGTTATACAGGCTCTGGAAAAACATGAAGGAAAACACCAGAAATTATTGTTGGCAGTTTTTGTGACTCCTCTTACTGATCTTCGTTCTGACTTCTCCAAGTTTCAGGAAATGATAGAAACAACTTTAGATATGGATCAGGTGGAAAACCATGAATTCCTTGTAAAACCTTCATTTGATCCTAATCTCAGTGAATTAAGAGAAATAATGAATGACTTGGAAAAGAAGATGCAGTCAACATTAATAAGTGCAGCCAGAGATCTTGGCTTGGACCCTGGCAAACAGATTAAACTGGATTCCAGTGCACAGTTTGGATATTACTTTCGTGTAACCTGTAAGGAAGAAAAAGTCCTTCGTAACAATAAAAACTTTAGTACTGTAGATATCCAGAAGAATGGTGTTAAATTTACCAACAGCAAATTGACTTCTTTAAATGAAGAGTATACCAAAAATAAAACAGAATATGAAGAAGCCCAGGATGCCATTGTTAAAGAAATTGTCAATATTTCTTCAGGCTATGTAGAACCAATGCAGACACTCAATGATGTGTTAGCTCAGCTAGATGCTGTTGTCAGCTTTGCTCACGTGTCAAATGGAGCACCTGTTCCATATGTACGACCAGCCATTTTGGAGAAAGGACAAGGAAGAATTATATTAAAAGCATCCAGGCATGCTTGTGTTGAAGTTCAAGATGAAATTGCATTTATTCCTAATGACGTATACTTTGAAAAAGATAAACAGATGTTCCACATCATTACTGGCCCCAATATGGGAGGTAAATCAACATATATTCGACAAACTGGGGTGATAGTACTCATGGCCCAAATTGGGTGTTTTGTGCCATGTGAGTCAGCAGAAGTGTCCATTGTGGACTGCATCTTAGCCCGAGTAGGGGCTGGTGACAGTCAATTGAAAGGAGTCTCCACGTTCATGGCTGAAATGTTGGAAACTGCTTCTATCCTCAGGTCTGCAACCAAAGATTCATTAATAATCATAGATGAATTGGGAAGAGGAACTTCTACCTACGATGGATTTGGGTTAGCATGGGCTATATCAGAATACATTGCAACAAAGATTGGTGCTTTTTGCATGTTTGCAACCCATTTTCATGAACTTACTGCCTTGGCCAATCAGATACCAACTGTTAATAATCTACATGTCACAGCACTCACCACTGAAGAGACCTTAACTATGCTTTATCAGGTGAAGAAAGGTGTCTGTGATCAAAGTTTTGGGATTCATGTTGCAGAGCTTGCTAATTTCCCTAAGCATGTAATAGAGTGTGCTAAACAGAAAGCCCTGGAACTTGAGGAGTTTCAGTATATTGGAGAATCGCAAGGATATGATATCATGGAACCAGCAGCAAAGAAGTGCTATCTGGAAAGAGAGCAAGGTGAAAAAATTATTCAGGAGTTCCTGTCCAAGGTGAAACAAATGCCCTTTACTGAAATGTCAGAAGAAAACATCACAATAAAGTTAAAACAGCTAAAAGCTGAAGTAATAGCAAAGAATAATAGCTTTGTAAATGAAATCATTTCACGAATAAAAGTTACTACGTGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P43246",
                "url": "http://purl.uniprot.org/uniprot/P43246",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": {
                "offset": 0,
                "identifier": "NP_000242.1",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_000242.1",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000050-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000050-a-1",
        "variant_count": 17746,
        "experiment": "urn:mavedb:00000050-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-i-1",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "Samples are collected after 72h and sequenced by Illumina. The counts for each variant is first added by 1, then divided by total sequence counts at this time point to calculate variant frequency. The functional score equals the division of a variant frequency at this time point and its frequency in initial library. Further normalizing the functional scores by wild type scores will give the relative enrichment values. The score data includes scores from three replicates which are suffixed by: _rep1, _rep2 & _rep3. The final score is the median of them.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 72h",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "RAF",
            "reference_sequence": {
                "sequence": "TCTAAGACAAGCAACACTATCCGTGTTTTCTTGCCGAACAAGCAAAGAACAGTGGTCAATGTGCGAAATGGAATGAGCTTGCATGACTGCCTTATGAAAGCACTCAAGGTGAGGGGC",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 51,
                "identifier": "P04049",
                "url": "http://purl.uniprot.org/uniprot/P04049",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000061-i-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_rep1",
            "score_rep2",
            "score_rep3"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000061-i-1",
        "variant_count": 298,
        "experiment": "urn:mavedb:00000061-i",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-01",
        "modification_date": "2021-10-01",
        "urn": "urn:mavedb:00000077-a-1",
        "publish_date": "2021-10-01",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study determined the effect of amino acid substitutions on cohesin-dockerin binding using deep mutational scanning. Cohesins from *Clostridium thermocellum* and *Clostridium cellulolyticum* were analyzed using yeast display.",
        "method_text": "Sequencing data was processed using Enrich v0.2 and custom scripts. The fitness score $\\zeta_i$ for FACS data is described in Kowalsky et al. 2015 and as follows. $\\epsilon_i$ is the enrichment ratio of variant $i$, $\\epsilon_{wt}$ is the wild-type enrichment ratio, $\\sigma$ is the standard deviation of the population and $\\phi$ is the percentage of cells collected in the gating population.\r\n\r\n$$\\zeta_i = \\log_2 (e) \\sqrt{2} \\sigma^{\\prime} [erf ^{-1} (1 - \\phi 2^{(\\epsilon_{wt} + 1)} - erf ^{-1} (1 - \\phi 2^{(\\epsilon_{i} + 1)}]$$\r\n\r\nThe fitness score is listed as the score, and the raw $\\log_2$ ratios are also included.",
        "short_description": "Deep mutational scan of C. cellulolyticum cohesin binding affinity for dockerin.",
        "title": "C. cellulolyticum cohesin binding affinity",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "27699856",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27699856",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "25790064",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25790064",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-3537-3865"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "C. cellulolyticum cohesin fragment",
            "reference_sequence": {
                "sequence": "MASDGVVVEIGKVTGSVGTTVEIPVYFRGVPSKGIANCDFVFRYDPNVLEIIGIDPGDIIVDPNPTKSFDTAIYPDRKIIVFLFAEDSGTGAYAITKDGVFAKIRATVKSSAPGYITFDEVGGFADNDLVEQKVSFIDGGVNVGNATPTKGATPTNTATPTK",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000077-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_err",
            "log2_ratio",
            "log2_ratio_err"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000077-a-1",
        "variant_count": 3145,
        "experiment": "urn:mavedb:00000077-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-b-1",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes a sequence similar to an SRSF1 (ASF/SF2) binding site.",
        "method_text": "Reads were filtered by accepting only those that had an unmutated 6nt stretch at the end of the read and had no mutations other than those that were designed. FASTQ quality scores were not used.\r\n\r\nThe sum of the reads in each of the two replicate transfections was used to calculate the scores, defined as the ratio of RNA read count to DNA read count (called the Enrichment Index, or EI).\r\n\r\nThe score reported here is the “LEIsc”, which is $log_2 EI$ re-scaled from -1 to +1 with the target sequence at 0, which enables easier comparison between the different 6-mers tested in the study.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, similar to an SRSF1 (ASF/SF2) binding site.",
        "title": "Exonic splicing for SRSF1 (ASF/SF2) binding site",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Minigene exon - SRSF1 (ASF/SF2) binding site",
            "reference_sequence": {
                "sequence": "AGTTGAAGAAGGGAGCTCCAGCACAGTGAAATGGACAGAAGGGCAGAGCAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000083-b-1",
            "type": "Other noncoding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "EI"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000083-b-1",
        "variant_count": 556,
        "experiment": "urn:mavedb:00000083-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-02-24",
        "modification_date": "2022-05-15",
        "urn": "urn:mavedb:00000094-a-5",
        "publish_date": "2022-05-15",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "V1/2 of co-expressing 915  current-reduced variants with WT.",
        "method_text": "V1/2 of co-expressing 915  current-reduced variants with WT.",
        "short_description": "4. V1/2 of co-expressing 915  current-reduced variants with WT.",
        "title": "V1/2 of co-expressing 915  current-reduced variants with WT",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ4",
            "reference_sequence": {
                "sequence": "MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGGGSPRRLGLLGSPLPPGAPLPGPGSGSGSACGQRSSAAHKRYRRLQNWVYNVLERPRGWAFVYHVFIFLLVFSCLVLSVLSTIQEHQELANECLLILEFVMIVVFGLEYIVRVWSAGCCCRYRGWQGRFRFARKPFCVIDFIVFVASVAVIAAGTQGNIFATSALRSMRFLQILRMVRMDRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLVYLAEKDANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAGILGSGFALKVQEQHRQKHFEKRRMPAANLIQAAWRLYSTDMSRAYLTATWYYYDSILPSFRELALLFEHVQRARNGGLRPLEVRRAPVPDGAPSRYPPVATCHRPGSTSFCPGESSRMGIKDRIRMGSSQRRTGPSKQHLAPPTMPTSPSSEQVGEATSPTKVQKSWSFNDRTRFRASLRLKPRTSAEDAPSEEVAEEKSYQCELTVDDIMPAVKTVIRSIRILKFLVAKRKFKETLRPYDVKDVIEQYSAGHLDMLGRIKSLQTRVDQIVGRGPGDRKAREKGDKGPSDAEVVDEISMMGRVVKVEKQVQSIEHKLDLLLGFYSRCLRSGTSASLGAVQVPLFDPDITSDYHSPVDHEDISVSAQTLSISRSVSTNMD",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-5",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000094-a-5",
        "variant_count": 915,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-09-30",
        "modification_date": "2019-10-08",
        "urn": "urn:mavedb:00000043-a-2",
        "publish_date": "2019-10-08",
        "created_by": "0000-0001-7684-5841",
        "modified_by": "0000-0001-7684-5841",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "The DMS library was encoded in the retroviral expression system pMX-GW-PGK-PuroR-GFP. Each codon for amino acid positions 488-516 of the human TpoR protein, encompassing the TM and partial JM regions, was independently randomised using degenerate (NNN) primers (IDT) to encode all 64 possible codons. Plasmid preparations for all positions (488-516) were pooled together in equal amounts to obtain a library containing all 1,856 possible DNA variants. The frequencies of variants in each library were determined by Illumina sequencing, which confirmed 100% representation across the randomised region.\r\n\r\nThe library was transfected into HEK293T cells along with retroviral packaging vectors using calcium phosphate transfection. After 48 hrs, supernatants containing virus were harvested and sterile filtered for transduction into Ba/F3 cells.  The pooled retroviral library was used to transduce 10^6 Ba/F3 cells at a multiplicity of infection ~0.1, generating ~10^5 transductants for each of six biological replicates. These six cultures were treated with 5 μg/ml puromycin (on IL-3) for 48 hours to yield pure virus-positive cells. Cells for each replicate were split in half and cultured in the continued presence of IL-3, or were washed to remove IL-3, and subjected to another 48 hours culture. mRNA was prepared from the live cells that remained at the end of this procedure.\r\n\r\ncDNA was prepared from 1 μg of total RNA using the TpoR-specific reverse transcription primer containing a 16 bp unique molecular identifier (UMI) and an Illumina adapter. cDNA was amplified to add illumina adapters and indexes for sequencing using an Illumina NextSeq kit with 140 cycles in the forward direction and 160 cycles in the reverse direction.\r\n\r\nThe paired-end reads from Illumina sequencing runs were separated into samples based on Illumina index sequences using Cutadapt v1.157. De-duplication based on the UMI was performed using UMI Tools v1.15 after sample separation. Reads were trimmed to the region of interest and filtered for length using Cutadapt prior to analysis with Enrich2 v1.2.0. \r\n\r\nTo determine mutations that confer increased activity on the S505N background six replicates of library-containing BaF3 cells grown in IL-3 were compared to six replicates of library-containing BaF3 cells grown without growth factors.  Log ratio enrichment scores were calculated using “wild-type” (all synonymous DNA sequences encoding the WT amino acid sequence) count normalisation.",
        "short_description": "This screen was designed to identify all single-amino-acid substitutions in the human TpoR transmembrane (TM) and partial juxtamembrane (JM) regions (488-516) that enhance the known S505N TpoR transmembrane domain mutation that causes receptor constitutive activity.",
        "title": "Novel Modifiers of MPL-dependent Oncogenic Transformation",
        "keywords": [
            {
                "text": "Thrombopoietin Receptor"
            },
            {
                "text": "Transmembrane"
            },
            {
                "text": "Enrich2"
            },
            {
                "text": "mRNA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-7684-5841"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "S505N MPL",
            "reference_sequence": {
                "sequence": "ACCGAGACCGCCTGGATCTCCTTGGTGACCGCTCTGCATCTAGTGCTGGGCCTCAACGCCGTCCTGGGCCTGCTGCTGCTGAGGTGGCAGTTT",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 486,
                "identifier": "P40238",
                "url": "http://purl.uniprot.org/uniprot/P40238",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg16",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.10",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000043-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "SE",
            "epsilon",
            "SE_Replicate_1",
            "score_Replicate_1",
            "SE_Replicate_2",
            "score_Replicate_2",
            "SE_Replicate_3",
            "score_Replicate_3",
            "SE_Replicate_4",
            "score_Replicate_4",
            "SE_Replicate_5",
            "score_Replicate_5",
            "SE_Replicate_6",
            "score_Replicate_6"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "Replicate_1_c_0",
            "Replicate_1_c_1",
            "Replicate_2_c_0",
            "Replicate_2_c_1",
            "Replicate_3_c_0",
            "Replicate_3_c_1",
            "Replicate_4_c_0",
            "Replicate_4_c_1",
            "Replicate_5_c_0",
            "Replicate_5_c_1",
            "Replicate_6_c_0",
            "Replicate_6_c_1"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000043-a-2",
        "variant_count": 1966,
        "experiment": "urn:mavedb:00000043-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000055-0-1",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment identified candidate pharmacogenomic variants in NUDT15 that could contribute to thiopurine toxicity. Two functional assays were performed on the same variant library, one for NUDT15 activity and one for protein stability.",
        "method_text": "The smaller value of the thiopurine-cytotoxicity-based and protein stability assays was assigned as the final activity score, reported here.",
        "short_description": "NUDT15 activity scores from combining thiopurine-cytotoxicity and protein stability results.",
        "title": "NUDT15 combined scores",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32094176",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32094176",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "NUDT15",
            "reference_sequence": {
                "sequence": "ATGACGGCCAGCGCACAGCCGCGCGGGCGGCGGCCAGGAGTCGGAGTCGGAGTCGTGGTGACCAGCTGCAAGCATCCGCGTTGCGTCCTCCTGGGGAAGAGGAAAGGCTCGGTTGGAGCTGGCAGTTTCCAACTCCCTGGAGGTCATCTGGAGTTCGGTGAAACCTGGGAAGAATGTGCTCAAAGGGAAACCTGGGAAGAAGCAGCTCTTCACCTGAAAAATGTTCACTTTGCCTCAGTTGTGAATTCTTTCATTGAGAAGGAGAATTACCATTATGTTACTATATTAATGAAAGGAGAAGTGGATGTGACTCATGATTCAGAACCAAAGAATGTAGAGCCTGAAAAAAATGAAAGTTGGGAGTGGGTTCCTTGGGAAGAACTACCTCCCCTGGACCAGCTTTTCTGGGGACTGCGTTGTTTAAAAGAACAAGGCTATGATCCATTTAAAGAAGATCTGAACCATCTGGTGGGATACAAAGGAAATCATCTCTAG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "Q9NV35",
                "url": "http://purl.uniprot.org/uniprot/Q9NV35",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000055-0-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "abundance_score",
            "sensitivity_score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000055-0-1",
        "variant_count": 3015,
        "experiment": "urn:mavedb:00000055-0",
        "is_meta_analysis": true,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-09-05",
        "modification_date": "2022-09-05",
        "urn": "urn:mavedb:00000104-a-2",
        "publish_date": "2022-09-05",
        "created_by": "0000-0001-6624-4698",
        "modified_by": "0000-0001-6624-4698",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "As per MAVEDB conventions hgvs_nt is the 1 indexed location relative to transcript used for mapping (ENST000003366794.9)",
        "short_description": "PARP1 dense CRISPR screen, clone 8",
        "title": "PARP1 dense CRISPR screen clone 8",
        "keywords": [
            {
                "text": "PARP1"
            },
            {
                "text": "GFP"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-018-03917-2",
                "url": "http://doi.org/10.1038/s41467-018-03917-2",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "29748565",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29748565",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0001-6624-4698"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "PARP1",
            "reference_sequence": {
                "sequence": "CGGTGGCCGGTGCGGCGTGTTCGGTGGCGGCTCTGGCCGCTCAGGCGCCTGCGGCTGGGTGAGCGCACGCGAGGCGGCGAGGCGGCAGCGTGTTTCTAGGTCGTGGCGTCGGGCTTCCGGAGCTTTGGCGGCAGCTAGGGGAGGATGGCGGAGTCTTCGGATAAGCTCTATCGAGTCGAGTACGCCAAGAGCGGGCGCGCCTCTTGCAAGAAATGCAGCGAGAGCATCCCCAAGGACTCGCTCCGGATGGCCATCATGGTGCAGTCGCCCATGTTTGATGGAAAAGTCCCACACTGGTACCACTTCTCCTGCTTCTGGAAGGTGGGCCACTCCATCCGGCACCCTGACGTTGAGGTGGATGGGTTCTCTGAGCTTCGGTGGGATGACCAGCAGAAAGTCAAGAAGACAGCGGAAGCTGGAGGAGTGACAGGCAAAGGCCAGGATGGAATTGGTAGCAAGGCAGAGAAGACTCTGGGTGACTTTGCAGCAGAGTATGCCAAGTCCAACAGAAGTACGTGCAAGGGGTGTATGGAGAAGATAGAAAAGGGCCAGGTGCGCCTGTCCAAGAAGATGGTGGACCCGGAGAAGCCACAGCTAGGCATGATTGACCGCTGGTACCATCCAGGCTGCTTTGTCAAGAACAGGGAGGAGCTGGGTTTCCGGCCCGAGTACAGTGCGAGTCAGCTCAAGGGCTTCAGCCTCCTTGCTACAGAGGATAAAGAAGCCCTGAAGAAGCAGCTCCCAGGAGTCAAGAGTGAAGGAAAGAGAAAAGGCGATGAGGTGGATGGAGTGGATGAAGTGGCGAAGAAGAAATCTAAAAAAGAAAAAGACAAGGATAGTAAGCTTGAAAAAGCCCTAAAGGCTCAGAACGACCTGATCTGGAACATCAAGGACGAGCTAAAGAAAGTGTGTTCAACTAATGACCTGAAGGAGCTACTCATCTTCAACAAGCAGCAAGTGCCTTCTGGGGAGTCGGCGATCTTGGACCGAGTAGCTGATGGCATGGTGTTCGGTGCCCTCCTTCCCTGCGAGGAATGCTCGGGTCAGCTGGTCTTCAAGAGCGATGCCTATTACTGCACTGGGGACGTCACTGCCTGGACCAAGTGTATGGTCAAGACACAGACACCCAACCGGAAGGAGTGGGTAACCCCAAAGGAATTCCGAGAAATCTCTTACCTCAAGAAATTGAAGGTTAAAAAACAGGACCGTATATTCCCCCCAGAAACCAGCGCCTCCGTGGCGGCCACGCCTCCGCCCTCCACAGCCTCGGCTCCTGCTGCTGTGAACTCCTCTGCTTCAGCAGATAAGCCATTATCCAACATGAAGATCCTGACTCTCGGGAAGCTGTCCCGGAACAAGGATGAAGTGAAGGCCATGATTGAGAAACTCGGGGGGAAGTTGACGGGGACGGCCAACAAGGCTTCCCTGTGCATCAGCACCAAAAAGGAGGTGGAAAAGATGAATAAGAAGATGGAGGAAGTAAAGGAAGCCAACATCCGAGTTGTGTCTGAGGACTTCCTCCAGGACGTCTCCGCCTCCACCAAGAGCCTTCAGGAGTTGTTCTTAGCGCACATCTTGTCCCCTTGGGGGGCAGAGGTGAAGGCAGAGCCTGTTGAAGTTGTGGCCCCAAGAGGGAAGTCAGGGGCTGCGCTCTCCAAAAAAAGCAAGGGCCAGGTCAAGGAGGAAGGTATCAACAAATCTGAAAAGAGAATGAAATTAACTCTTAAAGGAGGAGCAGCTGTGGATCCTGATTCTGGACTGGAACACTCTGCGCATGTCCTGGAGAAAGGTGGGAAGGTCTTCAGTGCCACCCTTGGCCTGGTGGACATCGTTAAAGGAACCAACTCCTACTACAAGCTGCAGCTTCTGGAGGACGACAAGGAAAACAGGTATTGGATATTCAGGTCCTGGGGCCGTGTGGGTACGGTGATCGGTAGCAACAAACTGGAACAGATGCCGTCCAAGGAGGATGCCATTGAGCACTTCATGAAATTATATGAAGAAAAAACCGGGAACGCTTGGCACTCCAAAAATTTCACGAAGTATCCCAAAAAGTTCTACCCCCTGGAGATTGACTATGGCCAGGATGAAGAGGCAGTGAAGAAGCTGACAGTAAATCCTGGCACCAAGTCCAAGCTCCCCAAGCCAGTTCAGGACCTCATCAAGATGATCTTTGATGTGGAAAGTATGAAGAAAGCCATGGTGGAGTATGAGATCGACCTTCAGAAGATGCCCTTGGGGAAGCTGAGCAAAAGGCAGATCCAGGCCGCATACTCCATCCTCAGTGAGGTCCAGCAGGCGGTGTCTCAGGGCAGCAGCGACTCTCAGATCCTGGATCTCTCAAATCGCTTTTACACCCTGATCCCCCACGACTTTGGGATGAAGAAGCCTCCGCTCCTGAACAATGCAGACAGTGTGCAGGCCAAGGTGGAAATGCTTGACAACCTGCTGGACATCGAGGTGGCCTACAGTCTGCTCAGGGGAGGGTCTGATGATAGCAGCAAGGATCCCATCGATGTCAACTATGAGAAGCTCAAAACTGACATTAAGGTGGTTGACAGAGATTCTGAAGAAGCCGAGATCATCAGGAAGTATGTTAAGAACACTCATGCAACCACACACAATGCGTATGACTTGGAAGTCATCGATATCTTTAAGATAGAGCGTGAAGGCGAATGCCAGCGTTACAAGCCCTTTAAGCAGCTTCATAACCGAAGATTGCTGTGGCACGGGTCCAGGACCACCAACTTTGCTGGGATCCTGTCCCAGGGTCTTCGGATAGCCCCGCCTGAAGCGCCCGTGACAGGCTACATGTTTGGTAAAGGGATCTATTTCGCTGACATGGTCTCCAAGAGTGCCAACTACTGCCATACGTCTCAGGGAGACCCAATAGGCTTAATCCTGTTGGGAGAAGTTGCCCTTGGAAACATGTATGAACTGAAGCACGCTTCACATATCAGCAAGTTACCCAAGGGCAAGCACAGTGTCAAAGGTTTGGGCAAAACTACCCCTGATCCTTCAGCTAACATTAGTCTGGATGGTGTAGACGTTCCTCTTGGGACCGGGATTTCATCTGGTGTGAATGACACCTCTCTACTATATAACGAGTACATTGTCTATGATATTGCTCAGGTAAATCTGAAGTATCTGCTGAAACTGAAATTCAATTTTAAGACCTCCCTGTGGTAATTGGGAGAGGTAGCCGAGTCACACCCGGTGGCTCTGGTATGAATTCACCCGAAGCGCTTCTGCACCAACTCACCTGGCCGCTAAGTTGCTGATGGGTAGTACCTGTACTAAACCACCTCAGAAAGGATTTTACAGAAACGTGTTAAAGGTTTTCTCTAACTTCTCAAGTCCCTTGTTTTGTGTTGTGTCTGTGGGGAGGGGTTGTTTTGGGGTTGTTTTTGTTTTTTCTTGCCAGGTAGATAAAACTGACATAGAGAAAAGGCTGGAGAGAGATTCTGTTGCATAGACTAGTCCTATGGAAAAAACCAAGCTTCGTTAGAATGTCTGCCTTACTGGTTTCCCCAGGGAAGGAAAAATACACTTCCACCCTTTTTTCTAAGTGTTCGTCTTTAGTTTTGATTTTGGAAAGATGTTAAGCATTTATTTTTAGTTAAAAATAAAAACTAATTTCATACTATTTAGATTTTCTTTTTTATCTTGCACTTATTGTCCCCTTTTTAGTTTTTTTTGTTTGCCTCTTGTGGTGAGGGGTGTGGGAAGACCAAAGGAAGGAACGCTAACAATTTCTCATACTTAGAAACAAAAAGAGCTTTCCTTCTCCAGGAATACTGAACATGGGAGCTCTTGAAATATGTAGTATTAAAAGTTGCATTTGAAATTCTTGACTTTCTTATGGGCACTTTTGTCTTCCAAATTAAAACTCTACCACAAATATACTTACCCAAGGGCTAATAGTAATACTCGATTAAAAATGCAGATGCCTTCTCTA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": {
                "offset": 0,
                "identifier": "ENST00000366794",
                "url": "http://www.ensembl.org/id/ENST00000366794",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000104-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "indel",
            "frame",
            "reads",
            "coverage"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000104-a-2",
        "variant_count": 46834,
        "experiment": "urn:mavedb:00000104-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-10-04",
        "modification_date": "2019-10-22",
        "urn": "urn:mavedb:00000005-a-6",
        "publish_date": "2019-10-22",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Success in precision medicine depends on our ability to determine which rare human genetic variants have functional effects. Classical homocystinuria - characterized by elevated homocyst(e)ine in plasma and urine - is caused by primarily-rare variants in the cystathionine beta-synthase (CBS) gene. About half of patients respond to vitamin B6 therapy. With early detection in newborns, existing therapies are highly effective. Functional CBS variants, especially those that respond to vitamin B6, can be detected based on their ability to restore growth in yeast cells lacking CYS4 (the yeast ortholog of CBS). This assay has previously been carried out only reactively after first observation of a variant in patients. Here we describe a proactive comprehensive missense variant effect map for human CBS. Together, saturation codon-replacement mutagenesis, en masse growth selection at different vitamin B6 levels, and sequencing yielded a look-up table for CBS missense variant function and vitamin B6-remediability in yeast. The CBS variant effect map identified disease variants and predicted both disease severity (r = 0.82) and human clinical response to vitamin B6 (r = 0.89). Thus, highly-multiplexed cell-based assays can yield proactive maps of variant function and patient response to therapy, even for rare variants not previously seen in the clinic.\r\n\r\nSee Sun et al 2018",
        "method_text": "Scoring procedure:\r\nDMS-TileSeq reads were processed using the tileseq_package and tileseqMave softwares. Briefly, TileSeq read counts were used to establish relative allele frequencies in each condition. Non-mutagenized control counts were subtracted from counts (as estimates of sequencing error). Log-ratios of selection over non-selection counts were calculated. The resulting TileSeq fitness values were then normalized to 0-1 scale where 0 corresponds to the median nonsense score and 1 corresponds to the median synonymous score. \r\n\r\nSee Sun et al 2018 for more details.",
        "short_description": "A Deep Mutational Scan of the human cystathionine-beta-synthase (CBS) using functional complementation in yeast via DMS-TileSeq at high levels of Vitamin B6.",
        "title": "CBS high-B6",
        "keywords": [
            {
                "text": "Vitamin B6"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "homocystinuria"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "CBS",
            "reference_sequence": {
                "sequence": "ATGCCTTCTGAGACCCCCCAGGCAGAAGTGGGGCCCACAGGCTGCCCCCACCGCTCAGGGCCACACTCGGCGAAGGGGAGCCTGGAGAAGGGGTCCCCAGAGGATAAGGAAGCCAAGGAGCCCCTGTGGATCCGGCCCGATGCTCCGAGCAGGTGCACCTGGCAGCTGGGCCGGCCTGCCTCCGAGTCCCCACATCACCACACTGCCCCGGCAAAATCTCCAAAAATCTTGCCAGATATTCTGAAGAAAATCGGGGACACCCCTATGGTCAGAATCAACAAGATTGGGAAGAAGTTCGGCCTGAAGTGTGAGCTCTTGGCCAAGTGTGAGTTCTTCAACGCGGGCGGGAGCGTGAAGGACCGCATCAGCCTGCGGATGATTGAGGATGCTGAGCGCGACGGGACGCTGAAGCCCGGGGACACGATTATCGAGCCGACATCCGGGAACACCGGGATCGGGCTGGCCCTGGCTGCGGCAGTGAGGGGCTATCGCTGCATCATCGTGATGCCAGAGAAGATGAGCTCCGAGAAGGTGGACGTGCTGCGGGCACTGGGGGCTGAGATTGTGAGGACGCCCACCAATGCCAGGTTCGACTCCCCGGAGTCACACGTGGGGGTGGCCTGGCGGCTGAAGAACGAAATCCCCAATTCTCACATCCTAGACCAGTACCGCAACGCCAGCAACCCCCTGGCTCACTACGACACCACCGCTGATGAGATCCTGCAGCAGTGTGATGGGAAGCTGGACATGCTGGTGGCTTCAGTGGGCACGGGCGGCACCATCACGGGCATTGCCAGGAAGCTGAAGGAGAAGTGTCCTGGATGCAGGATCATTGGGGTGGATCCCGAAGGGTCCATCCTCGCAGAGCCGGAGGAGCTGAACCAGACGGAGCAGACAACCTACGAGGTGGAAGGGATCGGCTACGACTTCATCCCCACGGTGCTGGACAGGACGGTGGTGGACAAGTGGTTCAAGAGCAACGATGAGGAGGCGTTCACCTTTGCCCGCATGCTGATCGCGCAAGAGGGGCTGCTGTGCGGTGGCAGTGCTGGCAGCACGGTGGCGGTGGCCGTGAAGGCCGCGCAGGAGCTGCAGGAGGGCCAGCGCTGCGTGGTCATTCTGCCCGACTCAGTGCGGAACTACATGACCAAGTTCCTGAGCGACAGGTGGATGCTGCAGAAGGGCTTTCTGAAGGAGGAGGACCTCACGGAGAAGAAGCCCTGGTGGTGGCACCTCCGTGTTCAGGAGCTGGGCCTGTCAGCCCCGCTGACCGTGCTCCCGACCATCACCTGTGGGCACACCATCGAGATCCTCCGGGAGAAGGGCTTCGACCAGGCGCCCGTGGTGGATGAGGCGGGGGTAATCCTGGGAATGGTGACGCTTGGGAACATGCTCTCGTCCCTGCTTGCCGGGAAGGTGCAGCCGTCAGACCAAGTTGGCAAAGTCATCTACAAGCAGTTCAAACAGATCCGCCTCACGGACACGCTGGGCAGGCTCTCGCACATCCTGGAGATGGACCACTTCGCCCTGGTGGTGCACGAGCAGATCCAGTACCACAGCACCGGGAAGTCCAGTCAGCGGCAGATGGTGTTCGGGGTGGTCACCGCCATTGACTTGCTGAACTTCGTGGCCGCCCAGGAGCGGGACCAGAAGTGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P35520",
                "url": "http://purl.uniprot.org/uniprot/P35520",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000160200",
                "url": "http://www.ensembl.org/id/ENSG00000160200",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000005-a-6",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "se"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "nonselect1",
            "nonselect2",
            "nonselect3",
            "nonselect4",
            "select1",
            "select2",
            "select3",
            "select4",
            "controlNS1",
            "controlNS2",
            "controlNS3",
            "controlNS4",
            "controlS1",
            "controlS2",
            "controlS3",
            "controlS4"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000005-a-6",
        "variant_count": 10802,
        "experiment": "urn:mavedb:00000005-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-h-1",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes the sequence for a CG-containing RNA-seq enhancer sequence.",
        "method_text": "Reads were filtered by accepting only those that had an unmutated 6nt stretch at the end of the read and had no mutations other than those that were designed. FASTQ quality scores were not used.\r\n\r\nThe sum of the reads in each of the two replicate transfections was used to calculate the scores, defined as the ratio of RNA read count to DNA read count (called the Enrichment Index, or EI).\r\n\r\nThe score reported here is the “LEIsc”, which is $log_2 EI$ re-scaled from -1 to +1 with the target sequence at 0, which enables easier comparison between the different 6-mers tested in the study.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, CG-containing RNA-seq enhancer sequence.",
        "title": "Exonic splicing for CG-containing enhancer",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Minigene exon - CG-containing enhancer",
            "reference_sequence": {
                "sequence": "AGTTCGCGCCGGGAGCTCCAGCACAGTGAAATGGACAGAAGGGCAGAGCAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000083-h-1",
            "type": "Other noncoding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "EI"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000083-h-1",
        "variant_count": 556,
        "experiment": "urn:mavedb:00000083-h",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-28",
        "modification_date": "2022-07-28",
        "urn": "urn:mavedb:00000098-a-1",
        "publish_date": "2022-07-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Deep mutational scan of 12 amino acids in voltage-sensing helix 4 of human SCN5A, screened for functional protein by challenging HEK293T cells with drug mixture of veratridine+brevetoxin+ouabain.",
        "method_text": "Variant scores were calculated by taking the frequency of all barcode counts for each variant and taking the $log_10\\left(\\frac{f_d}{f_i}\\right)$ where $f_d$ is the frequency post-drug challenge and $f_i$ is the frequency in the initial library. These scores were averaged across the 6 replicates and linearly rescaled such that the mean nonsense variants score was 0 and the mean synonymous variant score was 100. The 95% confidence interval was calculated using the replicate measurements.\r\n\r\nVariants with a score and 95% confidence interval falling completely within, above, or below the target sequence 95% confidence interval were considered wild-type-like, gain-of-function, or loss-of-function, respectively.",
        "short_description": "Deep mutational scan of human SCN5A by measuring response to veratridine+brevetoxin+ouabain drugs.",
        "title": "SCN5A response to veratridine+brevetoxin+ouabain mixture",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "31928070",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31928070",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-8037-6045"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "SCN5A",
            "reference_sequence": {
                "sequence": "LFRVIRLARIGR",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 1620,
                "identifier": "Q14524",
                "url": "http://purl.uniprot.org/uniprot/Q14524",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000098-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "ci95_lower",
            "ci95_upper"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000098-a-1",
        "variant_count": 248,
        "experiment": "urn:mavedb:00000098-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-31",
        "modification_date": "2021-10-31",
        "urn": "urn:mavedb:00000084-a-1",
        "publish_date": "2021-10-31",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study demonstrated the applicability of deep mutational scanning for inference of protein structural features (e.g. residue depth and active-site identity) and sequence-function relationships. A library of bacterial toxin CcdB variants was generated via site-directed mutagenesis. The library was then treated to induce expression at increasing levels, which were assigned rank numbers and these ranks were used to score each mutation.",
        "method_text": "Mutational sensitivity ($MS_{seq}$) scores were assigned to mutants as the condition barcode (MID) at which the number of reads for a particular mutant decreases by 5-fold or more relative to the previous MID.\r\n\r\nThe score was defined as the percentile at which $n + 1%$ of mutants have a lower $MS_{seq}$, and is therefore related to the cumulative distribution of mutants by their activity. The most active (most toxic) mutants have low scores and the least active (least toxic) have high scores.",
        "short_description": "Deep mutational scan against CcdB toxicity in E. coli",
        "title": "CcdB toxicity",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "22325784",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/22325784",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2072-3436"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "CcdB",
            "reference_sequence": {
                "sequence": "ATGCAGTTTAAGGTTTACACCTATAAAAGAGAGAGCCGTTATCGTCTGTTTGTGGATGTACAGAGTGATATTATTGACACGCCCGGGCGACGGATGGTGATCCCCCTGGCCAGTGCACGTCTGCTGTCAGATAAAGTCTCCCGTGAACTTTACCCGGTGGTGCATATCGGGGATGAAAGCTGGCGCATGATGACCACCGATATGGCCAGTGTGCCGGTCTCCGTTATCGGGGAAGAAGTGGCTGATCTCAGCCACCGCGAAAATGACATCAAAAACGCCATTAACCTGATGTTCTGGGGAATATAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P62554",
                "url": "http://purl.uniprot.org/uniprot/P62554",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000084-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "MSseq"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "MID 1",
            "MID 2",
            "MID 3",
            "MID 4",
            "MID 5",
            "MID 6",
            "MID 7",
            "MID 8"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000084-a-1",
        "variant_count": 1208,
        "experiment": "urn:mavedb:00000084-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-11-13",
        "modification_date": "2021-11-13",
        "urn": "urn:mavedb:00000088-b-1",
        "publish_date": "2021-11-13",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "A deep mutational scan of influenza nucleoprotein was performed to measure the fitness landscape, e.g. enumerate the mutants likely to produce viable viruses. Two homologs of nucleoprotein were scanned: one from H1N1 PR/1934 and one from H3N2 Aichi/1968. Because effects of single mutants in two highly similar (94% identical) sequence contexts were measured, small contrasts can be drawn between the score sets.",
        "method_text": "Overlapping paired-end read data was merged and aligned to the reference gene sequence. Sequence data were processed using the `mapmuts` package to calculate site preferences for each position.",
        "short_description": "Deep mutational scan of H3N2 Aichi/1968 nucleoprotein assaying for viral replication.",
        "title": "Influenza H3N2 Aichi/1968 nucleoprotein",
        "keywords": [
            {
                "text": "Influenza"
            },
            {
                "text": "Viral replication"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "26226986",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/26226986",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "NP, H3N2 Aichi/1968",
            "reference_sequence": {
                "sequence": "MASQGTKRSYEQMETDGERQNATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYKRVDRKWMRELVLYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDTTYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRKTRSAYERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGPAVASGYDFEKEGYSLVGIDPFKLLQNSQVYSLIRPNENPAHKSQLVWMACNSAAFEDLRVLSFIRGTKVSPRGKLSTRGVQIASNENMDAMESSTLELRSRYWAIRTRSGGNTNQQRASAGQISVQPAFSVQRNLPFDKPTIMAAFTGNTEGRTSDMRAEIIRMMEGAKPEEMSFQGRGVFELSDERAANPIVPSFDMSNEGSYFFGDNAEEYDN",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "I6TAH8",
                "url": "http://purl.uniprot.org/uniprot/I6TAH8",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000088-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000088-b-1",
        "variant_count": 9960,
        "experiment": "urn:mavedb:00000088-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2018-06-26",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-a-4",
        "publish_date": "2018-06-29",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957)",
        "method_text": "##Scoring procedure:\r\nDMS-BarSeq and DMS-TileSeq reads were processed using the [dmsPipeline](https://bitbucket.org/rothlabto/dmspipeline) software. Briefly, Barseq read counts were used to establish relative frequencies of each strain at each timepoint and converted to estimates of absolute frequencies using OD measurement data. Absolute counts were used to establish growth curves from which fitness parameters were estimated and then normalized to 0-1 scale where 0 corresponds to null controls and 1 corresponds to WT controls. Meanwhile, TileSeq read counts were used to establish relative allele frequencies in each condition. Non-mutagenized control counts were subtracted from counts (as estimates of sequencing error). log ratios of selection over non-selection counts were calculated. The resulting TileSeq fitness values were then rescaled to the distribution of the BarSeq fitness scores. Fitness scores were joined using confidence-weighted averages. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for more details.",
        "short_description": "A joint Deep Mutational Scan dataset of the human SUMO E2 conjugase UBE2I using functional complementation in yeast, combining DMS-BarSeq and DMS-TileSeq",
        "title": "UBE2I joint data",
        "keywords": [
            {
                "text": "DMS-BarSeq"
            },
            {
                "text": "E2"
            },
            {
                "text": "sumoylation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "UBE2I",
            "reference_sequence": {
                "sequence": "ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCATGGAGGAAAGACCACCCATTTGGTTTCGTGGCTGTCCCAACAAAAAATCCCGATGGCACGATGAACCTCATGAACTGGGAGTGCGCCATTCCAGGAAAGAAAGGGACTCCGTGGGAAGGAGGCTTGTTTAAACTACGGATGCTTTTCAAAGATGATTATCCATCTTCGCCACCAAAATGTAAATTCGAACCACCATTATTTCACCCGAATGTGTACCCTTCGGGGACAGTGTGCCTGTCCATCTTAGAGGAGGACAAGGACTGGAGGCCAGCCATCACAATCAAACAGATCCTATTAGGAATACAGGAACTTCTAAATGAACCAAATATCCAAGACCCAGCTCAAGCAGAGGCCTACACGATTTACTGCCAAAACAGAGTGGAGTACGAGAAAAGGGTCCGAGCACAAGCCAAGAAGTTTGCGCCCTCATAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P63279",
                "url": "http://purl.uniprot.org/uniprot/P63279",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000103275",
                "url": "http://www.ensembl.org/id/ENSG00000103275",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 159,
                "identifier": "NM_003345",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_003345",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000001-a-4",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "se",
            "df"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000001-a-4",
        "variant_count": 10438,
        "experiment": "urn:mavedb:00000001-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-14",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000012-a-2",
        "publish_date": "2019-02-18",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment demonstrated the programmed allelic series (PALS) method for site-directed mutagenesis using microarrays. The impact of nearly all singleton missense mutation in the Gal4 yeast transcription factor was measured in multiple selections.",
        "method_text": "Variant counts were calculated by summing the read counts of barcodes associated with each variant. The enrichment score for each variant is the $\\log_2$ ratio of the mutant count over the wild type count for the selected time point minus the $\\log_2$ ratio of the mutant count over the wild type count for the input time point (ratio of ratios).",
        "short_description": "Deep mutational scan of Gal4 DNA-binding domain using a yeast growth assay. 24 hours of selection.",
        "title": "Deep mutational scan of Gal4 DNA-binding domain, SEL_A_24h",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "log ratios"
            },
            {
                "text": "Yeast two-hybrid"
            },
            {
                "text": "Binding"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25559584",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25559584",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Gal4",
            "reference_sequence": {
                "sequence": "AAGCTACTGTCTTCTATCGAACAAGCATGCGATATTTGCCGACTTAAAAAGCTCAAGTGCTCCAAAGAAAAACCGAAGTGCGCCAAGTGTCTGAAGAACAACTGGGAGTGTCGCTACTCTCCCAAAACCAAAAGGTCTCCGCTGACTAGGGCACATCTGACAGAAGTGGAATCAAGGCTAGAAAGACTGGAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 1,
                "identifier": "P04386",
                "url": "http://purl.uniprot.org/uniprot/P04386",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000012-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000012-a-2",
        "variant_count": 1319,
        "experiment": "urn:mavedb:00000012-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-02-24",
        "modification_date": "2022-05-15",
        "urn": "urn:mavedb:00000094-a-6",
        "publish_date": "2022-05-15",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "Normalized currents of co-expressing 153 variants (normal currents and large rightward shifts in V1/2 in the homozygous state) with WT.",
        "method_text": "Normalized currents of co-expressing 153 variants (normal currents and large rightward shifts in V1/2 in the homozygous state) with WT.",
        "short_description": "5. Normalized currents of co-expressing 153 variants (normal currents and large rightward shifts in V1/2 in the homozygous state) with WT.",
        "title": "Normalized currents of co-expressing 153 variants (normal currents and large rightward shifts in V1/2 in the homozygous state) with WT",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ4",
            "reference_sequence": {
                "sequence": "MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGGGSPRRLGLLGSPLPPGAPLPGPGSGSGSACGQRSSAAHKRYRRLQNWVYNVLERPRGWAFVYHVFIFLLVFSCLVLSVLSTIQEHQELANECLLILEFVMIVVFGLEYIVRVWSAGCCCRYRGWQGRFRFARKPFCVIDFIVFVASVAVIAAGTQGNIFATSALRSMRFLQILRMVRMDRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLVYLAEKDANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAGILGSGFALKVQEQHRQKHFEKRRMPAANLIQAAWRLYSTDMSRAYLTATWYYYDSILPSFRELALLFEHVQRARNGGLRPLEVRRAPVPDGAPSRYPPVATCHRPGSTSFCPGESSRMGIKDRIRMGSSQRRTGPSKQHLAPPTMPTSPSSEQVGEATSPTKVQKSWSFNDRTRFRASLRLKPRTSAEDAPSEEVAEEKSYQCELTVDDIMPAVKTVIRSIRILKFLVAKRKFKETLRPYDVKDVIEQYSAGHLDMLGRIKSLQTRVDQIVGRGPGDRKAREKGDKGPSDAEVVDEISMMGRVVKVEKQVQSIEHKLDLLLGFYSRCLRSGTSASLGAVQVPLFDPDITSDYHSPVDHEDISVSAQTLSISRSVSTNMD",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-6",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000094-a-6",
        "variant_count": 153,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-02",
        "modification_date": "2021-10-02",
        "urn": "urn:mavedb:00000078-a-1",
        "publish_date": "2021-10-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the carboxylation activity change of vitamin K epoxide reductase (VKOR) variants. The functioning VKOR is able to carboxylate Factor IX domain which is secreted and retained on the cell surface. By culturing the cells with fluorophore-labeled carboxylation-specific antibody, the impact of VKOR variants to its carboxylation activity can be determined by FACS.",
        "method_text": "During the selection process, the histogram of the APC intensity is created and gates dividing the library into four equal bins on APC fluorescence intensity. And the deep sequencing result from each bin is quantified by Enrich2. For each variant in each bin, the frequency is calculated by the division of counts against total counts. Variants with lower frequency (0.0001) and observed times (2) are filtered out. The frequency values are weighted by their bins with 0.25, 0.5, 0.75 and 1. Then the weighted scores are normalized by the median of synonymous (to 1) and nonsense (to 0) mutations. The final scores are the average of six replicates.",
        "short_description": "Carboxylation activity of VKOR variants by substrate surface expression.",
        "title": "VKOR carboxylation activity",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32870157",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32870157",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-3537-3865",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "VKOR",
            "reference_sequence": {
                "sequence": "MGSTWGSPGWVRLALCLTGLVLSLYALHVKAARARDRDYRALCDVGTAISCSRVFSSRWGRGFGLVEHVLGQDSILNQSNSIFGCIFYTLQLLLGCLRTRWASVLMLLSSLVSLAGSVYLAWILFFVLYDFCIVCITTYAINVSLMWLSFRKVQEPQGKAKRH",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000078-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "lower_ci",
            "upper_ci"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000078-a-1",
        "variant_count": 747,
        "experiment": "urn:mavedb:00000078-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-08-26",
        "modification_date": "2022-08-26",
        "urn": "urn:mavedb:00000103-c-1",
        "publish_date": "2022-08-26",
        "created_by": "0000-0001-6624-4698",
        "modified_by": "0000-0001-6624-4698",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "MAPK1\r\nInduced with DOX and selected with 2 microM SCH772984",
        "title": "MAPK1 SCH772984",
        "keywords": [
            {
                "text": "resistance"
            },
            {
                "text": "complementation"
            },
            {
                "text": "MAPK1"
            },
            {
                "text": "ERK2"
            },
            {
                "text": "MITE"
            },
            {
                "text": "VRT-11E"
            },
            {
                "text": "SCH772984"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1016/j.celrep.2016.09.061",
                "url": "http://doi.org/10.1016/j.celrep.2016.09.061",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "27760319",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27760319",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0001-6624-4698"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MAPK1",
            "reference_sequence": {
                "sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000103-c-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "SCH_REP_A",
            "SCH_REP_B",
            "SCH_REP_C",
            "SCH_REP_D",
            "SCH_REP_E",
            "SCH_REP_F",
            "SCH_SD"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000103-c-1",
        "variant_count": 6810,
        "experiment": "urn:mavedb:00000103-c",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-09-30",
        "modification_date": "2019-10-08",
        "urn": "urn:mavedb:00000043-a-1",
        "publish_date": "2019-10-08",
        "created_by": "0000-0001-7684-5841",
        "modified_by": "0000-0001-7684-5841",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "The DMS library was encoded in the retroviral expression system pMX-GW-PGK-PuroR-GFP. Each codon for amino acid positions 488-516 of the human TpoR protein, encompassing the TM and partial JM regions, was independently randomised using degenerate (NNN) primers (IDT) to encode all 64 possible codons. Plasmid preparations for all positions (488-516) were pooled together in equal amounts to obtain a library containing all 1,856 possible DNA variants. The frequencies of variants in each library were determined by Illumina sequencing, which confirmed 100% representation across the randomised region and constitutes the unselected control sample.\r\n\r\nThe library was transfected into HEK293T cells along with retroviral packaging vectors using calcium phosphate transfection. After 48 hrs, supernatants containing virus were harvested and sterile filtered for transduction into Ba/F3 cells.  The pooled retroviral library was used to transduce 10^6 Ba/F3 cells at a multiplicity of infection ~0.1, generating ~10^5 transductants for each of six biological replicates. These six cultures were treated with 5 μg/ml puromycin (on IL-3) for 48 hours to yield pure virus-positive cells. Cells for each replicate were split in half and cultured in the continued presence of IL-3, or were washed to remove IL-3, and subjected to another 48 hours culture. mRNA was prepared from the live cells that remained at the end of this procedure.\r\n\r\ncDNA was prepared from 1 μg of total RNA using the TpoR-specific reverse transcription primer containing a 16 bp unique molecular identifier (UMI) and an Illumina adapter. cDNA was amplified to add illumina adapters and indexes for sequencing using an Illumina NextSeq kit with 140 cycles in the forward direction and 160 cycles in the reverse direction.\r\n\r\nThe paired-end reads from Illumina sequencing runs were separated into samples based on Illumina index sequences using Cutadapt v1.15. De-duplication based on the UMI was performed using UMI Tools v1.15 after sample separation. Reads were trimmed to the region of interest and filtered for length using Cutadapt7 prior to analysis with Enrich2 v1.2.0. \r\n\r\nTo determine mutations that confer constitutive activity log ratio enrichment scores were calculated for each of the six replicates by comparing the variant counts in the unselected plasmid library with those remaining in Ba/F3 cells after 2 days of culture in growth factor free media using “wild-type” (all synonymous DNA sequences encoding the WT amino acid sequence) count normalisation.",
        "short_description": "The screen was designed to identify all single-amino-acid substitutions in the human TpoR transmembrane (TM) and partial juxtamembrane (JM) regions (488-516) that confer factor-free growth.",
        "title": "Novel Drivers of MPL-dependent Oncogenic Transformation",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-7684-5841"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MPL",
            "reference_sequence": {
                "sequence": "ACCGAGACCGCCTGGATCTCCTTGGTGACCGCTCTGCATCTAGTGCTGGGCCTCAGCGCCGTCCTGGGCCTGCTGCTGCTGAGGTGGCAGTTT",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 486,
                "identifier": "P40238",
                "url": "http://purl.uniprot.org/uniprot/P40238",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg16",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.10",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000043-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "SE",
            "epsilon",
            "SE_Replicate_A",
            "score_Replicate_A",
            "SE_Replicate_B",
            "score_Replicate_B",
            "SE_Replicate_C",
            "score_Replicate_C",
            "SE_Replicate_D",
            "score_Replicate_D",
            "SE_Replicate_E",
            "score_Replicate_E",
            "SE_Replicate_F",
            "score_Replicate_F"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "Replicate_A_c_0",
            "Replicate_A_c_1",
            "Replicate_B_c_0",
            "Replicate_B_c_1",
            "Replicate_C_c_0",
            "Replicate_C_c_1",
            "Replicate_D_c_0",
            "Replicate_D_c_1",
            "Replicate_E_c_0",
            "Replicate_E_c_1",
            "Replicate_F_c_0",
            "Replicate_F_c_1"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000043-a-1",
        "variant_count": 2415,
        "experiment": "urn:mavedb:00000043-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-01",
        "modification_date": "2021-10-01",
        "urn": "urn:mavedb:00000077-b-1",
        "publish_date": "2021-10-01",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study determined the effect of amino acid substitutions on cohesin-dockerin binding using deep mutational scanning. Cohesins from *Clostridium thermocellum* and *Clostridium cellulolyticum* were analyzed using yeast display.",
        "method_text": "Sequencing data was processed using Enrich v0.2 and custom scripts. The fitness score $\\zeta_i$ for FACS data is described in Kowalsky et al. 2015 and as follows. $\\epsilon_i$ is the enrichment ratio of variant $i$, $\\epsilon_{wt}$ is the wild-type enrichment ratio, $\\sigma$ is the standard deviation of the population and $\\phi$ is the percentage of cells collected in the gating population.\r\n\r\n$$\\zeta_i = \\log_2 (e) \\sqrt{2} \\sigma^{\\prime} [erf ^{-1} (1 - \\phi 2^{(\\epsilon_{wt} + 1)} - erf ^{-1} (1 - \\phi 2^{(\\epsilon_{i} + 1)}]$$\r\n\r\nThe fitness score is listed as the score, and the raw $\\log_2$ ratios are also included.",
        "short_description": "Deep mutational scan of C. thermocellum cohesin binding affinity for dockerin.",
        "title": "C. thermocellum cohesin binding affinity",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "27699856",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27699856",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "25790064",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25790064",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-3537-3865"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "C. thermocellum cohesin fragment",
            "reference_sequence": {
                "sequence": "MTVLPKDIPGDSLKVTVGTANGKPGDTVTVPVTFADVAKMKNVGTCNFYLGYDASLLEVVSVDAGPIVKNAAVNFSSSASNGTISFLFLDNTITDELITADGVFANIKFKLKSVTAKTTTPVTFKDGGAFGDGTMSKIASVTKTNGSVTIDP",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000077-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_err",
            "log2_ratio",
            "log2_ratio_err"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000077-b-1",
        "variant_count": 2924,
        "experiment": "urn:mavedb:00000077-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-d-1",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "Samples are collected after 8h and sequenced by Illumina. The counts for each variant is first added by 1, then divided by total sequence counts at this time point to calculate variant frequency. The functional score equals the division of a variant frequency at this time point and its frequency in initial library. Further normalizing the functional scores by wild type scores will give the relative enrichment values. The score data includes scores from three replicates which are suffixed by: _rep1, _rep2 & _rep3. The final score is the median of them.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 8h",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "RAF",
            "reference_sequence": {
                "sequence": "TCTAAGACAAGCAACACTATCCGTGTTTTCTTGCCGAACAAGCAAAGAACAGTGGTCAATGTGCGAAATGGAATGAGCTTGCATGACTGCCTTATGAAAGCACTCAAGGTGAGGGGC",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 51,
                "identifier": "P04049",
                "url": "http://purl.uniprot.org/uniprot/P04049",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000061-d-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_rep1",
            "score_rep2",
            "score_rep3"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000061-d-1",
        "variant_count": 298,
        "experiment": "urn:mavedb:00000061-d",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-17",
        "modification_date": "2022-08-16",
        "urn": "urn:mavedb:00000070-a-4",
        "publish_date": "2022-08-16",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the experimental fitness of variants in the TEM-1 $\\beta$-lactamase gene in _Escherichia coli_. Fitness measurements were estimated based on growth under increasing concentrations of ampicillin using a band-pass selection system.",
        "method_text": "Variant reads were aligned to the template sequence and all codon substitution variants were mapped. Indels were assumed to be sequencing errors and ignored. Reads were removed if the average quality score was less than 30, if the read did not span the full sub-region, or if the read contained mutations in more than one codon.\r\n\r\nReads were counted for each of 13 concentrations of Amp used in the experiment. The raw fitness score $f$ of allele $i$ was calculated as:\r\n\r\n$$ f_i = \\frac{\\sum_{p=1}^{13} c_{i,p} \\log_2\\left(a_p\\right)}{\\sum_{p=1}^{13} c_{i,p}} $$\r\n\r\nVariants with five or fewer total counts were not assigned a fitness value. Additional measures were taken to calculate fitness values for variants with counts at many Amp concentrations (see manuscript SI for details).\r\n\r\nRaw fitness scores were normalized to wild type to get a normalized fitness $w_i$ using:\r\n\r\n$$ w_i = \\frac{2^{f_i}}{2^f_{wt}} $$\r\n\r\nThe wild type fitness score was calculated using the counts of all alleles with synonymous substitutions. Therefore a normalized fitness value of 1.0 is equivalent to wild type, greater than 1.0 is beneficial, and 0 to 1.0 is deleterious. Only the normalized scores were reported.\r\n\r\nThe score for a protein variant was calculated as the average fitness of all equivalent nucleotide variants.\r\n\r\nThe estimated error ('err' column) is based on the percent difference in fitness between the nucleotide variant fitness and the average fitness of the corresponding amino acid variant.\r\n\r\nThe 'ambler' column provides the [Ambler position](https://pubmed.ncbi.nlm.nih.gov/2039479/) of the amino acid .",
        "short_description": "Amino acid fitness scores for variants in the TEM-1 β-lactamase gene in the presence of ampicillin.",
        "title": "Amino acid fitness scores of TEM-1 β-lactamase",
        "keywords": [
            {
                "text": "normalized"
            },
            {
                "text": "band-pass selection"
            },
            {
                "text": "resistance"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24567513",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24567513",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TEM-1 β-lactamase",
            "reference_sequence": {
                "sequence": "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P62593",
                "url": "http://purl.uniprot.org/uniprot/P62593",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000070-a-4",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "err",
            "ambler"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "c_0.25",
            "c_0.5",
            "c_1",
            "c_2",
            "c_4",
            "c_8",
            "c_16",
            "c_32",
            "c_64",
            "c_128",
            "c_256",
            "c_512",
            "c_1024",
            "c_total",
            "ambler"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000070-a-4",
        "variant_count": 5740,
        "experiment": "urn:mavedb:00000070-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-14",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000012-a-1",
        "publish_date": "2019-02-18",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment demonstrated the programmed allelic series (PALS) method for site-directed mutagenesis using microarrays. The impact of nearly all singleton missense mutation in the Gal4 yeast transcription factor was measured in multiple selections.",
        "method_text": "Variant counts were calculated by summing the read counts of barcodes associated with each variant. The enrichment score for each variant is the $\\log_2$ ratio of the mutant count over the wild type count for the selected time point minus the $\\log_2$ ratio of the mutant count over the wild type count for the input time point (ratio of ratios).",
        "short_description": "Deep mutational scan of Gal4 DNA-binding domain using a yeast growth assay. 24 hours of nonselective growth.",
        "title": "Deep mutational scan of Gal4 DNA-binding domain, NONSEL_24h",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "log ratios"
            },
            {
                "text": "DNA-binding"
            },
            {
                "text": "Yeast two-hybrid"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25559584",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25559584",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Gal4",
            "reference_sequence": {
                "sequence": "AAGCTACTGTCTTCTATCGAACAAGCATGCGATATTTGCCGACTTAAAAAGCTCAAGTGCTCCAAAGAAAAACCGAAGTGCGCCAAGTGTCTGAAGAACAACTGGGAGTGTCGCTACTCTCCCAAAACCAAAAGGTCTCCGCTGACTAGGGCACATCTGACAGAAGTGGAATCAAGGCTAGAAAGACTGGAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 1,
                "identifier": "P04386",
                "url": "http://purl.uniprot.org/uniprot/P04386",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000012-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000012-a-1",
        "variant_count": 1319,
        "experiment": "urn:mavedb:00000012-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-09-05",
        "modification_date": "2020-09-05",
        "urn": "urn:mavedb:00000046-a-1",
        "publish_date": "2020-09-05",
        "created_by": "0000-0001-7684-5841",
        "modified_by": "0000-0001-7684-5841",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "HeLa cells were transduced with the CD86 library containing a GFP reporter and GFP positive cells isolated by FACS.  This population was stained for cell surface expression of CD86 and sorted for CD86 positive cells.  Variant ratios between CD86+ and GFP+ populations were calculated in Enrich2 using Enrich2 Log ratios with wild-type normalisation.",
        "short_description": "Library pre-screened for variants that support expression of CD86 at the cell surface.",
        "title": "CD86 Surface Expression",
        "keywords": [
            {
                "text": "MIR2"
            },
            {
                "text": "CD86"
            },
            {
                "text": "DMS"
            },
            {
                "text": "mRNA"
            },
            {
                "text": "MARCH1"
            },
            {
                "text": "Flow Cytometry"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-7684-5841"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "CD86",
            "reference_sequence": {
                "sequence": "GACCACATTCCTTGGATTACAGCTGTACTTCCAACAGTTATTATATGTGTGATGGTTTTCTGTCTAATTCTATGGAAATGG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 243,
                "identifier": "P42081",
                "url": "http://purl.uniprot.org/uniprot/P42081",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg16",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.10",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000046-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "SE",
            "epsilon",
            "SE_Replicate_1",
            "score_Replicate_1",
            "SE_Replicate_2",
            "score_Replicate_2",
            "SE_Replicate_3",
            "score_Replicate_3"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "Replicate_1_c_0",
            "Replicate_1_c_1",
            "Replicate_2_c_0",
            "Replicate_2_c_1",
            "Replicate_3_c_0",
            "Replicate_3_c_1"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000046-a-1",
        "variant_count": 32347,
        "experiment": "urn:mavedb:00000046-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-08-07",
        "modification_date": "2019-08-07",
        "urn": "urn:mavedb:00000039-a-6",
        "publish_date": "2019-08-07",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effects of yeast HSP90 variants under the control of different promoters to explore the relationship between protein sequence and expression level. The results showed that reduced expression level (compared to wild-type expression) revealed new partial loss of function mutations.",
        "method_text": "Growth rates were calculated for each variant and converted into selection coefficients. The selection coefficient for each variant under control of this promoter/UTR combination is reported as the score. For variants with multiple synonymous codons, the reported coefficient is the average of all synonymous variant's selection coefficients.\r\n\r\nVariants annotated as \"null-like\" have a score of -1.",
        "short_description": "Deep mutational scan of all single mutants in a nine-amino acid region of Hsp90 (Hsp82) in Saccharomyces cerevisiae under the control of the TEF promoter with CYC 3'UTR.",
        "title": "Deep mutational scan of HSP90, TEF construct",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "promoter"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23825969",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23825969",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "HSP90",
            "reference_sequence": {
                "sequence": "CAATTTGGTTGGTCTGCTAATATGGAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 581,
                "identifier": "P02829",
                "url": "http://purl.uniprot.org/uniprot/P02829",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000039-a-6",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000039-a-6",
        "variant_count": 187,
        "experiment": "urn:mavedb:00000039-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000076-d-1",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilized site directed mutagenesis to generate variants in the  carboxyl-terminal tail anchor (TA) on the Fis1p protein within yeast. All possible codons at 27 amino acid positions were assayed for their ability to target the mitochondrial membrane.",
        "method_text": "FASTQ paired end data were stripped of adapters and combined using PANDAseq assembler. Sequences not encoding the Fis1p tail anchor were removed.\r\n\r\nScores were calculated by taking the $\\log_2$ ratio of the variant count in the experimental condition to the variant count in the SC -Trp condition. If the variant count in the SC -Trp condition was 0, it was set to 1 to avoid a divide-by-zero error.",
        "short_description": "Amino acid scores for deep mutational scan of the yeast Fis1 tail anchor, SMM -Trp -His medium.",
        "title": "Fis1 tail anchor, SMM -Trp -His",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.5061/dryad.j14r5",
                "url": "http://doi.org/10.5061/dryad.j14r5",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "28007883",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28007883",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Fis1 tail anchor",
            "reference_sequence": {
                "sequence": "LKGVVVAGGVLAGAVAVASFFLRNKRR",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 128,
                "identifier": "P40515",
                "url": "http://purl.uniprot.org/uniprot/P40515",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000076-d-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000076-d-1",
        "variant_count": 536,
        "experiment": "urn:mavedb:00000076-d",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-03",
        "modification_date": "2021-10-03",
        "urn": "urn:mavedb:00000081-a-1",
        "publish_date": "2021-10-03",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study aimed to functionally characterize BRCA1 missense variants at scale in order to provide the additional information necessary for more definitive interpretation of VUSs in the clinic. To do so, the authors performed a DMS on the RING and BRCT domains of BRCA1 for the ability to perform homology-directed DNA repair.",
        "method_text": "Scores for all variants in control siRNA and double-strand break inducing siRNA were computed using Enrich2. Variants with a false-discovery-rate-adjusted q value indicating it was significantly different from the control siRNA experiment (q < 0.055) were considered depleted. The depletion score reported here is the number of replicates where the variant was depleted relative to the corresponding control siRNA replicate. The total number of replicates that passed the read count filter are also reported here. Only variants that passed the read count filter in at least three replicates are included.",
        "short_description": "Depletion scores for BRCA1 RING and BRCT domain variants in homology-directed DNA repair function assay.",
        "title": "BRCA1 RING and BRCT domains depletion scores",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30219179",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30219179",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2072-3436"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1",
            "reference_sequence": {
                "sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPENPSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEISLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENSSLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPCSENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLLASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKRKRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEKESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSEEIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKEFVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLGKAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVSKRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKDKPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSMSPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKLNAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDDLLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELPCFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLFSSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEAASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALEDLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHSCSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRAPESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKMLNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P38398",
                "url": "http://purl.uniprot.org/uniprot/P38398",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000081-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000081-a-1",
        "variant_count": 1061,
        "experiment": "urn:mavedb:00000081-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-r-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 19, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 19 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 19 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 19",
            "reference_sequence": {
                "sequence": "TTTCTTTCAGCATGATTTTGAAGTCAGAGGAGATGTGGTCAATGGAAGAAACCACCAAGGTCCAAAGCGAGCAAGAGAATCCCAGGACAGAAAGGTAAAGCTCC",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-r-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-r-1",
        "variant_count": 303,
        "experiment": "urn:mavedb:00000097-r",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000076-a-1",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilized site directed mutagenesis to generate variants in the  carboxyl-terminal tail anchor (TA) on the Fis1p protein within yeast. All possible codons at 27 amino acid positions were assayed for their ability to target the mitochondrial membrane.",
        "method_text": "FASTQ paired end data were stripped of adapters and combined using PANDAseq assembler. Sequences not encoding the Fis1p tail anchor were removed.\r\n\r\nScores were calculated by taking the $\\log_2$ ratio of the variant count in the experimental condition to the variant count in the SC -Trp condition. If the variant count in the SC -Trp condition was 0, it was set to 1 to avoid a divide-by-zero error.",
        "short_description": "Amino acid scores for deep mutational scan of the yeast Fis1 tail anchor, SMM -Trp -His medium with 20mM 3-aminotriazole.",
        "title": "Fis1 tail anchor, SMM -Trp -His with 20mM 3-AT",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.5061/dryad.j14r5",
                "url": "http://doi.org/10.5061/dryad.j14r5",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "28007883",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28007883",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Fis1 tail anchor",
            "reference_sequence": {
                "sequence": "LKGVVVAGGVLAGAVAVASFFLRNKRR",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 128,
                "identifier": "P40515",
                "url": "http://purl.uniprot.org/uniprot/P40515",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000076-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000076-a-1",
        "variant_count": 535,
        "experiment": "urn:mavedb:00000076-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-08-16",
        "modification_date": "2021-08-16",
        "urn": "urn:mavedb:00000067-a-1",
        "publish_date": "2021-08-16",
        "created_by": "0000-0001-6465-5776",
        "modified_by": "0000-0001-6465-5776",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "TECR variant effect map score set (Short description - to be updated)",
        "title": "TECR variant effect map score set",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-6465-5776"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TECR",
            "reference_sequence": {
                "sequence": "ATGAAGCATTACGAGGTGGAGATTCTGGACGCAAAGACAAGGGAGAAGCTGTGTTTCTTGGACAAGGTGGAGCCCCACGCCACCATTGCGGAGATCAAGAACCTCTTCACTAAGACCCATCCGCAGTGGTACCCCGCCCGCCAGTCCCTCCGCCTGGACCCCAAGGGCAAGTCCCTGAAGGATGAGGATGTTCTGCAGAAGCTGCCCGTGGGCACCACGGCCACACTGTACTTCCGGGACCTGGGGGCCCAGATCAGCTGGGTGACGGTCTTCCTAACAGAGTACGCGGGGCCCCTTTTCATCTACCTGCTCTTCTACTTCCGAGTGCCCTTCATCTATGGCCACAAATATGACTTTACGTCCAGTCGGCATACAGTGGTGCACCTCGCCTGCATCTGTCACTCATTCCACTACATCAAGCGCCTGCTGGAGACGCTCTTCGTGCACCGCTTCTCCCATGGCACTATGCCTTTGCGCAACATCTTCAAGAACTGCACCTACTACTGGGGCTTCGCCGCGTGGATGGCCTATTACATCAATCACCCTCTCTACACTCCCCCTACCTACGGAGCTCAGCAGGTGAAACTGGCGCTCGCCATCTTTGTGATCTGCCAGCTCGGCAACTTCTCCATCCACATGGCCCTGCGGGACCTGCGGCCCGCTGGGTCCAAGACGCGGAAGATCCCATACCCCACCAAGAACCCCTTCACGTGGCTCTTCCTGCTGGTGTCCTGCCCCAACTACACCTACGAGGTGGGGTCCTGGATCGGTTTCGCCATCATGACGCAGTGTCTCCCAGTGGCCCTGTTCTCCCTGGTGGGCTTCACCCAGATGACCATCTGGGCCAAGGGCAAGCACCGCAGCTACCTGAAGGAGTTCCGGGACTACCCGCCCCTGCGCATGCCCATCATCCCCTTCCTGCTCTGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "Q9NZ01",
                "url": "http://purl.uniprot.org/uniprot/Q9NZ01",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000067-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_sd",
            "quality_score",
            "num_replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000067-a-1",
        "variant_count": 4235,
        "experiment": "urn:mavedb:00000067-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2018-06-29",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-c-2",
        "publish_date": "2018-06-29",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957)",
        "method_text": "##Scoring procedure:\r\nDMS-TileSeq reads were processed using the [dmsPipeline](https://bitbucket.org/rothlabto/dmspipeline) software. Briefly, TileSeq read counts were used to establish relative allele frequencies in each condition. Non-mutagenized control counts were subtracted from counts (as estimates of sequencing error). log ratios of selection over non-selection counts were calculated. The resulting TileSeq fitness values were then normalized to 0-1 scale where 0 corresponds to the median nonsense score and 1 corresponds to the median synonymous score. Random-Forest-based machine learning was used to impute missing values and refine low-confidence measurements, based on intrinsic, structural, and biochemical features.\r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for more details.\r\n\r\n## Additional columns:\r\n* exp.score = experimental score from the joint DMS-BarSeq/DMS-TileSeq screens\r\n* exp.sd = standard deviation of the experimental score\r\n* df = degrees of freedom (number of replicates contributing to the experimental score)\r\n* pred.score = machine-learning predicted score",
        "short_description": "A machine-learning imputed and refined Deep Mutational Scan of human Calmodulin using functional complementation in yeast.",
        "title": "Human Calmodulin imputed and refined",
        "keywords": [
            {
                "text": "imputation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29269382",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29269382",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "CALM1",
            "reference_sequence": {
                "sequence": "ATGGCTGATCAGCTGACCGAAGAACAGATTGCTGAATTCAAGGAAGCCTTCTCCCTATTTGATAAAGATGGCGATGGCACCATCACAACAAAGGAACTTGGAACTGTCATGAGGTCACTGGGTCAGAACCCAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGTAATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAATGAAAGATACAGATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTGACAAGGATGGCAATGGTTATATCAGTGCAGCAGAACTACGTCACGTCATGACAAACTTAGGAGAAAAACTAACAGATGAAGAAGTAGATGAAATGATCAGAGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAAGAATTCGTACAGATGATGACTGCAAAATGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P0DP23",
                "url": "http://purl.uniprot.org/uniprot/P0DP23",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000198668",
                "url": "http://www.ensembl.org/id/ENSG00000198668",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 833,
                "identifier": "NM_001363670.1",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_001363670.1",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000001-c-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "se",
            "exp.score",
            "exp.sd",
            "df",
            "pred.score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000001-c-2",
        "variant_count": 2980,
        "experiment": "urn:mavedb:00000001-c",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-11-04",
        "modification_date": "2021-11-04",
        "urn": "urn:mavedb:00000086-d-1",
        "publish_date": "2021-11-04",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study examined the fitness effects of single amino acid mutations in TEM-1 β-lactamase in *Escherichia coli* under selection for ampicillin resistance or cefotaxime resistance.",
        "method_text": "Scores were calculated as the fitness value $F_i^a$ for an amino acid change $a$ at position $i$. The counts $N$ from either the selection condition or the unselected 0 μg/ml condition were used for the variant or wild-type TEM-1:\r\n\r\n$$F_i^a = \\log_{10} \\left( \\frac{N_i^{a,sel}}{N_i^{a,unsel}} \\right) -  \\log_{10} \\left( \\frac{N_i^{wt,sel}}{N_i^{wt,unsel}} \\right)$$\r\n\r\nTwo replicate selections were performed. The first replicate’s fitness is presented as the score, and the second replicate’s fitness is included as an additional column.",
        "short_description": "Effects of TEM-1 mutations on ampicillin resistance at 625 μg/ml",
        "title": "TEM-1 625 μg/ml Amp",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25723163",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25723163",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TEM-1 β-lactamase",
            "reference_sequence": {
                "sequence": "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P62593",
                "url": "http://purl.uniprot.org/uniprot/P62593",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000086-d-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "rep_score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000086-d-1",
        "variant_count": 4997,
        "experiment": "urn:mavedb:00000086-d",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-11-20",
        "modification_date": "2020-11-20",
        "urn": "urn:mavedb:00000049-a-7",
        "publish_date": "2020-11-20",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "A deep mutational scan of human MTHFR via functional complementation in yeast at 200ug/ml folate in WT background",
        "title": "MTHFR at 200ug/ml folate in WT background",
        "keywords": [
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "homocystinuria"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1628-9390",
            "0000-0002-9219-4310",
            "0000-0002-2550-2141",
            "0000-0001-6465-5776"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MTHFR",
            "reference_sequence": {
                "sequence": "ATGGTGAACGAAGCCAGAGGAAACAGCAGCCTCAACCCCTGCTTGGAGGGCAGTGCCAGCAGTGGCAGTGAGAGCTCCAAAGATAGTTCGAGATGTTCCACCCCGGGCCTGGACCCCGAGCGGCATGAGAGACTCCGGGAGAAGATGAGGCGGCGATTGGAATCTGGTGACAAGTGGTTCTCCCTGGAATTCTTCCCTCCTCGAACTGCTGAGGGAGCTGTCAATCTCATCTCAAGGTTTGACCGGATGGCAGCAGGTGGCCCCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCCTGGCTCAGACAAGGAGACCTCCTCCATGATGATCGCCAGCACCGCCGTGAACTACTGTGGCCTGGAGACCATCCTGCACATGACCTGCTGCCGTCAGCGCCTGGAGGAGATCACGGGCCATCTGCACAAAGCTAAGCAGCTGGGCCTGAAGAACATCATGGCGCTGCGGGGAGACCCAATAGGTGACCAGTGGGAAGAGGAGGAGGGAGGCTTCAACTACGCAGTGGACCTGGTGAAGCACATCCGAAGTGAGTTTGGTGACTACTTTGACATCTGTGTGGCAGGTTACCCCAAAGGCCACCCCGAAGCAGGGAGCTTTGAGGCTGACCTGAAGCACTTGAAGGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGCTTTTCTTTGAGGCTGACACATTCTTCCGCTTTGTGAAGGCATGCACCGACATGGGCATCACTTGCCCCATCGTCCCCGGGATCTTTCCCATCCAGGGCTACCACTCCCTTCGGCAGCTTGTGAAGCTGTCCAAGCTGGAGGTGCCACAGGAGATCAAGGACGTGATTGAGCCAATCAAAGACAACGATGCTGCCATCCGCAACTATGGCATCGAGCTGGCCGTGAGCCTGTGCCAGGAGCTTCTGGCCAGTGGCTTGGTGCCAGGCCTCCACTTCTACACCCTCAACCGCGAGATGGCTACCACAGAGGTGCTGAAGCGCCTGGGGATGTGGACTGAGGACCCCAGGCGTCCCCTACCCTGGGCTCTCAGCGCCCACCCCAAGCGCCGAGAGGAAGATGTACGTCCCATCTTCTGGGCCTCCAGACCAAAGAGTTACATCTACCGTACCCAGGAGTGGGACGAGTTCCCTAACGGCCGCTGGGGCAATTCCTCTTCCCCTGCCTTTGGGGAGCTGAAGGACTACTACCTCTTCTACCTGAAGAGCAAGTCCCCCAAGGAGGAGCTGCTGAAGATGTGGGGGGAGGAGCTGACCAGTGAAGAAAGTGTCTTTGAAGTCTTCGTTCTTTACCTCTCGGGAGAACCAAACCGGAATGGTCACAAAGTGACTTGCCTGCCCTGGAACGATGAGCCCCTGGCGGCTGAGACCAGCCTGCTGAAGGAGGAGCTGCTGCGGGTGAACCGCCAGGGCATCCTCACCATCAACTCACAGCCCAACATCAACGGGAAGCCGTCCTCCGACCCCATCGTGGGCTGGGGCCCCAGCGGGGGCTATGTCTTCCAGAAGGCCTACTTAGAGTTTTTCACTTCCCGCGAGACAGCGGAAGCACTTCTGCAAGTGCTGAAGAAGTACGAGCTCCGGGTTAATTACCACCTTGTCAATGTGAAGGGTGAAAACATCACCAATGCCCCTGAACTGCAGCCGAATGCTGTCACTTGGGGCATCTTCCCTGGGCGAGAGATCATCCAGCCCACCGTAGTGGATCCCGTCAGCTTCATGTTCTGGAAGGACGAGGCCTTTGCCCTGTGGATTGAGCGGTGGGGAAAGCTGTATGAGGAGGAGTCCCCGTCCCGCACCATCATCCAGTACATCCACGACAACTACTTCCTGGTCAACCTGGTGGACAATGACTTCCCACTGGACAACTGCCTCTGGCAGGTGGTGGAAGACACATTGGAGCTTCTCAACAGGCCCACCCAGAATGCGAGAGAAACGGAGGCTCCATGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P42898",
                "url": "http://purl.uniprot.org/uniprot/P42898",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000177000",
                "url": "http://www.ensembl.org/id/ENSG00000177000",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 230,
                "identifier": "NM_005957",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_005957",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000049-a-7",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "se"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000049-a-7",
        "variant_count": 12538,
        "experiment": "urn:mavedb:00000049-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-01-29",
        "modification_date": "2021-01-29",
        "urn": "urn:mavedb:00000060-a-2",
        "publish_date": "2021-01-29",
        "created_by": "0000-0002-9712-9163",
        "modified_by": "0000-0002-9712-9163",
        "extra_metadata": {},
        "abstract_text": "Insoluble protein aggregates are the hallmarks of many neurodegenerative diseases. For example, aggregates of TDP-43 occur in nearly all cases of amyotrophic lateral sclerosis (ALS). However, whether aggregates cause cellular toxicity is still not clear, even in simpler cellular systems. We reasoned that deep mutagenesis might be a powerful approach to disentangle the relationship between aggregation and toxicity. We generated >50,000 mutations in the prion-like domain (PRD) of TDP-43 and quantified their toxicity in yeast cells. Surprisingly, mutations that increase hydrophobicity and aggregation strongly decrease toxicity. In contrast, toxic variants promote the formation of dynamic liquid-like condensates. Mutations have their strongest effects in a hotspot that genetic interactions reveal to be structured in vivo, illustrating how mutagenesis can probe the in vivo structures of unstructured proteins. Our results show that aggregation of TDP-43 is not harmful but protects cells, most likely by titrating the protein away from a toxic liquid-like phase.",
        "method_text": "Variants for TDP-43 were constructed using a doped oligo for each of the TDP-43 libraries (290-331 and 332-373). Libraries were transformed in Saccharomyces cerevisiae and TDP-43 expression was induced for 5-6 generations. Variant counts were processed with DiMSum (Faure et al. 2020) to obtain a toxicity score for each variant. See Bolognesi et al. 2019 for details.",
        "short_description": "Deep mutational scanning of TDP-43 prion-like domain (AA 332-373) using a toxicity assay",
        "title": "TDP-43 toxicity",
        "keywords": [
            {
                "text": "prion-like domain"
            },
            {
                "text": "TDP-43"
            },
            {
                "text": "toxicity"
            },
            {
                "text": "intrinsic disorder"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-12101-z",
                "url": "https://doi.org/10.1038/s41467-019-12101-z",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-9712-9163",
            "0000-0002-6632-947X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TARDBP",
            "reference_sequence": {
                "sequence": "ATGTCTGAATATATTCGGGTAACCGAAGATGAGAACGATGAGCCCATTGAAATACCATCGGAAGACGATGGGACGGTGCTGCTCTCCACGGTTACAGCCCAGTTTCCAGGGGCGTGTGGGCTTCGCTACAGGAATCCAGTGTCTCAGTGTATGAGAGGTGTCCGGCTGGTAGAAGGAATTCTGCATGCCCCAGATGCTGGCTGGGGAAATCTGGTGTATGTTGTCAACTATCCAAAAGATAACAAAAGAAAAATGGATGAGACAGATGCTTCATCAGCAGTGAAAGTGAAAAGAGCAGTCCAGAAAACATCCGATTTAATAGTGTTGGGTCTCCCATGGAAAACAACCGAACAGGACCTGAAAGAGTATTTTAGTACCTTTGGAGAAGTTCTTATGGTGCAGGTCAAGAAAGATCTTAAGACTGGTCATTCAAAGGGGTTTGGCTTTGTTCGTTTTACGGAATATGAAACACAAGTGAAAGTAATGTCACAGCGACATATGATAGATGGACGATGGTGTGACTGCAAACTTCCTAATTCTAAGCAAAGCCAAGATGAGCCTTTGAGAAGCAGAAAAGTGTTTGTGGGGCGCTGTACAGAGGACATGACTGAGGATGAGCTGCGGGAGTTCTTCTCTCAGTACGGGGATGTGATGGATGTCTTCATCCCCAAGCCATTCAGGGCCTTTGCCTTTGTTACATTTGCAGATGATCAGATTGCGCAGTCTCTTTGTGGAGAGGACTTGATCATTAAAGGAATCAGCGTTCATATATCCAATGCCGAACCTAAGCACAATAGCAATAGACAGTTAGAAAGAAGTGGAAGATTTGGTGGTAATCCAGGTGGCTTTGGGAATCAGGGTGGATTTGGTAATAGCAGAGGGGGTGGAGCTGGTTTGGGAAACAATCAAGGTAGTAATATGGGTGGTGGGATGAACTTTGGTGCGTTCAGCATTAATCCAGCCATGATGGCTGCCGCCCAGGCAGCACTACAGAGCAGTTGGGGTATGATGGGCATGTTAGCCAGCCAGCAGAACCAGTCAGGCCCATCGGGTAATAACCAAAACCAAGGCAACATGCAGAGGGAGCCAAACCAGGCCTTCGGTTCTGGAAATAACTCTTATAGTGGCTCTAATTCTGGTGCAGCAATTGGTTGGGGATCAGCATCCAATGCAGGGTCGGGCAGTGGTTTTAATGGAGGCTTTGGCTCAAGCATGGATTCTAAGTCTTCTGGCTGGGGAATG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 994,
                "identifier": "Q13148",
                "url": "http://purl.uniprot.org/uniprot/Q13148",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000120948",
                "url": "http://www.ensembl.org/id/ENSG00000120948",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 0,
                "identifier": "NP_031401.1",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_031401.1",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000060-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "se"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000060-a-2",
        "variant_count": 714,
        "experiment": "urn:mavedb:00000060-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-08-23",
        "modification_date": "2021-01-18",
        "urn": "urn:mavedb:00000058-a-1",
        "publish_date": "2021-01-18",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the molecular determinants of A$\\beta$ 42 aggregation in a cell-based system, by combining a yeast DHFR aggregation assay with deep mutational scanning. The effect of 791 of the 798 possible single amino acid substitutions on the aggregation propensity of A$\\beta$ 42 was measured using a yeast growth-based aggregation assay. This record contains amino acid level scores.",
        "method_text": "Enrich2 was used to calculate solubility scores for each A$\\beta$ variant from the FASTQ files. Sequencing reads were required to have a Phred score greater than 20 for every base and no uncalled bases. Scoring was performed using a weighted linear least squares regression line fit to the normalized frequency ratios across time points. The score is the slope of the regression line. The three replicates were combined using Enrich2's random-effects model. Solubility scores below 0 denote variants that are more aggregation-prone than wild-type. Scores above 0 indicate that a variant has increased solubility compared to wild-type.",
        "short_description": "Amino acid level scores for molecular determinants of Aβ aggregation with deep mutational scanning",
        "title": "Amino acid scores for Aβ42 variants",
        "keywords": [
            {
                "text": "Enrich2"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "31558564",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31558564",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Aβ42",
            "reference_sequence": {
                "sequence": "GATGCAGAATTCCGACATGACTCAGGATATGAAGTTCATCATCAAAAATTGGTGTTCTTTGCAGAAGATGTGGGTTCAAACAAAGGTGCAATCATTGGACTCATGGTGGGCGGTGTTGTCATAGCG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 670,
                "identifier": "P05067",
                "url": "http://purl.uniprot.org/uniprot/P05067",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000058-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "SE",
            "epsilon"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000058-a-1",
        "variant_count": 2162,
        "experiment": "urn:mavedb:00000058-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-k-1",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\n\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The expression level of alpha-synuclein missense variants was determined by cell sorting of yeast expressing each variant fused to GFP",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Expression Level in Yeast",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41589-020-0480-6",
                "url": "https://doi.org/10.1038/s41589-020-0480-6",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32152544",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32152544",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "alpha-synuclein",
            "reference_sequence": {
                "sequence": "ATGGATGTATTCATGAAAGGACTTTCAAAGGCCAAGGAGGGAGTTGTGGCTGCTGCTGAGAAAACCAAACAGGGTGTGGCAGAAGCAGCAGGAAAGACAAAAGAGGGTGTTCTCTATGTAGGCTCCAAAACCAAGGAGGGAGTGGTGCATGGTGTGGCAACAGTGGCTGAGAAGACCAAAGAGCAAGTGACAAATGTTGGAGGAGCAGTGGTGACGGGTGTGACAGCAGTAGCCCAGAAGACAGTGGAGGGAGCAGGGAGCATTGCAGCAGCCACTGGCTTTGTCAAAAAGGACCAGTTGGGCAAGAATGAAGAAGGAGCCCCACAGGAAGGAATTCTGGAAGATATGCCTGTGGATCCTGACAATGAGGCTTATGAAATGCCTTCTGAGGAAGGGTATCAAGACTACGAACCTGAAGCCTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P37840",
                "url": "http://purl.uniprot.org/uniprot/P37840",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg16",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.10",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000045-k-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000045-k-1",
        "variant_count": 2800,
        "experiment": "urn:mavedb:00000045-k",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-06-16",
        "modification_date": "2022-06-16",
        "urn": "urn:mavedb:00000094-a-14",
        "publish_date": "2022-06-16",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "13. Normalized currents of 62 KCNQ1 missense SNVs in the homozygous state.",
        "method_text": "",
        "short_description": "13. Normalized currents of 62 KCNQ1 missense SNVs in the homozygous state.",
        "title": "Normalized currents of 62 KCNQ1 missense SNVs in the homozygous state",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ1",
            "reference_sequence": {
                "sequence": "MAAASSPPRAERKRWGWGRLPGARRGSAGLAKKCPFSLELAEGGPAGGALYAPIAPGAPGPAPPASPAAPAAPPVASDLGPRPPVSLDPRVSIYSTRRPVLARTHVQGRVYNFLERPTGWKCFVYHFAVFLIVLVCLIFSVLSTIEQYAALATGTLFWMEIVLVVFFGTEYVVRLWSAGCRSKYVGLWGRLRFARKPISIIDLIVVVASMVVLCVGSKGQVFATSAIRGIRFLQILRMLHVDRQGGTWRLLGSVVFIHRQELITTLYIGFLGLIFSSYFVYLAEKDAVNESGRVEFGSYADALWWGVVTVTTIGYGDKVPQTWVGKTIASCFSVFAISFFALPAGILGSGFALKVQQKQRQKHFNRQIPAAASLIQTAWRCYAAENPDSSTWKIYIRKAPRSHTLLSPSPKPKKSVVVKKKKFKLDKDNGVTPGEKMLTVPHITCDPPEERRLDHFSVDGYDSSVRKSPTLLEVSMPHFMRTNSFAEDLDLEGETLLTPITHISQLREHHRATIKVIRRMQYFVAKKKFQQARKPYDVRDVIEQYSQGHLNLMVRIKELQRRLDQSIGKPSLFISVSEKSKDRGSNTIGARLNRVEDKVTQLDQRLALITDMLHQLLSLHGGSTPGSGGPPREGGAHITQPCGSGGSVDPELFLPSNTLPTYEQLTVPRRGPDEGS",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-14",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": "urn:mavedb:00000094-a-15",
        "current_version": "urn:mavedb:00000094-a-15",
        "variant_count": 62,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-18",
        "modification_date": "2021-09-18",
        "urn": "urn:mavedb:00000070-a-1",
        "publish_date": "2021-09-18",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the experimental fitness of variants in the TEM-1 $\\beta$-lactamase gene in _Escherichia coli_. Fitness measurements were estimated based on growth under increasing concentrations of ampicillin using a band-pass selection system.",
        "method_text": "Variant reads were aligned to the template sequence and all codon substitution variants were mapped. Indels were assumed to be sequencing errors and ignored. Reads were removed if the average quality score was less than 30, if the read did not span the full sub-region, or if the read contained mutations in more than one codon.\r\n\r\nReads were counted for each of 13 concentrations of Amp used in the experiment. The raw fitness score $f$ of allele $i$ was calculated as:\r\n\r\n$$ f_i = \\frac{\\sum_{p=1}^{13} c_{i,p} \\log_2\\left(a_p\\right)}{\\sum_{p=1}^{13} c_{i,p}} $$\r\n\r\nVariants with five or fewer total counts were not assigned a fitness value. Additional measures were taken to calculate fitness values for variants with counts at many Amp concentrations (see manuscript SI for details).\r\n\r\nRaw fitness scores were normalized to wild type to get a normalized fitness $w_i$ using:\r\n\r\n$$ w_i = \\frac{2^{f_i}}{2^f_{wt}} $$\r\n\r\nThe wild type fitness score was calculated using the counts of all alleles with synonymous substitutions. Therefore a normalized fitness value of 1.0 is equivalent to wild type, greater than 1.0 is beneficial, and 0 to 1.0 is deleterious. Only the normalized scores were reported.\r\n\r\nThe score for a protein variant was calculated as the average fitness of all equivalent nucleotide variants.\r\n\r\nThe estimated error ('err' column) is based on the percent difference in fitness between the nucleotide variant fitness and the average fitness of the corresponding amino acid variant.\r\n\r\nThe 'ambler' column provides the [Ambler position](https://pubmed.ncbi.nlm.nih.gov/2039479/) of the amino acid .",
        "short_description": "Nucleotide fitness scores for variants in the TEM-1 β-lactamase gene in the presence of ampicillin.",
        "title": "Nucleotide fitness scores of TEM-1 β-lactamase",
        "keywords": [
            {
                "text": "normalized"
            },
            {
                "text": "band-pass selection"
            },
            {
                "text": "resistance"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24567513",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24567513",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TEM-1 β-lactamase",
            "reference_sequence": {
                "sequence": "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P62593",
                "url": "http://purl.uniprot.org/uniprot/P62593",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000070-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "err",
            "ambler"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000070-a-1",
        "variant_count": 18081,
        "experiment": "urn:mavedb:00000070-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-16",
        "modification_date": "2021-09-16",
        "urn": "urn:mavedb:00000069-a-2",
        "publish_date": "2021-09-16",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study used deep mutagenesis to identify ACE2 variants with increased binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein in a cell-based assay. Cells expressing ACE2 variants with high or low binding to RBD were sorted based on fluorescence detection of bound RBD fused to superfolder GFP (sfGFP) and myc-tagged ACE2 expression.",
        "method_text": "Data analysis was performed using Enrich (version unspecified) and commands are provided in the GEO deposit. Log2 enrichment ratios of all 2,340 single amino acid variants in the library were calculated by comparing the frequencies of mutations in the transcripts of the sorted population (nCoV-S-Low) to the naive plasmid DNA library. Values were normalized by the same calculation for wild type (WT) by setting WT as log2 enrichment ratio as 0. Wild type sequences were neither substantially enriched or depleted, and had log2 enrichment ratios of -0.2 to +0.2. Normalized log2 enrichment ratios of  ≤-3 represent depleted/deleterious mutations, while ≥ +3 are enriched and -2 to +2 are neutral. Enrichment ratios serve as a proxy for relative binding to the RBD of SARS-CoV-2. This binding signal is a product both of ACE2 affinity and surface display of properly folded ACE2.",
        "short_description": "ACE2 variants with low binding affinity to the SARS-CoV-2 spike protein.",
        "title": "ACE2 binding to SARS-CoV-2 spike protein, low affinity",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-1494-8030"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "ACE2",
            "reference_sequence": {
                "sequence": "MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKNQMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDNSLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENPYASIDISKGENNPGFQNTDDVQTSF",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "Q9BYF1",
                "url": "http://purl.uniprot.org/uniprot/Q9BYF1",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000069-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "rep1",
            "rep2"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "reads_in_naive_library"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000069-a-2",
        "variant_count": 2341,
        "experiment": "urn:mavedb:00000069-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-09-05",
        "modification_date": "2020-09-05",
        "urn": "urn:mavedb:00000046-a-2",
        "publish_date": "2020-09-05",
        "created_by": "0000-0001-7684-5841",
        "modified_by": "0000-0001-7684-5841",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "MIR2, which targets CD86 for down-regulation, was expressed in cells with CD86 at the cell surface. Cells that remained CD86 positive were sorted. Enrich2 log ratios were calculated with wild-type normalisation to determine which variants were enriched after selection thereby determining which variants were resistant to MIR2-mediated down-regulation.",
        "title": "CD86 susceptibility to MIR2",
        "keywords": [
            {
                "text": "MIR2"
            },
            {
                "text": "CD86"
            },
            {
                "text": "DMS"
            },
            {
                "text": "mRNA"
            },
            {
                "text": "MARCH1"
            },
            {
                "text": "Flow Cytometry"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-7684-5841"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "CD86",
            "reference_sequence": {
                "sequence": "GACCACATTCCTTGGATTACAGCTGTACTTCCAACAGTTATTATATGTGTGATGGTTTTCTGTCTAATTCTATGGAAATGG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 243,
                "identifier": "P42081",
                "url": "http://purl.uniprot.org/uniprot/P42081",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg16",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.10",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000046-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "SE",
            "epsilon",
            "SE_Replicate_1",
            "score_Replicate_1",
            "SE_Replicate_2",
            "score_Replicate_2",
            "SE_Replicate_3",
            "score_Replicate_3"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "Replicate_1_c_0",
            "Replicate_1_c_3",
            "Replicate_2_c_0",
            "Replicate_2_c_3",
            "Replicate_3_c_0",
            "Replicate_3_c_3"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000046-a-2",
        "variant_count": 4360,
        "experiment": "urn:mavedb:00000046-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-16",
        "modification_date": "2021-09-16",
        "urn": "urn:mavedb:00000069-a-1",
        "publish_date": "2021-09-16",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study used deep mutagenesis to identify ACE2 variants with increased binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein in a cell-based assay. Cells expressing ACE2 variants with high or low binding to RBD were sorted based on fluorescence detection of bound RBD fused to superfolder GFP (sfGFP) and myc-tagged ACE2 expression.",
        "method_text": "Data analysis was performed using Enrich (version unspecified) and commands are provided in the GEO deposit. Log2 enrichment ratios of all 2,340 single amino acid variants in the library were calculated by comparing the frequencies of mutations in the transcripts of the sorted population (nCoV-S-High) to the naive plasmid DNA library. Values were normalized by the same calculation for wild type (WT) by setting WT as log2 enrichment ratio as 0. Wild type sequences were neither substantially enriched or depleted, and had log2 enrichment ratios of -0.2 to +0.2. Normalized log2 enrichment ratios of  ≤-3 represent depleted/deleterious mutations, while ≥ +3 are enriched and -2 to +2 are neutral. Enrichment ratios serve as a proxy for relative binding to the RBD of SARS-CoV-2. This binding signal is a product both of ACE2 affinity and surface display of properly folded ACE2.",
        "short_description": "ACE2 variants with high binding affinity to the SARS-CoV-2 spike protein.",
        "title": "ACE2 binding to SARS-CoV-2 spike protein, high affinity",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32753553",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32753553",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-1494-8030"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "ACE2",
            "reference_sequence": {
                "sequence": "MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKNQMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDNSLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENPYASIDISKGENNPGFQNTDDVQTSF",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000069-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "rep1",
            "rep2"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "reads_in_naive_library"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000069-a-1",
        "variant_count": 2341,
        "experiment": "urn:mavedb:00000069-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-03-14",
        "modification_date": "2021-04-15",
        "urn": "urn:mavedb:00000063-a-1",
        "publish_date": "2021-04-15",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the variant effects of <i>E.coli</i> dihydrofolate reductase (DHFR) whose function is necessary for the survival of the bacteria. The study cultured the bacteria in an early Log phase growth period under the control of Lon protease and determined the variant frequency change after cultivation, indicating the impact of DHFR variants.",
        "method_text": "This variant library consists of four sub-libraries which cover different positions in the target protein (40 residues each). Each mutant library is generated by parallel inverse PCR reactions. The libraries are transformed to <i>E.coli</i> with deficient Lon gene by electroporation, and the selection experiments take 2 libraries at a time. Samples after 0, 2, 4, 6, 8, 12, 16 and 18 hours of cultivation are collected and sequenced by Illumina NextSeq. \r\nThe results with less than four timepoints reported and larger standard error from regression are discarded. The rest are analyzed by Enrich2 and normalized. Each sub-library is tested three times and the final scores are the average of them. The results are discarded when there are less than two replicates available or the standard deviation is larger than the threshold.\r\nThe count data records the counts result from transformation rescue medium, overnight outgrowth and each timepoint outgrowth. Each library is tested three times and two of the four libraries are tested at the same time which gives the six repeats in the count data.",
        "short_description": "Growth rate of E.coli with mutated dihydrofolate reductase (DHFR) with functioning Lon protease",
        "title": "Growth rate of mutated DHFR with functioning Lon",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.7554/eLife.53476",
                "url": "https://doi.org/10.7554/eLife.53476",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32701056",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32701056",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "DHFR",
            "reference_sequence": {
                "sequence": "ATGATCAGTCTGATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCCGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATGGGCCGCCATACCTGGGAATCAATCGGTCGTCCGTTGCCAGGACGCAAAAATATTATCCTCAGCAGTCAACCGGGTACGGACGATCGCGTAACGTGGGTGAAGTCGGTGGATGAAGCCATCGCGGCGTGTGGTGACGTACCAGAAATCATGGTGATTGGCGGCGGTCGCGTTTATGAACAGTTCTTGCCAAAAGCGCAAAAACTGTATCTGACGCATATCGACGCAGAAGTGGAAGGCGACACCCATTTCCCGGATTACGAGCCGGATGACTGGGAATCGGTATTCAGCGAATTCCACGATGCTGATGCGCAGAACTCTCACAGCTATTGCTTTGAGATTCTGGAGCGGCGGTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P0ABQ4",
                "url": "http://purl.uniprot.org/uniprot/P0ABQ4",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000063-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "standard deviation",
            "standard error"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "Repeat1_library_transformation",
            "Repeat1_outgrowth",
            "Repeat1_t_00hrs",
            "Repeat1_t_02hrs",
            "Repeat1_t_04hrs",
            "Repeat1_t_06hrs",
            "Repeat1_t_08hrs",
            "Repeat1_t_12hrs",
            "Repeat1_t_16hrs",
            "Repeat1_t_18hrs",
            "Repeat2_library_transformation",
            "Repeat2_outgrowth",
            "Repeat2_t_00hrs",
            "Repeat2_t_02hrs",
            "Repeat2_t_04hrs",
            "Repeat2_t_06hrs",
            "Repeat2_t_08hrs",
            "Repeat2_t_12hrs",
            "Repeat2_t_16hrs",
            "Repeat2_t_18hrs",
            "Repeat3_library_transformation",
            "Repeat3_outgrowth",
            "Repeat3_t_00hrs",
            "Repeat3_t_02hrs",
            "Repeat3_t_04hrs",
            "Repeat3_t_06hrs",
            "Repeat3_t_08hrs",
            "Repeat3_t_12hrs",
            "Repeat3_t_16hrs",
            "Repeat3_t_18hrs",
            "Repeat4_library_transformation",
            "Repeat4_outgrowth",
            "Repeat4_t_00hrs",
            "Repeat4_t_02hrs",
            "Repeat4_t_04hrs",
            "Repeat4_t_06hrs",
            "Repeat4_t_08hrs",
            "Repeat4_t_12hrs",
            "Repeat4_t_16hrs",
            "Repeat4_t_18hrs",
            "Repeat5_library_transformation",
            "Repeat5_outgrowth",
            "Repeat5_t_00hrs",
            "Repeat5_t_02hrs",
            "Repeat5_t_04hrs",
            "Repeat5_t_06hrs",
            "Repeat5_t_08hrs",
            "Repeat5_t_12hrs",
            "Repeat5_t_16hrs",
            "Repeat5_t_18hrs",
            "Repeat6_library_transformation",
            "Repeat6_outgrowth",
            "Repeat6_t_00hrs",
            "Repeat6_t_02hrs",
            "Repeat6_t_04hrs",
            "Repeat6_t_06hrs",
            "Repeat6_t_08hrs",
            "Repeat6_t_12hrs",
            "Repeat6_t_16hrs",
            "Repeat6_t_18hrs"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000063-a-1",
        "variant_count": 3132,
        "experiment": "urn:mavedb:00000063-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-08-07",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000040-a-2",
        "publish_date": "2019-08-07",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effect of variants in yeast HSP90 under different combinations of temperature (30C or 36C) and presence/absence of salt (0.5 M NaCl). The results explore the adaptive potential of this essential gene.",
        "method_text": "Sequencing reads were filtered based on a minimum Phred quality score of 20 across all 36 bases. For each time point, the log2 ratio of each variant's count to the wild type count was calculated. The score of each variant was calculated as the slope of these log ratios to time in wild type generations. Scores of -0.5 are considered null-like.",
        "short_description": "Deep mutational scan of all single mutants in a nine-amino acid region of Hsp90 (Hsp82) in Saccharomyces cerevisiae at 30C with 0.5 M NaCl.",
        "title": "Deep mutational scan of HSP90, 30C with salt",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24299404",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24299404",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "HSP90",
            "reference_sequence": {
                "sequence": "CAATTTGGTTGGTCTGCTAATATGGAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 581,
                "identifier": "P02829",
                "url": "http://purl.uniprot.org/uniprot/P02829",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000040-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000040-a-2",
        "variant_count": 189,
        "experiment": "urn:mavedb:00000040-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-20",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000034-b-1",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {
            "chr": "7",
            "end": 156791604,
            "start": 156791119,
            "reference": "hg38"
        },
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "The effect of each variant was calculated using a multiple linear regression model based on the DNA counts and RNA counts. Each variant needed to have 10 unique barcode tags to be included in the downstream analyses.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>\r\n\r\nMetadata contains the genomic coordinates for the target sequence.\r\n\r\nColumn descriptions:\r\n\r\n- 'score' is the Log2 variant expression effect derived from the fit of the linear model (coefficient).\r\n- 'p-value' is the P-value of the coefficient.\r\n- 'unique_tags' is the number of unique tags associated with the variant.\r\n- 'dna_sequences' is the count of DNA sequences that contain the variant (used for fitting the linear model).\r\n- 'rna_sequences' is the count of RNA sequences that contain the variant (used for fitting the linear model).",
        "short_description": "Saturation mutagenesis MPRA of ZRS enhancer in NIH3T3 cells. Co-transfected with Hoxd13 and Hand2.",
        "title": "Saturation mutagenesis MPRA of ZRS enhancer, Hoxd13+Hand2",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "ZRS enhancer",
            "reference_sequence": {
                "sequence": "TGAGATATGGCTTCATTTTCTGTAATAAACACTAAGATCAAAACATGACCCAAGTTAAATTTCCTTGCAGGGTTCCCAGCAGGGGCTTCCCTTTTGTCTGTGATTTCCTCTCACCCACCAGAACCAGGCCAAATATGCGCATGTGCCACTAACACTAAGCAGCACTTCCTTAATCACTCATTTCCAACAATTTATGGATCATCAGTGGCAAAAAACGAGCAAAAATAATGAAAGAATGCAATGAAAGCTCGTGGAGACAGAGGCTGGACTTCCTACTCACTCTGTGTCTCTTTAAGATGGAGGCCTGATACAAATTAGCCACTGGGGGGAAAAAGTCATCTGGTCATAAAATACAGTACAAGGTCACTTTTATGTAAGTTTGCCAAAAGGGACATAAACCAGGACAATTTCAAACTGTGACACAGGATAGAAACATATTAAAAAAATCTTTGTTCCTCCTCTATTGTGCTGTCATGTTGCTCAGCA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000034-b-1",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "p-value",
            "unique_tags",
            "dna_sequences",
            "rna_sequences"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000034-b-1",
        "variant_count": 1662,
        "experiment": "urn:mavedb:00000034-b",
        "is_meta_analysis": false,
        "data_usage_policy": "We are making our data available prior to publication in line with Fort Lauderdale principle, allowing others to use the data but allowing the data producers to make the first presentations and to publish the first paper with global analyses of the data. In addition, we also reserve the right to publish the first analysis of the differences seen in the TERT knock-down experiments and alternative cell-type experiments. Studies that do not overlap with these intentions may be submitted for publication at any time, but must appropriately cite the data source. After publication of the data, the first publication of the data producers should be cited for any use of these data."
    },
    {
        "creation_date": "2020-11-20",
        "modification_date": "2020-11-20",
        "urn": "urn:mavedb:00000049-a-8",
        "publish_date": "2020-11-20",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "A deep mutational scan of human MTHFR via functional complementation in yeast at 200ug/ml folate in A222V background",
        "title": "MTHFR at 200ug/ml folate in A222V background",
        "keywords": [
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "homocystinuria"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1628-9390",
            "0000-0002-9219-4310",
            "0000-0002-2550-2141",
            "0000-0001-6465-5776"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MTHFR",
            "reference_sequence": {
                "sequence": "ATGGTGAACGAAGCCAGAGGAAACAGCAGCCTCAACCCCTGCTTGGAGGGCAGTGCCAGCAGTGGCAGTGAGAGCTCCAAAGATAGTTCGAGATGTTCCACCCCGGGCCTGGACCCCGAGCGGCATGAGAGACTCCGGGAGAAGATGAGGCGGCGATTGGAATCTGGTGACAAGTGGTTCTCCCTGGAATTCTTCCCTCCTCGAACTGCTGAGGGAGCTGTCAATCTCATCTCAAGGTTTGACCGGATGGCAGCAGGTGGCCCCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCCTGGCTCAGACAAGGAGACCTCCTCCATGATGATCGCCAGCACCGCCGTGAACTACTGTGGCCTGGAGACCATCCTGCACATGACCTGCTGCCGTCAGCGCCTGGAGGAGATCACGGGCCATCTGCACAAAGCTAAGCAGCTGGGCCTGAAGAACATCATGGCGCTGCGGGGAGACCCAATAGGTGACCAGTGGGAAGAGGAGGAGGGAGGCTTCAACTACGCAGTGGACCTGGTGAAGCACATCCGAAGTGAGTTTGGTGACTACTTTGACATCTGTGTGGCAGGTTACCCCAAAGGCCACCCCGAAGCAGGGAGCTTTGAGGCTGACCTGAAGCACTTGAAGGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGCTTTTCTTTGAGGCTGACACATTCTTCCGCTTTGTGAAGGCATGCACCGACATGGGCATCACTTGCCCCATCGTCCCCGGGATCTTTCCCATCCAGGGCTACCACTCCCTTCGGCAGCTTGTGAAGCTGTCCAAGCTGGAGGTGCCACAGGAGATCAAGGACGTGATTGAGCCAATCAAAGACAACGATGCTGCCATCCGCAACTATGGCATCGAGCTGGCCGTGAGCCTGTGCCAGGAGCTTCTGGCCAGTGGCTTGGTGCCAGGCCTCCACTTCTACACCCTCAACCGCGAGATGGCTACCACAGAGGTGCTGAAGCGCCTGGGGATGTGGACTGAGGACCCCAGGCGTCCCCTACCCTGGGCTCTCAGCGCCCACCCCAAGCGCCGAGAGGAAGATGTACGTCCCATCTTCTGGGCCTCCAGACCAAAGAGTTACATCTACCGTACCCAGGAGTGGGACGAGTTCCCTAACGGCCGCTGGGGCAATTCCTCTTCCCCTGCCTTTGGGGAGCTGAAGGACTACTACCTCTTCTACCTGAAGAGCAAGTCCCCCAAGGAGGAGCTGCTGAAGATGTGGGGGGAGGAGCTGACCAGTGAAGAAAGTGTCTTTGAAGTCTTCGTTCTTTACCTCTCGGGAGAACCAAACCGGAATGGTCACAAAGTGACTTGCCTGCCCTGGAACGATGAGCCCCTGGCGGCTGAGACCAGCCTGCTGAAGGAGGAGCTGCTGCGGGTGAACCGCCAGGGCATCCTCACCATCAACTCACAGCCCAACATCAACGGGAAGCCGTCCTCCGACCCCATCGTGGGCTGGGGCCCCAGCGGGGGCTATGTCTTCCAGAAGGCCTACTTAGAGTTTTTCACTTCCCGCGAGACAGCGGAAGCACTTCTGCAAGTGCTGAAGAAGTACGAGCTCCGGGTTAATTACCACCTTGTCAATGTGAAGGGTGAAAACATCACCAATGCCCCTGAACTGCAGCCGAATGCTGTCACTTGGGGCATCTTCCCTGGGCGAGAGATCATCCAGCCCACCGTAGTGGATCCCGTCAGCTTCATGTTCTGGAAGGACGAGGCCTTTGCCCTGTGGATTGAGCGGTGGGGAAAGCTGTATGAGGAGGAGTCCCCGTCCCGCACCATCATCCAGTACATCCACGACAACTACTTCCTGGTCAACCTGGTGGACAATGACTTCCCACTGGACAACTGCCTCTGGCAGGTGGTGGAAGACACATTGGAGCTTCTCAACAGGCCCACCCAGAATGCGAGAGAAACGGAGGCTCCATGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P42898",
                "url": "http://purl.uniprot.org/uniprot/P42898",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000177000",
                "url": "http://www.ensembl.org/id/ENSG00000177000",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 230,
                "identifier": "NM_005957",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_005957",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000049-a-8",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "se"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000049-a-8",
        "variant_count": 12141,
        "experiment": "urn:mavedb:00000049-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-11-11",
        "modification_date": "2021-11-11",
        "urn": "urn:mavedb:00000087-a-1",
        "publish_date": "2021-11-11",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Deep mutational scan of Influenza Nucleoprotein, selecting for viral replication in human MDCK-SIAT1-CMV-PB1 cells.",
        "method_text": "Site-specific amino acid preferences were calculated using MCMC implemented by the `mapmuts` package. The score is the site-specific amino acid preference for that position, so all scores for a given position sum to 1.\r\n\r\nScores for the N-terminal methionine are included, but this position was not mutagenized.",
        "short_description": "Site-specific preferences for deep mutational scan of Influenza A (H3N2 Aichi/1968) Nucleoprotein for viral replication.",
        "title": "Influenza A nucleoprotein",
        "keywords": [
            {
                "text": "Influenza"
            },
            {
                "text": "Viral replication"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24859245",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24859245",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-8037-6045"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "NP",
            "reference_sequence": {
                "sequence": "MASQGTKRSYEQMETDGERQNATEIRASVGKMIDGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYKRVDRKWMRELVLYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDTTYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRKTRSAYERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGPAVASGYDFEKEGYSLVGIDPFKLLQNSQVYSLIRPNENPAHKSQLVWMACNSAAFEDLRVLSFIRGTKVSPRGKLSTRGVQIASNENMDAMESSTLELRSRYWAIRTRSGGNTNQQRASAGQISVQPAFSVQRNLPFDKPTIMAAFTGNTEGRTSDMRAEIIRMMEGAKPEEMSFQGRGVFELSDERAANPIVPSFDMSNEGSYFFGDNAEEYDN",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "I6TAH8",
                "url": "http://purl.uniprot.org/uniprot/I6TAH8",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000087-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000087-a-1",
        "variant_count": 9960,
        "experiment": "urn:mavedb:00000087-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-11-11",
        "modification_date": "2020-11-11",
        "urn": "urn:mavedb:00000047-c-1",
        "publish_date": "2020-11-11",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilised site-saturation mutagenesis (SSM) to measure the functional consequences of mutations in the human chemokine receptor, CCR5 and to map ligand interaction sites. Cells were selected for binding to HIV-1~BaL~ gp120-CD4.",
        "method_text": "Data obtained from sorting cells for both surface expression and HIV-1~BaL~ gp120-CD4 interaction was analysed using Enrich (version unspecified). Log~2~ enrichment ratios were calculated and normalised by subtracting the frequency of the WT sequence. Log~2~ enrichment ratios for two replicates were averaged to obtain variant scores. Note that the scores here were not reported in the manuscript tables, but were calculated from the replicate enrichment ratios that were reported.",
        "short_description": "Deep mutational scan selecting for CCR5 binding to HIV-1(BaL) gp120-CD4 in Expi293F cells.",
        "title": "CCR5 HIV binding",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29678950",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29678950",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-6681-7994"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "CCR5",
            "reference_sequence": {
                "sequence": "GATTATCAAGTGTCAAGTCCAATCTATGACATCAATTATTATACATCGGAGCCCTGCCAAAAAATCAATGTGAAGCAAATCGCAGCCCGCCTCCTGCCTCCGCTCTACTCACTGGTGTTCATCTTTGGTTTTGTGGGCAACATGCTGGTCATCCTCATCCTGATAAACTGCAAAAGGCTGAAGAGCATGACTGACATCTACCTGCTCAACCTGGCCATCTCTGACCTGTTTTTCCTTCTTACTGTCCCCTTCTGGGCTCACTATGCTGCCGCCCAGTGGGACTTTGGAAATACAATGTGTCAACTCTTGACAGGGCTCTATTTTATAGGCTTCTTCTCTGGAATCTTCTTCATCATCCTCCTGACAATCGATAGGTACCTGGCTGTCGTCCATGCTGTGTTTGCTTTAAAAGCCAGGACGGTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGAATCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTCTCATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAAAGATAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTCATGGTCATCTGCTACTCGGGAATCCTAAAAACTCTGCTTCGGTGTCGAAATGAGAAGAAGAGGCACAGGGCTGTGAGGCTTATCTTCACCATCATGATTGTTTATTTTCTCTTCTGGGCTCCCTACAACATTGTCCTTCTCCTGAACACCTTCCAGGAATTCTTTGGCCTGAATAATTGCAGTAGCTCTAACAGGTTGGACCAAGCTATGCAGGTGACAGAGACTCTTGGGATGACGCACTGCTGCATCAACCCCATCATCTATGCCTTTGTCGGGGAGAAGTTCAGAAACTACCTCTTAGTCTTCTTCCAAAAGCACATTGCCAAACGCTTCTGCAAATGCTGTTCTATTTTCCAGCAAGAGGCTCCCGAGCGAGCAAGCTCAGTTTACACCCGATCCACTGGGGAGCAGGAAATATCTGTGGGCTTG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 1,
                "identifier": "P51681",
                "url": "http://purl.uniprot.org/uniprot/P51681",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000047-c-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "rep1",
            "rep2"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000047-c-1",
        "variant_count": 7020,
        "experiment": "urn:mavedb:00000047-c",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-11-04",
        "modification_date": "2021-11-04",
        "urn": "urn:mavedb:00000086-c-1",
        "publish_date": "2021-11-04",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study examined the fitness effects of single amino acid mutations in TEM-1 β-lactamase in *Escherichia coli* under selection for ampicillin resistance or cefotaxime resistance.",
        "method_text": "Scores were calculated as the fitness value $F_i^a$ for an amino acid change $a$ at position $i$. The counts $N$ from either the selection condition or the unselected 0 μg/ml condition were used for the variant or wild-type TEM-1:\r\n\r\n$$F_i^a = \\log_{10} \\left( \\frac{N_i^{a,sel}}{N_i^{a,unsel}} \\right) -  \\log_{10} \\left( \\frac{N_i^{wt,sel}}{N_i^{wt,unsel}} \\right)$$\r\n\r\nTwo replicate selections were performed. The first replicate’s fitness is presented as the score, and the second replicate’s fitness is included as an additional column.",
        "short_description": "Effects of TEM-1 mutations on ampicillin resistance at 156 μg/ml",
        "title": "TEM-1 156 μg/ml Amp",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25723163",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25723163",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TEM-1 β-lactamase",
            "reference_sequence": {
                "sequence": "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P62593",
                "url": "http://purl.uniprot.org/uniprot/P62593",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000086-c-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "rep_score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000086-c-1",
        "variant_count": 4997,
        "experiment": "urn:mavedb:00000086-c",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-02-24",
        "modification_date": "2022-05-15",
        "urn": "urn:mavedb:00000094-a-8",
        "publish_date": "2022-05-15",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "Normalized currents of co-expressing 43  current-enhanced variants with WT.",
        "method_text": "Normalized currents of co-expressing 43  current-enhanced variants with WT.",
        "short_description": "7. Normalized currents of co-expressing 43  current-enhanced variants with WT.",
        "title": "Normalized currents of co-expressing 43  current-enhanced variants  with WT",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ4",
            "reference_sequence": {
                "sequence": "MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGGGSPRRLGLLGSPLPPGAPLPGPGSGSGSACGQRSSAAHKRYRRLQNWVYNVLERPRGWAFVYHVFIFLLVFSCLVLSVLSTIQEHQELANECLLILEFVMIVVFGLEYIVRVWSAGCCCRYRGWQGRFRFARKPFCVIDFIVFVASVAVIAAGTQGNIFATSALRSMRFLQILRMVRMDRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLVYLAEKDANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAGILGSGFALKVQEQHRQKHFEKRRMPAANLIQAAWRLYSTDMSRAYLTATWYYYDSILPSFRELALLFEHVQRARNGGLRPLEVRRAPVPDGAPSRYPPVATCHRPGSTSFCPGESSRMGIKDRIRMGSSQRRTGPSKQHLAPPTMPTSPSSEQVGEATSPTKVQKSWSFNDRTRFRASLRLKPRTSAEDAPSEEVAEEKSYQCELTVDDIMPAVKTVIRSIRILKFLVAKRKFKETLRPYDVKDVIEQYSAGHLDMLGRIKSLQTRVDQIVGRGPGDRKAREKGDKGPSDAEVVDEISMMGRVVKVEKQVQSIEHKLDLLLGFYSRCLRSGTSASLGAVQVPLFDPDITSDYHSPVDHEDISVSAQTLSISRSVSTNMD",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-8",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000094-a-8",
        "variant_count": 43,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-08-07",
        "modification_date": "2019-08-07",
        "urn": "urn:mavedb:00000039-a-2",
        "publish_date": "2019-08-07",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effects of yeast HSP90 variants under the control of different promoters to explore the relationship between protein sequence and expression level. The results showed that reduced expression level (compared to wild-type expression) revealed new partial loss of function mutations.",
        "method_text": "Growth rates were calculated for each variant and converted into selection coefficients. The selection coefficient for each variant under control of this promoter/UTR combination is reported as the score. For variants with multiple synonymous codons, the reported coefficient is the average of all synonymous variant's selection coefficients.\r\n\r\nVariants annotated as \"null-like\" have a score of -1.",
        "short_description": "Deep mutational scan of all single mutants in a nine-amino acid region of Hsp90 (Hsp82) in Saccharomyces cerevisiae under the control of the ADH promoter, no 3'UTR added.",
        "title": "Deep mutational scan of HSP90, ADHdter construct",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "promoter"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23825969",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23825969",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "HSP90",
            "reference_sequence": {
                "sequence": "CAATTTGGTTGGTCTGCTAATATGGAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 581,
                "identifier": "P02829",
                "url": "http://purl.uniprot.org/uniprot/P02829",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000039-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000039-a-2",
        "variant_count": 185,
        "experiment": "urn:mavedb:00000039-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-08-08",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000041-b-1",
        "publish_date": "2019-08-08",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study infers the activity of variants in Src kinases's SH4 domain by measuring their effects on yeast growth, and therefore phosphotransferase activity. The resulting dataset includes variants classified as gain of function, loss of function. or neutral.",
        "method_text": "Variant scores were calculated using Enrich2 weighted least squares regression and wild-type normalization. The `activity_score` is `-1 * score`, because negative scores indicate depletion in the population, which is associated with higher kinase activity.\r\n\r\nVariants were classified as \"gain of function\" \"neutral\" or \"loss of function\" based on whether they were within +/- 2 standard deviations of the mean score of synonymous variants (variants with wild type amino acid sequence). These categories are denoted by 1, 0, or -1 in the table respectively.",
        "short_description": "Amino acid scores for deep mutational scan of the Src kinase catalytic domain.",
        "title": "Deep mutational scan of Src SH4",
        "keywords": [
            {
                "text": "kinase"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "Enrich2"
            },
            {
                "text": "NNK mutagenesis"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30956043",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30956043",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Src SH4 domain",
            "reference_sequence": {
                "sequence": "GGTAGCAACAAGAGCAAGCCCAAGGATGCCAGCCAGCGGCGCCGCAGCCTGGAG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 1,
                "identifier": "P12931",
                "url": "http://purl.uniprot.org/uniprot/P12931",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000041-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "std",
            "epsilon",
            "activity_score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000041-b-1",
        "variant_count": 360,
        "experiment": "urn:mavedb:00000041-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-o-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 18, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 18 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 18 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 18",
            "reference_sequence": {
                "sequence": "TGTAACCTGTCTTTTCTATGATCTCTTTAGGGGTGACCCAGTCTATTAAAGAAAGAAAAATGCTGAATGAGGTAAGTACTTGATGTTACAAACTAACCAGA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-o-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-o-1",
        "variant_count": 294,
        "experiment": "urn:mavedb:00000097-o",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-a-1",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\n\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with MG-132",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "alpha-synuclein",
            "reference_sequence": {
                "sequence": "ATGGATGTATTCATGAAAGGACTTTCAAAGGCCAAGGAGGGAGTTGTGGCTGCTGCTGAGAAAACCAAACAGGGTGTGGCAGAAGCAGCAGGAAAGACAAAAGAGGGTGTTCTCTATGTAGGCTCCAAAACCAAGGAGGGAGTGGTGCATGGTGTGGCAACAGTGGCTGAGAAGACCAAAGAGCAAGTGACAAATGTTGGAGGAGCAGTGGTGACGGGTGTGACAGCAGTAGCCCAGAAGACAGTGGAGGGAGCAGGGAGCATTGCAGCAGCCACTGGCTTTGTCAAAAAGGACCAGTTGGGCAAGAATGAAGAAGGAGCCCCACAGGAAGGAATTCTGGAAGATATGCCTGTGGATCCTGACAATGAGGCTTATGAAATGCCTTCTGAGGAAGGGTATCAAGACTACGAACCTGAAGCCTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P37840",
                "url": "http://purl.uniprot.org/uniprot/P37840",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg16",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.10",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000045-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000045-a-1",
        "variant_count": 2800,
        "experiment": "urn:mavedb:00000045-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-0-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the normalized scores for the full BRCA1 saturation genome editing (SGE) experiment as originally published. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "The LOESS-corrected log2 ratio scores for each exon were normalized across exon replicates and then normalized across all exons in the assay. The scores within each replicate exon were linearly rescaled so that the median synonymous and median nonsense variant scores within each replicate would match the median synonymous and medain nonsene variant scores across replicates. The result is that each exon’s median synonymous and median nonsense variant function score matches the global median across the full dataset.",
        "short_description": "BRCA1 SGE normalized scores for all exons",
        "title": "BRCA1 SGE Normalized Scores",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Locus",
            "reference_sequence": {
                "sequence": "AAGTTCATTGGAACAGAAAGAAATGGATTTATCTGCTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATTCCTATGATTATCTCCTATGCAAATGAACAGAATTGACCTTACATACTAGGGAAGAAAAGACATGTCTAGTAAGATTAGGCTATTGTAATTGCTGATTTTCTTAACTGAAGAACTTTAAAAATATAGAAAATGATTCCTTGTTCTCCATCCACTCTGCCTCTCCCACTCCTCTCCTTTTCAACACAAATCCTGTGGTCCGGGAAAGACAGGGACTCTGTCTTGATTGGTTCTGCACTGGGGCAGGAATCTAGTTTAGATTAACTGGCATTTTGGCTTTTCTTCCAGCTCTAAAACAAGCTCCATCACTTGAAATGGCAAAATAAAATCATGGATGAGGCCGAGGGCGGTGGCTTATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGTAGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCCAACATGGTGAAACCCCCTCTCCACTAAAAATACAAAAATTAGCTGGGCGTAGTGGCATGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCACTTGAACCAGGAGGCAGATGTTGCTGTGAGCCAATATGGCACCACTGAACTCCAGCGACAGAGCTAAACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAACATGGATGATCGGTGTCGTTGAGAGGATAGGTATTTGGAAGAACCTTTGTTTGAAACTGGCTCTGTACATACAATGAAATTACATACTTATTTACATACAATGAAATGCAGAGGTTTTTTTTTTATATAGGATCTCTGTCGAGAGGCTGGAGTGCAGTGGTGCTATCACAGCTCACTGCAGCCTCAACCTCGTCAGGCTCAAGCAATCCTCCCACCTCAGCCTCCAGAGTAGCAGGGACGATAGGTGTGCACCACCATGCCCAGCTAATTTTTGTATTTTTTTTTCTTTTTTTGAGATGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCGCGATCTCAGCTCACTGCAAACTCTGCCTCCCGGGTTCATGCCATTCTTCTGCCTGAGCCTCCTGAATAGCTGGGACTACAAGCACCCACTACCACGCCCGGCTAATTTTTTGTATTTTTTTTTCTTTTTTAGTAGAGGCGGGATTTCACCGTGTTAGCCAGGATAGTCTTGATCTCCTGACCTTGTGATCCACCCGCCTGGGCCTCCCAAAGTGCTAGGATTACAGGCATAAGCCACTGCGTCCAGCCATTCTTGTATTTTTCTGTTGTAGAGATAGGGTTTTGCTATGTTGGCCATGCTGGTCTCAAACTCCTGACCTCAAGTGATCTACCCTCCCTTGGCCTCTCAAGGTGCTGGGATTACAGGCCTGAGCCATTGCACCCAGCCATGGTCTAAAAATCTTGATTGAAATACCACCTTTTCATTTCCAGACACCCCTATTTAAAATTACCACACCCCCAGCACACACTTTATCTTCTATTCCTGCTGCTTCTCCATAACACTGATTACTAGCTGACATTCTATGTAATGTATCCATTTTTTATCTCTAGTCCCACAGAATGTAAACTCCAGGATGGGATTTTTGTTTTGTTTACATACATCTGTATGTTCAGTAGTTAGAACGGTACTTGGGACCTAGTTGCCACTCAATAAACATTTGTCAAATAAATAATAAACTAAACTAAATTAGTTCTTTAATTTTTTTAAATATGGTGATGGTTAGTAGTGAGTAACATTCAAAAAATAAGTTGAAAAGTTGTACCATTGCCTCTTACCCACAATAAAAAAGGGTAAATTCTTTTCTGCTTTATGAAAGTTGTTTTTCATATTTGAAGTCAAGTTAATCAGATTAAGGAAAATGTATGTTGTGTTTTCAGAGCGATACAAGATTTATAAATAACCATCCTCTCCCTTGCCCTTCAACATTATAGCTAAACAAAAATAAGAGGAAAACAGGATTCACAATTTATCAATTTATTGAAAATCAGAGCCAGAGAAGCAGGAAATGACATTGTAGGAAAAAACTGCTTTTGAAAAAGCACAAAACTTACTCATGACAATCAGTGATCAGGAAAATCCTCAATAGTGTGGCATTTGGATACATTTATGTTTCATTTCCATGGGAGAGAGTCATAAAAATAGGATGTTCTTTCTCATTCTGGCAAATTAAACCATCAATTAAAAACTCAGATACATAAAAATTAAAGATGTAAGAATGAAAATGCTAAATTGTTATTTTCAATCAACTATTATGTTTTCTAGCTTTTCATTGCTTTTTTCTGTTTCCTGTTAAGATTAATTTCTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGACTTTGGCTCTTGTTGCCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTACAACCTCCACCTCCCGGGTTCAAGCAATTCTGCTGCCTCAGCCTCCGGAGTACCTGGGATTGCAGGCATGTGCCATCACACCAGCTAATTTTGTATTTTTAGTAGAGACAGGGTTTCTCCATATTGGTCAGGTTGGTCTCGAACTCCTGACCTCAGGTGATCCTCCTGCCTTGGCCTCCGAAAGTGCTGGGATTACAGGCGTGAGCCACCGCTCCCAGACTTTTTGTTTTGTTTTGTTTTGTTTTTTTGAGACACGGTCTCGCTCTGCTGCCTAGGCTGGAGTGCAGTGGCACGATCTTGGCTCACTGCCAGCTCCGCCTCCCGGGTTCAGGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCACCACTATGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTAGCCAAGATGGTCTCGATCTCCTGACCTTGTGATCCACCCGCCTCAGCCTTCCAAAGTGCTGGGATTACAGTCCTGAGCCACTGCGCCCGGCCTGGACCTTTTTTTTTCGGGGTGGGGGGTTGGAGTCTGGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCCATCTTGGCTCACTGCAACCTCCGCCTGCCAGGTTCAAGTTCAAGCGCTTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTATAGGCGCACGCCACCGTGGCCGGCTAATTTTGTATTTTTAGTAGAGATAGGGTTTCATCACGTTGGTCAGGCTGGTCTTGAAGTCCTGATCTCGTGATCCACCCGCCTCGGCCTTCCAAAGTGCTGGCGTGAGCCACTGCGCCTGGCTTAAGATTAATTTTTGTTTGTTTTGTTTTTGAGACGGAGTCTCGCTCTTTCACCCAGGCCGGAGTGCAGTGGCGCCATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCGGCCCCCCAAGTAGCTGGGACTACAGGCGTCCACCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCCACTTCCTGACCTCGTGATCCGCCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTAAGATTAATTTTTATGGTGTTTTACATTCATTTGTATGGAAAGTTCTAGGATAGGGATCATATTTCACTTCCTTTTAATATAGTACAGTATAGCACAATTTGCAGTTATGTCTTAATATGTGATCAGGAATGATCATGACTGGAAACAGTGTTATTTGTGGTAGCTATAGGGTAGGTAAGGTTTTCAGCCTGTTTTAGGTTTCTTGAACTAAAATTCCTTCTGCTGTCTTCTAAGTCAATATTGGCAGCTATTTCTGACAATTGGTAGTTCTTTGTAACTTTTTACCTATGACTATAACATTTTTGACTTTCAGAAGAATTTGCTAAAATGTGTTCCCCGGTGGGTTGTTGTTTTTCAACCTAAACCTAGCTGCTTTTTCCAGTCACTTATCCGTATTGGAAGCTCAAAATGCAAATATACAGTAGGCCTAAAATATTGCCTGGTTTGAAAAGTGTTTAAAATATTTGAATCATTTTTATAGTAAACATTTACTCTCATCAGGACCTAGAAGGGGAACATTTTAATTTTTTTTCTTTTCCCTTTTCACAGTCTTCCTTCAACATTCATTACCTTTTTACATATCGGAGTTTTCATCTGTTCAAAGTTTGTGTTTACAGTGTGTTTATATAGTTTAGATTATAATTACCATACTGAAATATAATTGTTTCAGAATTGAGTCAGTGGTGAGAATGAAAGCCATCTGGTATGATAACTGAATCCAATTTTTCTTTTACGGAGAATTTCTTTGAAATGTAGCTTATCTCAGAAATAGGGATTTAGTAACCAATCAGAGTTTTCTTTGTCAAGGTTGTTTTTCTTTTTAAAGTCACATTTGGTCCCAGTAATAATACCAATGTTGGTACAAGTTATCTCAGGTTGTGAAGCATTTTTCCCAAGTCATCTCAGGTTGTGAAGCATTTTCCCAAGTAGCATTTAATTTTATTCTTGCAATAGCCCAAGGAGTCTGGCAGGGTGAATGGCAAGAGAAGGAAACAGGTTCAGGTAGAGTGGTTAGCCCAAGGTGGCTCTGCTTATATACACAACTGGTAGTAGAAACCCAGCCTCCTGACTTAGTTCATTGTTTTTCTTTTCACTGCCCTGTGCTATGTCAAAAACCCCATGATTACAAGAGTTGTATTACAACCCTTCACAATAAGGTTACTGTCCACAAGCTTTTCTTGTGATCCTTTTCTTTTTTTTTTTTCTTTTTTTGAGATGGATTCTCTGTCACCCAGGCTGGCCCGCCTTGGCCTCCCAAAATGCTGGGATTACAGCGTGAGCCACCGCACCTGGCCCTTGTGATCCTTTTCTAAAAAGTTAAATATTTAAGGAAAAAACCACATTCTTGTCACACTGCCAGGTTAGTCGTTCTTTGATATCTTGCCTGGACTTTATCCAAAAAATCCGTTTCAAAAATTCACATTTAGAGCTAAGTGTAGTGGCTCACGCCTGTAATCCCGGTCGAGGCAGATGGATCACTTGAGGTCAGGACTTCAAGACCAGCCTGGGCAATATGGTGAAACCCCTTCCCTACCAAAAATACAAAAAAATTAGCCGGGTGTGGCAGCACGCGCCTGTAGTCCCAGCTACTTGGAATGCTGAGGCACAAGAATCACTTCAATCCGAGAGGCAGAGGTTGCAGTGAGCCAAGACCACACCACTGCACTCCAGCCTGAGCAGCAGAGTGAGTGAGACTCCATCTCCAAAAAAAAAAAAAAAGGTTCACATTCAGAAGAAAGCTAAAGGCCGGGTATAGTAGCTCACACCTGTAATCCCAGCACTTTGGGAAGCCGAAGCAGGAAGATTGCTTGATGCCAGGCATTCAAGACCAGCATGGGCATCATAGTGAGATCCTGTCTCTACAAAAATTAATTAACATTAAAAATTAAAAAGATGGCTGGCATGGTGGCTCACTCCTGTAATCCCAGTACTTTGGGAGGCCAAGGCATGGTGGTGCATGCCTTTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAATTCAGGAGGCGGAGGTTACAGAGAGCCGAGATGGTGCCACTGCACTCCAGCCTGGGCGACAGAACGAGACTCTGTCTGAAAAAAAAAAAGAAAATTAAAAAGACCAGAATAAAGCTAAAGATTTAAAATAGCCTATAGGTTCCTACCAGAAGTTACCAGCTACCTCTCTGATAGTCTTTCCCTACAATATCCTCCTGGATTATTACATTTTAGCACCTTGACCTATCTGATGTCCTGCATACACAGGCATGGTCCTGCTCAGGGTTTGCCTTCTCTGCTCCCTCTTTCTTGGAATGCTCTTCCCCTAATTGTTGCATAGTGTGTTTCTTTACATTATTAAGCTATCCTCTAGTCTCACCTCAGTGAAACCTTTCCTGACTCCCCCCATGTACATCTCACCCCCACATAGATATTGAACTACCTGTTTCCCCTTACCCTGCTTAATTTTTCTCTTTAATGCACTTATTCCCATGTATTCTTTAATTCCGTATCAACTGTCTACCACACTAGAATATGAGCTCTATGAGAGCAGGCTTTATTTTGTAAACTGCTACATTTCTATCTCCTAGAATAGTACTTGAATATAGTAGTAGATACTTAATAAACACTTGTTATATTAGTATAATAAATGAACTAATCTCAGGAATGCCTTGGTTTTGTGGATAGACAGGTAGGGATGGGAACTTGGGTGATGTATTTTCTGAAGTTTTTATTTTTAAGCTTATTATTATTTTGAGATGGAGTCCAGCTCTGTCGCCCAGGTTGGAGTACAGTGGCGCGATCTTGGCTCACTGCAACGTGCACTTCCCCGGTTCAAGCGATTCTCCTGCCTTAGCCTCCCAAGTAGCTGGGATTACAGGCGCATGCCACCATGCCCAGTTAGTTTTGGTATTTTTAGTAGAGACAGCGTTTCACTGTGTTGGCCAGGCTGGTCTCGAAATCCTGACCTCATGATCCGCCCGCCTCGGCCTCCCAAGTGCTGGGATTACAAGCATGAGCCCCCGTGTCTGGCCTTATTTTCTTTTTTTTGAGACAGAGTCTTCCTCTGTCACCTAGGCTGGAGTGCAGTGGCACGATATTGGCTCACTCTGCAACCTCCACCTCCAGGATTCAAGTGATCCTTCTACCTTAGTCTCCAAAGTAGCTGAGACCACAGGCATGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGCGTAGACAGGGTTTCACCATATTGTCCAGGATGATCTGGAACTCCTGAGCTCAGGTGATCCACCCACCTCAGCCTCCCAAAGTGCTAGGATTACAGGCATGAGGCACCATGCCCGGCCTTAAGCTTATCATTTTCTAAATTTCCTTTAGTGAGTACTTATTACACTGTTTTTACAAAGTAATCACAAACCAAACATCATGCCTCTTCTGAAGTGATCTAATAAGAGTACACAGTACCATCTGTAAAGTGTTCTTGCCAGAAAGTTGAACCTGAATGATTAAGCCTGTAAGTCTAGTTTATAGGAAATAAGGCTAGAGGAACAAGTTAAACCTCACCATAGGGTTATACAATCAGCAAAATCCAGAATGGGGGAAACTCCACAGGTCAAATGACCTAATTTTAAAAATAAATGACAAGGGAGAAAAAGTAAGAGACACCTATAGATCAGAAGACACTTGGGGCTGGGCATGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCGGATCACCTGAGGTCAGGAGTTCAAGACCAGCCGGCCAACATGGTGAAACCCCAACTCTACTAAAAATACGAAAAATCAGCCGGGCGTGGTGGCGCACGCCTGTAGTTCCAACTACCTGGGAGGCTGAGGCAGGAGAATCACTTGAACTTGGGAGGCAGAGGTTGCAGTGAGCCGAGATCGCACCATTGCATGCCAGTCTGGGCTACAAAAGCAAAACCCCATCTCAAAAAAAAGAAGACACTTGGGTTTGGGTGTGTTGGCTCATGCCTGTAAACCCCGTGCTGGGAGGATTGCTTGAGCCCAGGAGTTCAAGGCTGCAGTGAGGTATGTTTGCACCACTGCACTCCAGCCTAGGTGACAGAGTGTGACCTTATCTTAAAAGTAATAATAATTAAAATAATCTGGGGTAGGGGTGGATATGGGTGAAACAGCTTGGCCATGAGTTGATGGTTGTTGGACCAGGGTGATGGTCCATATAGTTCATTTTATTATTTTATTTACTTGAAATTTTGAAATACTTGAAATTTTCCATATTAAGTTAAAAAGGCATTTACAGTAAACAAAAAAAAGTTCTAGGAAGGAATTCAAAAGAAATATAAGCAGAAAATTTTGTCTTTATGGAGCTTAAAGATGAGATGTGCACCCACAGTGATAGTGCAGAAAAATATATCACTGGAAATGAATTCGTACGAACTATTATCAACTAATCTTTTAAATGCTGATGATAGTATAGAGTATTGAAGGGATCAATATAATTCTGTTTTGATATCTGAAAGCTCACTGAAGGTAAGGATCGTATTCTCTGCTGTATTCTCAGTTCCTGACACAGCAGACATTTAATAAATATTGAACGAACTTGAGGCCTTATGTTGACTCAGTCATAACAGCTCAAAGTTGAACTTATTCACTAAGAATAGCTTTATTTTTAAATAAATTATTGAGCCTCATTTATTTTCTTTTTCTCCCCCCCTACCCTGCTAGTCTGGAGTTGATCAAGGAACCTGTCTCCACAAAGTGTGACCACATATTTTGCAAGTAAGTTTGAATGTGTTATGTGGCTCCATTATTAGCTTTTGTTTTTGTCCTTCATAACCCAGGAAACACCTAACTTTATAGAAGCTTTACTTTCTTCAATTAAGTGAGAACGAAAAATCCAACTCCATTTCATTCTTTCTCAGAGAGTATATAGTTATCAAAAGTTGGTTGTAATCATAGTTCCTGGTAAAGTTTTGACATATATTATCTTTTTTTTTTTTTTTGAGACAAAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCATGATCTTGGCTCACTGCAACCTCCGCCCCCCGAGTTCAAGCGATTCTTCTACCTCAGCCTCCCAGGTAGCTGGGACTACAGGCACCCGCCACCATGCTTGGCTAATTTTTGTACTTTTAGTAGAGATAAGGTTTCACCATATTGGCCAGGCTGGTCTCGAACTCCTGACCTTGTGATCCACCTGCCTCGGCCTCCCAAAGTTCTGGGATTACAGGCGTGAGCCACCACACCCGACTGACATATATTATCTATTAGGATGTAACATCATTTTGAACAGTGTTTTGTATTTTTTGTGTCCATCAGTGAAAGCAAACTGCAAGCAGTTTTGAAATAAGCACATTGTGTTTGAGCCTTCCCAGTTTCTCCTTTCTGTTCATTTCTGCATATCCTTATGCATTCCCCCTTCTAAGGGTCAGTGTTTGCCCGCTTTGTAATCATTGTGAAGACAGGAAAGGACCTGATACCAGTTTCTATTTAGGCCAAAATTCATTTATAGCAGTGATTCAAGTTATATTTACGTATTTGATGATCTTGTCTTTTGAAATGAAAATGTTTGTTTCTTAATAAAAGAATTTCAGAAAAAGTAGAGTAGGTAATTTAGTAGAACAAGTGGGCTTTCTCCTTTTCTTTATGTTAAGCTATGGCTCACATCTTACCTTAAATGTCAACTAATTTGTTTTTAAGTATTTATGTACCTGGTACATAACCTGGTACCAGGTACAAACTATGTACTTGGTAAAAAGTTTATTAGCACAAAAAGGTATATGATGCAAAGTATACTTCCCTCTTACCCTACAACCCCTGCCTCCCTGTTCCCTCCCCAGACAACCACAATGATCAATTTCTTATGTATCCTTTGAGGAATTTTTAAATTCCAGAGTTCTTAACTTGGGGTTTATGAATAGTCTTTATGAATTTCCTAGAATTATATTTAAATTGTATTCAAAACTATGGCCATGTACATTTTTCTGGGAAGATAGTCCATAATTTTCATCTGAGTGAGCTAAGATCATGCCACTGCATTCCAGCCTGGGCGACAAGAGGGAGACTCAAAAAAAAAAAAAAAAGTCCCAGTATTTACTACAGAGAGCTAAAGATTAACCTTTAAAGCCCTGGGGCTTTCAATTTATCTGGATGAGAATCTTTCTGGAATGAACTGTATGTTTTCTTGTCAGCTTGAGTAACAAATGCTGAACATACTATACTATTATTACAGGGACTCAAGGGCCCAGTGTGGTAGCTCCTGCCCATAACCCCAGCACTTTGGGAGGCCAAGGCAGGAAGATCACTTAAGGCCAGGAGTTCGAAGCTGTAGTGAGCTATGATCACACCACTGCACTCCAGCCTAGATGACAGAGTGAGACCCTGTCTTTTTTTTTTTTTGAGATGGTGTTTCACTCTATTGCCCAGGCTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCTTGAGTAGCTGGGATTACAGGCATCTGCCACCACACCCAGCTAATTTTTGTATTTTTAGTCGAGACAGGGTTTTCACCATGTTGGCCAGGCTGCTCTCAAACTCCTGACTTCAGCTACCTTGGCCTTAAAAAGTGTTGGGATTACAGGTGTAAGCCACCGCGCCTGGCTGACCCTGTCTCTTAACAAAAAAAGAGAGATTAAGTTATGAATATAGTTGCTTTGAGAACTTGTGGAAGAAGGAAATTATAGGCTTATAGGCAGAGATAATAATACGAGCAAATGTACAAATAAAAGAAAATAGAGGACGGGCGCGGTGGCTCACGCCTATAATACCAGCACTTTGGGAGGTCGAGGTGGGCGGATCACGAGGTCAGGAAATTAAGACCATCCTGGCCAAAATGGCGAAACACTGTCTCTACTAAAACACACAAAAAACTAGCCTGGCATGGTGGCACGTACCTGTAGTCCCAGCTACTTGGTAGGCTGCGGCAGGGGTATCACTTGAACCTGGGAGGCAGAGGTTGCCCTGAGCCGAGATCATGCCAATGCACTCCAGCCTGACAACAGAGTGAGACTCTGTCTGAAAAAAAAGAAAAGAAAAGAAAATACATCCAGGAAAAATAAGCTAACTTTGCATATGTGTATAGGAGTTGTGTTAGAAAAGGAAGAAGCCCTCAAAGATGGGAAGCCATTTGCAAGAAAGAGAAGGTCCAAGAGGAGGCAGAAGGGATTGGAAATAGAAAAAGGATGTAAGAAAGAGTTGATTATTACTCATAAACAGTAATGAAGGAAAAGGAGAGTAATTCTACAGGAAGATGCTGAGGTGCTTTGAGCCCAGTGAAGTTGGAGGTAAAGACAGCTGTTGAGGCCGGGCACGGTGGCTCACGCCTCTAATCCTAGCACTTTTGGAGCCCAAGGCAGGTGGATCACCTGAGGTCAGGAGCTCAAGACCAGCCTGACCAACATAGAGAAACCCCATCTCTACTAAAAATACAAAATTAGACGGGCGTGGAGGCGCATGCCTGTAATCCCAGTTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGCGGAGGTTGCAGTGAGCCGAGATTGCGCCATTGCACTCCAGCCTGGGCGACAAGAGTGAAAACTGTCTCAAAAAAAAAAAACAACAAAAAACAGCTGTTGAGATTGAGAGGATTAGAGTTGGCAACTGGAGAAGAGTGAGAAGCTTGGTTTCAAGCTTGTGATAGTCAGGATTGTGATAGTCAGGAAAGAACCAGTCATAAAGATATATGTGTGTGTATACATATAAATATGTTATATATATGTGTGTGTGTGACACATATATATTTTTGTTTGTTTCTTTGAGACAGTGTCTCCCTCTGACACCCAGGCTGGAGTTCAGTGGTGTGATCATAGTTCACTTTTACCTTGCAATCTGGGTTCAAGCAATCTCTCATCTCAGCCCCTCAAGTAGCTAGGACTACAGGTACATGGCATTTGCCCAGCTAATTTTTAAGTTTCTTGTAGAGATGGGCCAGCCATATTTTAAATTGTGTTTTGAATGTTATATTAGAATTAAAAGTCCAAAGCCGGGTGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCGGATCACGAGGTCAGGAGTTCGAGACCAGCCTGGCCAATATGGTAACACCATCTCTACTAAAAATACAAAAATTAGCTGGGTATGGGGGCACATGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGAGGAACCTCTTGAACCCAGGAGGCAGAGGCTGCAGTGAGTTGAGATCGTGCCACTGTACTCTAGCCTGGGCGACAGAGCAAGATTCCGTCTCAAAAAAAAAAAAAGTCCAGTATAATGCCCATGTGATAGATCGACTTTTTCATGAAATCTCTTCTGTAATATCAATATAATCTGAATAACACTTTGATCTATATGATGAGAAAGCTGGGAGCCTGGGAGCGATACCCCCATGCTTTTGTTGTATTAATTGTATTTTCTACGGATAAACTCTAATTGCTAAAAATAAAACAACTTTATTGACCCAAGCAAGCCTAAAGTTCTGAAATCTTTTTTTTATTTTTGTTTGTTTGTTTGTTTGTTTTTGTTTGTTTTGTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCGGTGGTGCAGTCTCGGCTCACTGCAAGCTCCACCTCCCGGGTTCACACCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGACGCCTGCCACCACGCCCAGCTAATTTTTTTGTATTTTTAGTAGAGAAAGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTTGGCCTCCCTAAGTTCTGGGATTACAAGTGTGAGCCACCACGCCCGGCTGTTTTTTTTTGTTTTGTTTTGAGACGGAGTCTCACTGTGTTGCCCAGACTGGAGTGCAGTGGCATGATCTCAGCTCACTGCCACCTCCATCTCCTGGGTTCAAGCAAATCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCATGTGCCACCACACCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACTATGTTGGCCAGGCTGGTCCAAAACTCCTGACCTCAGGTGATCTGCTCGCCTTGGCCTCCCACAGTGCCAGGATTACAGGCATGAGCCACCTTGCCCAGCCAGTTCTGAAATCTTTTATGAAGCCTATAAAAAAAGATAATAATACCAATCTAGAAAATATTTCTTAAGGCAGTCATGCATTAGTTTGAACTTTCCAAACAAAAAAATGCAATGTGTAATACTTTTTTTTTTTTTTTTGAGATGGAGTCTTGTTCTGTTGCCCAGGCTGGAGTGCAGTGGTACAATCTCGGCTCACTGCAGCCTCTGCCTCTCTGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCGTGCACCACCATGCATGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGACAAGGCTGATCTCGAACTCCTGACCTCAGGTGATCCGCCCACCTCAGCCTCCCAAAGTGCTGAGATTACAGGCATTAGCCACCACGCCCAGCCTTTTATTTTAGTAGAGACCATGTTTCACCATGTTGACCAAGCTGGTCTTGAGCTGACCTCAAGTGATCCGCCCACCTCCACCTCCCAAAATGGTGGGATTATAGGCATGAGCCACCGCACCCAGCCTGTAATACTTTTTTGAAGATCTAGAACCACATTGTTCAAAGAGATAGAATGTGAGCAATAAATGTAACTTAAATTTTTCAACAGCTACTTTTTTTTTTTTTTTTTGAGACAGGGTCTTACTCTGTTGTCCCAGCTGGAGTACAGTGGTGCGATCATGAGGCTTACTGTTGCCTTGACCTCCTAGGCTCAAGCGATCCTATCACCTCAGTCTCCCAAGTAGCTGGGACTGTAAGTGCACACCACCATATCCAGCTAAATTTTGTGTTTTCTGTAGAGACGGGGTTTCGCCATGTTTCCCAGGCTGGTCTTGAACTTTGGGCTTAACCCGTCTGCCCACCTAGGCATCCCAAAGTGCTAGGATTACAGGTGTGAGTCATCATGCCTGGCCAGTATTTTAGTTAGCTCTGTCTTTTCAAGTCATATACAAGTTCATTTTCTTTTAAGTTTAGTTAACAACCTTTATACATGTATTCTTTTTCTAGCATAAAGAAAGATTCGAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGATGGGCACATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACATGGTGAAACCCCGCCTCTACTAAAATTACAAAAAGTTAGCCAGGCGTGGTAGCGGGCACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGGCAGAGCTTGCAGTGAGCAGAGATTGTGCCACTGCACTCCAGCCTGAGAGACAGAGCGAGACTCCGTCTAAAAAAAAAAAAAAAGATTCGAATCCTTATCTTGGTTGATTTTTGCGTATCTAGTTCCACTGAATTATTTATATAATTGTATAGACTACAGCACGAGACAGCTTAGCTTGTCACTCTACTGTACTATATTCTGCAGTACTATCATAAGGGAATTTCCTCCCTACCCCTGCTCTGAATTGTTCAATTGTACTATTTGCTGGAGTAATGCTTGATGCCTTCTTGATCCATTATACTAGAGTATATGTAGTATTTGTAGATTCTGAAGGAGTGGGAGCCTCTATTCTGAGTTTTAAAGGTACTTATGTACAGTGGAGGTAGCTTTTTGACAGCCTCATCTTCCAAACTATAGAGTCATTGTTTTGTTGAGTGCAATATGGTACTTGAAGCATCTATATCGGCGAAGAAGGACCCAAGTCTCCTTGACCTTACCTACCTACATTCACTTTCTCTGGTAGGAAGATTGTGGGTGCCTCTCTCCAGACTTAGTTTCCATGTCAAAAAAGAAAAAAGGAAGATTGTGGGCTTTGCTACAATCCAATTCTGGATCCAATATAACCTTCATTGCTTAATTACTGTGTGATCTGGGACAAGCCTCTACTCTATAAAAATGAAGATAAGGCCAGGCTTGATGGCTCATGCCTGTAATCCCAGCACGTTGGGATGCCAAGGCAGGAGGATCACTTGAGGTCAGGAGTTCGAGACCAGACTGGGCAATATAGTGAAACCACATCTGTACAAAAATAAAGATAGAAAGTAGCCCAGCGCAATGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAAGCAGGCGATCACTTGAGGTCGGGAGTTCAAGACTGTAGACAGATAGATAGGTAGGTAGATAGATAGAGATATAGATATAGTTGGGGTTTTTTTGTTTTGTTTTGTTTTGTTTTTGAGATGGAGTTTCGCTCTTGTTGCCCAGGCTGGAGTGCAATGGCGCGATCTCAGTTTACTGCAACCTCCGCCTCCCGGGTTCAAGAGATTCTCCTGCCTCAGCCTCCTGAGTAGCCAGGATTACAGGCATATGCCACCATGCCCGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCTCCGTGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACCGCTCCTGGCCTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTCCTCTGTTGCCCAGGGTGGAGTGCAGTGGCACTCTTCTCAGCTCATTGCAACCTCTGCCATCCTGGGTTCCAGTGATTCTCATGCCTCAGCCTCCCAAGTAGCTGGGACTCAGGCGTGTGCCCACCACGCCTGGCTAATTTTGTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGCTGGTCTCAAACTCCAGGCCTCAAGTGATCTGCCTGCCTCAGCCTCCTGGGATTGCAGACATGAGCCACTGCACCCGGCCAAGAGAGGGTAATAAATGTTAAATTACCTGGCTAGTAAAAAATATTCTCTAAGTGTCTTTTCTCACAATTCCCAATGCCTTTTTTTTTTTTTTGGCACAATCTCACTCTGTTGCCCAGGCTGGAATGCAATGGTGCAATATTGGCTCACTGTAACCCCCGCCTCACAGGTTCAACTTATTCTCATGCCTCAGCCTCCCGAGTAACTGGGACTACAGTGCACCACCACCACACCCAGCTAATTTTTGAATATTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGGCCTCAAGTGATTCACCCACCCCGCAAGTGCTGGGATTACAGGTGTGGACCACCGTGCACAGCCCTAGTGACTTTTTTTTTAGCCCCTTAATCTTTTCTTTCCTGGGTCTCTTCATTGTCAGTGTCTGCTATTTACTCCCTACCTAGTCACCCCCTTCACCAGTATATTATGTCCTTTATGTTTTATTTTGCAGGATCTTATTTTGCTTTTCTATTGAATCCCCTCCATCTAGAATAGTACTAGACATAGTAAATATTGGTTGTATGAGTGAATCGCTGCTTTTAATTATCATCACCATTGCTCTCTCTACTTCTGGTCTATGATCCACTTTGAGTTAACTTTTGTTATTTGGTGTGAGATAGGAGTATAATTTCATTCTTTTACATGTGGTTATACTTTTGTCTCAACACTGTTTGTTAAAAACACAAAAAGTATTATTTTCCCATTTAATCATCTTTGGCCTGGGCACGGTGGCTCATGCCTGTAATCCCAGCACTCTGGAAGGCCAAGGCAGATGGATCAATTTGAGGCCAGGAGTTCAAGACTAGCCAACATGGTGAAACTAAAAATACAAAAAATTAGCTGGGTATGGTGGTGCATGTCTGTAATCCCAGCTACTCGGGAGGCTGAGGCACGAGAATTGCTTGAGCCTAGGAGGTGGAGGTTGTAGTGAGCTGAGATTGTGTCACTACCCTCCAGCCTGGGTGATAGAGTGAGTCTGTCTCAAAAAAAAAAAAAAAAAATTAAGAAAATAAAAATCGTCGGCCAGGCATGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCAGAGGCGGGCAGATCACGAGGTCAGGAGATGGAGACCATCCTGGCTAACATGGTGAAACCCCGTCTCTACTAAAAATAAAAAAATTAGCCGGGCATGGTGCTGGGCGCCTGTAGTCCCAGCTGCTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGGTGGAGCTTGCAGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGAGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAATTGTCTTGGTATTTATTATTGTTGAAAATCGCTTGATCACAGATGTATGTATGAGTTTATTTCTGTACTGTCAATTCCATTTTATTGATGTATGTGTCTATTCTTATGCTATTACCACACTTTCTTGATTACTATAGCTTTGTGGTGAGGTGTTGAGATTTTAAACTAATTATAAGCATCTTACATGAACTACTTACCGTTTATATTTGATTATGCAGCATGAAATAATTATGAATATATCATTAAATATGCCATATTAACTTTTATTAAGTTTTATGTGATCATAACAGTAAGCCATATGCATGTAAGTTCAGTTTTCATAGATCATTGCTTATGTAGTTTAGGTTTTTGCTTATGCAGCATCCAAAAACAATTAGGAAACTATTGCTTGTAATTCACCTGCCATTACTTTTTAAATGGCTCTTAAGGGCAGTTGTGAGATTATCTTTTCATGGCTATTTGCCTTTTGAGTATTCTTTCTACAAAAGGAAGTAAATTAAATTGTTCTTTCTTTCTTTATAATTTATAGATTTTGCATGCTGAAACTTCTCAACCAGAAGAAAGGGCCTTCACAGTGTCCTTTATGTAAGAATGATATAACCAAAAGGTATATAATTTGGTAATGATGCTAGGTTGGAAGCAACCACAGTAGGAAAAAGTAGAAATTATTTAATAACATAGCGTTCCTATAAAACCATTCATCAGAAAAATTTATAAAAGAGTTTTTAGCACACAGTAAATTATTTCCAAAGTTATTTTCCTGAAAGTTTTATGGGACATCTGCCTTATACAGGTATTAGAAACTTACTGCCTTTCTCTAATGCTTCTAGTGTAAAAACTTGCAGACTTATGTAAAGTAGGGCTGTATCGCCGTGCCCCCATTGTCTGTTAATCTTGTTTTTATATTTTTGATTGTGTTTCCTTTTCTTTTTTTTTTTTTTTTTAAGACAGGGTCCTGCTCTGTCACTGAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCACTGTAGCCTCTGTCTCCCAGCCTCTTCCTGCCTTAGCCTCCCAAATAGCTGGGACTACAGGCACACGCTACCATGCCCGGCCAATTTTTGTATTTTTTGTAGAGATGAGGTTTTACCATGTTGCCCAGGCTGGTAACTCCTGAGCTCAGGTGATCTGCCCACCTCGGCCTCCCAAAGTGCTGGGGTTCACAGGTGTGTGTTTATTTCTATCTAATTATTTACACAAACACAATGTATTTATATATTGTGTATCTCTTCTGCTACAATGTAAATTCTATGAGAGTAGTAATTTTGTCTGTCTCAACACTGTTTTTCCTAAGTTTGGTACATAGTAGGCACTCAGATGCTTAAAGGAATGAATGAATTGTGCTTTAATTCCACTTTACTAAACCCAAATCTCCCTTTGGACATTGTTATCTATGTGTTTTCAAAGAAGTATAATCATAATTTGACAGAAATCCTTGAGAGGCAGAACTAAGTGAGGGATTGGGCAGGGTTCAGATGTTAAGAACAGTAAGCTCAGCAGGGTGTGATTGCTCATGCCTATAACCCTAGCACTCTAGGAGGCTGAGGTGGGATGATTGCTTGAGGCCAGGAGTTTGAAATCAGCCTGGGCAACATAGTGAGACCCCATCACTACCAACAAAATAAATAAATAAATGTACATGGTGGCATATGCCCATAGTCCTAGCTACTTGGGAGGCTATAGTGGGAGGATAGCTTGAGTACAGAAGTCTGAGGCTGCAGTGAGCTATGATTGTGGCACTGCATGCTAGCCTGGGCAATAGAGCAAGACCCTGTCTCTAAATTAAACAAAAAAAAAAGTACTCTAGTTTTCTATGCAATGCATTATATCTGCTGTGGATTTAGGGCAGTATTATATCAGATAATTTTAGGCATTTGGTAGGCTTAAATGAATGACAAAAAGTTACTAAATCACTGCCATCACACGGTTTATACAGATGTCAATGATGTATTGATTATAGAGGTTTTCTACTGTTGCTGCATCTTATTTTTATTTGTTTACATGTCTTTTCTTATTTTAGTGTCCTTAAAAGGTTGATAATCACTTGCTGAGTGTGTTTCTCAAACAATTTAATTTCAGGAGCCTACAAGAAAGTACGAGATTTAGTCAACTTGTTGAAGAGCTATTGAAAATCATTTGTGCTTTTCAGCTTGACACAGGTTTGGAGTGTAAGTGTTGAATATCCCAAGAATGACACTCAAGTGCTGTCCATGAAAACTCAGGAAGTTTGCACAATTACTTTCTATGACGTGGTGATAAGACCTTTTAGTCTAGGTTAATTTTAGTTCTGTATCTGTAATCTATTTTTAAAAAATTACTCCCACTGGTCTCACACCTTATTTTATCAATCGTAAGGTGCACATTTTTCACATCTTAACATCTCTGAAATTGGGAACATTTTACTATTGAGGGTGTGTCATTTGTTTAATTTGTGTGCTTTCTTTCTTAGTGATACAGAAAATAATAGTGCAACTTACATTGTTGGTGTCTTAGCTTTAGTGAAATACAGTATTGATAGGCAAATTTCTTAGTGTTAAGGTAGAAAACAAGGACTCTAAATAACTTTGATGGTCTGTGTATTTGTTTTTGTTTCCTAGGAGTAAAATTTCCAGTTGATTTTTTAAAATTTGATTTTTAAAAAAAATCACAGGTAACCTTAATGCATTGTCTTAACACAACAAAGAGCATACATAGGGTTTCTCTTGGTTTCTTTGATTATAATTCATACATTTTTCTCTAACTGCAAACATAATGTTTTCCCTTGTATTTTACAGATGCAAACAGCTATAATTTTGCAAAAAAGGAAAATAACTCTCCTGAACATCTAAAAGATGAAGTTTCTATCATCCAAAGTATGGGCTACAGAAACCGTGCCAAAAGACTTCTACAGAGTGAACCCGAAAATCCTTCCTTGGTAAAACCATTTGTTTTCTTCTTCTTCTTCTTCTTCTTTTCTTTTTTTTTTCTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTGGCCCAGGCTAGAAGCAGTCCTCCTGCCTTAGCCCCCTTAGTAGCTGGGATTACAGGCACGCGCCACCATGCCAGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCATCATGTTGGCCAGGCTGGTCTCGAACTCCTAACCTCAGGTGATCCACCCACCTCGGCTCCCCAAATTGCTGGGATTACAGGTGTGAGCCACTGTGCCCGGCCGGTAAAACCATTTTCATTTATTCTGGCAACATCTCTTTATTGAGCATTGTGAATATGTTAGTGAATGTGCTAGATGCTCATAGATTTATATAAAAAGTTAGTGAAGAAGGAAAGATGGTATATTAAGTGGTTAGACAAGTGTTCTAATCAGTTAGAGTTCAGAGAAGGTCAGGGTACCTGATATAATCAAGAGAGAGACCTTACAGCCAGGTGAGGTGAATGTACCTATAATCCCAGCTACTTAGGAGGCTGAAATGGGAGGATCACTTGAGTCCAGGTTTGAGACCAGCCCAGGCAACATAGCAAGATCCCCATCAGATACACCAAAAAGACAGATTTCTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCGCTCTGTCGCCCAGGCTGGAGCGCAGTGACACGATGTCAGCTCACTGCAACCTCCGCCTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGTTGGGACTACAGGGGTACGACACCAGACCTGGCTAATTTTTGTAATTTTAGTAGAGTCGGGGTTTCACCATATTGGTCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCACCCTCCTTGGCCTCCCAGAGTGCTGGGATTACAGGCGTGAGCCACCAAGCCCGGCCAAAAAAGAGAGCTCTTATAGGCCCTTCCTTGCTTTGGAGCTTTATCTGCTCTGTGATGCTTATCTAAAATAGCCATAAGGTCACTGATATTTTTAAGCATTTGGAAATTACTTCAGCTGGGTGCCATGGCTCATGCCTATAATCCCAACCCTTTGGGAGGCTGAGGTAGGAGGTCCTTTGAGCCCAGCTTGGGCAACACAGTGAGACACTGTCTCTGCAATTAAAAAAAAAAAAAAGTAGCTGGGTGCCGTGGCTCACGCCTGTAATTCCAGCACTAGGAGGCTTGAGGATTGCCTGAGCTCAGGAGTTCAAGACCAGTTTGGGCAACATAGCAAGTCCTTGTCTATATTAAAAGTTTTTTTAAATTATCTGGGCATGGTGGTGTGTGCCTGTAGTCCCAGCTACTTGGGAAGCTGAGACAGAAGGATCACTTGAGTCCAGGAGATGTAGACTACAGTGAGCTATGATCACTCCACTGCACTTCAGCGTGGGCGGCAAAGCAAGATCTAGTTGCAAAAAAAAAAAGAACTGGCTGGGTGCGGCGGCTAACACCTGCAATCCCAGCACCTTGGGAGGCTGAGGCCAGTGGATCATGAGGTCAGGAGATTGAGACCACCCTGGCCAACATGGTGAAACCCGGTCTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGGCACGTGCCTGTAATCCCAGCTACTCCAGAGGCTGAGGATGGAGAATCACTTGAACCTGAGAGTCGGAGGTTGCAGTGAGCCGAGATTGCGCCACTGCACTCCAGCCTGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAGCTTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGTCAAGTGGATCACGAGGTGTGGAGATCAAGACTATCCTGGCTCACATGGTGAAAGCCCGTCTCTACTAAAAACACAGAAAAATTAGCTGAGCGTGATGGCGGACTCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATAGCATGAACCCGGGAGGTGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCGATCCAGCCTGGGCGACAGAGTGAGACTCTGTCTCAAAAAAAAAACAAAAAAACTTAGCTGGGCGTGGTGGTATGCACCTGTGGTCCTAGCTACTTGGGAGGCTGAGGCTGGAGCATTGCTTTAACATAGAGAGTCAAGGCTGCAGTTGAGCTATGACTGTGCCACTGGACTCCAGCGCAGGTGACTGAGACCCTATCTTTTAAAAAAAGGGAAAATTACTTGAACTTAAAAGGTGTAATTGTTAAAGAAAATGTAGTGATTTGCTCTGTTGTTACTTATATGTGCATGAATGATGGAGATCTTAAAAAGTAATCATTCTGGGGCTGGGCGTAGTAGCTTGCACCTGTAATCCCAGCACTTCGGGAGGCTGAGGCAGGCAGATAATTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCATCTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGGCACGTACCTGTAATCCCAGCTACTCGGGAGGCGGAGGCACAAGAATTGCTTGAACCTAGGACGCGGAGGTTGCAGCGAGCCAAGATCGCGCCACTGCACTCCAGCCTGGGCCGTAGAGTGAGACTCTGTCTCAAAAAAGAAAAAAAAGTAATTGTTCTAGCTGGGCGCAGTGGCTCTTGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCGGGTGGATCTCGAGTCCTAGAGTTCAAGACCAGCCTAGGCAATGTGGTGAAACCCCATCGCTACAAAAAATACAAAAATTAGCCAGGCATGGTGGCGTGCGCATGTAGTCCCAGCTCCTTGGGAGGCTGAGGTGGGAGGATCACTTGAACCCAGGAGACAGAGGTTGCAGTGAACCGAGATCACGCCACCACGCTCCAGCCTGGGCAACAGAACAAGACTCTGTCTAAAAAAATACAAATAAAATAAAAGTAGTTCTCACAGTACCAGCATTCATTTTTCAAAAGATATAGAGCTAAAAAGGAAGGAAAAAAAAAGTAATGTTGGGCTTTTAAATACTCGTTCCTATACTAAATGTTCTTAGGAGTGCTGGGGTTTTATTGTCATCATTTATCCTTTTTAAAAATGTTATTGGCCAGGCACGGTGGCTCATGGCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGGTCAGGAGTGTGAGACCAGCCTGGCCAACATGGCGAAACCTGTCTCTACTAAAAATACAAAAATTAACTAGGCGTGGTGGTGTACGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCAACTGAACCAGGGAGGTGGAGGTTGCAGTGTGCCGAGATCACGCCACTGCACTCTAGCCTGGCAACAGAGCAAGATTCTGTCTCAAAAAAAAAAAACATATATACACATATATCCCAAAGTGCTGGGATTACATATATATATATATATATATATATTATATATATATATATATATATGTTATATATATGTTATATATATATAACATATATATATGTTATATATATGTTATATATATATAATATATATATGTTATATATATGTTATATATATATATACACACACACACACATATATATGTATATATATATACACACACACACACAAATTAGCCAGGCATAGTTGCACACGCTTGTAGACCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCTCTTGAACTTAGGAGGCGGAGGTTGCAGTGAGCTGAGATTGCGCCACTGCACTCCAGCCTGGGTGACAGAGCAGGACTCTGTACACCCCCCAAAACAAAAAAAAAAGTTATCAGATGTGATTGGAATGTATATCAAGTATCAGCTTCAAAATATGCTATATTAATACTTCAAAAATTACACAAATAATACATAATCAGGTTTGAAAAATTTAAGACAACAGAAAAAAAAATTCAAATCACACATATCCCACACATTTTATTATTACTACTACTATTATTTTGTAGAGACTGGGTCTCACTCTGTTGCTTATGCTGGTCTTGAACTCCTGGCCTCAAGCAGTCCTGCTCCAGCCTCCCAAAGTGCTGGGATTATAGGCATGAGCTACCGCTCCCAGCCCCAGACATTTTAGTGTGTAAATTCCTGGGCATTTTTTCCAGGCATCATACATGTTAGCTGACTGATGATGGTCAATTTATTTTGTCCATGGTGTCAAGTTTCTCTTCAGGAGGAAAAGCACAGAACTGGCCAACAATTGCTTGACTGTTCTTTACCATACTGTTTAGCAGGAAACCAGTCTCAGTGTCCAACTCTCTAACCTTGGAACTGTGAGAACTCTGAGGACAAAGCAGCGGATACAACCTCAAAAGACGTCTGTCTACATTGAATTGGGTAAGGGTCTCAGGTTTTTTAAGTATTTAATAATAATTGCTGGATTCCTTATCTTATAGTTTTGCCAAAAATCTTGGTCATAATTTGTATTTGTGGTAGGCAGCTTTGGGAAGTGAATTTTATGAGCCCTATGGTGAGTTATAAAAAATGTAAAAGACGCAGTTCCCACCTTGAAGAATCTTACTTTAAAAAGGGAGCAAAAGAGGCCAGGCATGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAAGTGGGTGGATCACCTGAGGTCGGGAGTTCGAGACCAGCCTAGCCAACATGGAGAAACTCTGTCTGTACCAAAAAATAAAAAATTAGCCAGGTGTGGTGGCACATAACTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGTGGAGGTTGCGGTGAACCGAGATCGCACCATTGCACTCCAGCCTGGGCAAAAATAGCGAAACTCCATCTAAAAAAAAAAAAGAGAGCAAAAGAAAGAATATCTGGTTTTAAATATGTGTAAATATGTTTTGGAAAGATGGAGAGTAGCAATAAGAAAAAACATGATGGATTGCTACAGTATTTAGTTCCAAGATAAATTGTACTAGATGAGGAAGCCTTTTAAGAAGAGCTGAATTGCCAGGCGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCACCTGAGGTCGGGAGTTCAAGACCAGCCTGACCAACATGGAGAAACCCCATCTCTACTAAAAAAAAAAAAAAAAAAATTAGCCGGGGTGGTGGCTTATGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAAGCAGAGGTTGCAGTGAGCCAAGATCGCACCATTGCACTCCAGCCTAGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAAAGAGCTGAATCTTGGCTGGGCAGGATGGCTCGTGCCTGTAATCCTAACGCTTTGGAAGACCGAGGCAGAAGGATTGGTTGAGTCCACGAGTTTAAGACCAGCCTGGCCAACATAGGGGAACCCTGTCTCTATTTTTAAAATAATAATACATTTTTGGCCGGTGCGGTGGCTCATGCCTGTAATCCCAATACTTTGGGAGGCTGAGGCAGGTAGATCACCTGAGGTCAGAGTTCGAGACCAGCCTGGATAACCTGGTGAAACCCCTCTTTACTAAAAATACAAAAAAAAAAAAAAATTAGCTGGGTGTGGTAGCACATGCTTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCAGGGAGGCGGAGGTTACAATGAGCCAACACTACACCACTGCACTCCAGCCTGGGCAATAGAGTGAGACTGCATCTCAAAAAAATAATAATTTTTAAAAATAATAAATTTTTTTAAGCTTATAAAAAGAAAAGTTGAGGCCAGCATAGTAGCTCACATCTGTAATCTCAGCAGTGGCAGAGGATTGCTTGAAGCCAGGAGTTTGAGACCAGCCTGGGCAACATAGCAAGACCTCATCTCTACAAAAAAATTTCTTTTTTAAATTAGCTGGGTGTGGTGGTGTGCATCTGTAGTCCCAGCTACTCAGGAGGCAGAGGTGAGTGGATACATTGAACCCAGGAGTTTGAGGCTGTAGTGAGCTATGATCATGCCACTGCACTCCAACCTGGGTGACAGAGCAAGACCTCCAAAAAAAAAAAAAAAAGAGCTGCTGAGCTCAGAATTCAAACTGGGCTCTCAAATTGGATTTTCTTTTAGAATATATTTATAATTAAAAAGGATAGCCATCTTTTGAGCTCCCAGGCACCACCATCTATTTATCATAACACTTACTGTTTTCCCCCCTTATGATCATAAATTCCTAGACAACAGGCATTGTAAAAATAGTTATAGTAGTTGATATTTAGGAGCACTTAACTATATTCCAGGCACTATTGTGCTTTTCTTGTATAACTCATTAGATGCTTGTCAGACCTCTGAGATTGTTCCTATTATACTTATTTTACAGATGAGAAAATTAAGGCACAGAGAAGTTATGAAATTTTTCCAAGGTATTAAACCTAGTAAGTGGCTGAGCCATGATTCAAACCTAGGAAGTTAGATGTCAGAGCCTGTGCTTTTTTTTTGTTTTTGTTTTTGTTTTCAGTAGAAACGGGGGTCTCACTTTGTTGGCCAGGCTGGTCTTGAACTCCTAACCTCAAATAATCCACCCATCTCGGCCTCCTCAAGTGCTGGGATTACAGGTGAGAGCCACTGTGCCTGGCGAAGCCCATGCCTTTAACCACTTCTCTGTATTACATACTAGCTTAACTAGCATTGTACCTGCCACAGTAGATGCTCAGTAAATATTTCTAGTTGAATATCTGTTTTTCAACAAGTACATTTTTTTAACCCTTTTAATTAAGAAAACTTTTATTGATTTATTTTTTGGGGGGAAATTTTTTAGGATCTGATTCTTCTGAAGATACCGTTAATAAGGCAACTTATTGCAGGTGAGTCAAAGAGAACCTTTGTCTATGAAGCTGGTATTTTCCTATTTAGTTAATATTAAGGATTGATGTTTCTCTCTTTTTAAAAATATTTTAACTTTTATTTTAGGTTCAGGGATGTATGTGCAGTTTGTTATATAGGTAAACACACGACTTGGGATTTGGTGTATAGATTTTTTTCATCATCCGGGTACTAAGCATACCCCACAGTTTTTTGTTTGCTTTCTTTCTGAATTTCTCCCTCTTCCCACCTTCCTCCCTCAAGTAGGCTGGTGTTTCTCCAGACTAGAATCATGGTATTGGAAGAAACCTTAGAGATCATCTAGTTTAGTTCTCTCATTTTATAGTGGAGGAAATACCCTTTTTGTTTGTTGGATTTAGTTATTAGCACTGTCCAAAGGAATTTAGGATAACAGTAGAACTCTGCACATGCTTGCTTCTAGCAGATTGTTCTCTAAGTTCCTCATATACAGTAATATTGACACAGCAGTAATTGTGACTGATGAAAATGTTCAAGGACTTCATTTTCAACTCTTTCTTTCCTCTGTTCCTTATTTCCACATATCTCTCAAGCTTTGTCTGTATGTTATATAATAAACTACAAGCAACCCCAACTATGTTACCTACCTTCCTTAGGAATTATTGCTTGACCCAGGTTTTTTTTTTTTTTTTTTTGGAGACGGGGTCTTGCCCTGTTGCCAGGATGGAGTGTAGTGGCGCCATCTCGGCTCACTGCAATCTCCAACTCCCTGGTTCAAGCGATTCTCCTGTCTCAATCTCACGAGTAGCTGGGACTACAGGTATACACCACCACGCCCGGTTAATTGACCATTCCATTTCTTTCTTTCTCTCTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTGCTCTGTTGCCCAGGCTGGAGTACAGAGGTGTGATCTCACCTCTCCGCAACGTCTGCCTCCCAGGTTGAAGCCATACTCCTGCCTCAGCCTCTCTAGTAGCTGGGACTACAGGCGCGCGCCACCACACCCGGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCATGACCTCAAGTGGTCCACCCGCCTCAGCCTCCCAAAGTGCTGGAATTACAGGCTTGAGCCACCGTGCCCAGCAACCATTTCATTTCAACTAGAAGTTTCTAAAGGAGAGAGCAGCTTTCACTAACTAAATAAGATTGGTCAGCTTTCTGTAATCGAAAGAGCTAAAATGTTTGATCTTGGTCATTTGACAGTTCTGCATACATGTAACTAGTGTTTCTTATTAGGACTCTGTCTTTTCCCTATAGTGTGGGAGATCAAGAATTGTTACAAATCACCCCTCAAGGAACCAGGGATGAAATCAGTTTGGATTCTGCAAAAAAGGGTAATGGCAAAGTTTGCCAACTTAACAGGCACTGAAAAGAGAGTGGGTAGATACAGTACTGTAATTAGATTATTCTGAAGACCATTTGGGACCTTTACAACCCACAAAATCTCTTGGCAGAGTTAGAGTATCATTCTCTGTCAAATGTCGTGGTATGGTCTGATAGATTTAAATGGTACTAGACTAATGTACCTATAATAAGACCTTCTGTAACTGATTGTTGCCCTTTCGTTTTTTTTTTTGTTTGTTTGTTTGTTTTTTTTTGAGATGGGGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGATGCAATCTTGGCTCACTGCAACCTCCACCTCCAAGGCTCAAGCTATCCTCCCACTTCAGCCTCCTGAGTAGCTGGGACTACAGGCGCATGCCACCACACCCGGTTAATTTTTTGTGGTTTTATAGAGATGGGGTTTCACCATGTTACCGAGGCTGGTCTCAAACTCCTGGACTCAAGCAGTCTGCCCACTTCAGCCTCCCAAAGTGCTGCAGTTACAGGCTTGAGCCACTGTGCCTGGCCTGCCCTTTACTTTTAATTGGTGTATTTGTGTTTCATCTTTTACCTACTGGTTTTTAAATATAGGGAGTGGTAAGTCTGTAGATAGAACAGAGTATTAAGTAGACTTAATGGCCAGTAATCTTTAGAGTACATCAGAACCAGTTTTCTGATGGCCAATCTGCTTTTAATTCACTCTTAGACGTTAGAGAAATAGGTGTGGTTTCTGCATAGGGAAAATTCTGAAATTAAAAATTTAATGGATCCTAAGTGGAAATAATCTAGGTAAATAGGAATTAAATGAAAGAGTATGAGCTACATCTTCAGTATACTTGGTAGTTTATGAGGTTAGTTTCTCTAATATAGCCAGTTGGTTGATTTCCACCTCCAAGGTGTATGAAGTATGTATTTTTTTAATGACAATTCAGTTTTTGAGTACCTTGTTATTTTTGTATATTTTCAGCTGCTTGTGAATTTTCTGAGACGGATGTAACAAATACTGAACATCATCAACCCAGTAATAATGATTTGAACACCACTGAGAAGCGTGCAGCTGAGAGGCATCCAGAAAAGTATCAGGGTAGTTCTGTTTCAAACTTGCATGTGGAGCCATGTGGCACAAATACTCATGCCAGCTCATTACAGCATGAGAACAGCAGTTTATTACTCACTAAAGACAGAATGAATGTAGAAAAGGCTGAATTCTGTAATAAAAGCAAACAGCCTGGCTTAGCAAGGAGCCAACATAACAGATGGGCTGGAAGTAAGGAAACATGTAATGATAGGCGGACTCCCAGCACAGAAAAAAAGGTAGATCTGAATGCTGATCCCCTGTGTGAGAGAAAAGAATGGAATAAGCAGAAACTGCCATGCTCAGAGAATCCTAGAGATACTGAAGATGTTCCTTGGATAACACTAAATAGCAGCATTCAGAAAGTTAATGAGTGGTTTTCCAGAAGTGATGAACTGTTAGGTTCTGATGACTCACATGATGGGGAGTCTGAATCAAATGCCAAAGTAGCTGATGTATTGGACGTTCTAAATGAGGTAGATGAATATTCTGGTTCTTCAGAGAAAATAGACTTACTGGCCAGTGATCCTCATGAGGCTTTAATATGTAAAAGTGAAAGAGTTCACTCCAAATCAGTAGAGAGTAATATTGAAGACAAAATATTTGGGAAAACCTATCGGAAGAAGGCAAGCCTCCCCAACTTAAGCCATGTAACTGAAAATCTAATTATAGGAGCATTTGTTACTGAGCCACAGATAATACAAGAGCGTCCCCTCACAAATAAATTAAAGCGTAAAAGGAGACCTACATCAGGCCTTCATCCTGAGGATTTTATCAAGAAAGCAGATTTGGCAGTTCAAAAGACTCCTGAAATGATAAATCAGGGAACTAACCAAACGGAGCAGAATGGTCAAGTGATGAATATTACTAATAGTGGTCATGAGAATAAAACAAAAGGTGATTCTATTCAGAATGAGAAAAATCCTAACCCAATAGAATCACTCGAAAAAGAATCTGCTTTCAAAACGAAAGCTGAACCTATAAGCAGCAGTATAAGCAATATGGAACTCGAATTAAATATCCACAATTCAAAAGCACCTAAAAAGAATAGGCTGAGGAGGAAGTCTTCTACCAGGCATATTCATGCGCTTGAACTAGTAGTCAGTAGAAATCTAAGCCCACCTAATTGTACTGAATTGCAAATTGATAGTTGTTCTAGCAGTGAAGAGATAAAGAAAAAAAAGTACAACCAAATGCCAGTCAGGCACAGCAGAAACCTACAACTCATGGAAGGTAAAGAACCTGCAACTGGAGCCAAGAAGAGTAACAAGCCAAATGAACAGACAAGTAAAAGACATGACAGCGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTCTTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAAGAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAGAAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCATTGGTACCTGGTACTGATTATGGCACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGTGTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATGACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGAAGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCCGTTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAACAAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAAGCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGATAAGCCAGTTGATAATGCCAAATGTAGTATCAAAGGAGGCTCTAGGTTTTGTCTATCATCTCAGTTCAGAGGCAACGAAACTGGACTCATTACTCCAAATAAACATGGACTTTTACAAAACCCATATCGTATACCACCACTTTTTCCCATCAAGTCATTTGTTAAAACTAAATGTAAGAAAAATCTGCTAGAGGAAAACTTTGAGGAACATTCAATGTCACCTGAAAGAGAAATGGGAAATGAGAACATTCCAAGTACAGTGAGCACAATTAGCCGTAATAACATTAGAGAAAATGTTTTTAAAGAAGCCAGCTCAAGCAATATTAATGAAGTAGGTTCCAGTACTAATGAAGTGGGCTCCAGTATTAATGAAATAGGTTCCAGTGATGAAAACATTCAAGCAGAACTAGGTAGAAACAGAGGGCCAAAATTGAATGCTATGCTTAGATTAGGGGTTTTGCAACCTGAGGTCTATAAACAAAGTCTTCCTGGAAGTAATTGTAAGCATCCTGAAATAAAAAAGCAAGAATATGAAGAAGTAGTTCAGACTGTTAATACAGATTTCTCTCCATATCTGATTTCAGATAACTTAGAACAGCCTATGGGAAGTAGTCATGCATCTCAGGTTTGTTCTGAGACACCTGATGACCTGTTAGATGATGGTGAAATAAAGGAAGATACTAGTTTTGCTGAAAATGACATTAAGGAAAGTTCTGCTGTTTTTAGCAAAAGCGTCCAGAAAGGAGAGCTTAGCAGGAGTCCTAGCCCTTTCACCCATACACATTTGGCTCAGGGTTACCGAAGAGGGGCCAAGAAATTAGAGTCCTCAGAAGAGAACTTATCTAGTGAGGATGAAGAGCTTCCCTGCTTCCAACACTTGTTATTTGGTAAAGTAAACAATATACCTTCTCAGTCTACTAGGCATAGCACCGTTGCTACCGAGTGTCTGTCTAAGAACACAGAGGAGAATTTATTATCATTGAAGAATAGCTTAAATGACTGCAGTAACCAGGTAATATTGGCAAAGGCATCTCAGGAACATCACCTTAGTGAGGAAACAAAATGTTCTGCTAGCTTGTTTTCTTCACAGTGCAGTGAATTGGAAGACTTGACTGCAAATACAAACACCCAGGATCCTTTCTTGATTGGTTCTTCCAAACAAATGAGGCATCAGTCTGAAAGCCAGGGAGTTGGTCTGAGTGACAAGGAATTGGTTTCAGATGATGAAGAAAGAGGAACGGGCTTGGAAGAAAATAATCAAGAAGAGCAAAGCATGGATTCAAACTTAGGTATTGGAACCAGGTTTTTGTGTTTGCCCCAGTCTATTTATAGAAGTGAGCTAAATGTTTATGCTTTTGGGGAGCACATTTTACAAATTTCCAAGTATAGTTAAAGGAACTGCTTCTTAAACTTGAAACATGTTCCTCCTAAGGTGCTTTTCATAGAAAAAAGTCCTTCACACAGCTAGGACGTCATCTTTGACTGAATGAGCTTTAACATCCTAATTACTGGTGGACTTACTTCTGGTTTCATTTTATAAAAGCAAATCCAGGTGTCCCAAAGCAAGGAATTTAATCATTTTGTGTGACATGAAAGTAAATCCAGTCCTGCCAATGAGAAGAAAAAGACACAGCAAGTTGCAGCGTTTATAGTCTGCTTTTACATCTGAACCTCTGTTTTTGTTATTTAAGGTGAAGCAGCATCTGGGTGTGAGAGTGAAACAAGCGTCTCTGAAGACTGCTCAGGGCTATCCTCTCAGAGTGACATTTTAACCACTCAGGTAAAAAGCGTGTGTGTGTGTGCACATGCGTGTGTGTGGTGTCCTTTGCATTCAGTAGTATGTATCCCACATTCTTAGGTTTGCTGACATCATCTCTTTGAATTAATGGCACAATTGTTTGTGGTTCATTGTCTCCTTAAATTAGACTGTAAGCACCTTGATGGAACTCATACTACCTTTTATTTCACACACACGCACACGCGCACACACAGCCTACACATACACTGCCTAGCTCATTGTAGCATACTAAATACTGATTTTAATGAATAAGCTAAACCTTCGAAACCCATTTGCTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGATCACCTCAGGTCAGAAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCCACATCTACTAAAAATACAAAAATTAGCTGGGCGTGGTGGCCAATGCCTTGTAATCCCAGCTATTCTGGAGGCTGAGACAGGAGAATCGCCTGAACCTGGGAGGCGGAGGTTGCACTGAGCTGGGATTGTACCACTGCACTCCAGCCTGGGTGACAAAGTGAGACTCCATCTCAAAAACAAACAAACAAAAACACATCATTTCCCCTATAGCAAAAACATGACGGCACTTACTGTATCAAGAGAGGTGAGAAAAAGGAGCCACAGCAGGATGATTCAAGGGACTCTGCATAGCTCCATTTTAAGAATATGCCTACTGCAGGTCAGAGAAGGTAAGCAAACTGCCTAAGGCCACACAGCCAGGTACAGAACTCTCACCAATATTATTGCCAGCAATCGCAATTTTGGTGTTTATTCTTGGTACCAAGTTGGAGACTATAGGGTTCTCTTCCTAATAGAGACCATCTAGCCTTTCACTGTTTTGTGGATACTTCTTTCTCTTCTTCTTTTTTTTTTTCCCTTTTAAAATCTAGTTATTTTTTTCTTTTTGGTTTCTTTGACACAGGGTCTCTTACTCTGTTACCCAGGCTGGAATGGAGTAGTGCAGTCATGGTTCACTGTAGCTTTGACTTCCTGGGCTCAAGCGATCCTCCTACCTCAGCTTCCCGAGTAGCTGGGACCACAGGCGCCCACCAACACCTCCAGCTAATTTTTAAGTTTTTACTAGAGACAACATCTCACTATGTTGCCCAGGCTGGTCTCAAAATCCTGGGCTCAAGTGATCCCACCTCAGCCTCCCAAAATGCTGGGATTACAGGTGTGTGCAACCACGCCTGGCCTATTTTTTTTTTAATTGCTCATAAATCATCTTTTTTCTTTAAAAAAAAGAAAGATGGGAGGCTAAAGCAGGAGAATCACTTGAACCCAGGAGGCGGAGGTTGCAGTGAGCTGAGATCATGCTGCTGCTCTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAAAGAAAGTACACAATTTTACTTTCTGGACCTAATGGTCAAGGCCAATAATTTGGTCACCTATGAAATAAATAAAAGCTTTACCATATATATGACCATTTGATAATGTAATATGAAATGTTTATGTACTAAAGGCAGAATAGTCTAGAAAAAACATTCTGTATCACAACGTCTAAAAATGAATATCATCTTCATCATAGAACCAGGCTCTTTCTCCTAATTTTTTTTTTTGAGATGGAGTTTTGCTCTGTCACCCAGGCTGGAATGCAGTGGCACAATTTTGGCTCACTGCAACCTTCAGCTCCCAGGTTCAGGATCAAGTGATTTTCGTGCTTCAGCCTTCTAAGTAGCTGGGATTACAGGTGACTGCCACCACACCCAGCTCATTTTTTTGTATTTTTTTAGTAGAGAGAGGGTTTCACCATGTTGGCCAGGCTCGTCTCGAACTCCTGACCTCAAATAATCCACCCGTCTCAGCCTCCCAAAGTGCTGAGATTACAGGCGTGAGCCACCAGGCCTGGCCTCCTAATTTTTATTTGTAGAAGTGGCACCAAAATTTTCCAAGTTCTCATGCAAAAATTCAGGCTCATCTCAGTTTATTTTTTTCATTTATTTATCTCCCACTAAATTGACAACTTCTAATAATTAGGTTGGTTCTTTGTATTCCCAGCACAGGGTTCTATGCAGAATACACACACAGCAGTTGCTGGCAATAATATTGGTGAGAGTTCTGTACTGGGCTATGTGATCTTAGACAGTTTGCTTATGTTCTCTGACCTGCCGTAGGCACATTCTTAAAATGAAGCTGTTCAGACCCCCTCGATTCATCCTGCTGTGGCTTCTTTTTCCCACCTAAATCTTAAATACCCTTTTAGCTGCTAGTAAGTGAATGATGTTTTTTTATGAACTTTCTGAAGTCAGATTAGATGAAGTTGAGAAAAGCCTGATATTCTTATAAAGTTATATATGTGCATCATAGAAAACTTAGAAAATACAGATAAACAAAAATCATCCATGGACGAACCTTGAAGACATTGTGTTAACTGAAATAAACCGGACACCAAAGGACACATGTTATATGCTTCCACTTATATGAGATACCTAGAATAGTTACATTTGGTTACTCTGGGTACATTGCCTATAGATAAGCCTTGCTCCACAAGGAGCAGTTAAAAAAAAAAAAAAGATAAATTCATAGGATGGAAGGTAGAATAGTGGTTACTAGGGACTTGGGGAGGGGGAAATGGGGAGTTACTGTTTGATGAGTGCAGATTTCAGTTTGGGATGATGAAAAAGTTCTGGAGATAGATAGTGGCAATGGTAACACAACAGTGTGAAAATAATGCCACTGAACTGTACACTTAAAATGATTAAAATGATAAGTTAATTGTAATTTGTGTTATCCAGAAATGGTTAGCAATTTATTGGTGTATATTCTTTTAGTATTCCTGTGTGTGCACAGGGGTGCTTGTATATACTTTATCTTTAAAATATATCCAGGAAGCTAGGCACAGTGGCTTACACCTGTAATCCCAGCACTTTGGGAGGGTGAGGCAGGAAGATTGCCTGAGCCCCGGAGGTCAAGGCTGCAGTGAGTTGTGATCACGCTACTGCACTCTGTTCTGGGCAACCCCTGTCTGGGAAAAAAAAAAAAATTAGTGAGGCTTAGTGGTGCACACCTGTAGTCTCAGCTACTTGAGTGGCTGGGGTAGGATTGCTTGATCCCAGCAAGTTGAGGCCGTGGTGAGCCATGATGGTGCCACTGCACTCCATCCTGGGTGATATGGTGAGACCCTGTCTCAAAAACAAGAAATCCAGATAATTCTGTGCATTATAATCTAGCTTTTACTGGATCATTAAAATTCTTTTTTCTTTTTTTTTTTTTTTTTCTGAGATGGAGTTTCACTCTTGTTGCCCAGGCTGGAGTGCAGTGGTGTGACCTTGGCTCACCGCATCCTCTGCCTCCCGGGTTCATGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCATGTGCCACCATGCCCAGCTAACTTTGTATTTTTAGTAGAGACAGGGTTTCTCCATGTTGACCAGGCTGGTCTCAAACTCCTGGCCTCAAGTGATCCACCCACCTCGGCCTCCCAAAGTGCTGGGGTTACAGGCGTGAGCCACCGCACTCAGCCTGGGTCGTTAAAATTCTTAAGTGACTTCATTTTTAATTACTATATGGGATTCTATCTTTCCAGTGTATCATGATTTATTTGACCTATTGCTGAATGTTGGAGGTTTCAGGGTAAGAGGCACAGTTTGCTATTATGTACATCACTATAGTGGCATCCTGATAGCTAAATATTTGCCTACATCCCTGATTATTTCCTTAGTCTAAATTACTGGGACTAGGATTTTGGTGTTTGATACATGTTACTAAATTGTTTTTTAGAAAGATTAAACCAGTTTATGCTCTTCCAGCCCCTGTGGTATATGATAGTTCCCATTTTCCTGTACCTTGCCAACACTGGGTGATATCCAGTTTTAAAATCTAAATCTTGCATTGCTATGAGAACTACAATTAGAGAAGGCTTATCTTCTACTGCCCATTCTCTGTACAGAGCAAATCCCTCTAGACCTGAAGCCCCTTGGAGTTGTCAAGAAACCTTTGAGATGACTCCCCACTCTGTATCTGAGCTGTCACCAGTATTCTCCACTTCTTCAGGATTGCCATGGCAACTAAATTGATGAAAAGATTTAGGAGGCCTTTTCTCTCTTTGCAATTCCTATGATCCTTTTTGAATGTGGGTTTGGGACTCTGTCAATATACCCATCATCTAATTCTGTCCATTGTGTTTTAAAGTTTAAGGTTGCAATTTCTGATTACATCTGCCTTAGCCATACTGTATTATATTTGACATTCAATATACAATGTCCTTGTTTTTCTGTATTTCTAATCTTATTCCCAGAGATGTGTCTATTTGTTCAGGATTCATTTTGCAACGTGTTTTTACTAAGCATCTACCCAAAACCGTTGAAGTCAGATTTCAGGCTGTCTTACGTCTAAAGTAGCACAGGCAGGAAAAACTATTGAAGTGGGATTTTTTTTTCCCTTTTTGTACTGAACCGAGAAAAAGTATATAGATGATAGAGAATTCCTAATTTGGTATCATTGATATCTGGGTTTTTGTTTGTTTTTACAGAAGACTGATTAACTATACTTATTTATTAATTTATCTTCTCATTAATAAACACTTGCTGAGTGCTTACTGTCTGCTAGGCATTAGGGAGACAAATATGATTAAGGGAAGCTTCCTCCTATCAAGGTCATGTGTTCCATTTGGGTATACTAATGCATTAGCAATGTAAATCAAGTAGTGAGAGATCATCTGTTCCCGATAGGAGATGGATTATTGGTGGGGACTTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTATGTGATAAAATAAATATAGGAAATGTTAATTATAGATTCTAAGTAGTAGATATATAAACACTCATTGCAAAGTTGCTTCAAGTTTTCTGTATATTTGAAAATATTCACAACATGTCGACAAAACTAGCATGATAAAGCCACTATTTGTGCTAAGACTTCAGCTTGTATCTGGATTAGGCTTATTATGTAGTAGTAGGAACATTAGAAATAGTTTTAACTCATTAAATACACATGTTTTATGGGAAGGTTTTATATATATATTTATATGTAATGAATGTGAACAAACAAGGGTCAGATATACACTCTGCTTCCCTCCAGACCAGTTCCGGCTGCTCTGCTGCACATTTCAGGAGTCTTATTAGAATTAGCCACATTCTGCCCACTTGCCCTTACTTCTCATATTTCACAACTCCTCCTGGTGGGGACTTAAGGAGACATTCAAACTAGGCCTTGAAAGATGAGAATTTTTCCAAGTGGAAAAAGAGGAGTGGCAGCAAGTAAGGTAAAGGTACAGAGTCATGGAATTCCCAGGAAACGTAAAGTTGTCATGTGTTATAGGAAAACAACTTGTGTGAGGGGTGTTGGGAGAAATGAGAGATAATACCAGGGTATAAAGGGCCTTTTGAATGCTATGTTGAGGAATTTTATCCTAATGGCAGTAATGACTAACAATTATATAGTGTTCAAAAAGTATAAATCAGCAGTGGTATACCACTAAGGGTTTTTTTCTTTTCTTTTTTTTTTTGAGACAGAGTTTTGCTCTGTTGCCCAGGCTGGAGTGCCGTGGCACGATCTCAGCTCACTGCACTTCCGCCACCTGGGTTCAAGTGATTCTTCTGCCTCAGCCAGTGTTTCACTGTGATGGCCAGGATGGAGCACTAAGGGTCTTTATGGAAGAAAAAGACATGATAAACAAGGCTTTTAGGGAACTTCTACAGTAATGTAGCTGTATTAAAAGTAGAGATCAGAGCAGCATAGTAGAAGTAGAAGGCTAGAGCTAATTGAAGGAGCACTTCAGAATTAGAATCAAGAAGTCTTAGAAACCTATTGGTTTTATTCTCCCTAATGTATTTGGCCACTTACCTGCTGGGGAATTTGTCTAAGTTATAAAAAATAATTCCTTTGGGAAACCCAAAGGAAAGTTATCTATTAATAATTACCCCACTACTTTTTCTGATTTATGTAATGGCCACGTAGAGGTTAGATGTGATGGTTGTGACAGTAGTGACTAATACAGCCTGTGAAGCATTTTGGTCAGATATCTATGTGCTTTCATTCCAGGTTGACTGAGGCAAGACTTTGGCTAGGGTTTGATCAGTGATGTAACTACTCACGAGTACCACGTGGTGGCAATGGCATTGCTGCAGACCTTGGCAGCAAAGCAGTGTTAGAGTAGCAGTAGAAACCTTTGTGAAGCTAGGAATACATTTTCTGGTCATAAAAACCTCCTGAAAATTGTGAACTCAGTGTAGCAGGAGAAAGAAGATGGCTTGTTTTTAGTAAAGGGCAAAGTCATTTTTAAGGATCAGAAGAAGAAACGGAGAGTGAAACAATGTGTTCCTGCCCTACTCCCCCACTGGACTTTTTGGCAACCATTGCTGTTCCTTCTAAAAGTGATTTTTAAACATGTATATTTTGAAGCCAGGCACAGTGACTCACGTCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGGCCAGGTGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGAGGATCATGTGGTCAGGAGATCCAGACCATCCTGGCTAACACGGTGAAACACCATTTCTACTAAAAATACAAAAAATTAGCTGGGCATGGTGGCGGGCGCCTGTAATCCCAGCTACTCAGGAGGCTGAAGCAGAAGAATGGCTTGAACCTGGGAGGCGGAGCTTGCAGTGAACCAAGATTGCGCCACTGCACTCCAGCCTGGGCAACAAAGTGAGACTCCGTCTCAAAAAAAAAAAAAAAAATTAGTCGGGCATGGTAACAGGTGCCTGTAATCCCAGCTACTTGAGAGGCTGAGGCAGGGAGAATTGCTTGAACCAGGTAGGCGGAGGTTGCAGTGAGCCAAGATCGCACCACTGCACTCCAGCCTGGGGCAACAGAGCAAGACTGTCTCAAAAAAAATAAATAAATAAAATAAATTCTTAAGAAGGATATTTTGGAAAACTCCTTACATACCTAAATTCTTTGTTTATCAAATACTTGGACTTAGCACACTCTTCTTTGAAATGGACCAATAAACAACAGGAGCCCATAAGCAAAAAGAACTCATTATTTTAAAAACAGTAACTATCCTTACAGGCTTTCTCAGGGCTCTTTCTGTTGGATCCTTCCCTCTCACAGGTCCTTGCTAATGATCTCTAGGTGGACACATTCTAGATGAGATGTCCCTGTCTAGAATGGCAGCACCATGAGGGCTATATCCTCAGTACTAGGACAGCGCCTGGTGCTTAATAGATAGTAAATAGTTGTCTAATTAACTGAGCAAACAGATAGATTCATGAATTAGCTTTTTGCTTTTTCTGTTAGAAACTAAAGGTTCAGGTCAGGCACAATGGCGCATGTCTCTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCTGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATAGTAAAACCCTGTTTCTACAAAAATTACCAAAATTAGCCGGGCGTCTTGGCAAGCACCTGTAATGCCAGCTACTTGAGAGGCTGAGGTGGGAGAATCGCTTGAACCTGGGAGGAAGAGGTTGCAGTGAGCCGAGATGGTGCCAACCTGGGTGACAGAGGGAGACTTAAAAAAAAAAAGAAAGAAAGAAAGAAAAGAAACTAAAGGTTCAAAGAATCCCAGAAAAGGAAGAGTCCTCACAAGCCAGTAATCTAGGCAGGATTACTGATAGTATTTTTATATTTGTTGTATTTTTATAAAATGCCATAGATAGAGGGCTTTTTTCAACATTACATCAGTCTAAAAATCACACATTTTTATATGAACTAACCTAAATGTCTGATGAATCTCACAACACCAAGTCTTTGAAATGTGCCCATATAAATAAAATGTTAACAGATTCATGCTAATTTTAAATATCGATAGTGTTTAAATGCCTTAATTATTTTTTCACTCCCTAGCTTTAAAAGAAAATAACCAACTTCAAAAGGACATCACAATAACATCAAGTCTATTTGGGGGAATTTGAGGATTTTTTCCCTCACTAACATCATTTGGAAATAATTTCATGGGCATTAATTGCATGAATGTGGTTAGATTAAAAGGTGTTCAGCTAGAACTTGTAGTTCCATACTAGGTGATTTCAATTCCTGTGCTAAAATTAATTTGTATGATATATTTTCATTTAATGGAAAGCTTCTCAAAGTATTTCATTTTCTTGGTGCCATTTATCGTTTTTGAAGCAGAGGGATACCATGCAACATAACCTGATAAAGCTCCAGCAGGAAATGGCTGAACTAGAAGCTGTGTTAGAACAGCATGGGAGCCAGCCTTCTAACAGCTACCCTTCCATCATAAGTGACTCTTCTGCCCTTGAGGACCTGCGAAATCCAGAACAAAGCACATCAGAAAAAGGTGTGTATTGTTGGCCAAACACTGATATCTTAAGCAAAATTCTTTCCTTCCCCTTTATCTCCTTCTGAAGAGTAAGGACCTAGCTCCAACATTTTATGATCCTTGCTCAGCACATGGGTAATTATGGAGCCTTGGTTCTTGTCCCTGCTCACAACTAATATACCAGTCAGAGGGACCCAAGGCAGTCATTCATGTTGTCATCTGAGTACCTACAACAAGTAGATGCTATGGGGAGCCCATGGAAGATACATGGTATACAACATAGCTCTTGCTCTATTGGAAGCTAAGTGGAATGGGAGAAATTGGTGACAGGCAACCCCATAATTTCAGAAAGCTATGAAAAAGTACTCAGACATATTCCTTATAACACTGGTGTCACATCACAAAGACCTATTTAATGTGCTTCTGATTTATAGGGAGAGACATCCTATACTTCAGGAACTGCACTTTGATCCACAGAAAGCCTAGTGATGTAGAGCTCCTGTTAGTTCAAAAGGAAAAGAAAAGAACAACACAGAAAGCCTAATTATGCAATAGAGTCAAGTGCTTTATAGCAATGTTACAGTTATCAAAAAAAATCCAGATGGACCTCTGAGAGGATGCCATTGGAGTAACCAGGCAGATGCAGTTGATCAGAGCTGACTTCCTATAAGAAGTGAGCACTGAGCTGAGGAATAATGGCATAAATGAAGGAAAGTGAGATGGAAATTTGAGTTTTTAATTGGAAAGACAATACATCAGGCAGATTTTTAAATAGGGGCAAACAAACAGACACATAGGAGATGCTAGGCATGGGGTCCCCACTAGGATGCTGCTTAGAAACATGCAGGGGTGGTGAGTACTCCCAAAGTACACTTCATTCCTAGCTCAGTGATTCTTATCTGAGTGTTAAAGTTCCTTCTTCAGCACCCCGTTCCACAGTCCAACTGGGAACTTTAAGACCTTTCTTGGAGTCTTTCTAGGAACTCAAGTCTGCTACTTATACAGAACAGTGGCTTTGGTCCCCAGTTGTGCCTTGCAGTATTTTTGTGTTCAGGAAGAAACAGTAGCTCTTGGATAAAGAAGCTAGCTAGAAACTCTGTTGCTATGGCAGTGCTTCAAAATGTATTTCCTTAAATGCTTTCTTTGTAACTATCTTCATTTAGTTCATCTCTCAGATAATGAGAGATCAGAGTCCCATCCCCAGTATAATACTCTTCTTTAGGGTACTTTCACCATCTTCAGTCTAAACACAGACTAGACTTTCAATTATAATGTGTAAGATTTAAAATGTTATTATTGTGTGACTTTGAATATCTGTGTAAATCTACTATCTCCTCTTTGGTATATACGTGTGTTTATTTTTTTCTGGAGATCTGTAACTGAAATGCTTAATTTCTGAATTGTTTTGGATATCACAACTTAATACCAACATAAGTTTTGAGCCTTTTTCTCCCTAAATCTGGTGTGAGTCTAACTGAAACTCAAATGAACTTTTTAAAAATAATTTTTTCTTTTCTTTAATTTTTTTTTTAAGTAGAGACAGGGACGCACTGTTAACTAGGCTGGTCTTGAACTCCTGATCTTGAGCCATCCTCCCCGACCTGAGCCTCACCTTATAGAGAGGGTCTTGCTCTGTTGCCCAAGCTGGAGGGCAGTGGCATAATCACAGCTCACTGCAGCCTCTCGACCTCCTCAAGCGATCCTCCTGCCTTAGCCTCCCAAGTAGCTGGGACTATAGGCGTCCACCACCATACCCAGCTAATTTTTTTTTTTATTTTTTGTAGAGACAAGGTCTCCCTATGTTGCCCAAGTTGGTCTCAAACTCCTGGACTCAAGCAGTCCTCTCACCTCAGCCTCCCAAAGTGCTGGGGTTACAGGTGTGAGCCATGGCACCTGGCCAGAACTTCTAGTAAAAAGAATATTGTTGCCGGGTACGGTGGCTCACGCCTGTAACCCCAGCACTTTGGGAGGCCAAGGCAGGCGAATCACCTGAGGTCGGGAGCTCGAGACCAGCCTGACCAACATGGAGAAACCACATCTCTACTAAAACTACAAAAAATTAGCCGGGCGTGGTGGCACATGCCTGTAATCCCACCTACTTGGGAGCTACGGTGCCTGGCCTAGTTTATTATTTCTTAATATCTGTTGTCTTCCAGTGTCTTCCTTAATTCTTCACAATACCCTGTACAATGCTTAGCACACAGTGGGCAGTCTGTAAGTTTATTAAATGTTTGGTGTGGCCCATACTTCCTATCCACAAAGAATGTAACATGTTAAGACATCTAGATGAGGGAATGATTTAAGAGGAACTACAATAATATTCTGAAACTTGGACTCTGGATCTCTGCATTTAGACTTTCCTAAACCAGCCAGCAAGTAGATCATCATGTCACAAGGCTTAGGTTGGGCTTGCTGTTCAGAGAATGAATTAAGGATTAAGGAGAAAAAAAAGCAGAAAGGTTTTGCTCTGTTTTTCAGGTTCTATTGAGTTGTTAACTTCTAACAAGTTATCTTATTTGCTTCATTGCATGAGGCCCATTGTAGTAAGAAGAGGAATTTATATGCTAAATGTTCTGGTGATAGAATGACTTTTCTTTTTTTTTACAGTCCAAAGGTCTTTTTTTTTTTTTTTTAACACCTATTATGCCATGAATTCATAGGGAATAGGTTCCAGCTGCTCAGGCTCCTTCCCATTGGTTCTCACAAAGTGTGCTTCTCTGGGTGGAGCAGGCTGGTGCTTCAGTTGAACCCACGTACCTTTCTCTTTGGCTTCTTTCTTTTTCTGATCATTTTCCTTCACGCGTTTCAGGAAGCTGTCTTGGCTCTTAGAGTGTTTAATGTGCTCAATACGCACATTAATTCTCTTGGCAAGAATCTTGCCCTTAACTTGTTTACAGCGATGCCAACAGCATGCTGGGTCACGTTGTAGACTTTTCCAGTTTTGCCATGGTAACACTTGTGGGGCATTCCTTTTTGAACAGTACCCGTTCCCTTGATGTCTACAATTTCACCTTTCTTACAGATTCGCATATACATGGCCAAAGGAACAACTCCATGTTTTCTAAAAGGCCTAGAGAACATATATCAGGTGCCTCTCCTCTTTCCCTTTGTGTTCGTCATTTTGGCAAATTACTGAAAGATGGTGGTTCTGGCCAAAAGGAGGAATGACTTTTTAATAGCTGTGTTTGTATCTGAGCCTTCCCTCTGCCTTTCATTTTTTTTGTTTTGTTTTGTTTTGTTTTTGTTTGAGATGAAGTTTCACTTTTGTTGCCCAGGCTGGAGTGCAATGGTGTGATTTCGGCTCATTACAATGTCCGCCTCAGCCTCCTGGGTAGCTGGGATTACAGGCACCCGCCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCGGGCTGGTCTCAAACTCCTGACCTCAGGTGATCTGTCCACCTCGGCCTCTCAAAGTGCTGGGATTGTAGGCGTGAGCCACATCACCTGGCCACTTTTTTAACTCTTTCCAATGGTTAATTCCGTTTGATATGGTTCCTTGGAACTTGCACATTACCCTTTATCAATTATCACCCTGTATTGGGGGTGGGGAGGATGATACCTCTCTTCATAGTTAGATCCTACTTACTTTCAACAGAGTTCTTAACAATCCTAGAAACTCACAGGTCCAGAAAAGACAAGCATAAAGGAAACTATAAATAATGCATTTGAAGACTAACTCAGGAAATCAATGATTATTTCCCCCCAGGCTACCCAGTGTCTTAAAAAAACAGTTTAATTAATACAATCTTTTGTTTCAATTTTCTACCTATATTTATGGCTTTTAGCTTTTCTAATAAAAGCTCAAAATGAATTACAGTCATCAGTGACTTTTTAATGAATAGAAGACTTTTGCAATTTTTAACTATTTGTTTTTACTTATTAAATATTTCCGCCTTGGCCAGGCATGGTGGCTCACGCCTATAATCCCAGCACTGTGAGATGCCAAGGCAGGAGGATCACTTGAGTTTAAGAGTTCTAGACCAGGCTGGGTATGGTGGCTCATGCCTATAATCCCAGCACTTTGTGAGGCCAAGGTTGGCGGATCACCTGAGGTCAGGAGTTTAAGACCAGCCTGGCCAACATGGTAAAACCCCATCTCTACAAAAAATACAAAAATTAGCCAAGGGGTGGTGGTGGGCACCTATAATCCCATCTTCTTGGGAGGCTAAGGCAGGAGAATCGCTTGAACCTGGAGGCAGAGGTTGCAGTGAGCCGAGATCATGCCACTGTATTCCAGCCTGGGTAACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAGTTTGAAACCAGCCTGGTCAACACAGCAAGACACCCATCTCGTTGAAAAATAACGGTCGGGCGCAGTGGCTCACGCCTGTAATCCCATCACTTTGGGAGGCCGAGGCAGGCAGATCACCTGAGGTCGGGAGTTCGAGACCAGCGTGACCAACATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGTTGGGCGAGGTGGTGCATACCTGTAATCCCAACTACTTGGGAGGCTGAGGCAGGAGAACAGCTTGAACCTGGGAGGCAGAGAGGTTGTGGTGAGCCAAGATCATGCCATTGCACTGCAGCCTGGGCAACAAGAGCAAACTCCATCTCAAAAAAAATAAATAAATAAAAATAAATAAATAAGTACTTCTGCCTTTAAGCCACTTCCTAGAAGGCAGTGGCACAAAGTGATACATTTGGAGGAGTAAATATATTACAAAATGAATTAGGCTGGGCGCAGTGGCTCATGTCTGTAATCCCCGCACTTTGGGAGGCCAAGGCGGGTGGATCACTTGAGGTCAGGAGTTCGAGACTAGCCTGATCAACAGGGTAAAATCCCATCTCTACTAAAAATACCAAAAAAACTAGCTGGGCGTGGTGGCAGGCACCTGTAATGTCAGCTACTAGGAAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCAAGATTGCACCATTGCACTTCAGCTTGGGCAACAGAGTGAGACTCCGTCTCAAAAAAAAAAAAAGAACTAACATGCCAGAACTTTGCCTTCAGTATGTTTTGTGATTTTTCCCTTCTTGTGCCATTTCATCATTAGTTCCATGTATTATTTAAGATTTCTTATCAACCAGCACCTTGGGATTTTTTTGTGTATGTGTTGGTTTAGGGGGTTTATTTGTTTTTTTCTTTTTTTTCGGTAATTGAAAATGTGAAGCAAAATGTCACCTGTTTTTTCTTTCATGTCTGACACTCATGTCTTGTTTACCCCCGACATGCAGAAGCTGAAATCCCCATTTCATACAGTCTTCAATGTGGAGGCAGTAGGGATGGAGAAAATAATGTACTTTGTGCTCTCCGGTACTCTTTCTTTCCTATTGTCTGAGGGGATTTGGGCATAATTTATTTTGCTGCAGAGATAAAAATTTGTTATATATATTTTTTATCATTCAGGGCCAAGGAATATAGATTTTTTTTTTCAGCCTTGTCTCAGCTGGGTGTCTTTATTTACTCTGTCTTAAAGTGTTCCTTTTATTATCATTATTATTTTTTAATCATTGAATTCCATTTGGTGCTAGCATCTGTCTGTTGCATTGCTTGTGTTTATAAAATTCTGCCTGATATACTTGTTTAAAAACCAATTTGTGTATCATAGATTGATGCTTTTGAAAAAAATCAGTATTCTAACCTGAATTATCACTATCAGAACAAAGCAGTAAAGTAGATTTGTTTTCTCATTCCATTTAAAGCAGTATTAACTTCACAGAAAAGTAGTGAATACCCTATAAGCCAGAATCCAGAAGGCCTTTCTGCTGACAAGTTTGAGGTGTCTGCAGATAGTTCTACCAGTAAAAATAAAGAACCAGGAGTGGAAAGGTAAGAAACATCAATGTAAAGATGCTGTGGTATCTGACATCTTTATTTATATTGAACTCTGATTGTTAATTTTTTTCACCATACTTTCTCCAGTTTTTTGCATACAGGCATTTATACACTTTTATTGCTCTAGGATACTTCTTTTGTTTAATCCTATATAGGTTTTTTGAACCTATAACATAAGCTACAACATGAGAAATGTGCGGTTAGATAGATATGTCCCTTCTGAAGGTCAGAAAAAAATATAATGGAGGTAAAACCTGAACAAGCTTGGAAACTGATGGTAGACTTCTTCAAGGCAGCCCTTGCCCTAATTAAAATTCTTGTCTTTCTAGAAAAAGTCTAGCTGTTGATTTACCACAGAAAATAATAATAATAATTACTATTATTATTATTTTTTGAGACAGGGTCGCCCTGTGTCACCTAGATTGCAGTGGTGCAGTCATGGCTCACTGCATCCTCCGTTTTTCAGGCTCAAGCAATCCTCCCACCTTAGCCTCCTGAGTAGCTGGGTCCACAAGCATGCGCCACCCACACCCACTAAGTTTTTGTATTTTTGGTAGAGATGGAGTTTTACCTTGTTGCCCAGGCTGGTCTCAAATTCCTGGACTCAAGTAGTCCGCCCGCCTTGCCCTCCCAAAGCCAGAAAACATTTAGAATATCTTTCAGAGATGTGTATTTACACCACTATTAACACAGGGCTGTATAGCAGTCCAGTACTGGACTATGTAGTCCAGTACTATTCTTTTCCTTACTGGAGGGCCAGGCGTGGTGGCAGGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCTGGGACCGTGCCATTGCACTCCAGCCTGGGCGACAGAGCAAGACTCCGTCTCAAAACAAAAAAAAAAAGAGAGAGAGAGCAGTAATTCAGGTCTCACCCATCTTCAATCCAGGGGGCCTAGCCTTAGTATTTGACCCATAGTAAGCACCCAATAATTGTTTAAATTAATTAACCTCTGAGGCCCTTTAAATCTGTTGATAAGTATCTTATTTTGCAAAGTCCTAAGCACTTGGAAGAGCAGAGGAACTATTTACTGGGTGTGTATGCTTTTCTAACAATATTTTATAGCTGGCTTTTGTTTTTAGAATGAATTTGAACATTGAAAAGGCAGGCAATAGGGATGATTCTGTGAATTCTGCTAAAACTGAGTAGAAAGAATGAGTGTAGAGATGTCGACATTGATCAACTTTCTATCTTCATAAGAGATCTGATTCTAACATATCCATTTAGACTCAAGTAGAATATTGTGTATAGAGTGAGTGGCAGTGAGTAATTTGGTAAAAATTTGCTGACCTGCTTTTATTCTTTCCTCCTTTCTTTCTTCCTTTCCTTCCTTCCTTCCTTCCGTCCTTTCCTTTCCTTTCCCTCCCTTCCTTCCTTCTTTCCTTCTTTCTTTCCTTTCTTTCCTTTCTTCCTTTCTTTCCTTCCTCCCTTCCTTTTCTTTTCTTTCTTTCCTTTCCTTTTCTTTCCTTTCTTTCCTTTCCTTTCTTTCTTGACAGAGTCTTGCTCTGTCACTCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCACTGCAACCTCTGTCTCCCAGGTTCAAGCAATTTTCCTGCCTCAGCCTCCCGAGTAGCTGAGATTACAGGCGCCAGCCACCACACCCAGCTACTGACCTGCTTTTAAACAGCTGGGAGATATGGTGCCTCAGACCAACCCAACCCCATGTTATATGTCAACCCTGACATATTGGCAGGCAACATGAATCCAGACTTCTAGGCTGTCTTGCGGGCTCTTTTTTGCCAGTCATTTCTGATCTCTCTGACATGAGCTGTTTCATTTATGCTTTGGCTGCCCAGCAAGTATGATTTGTCCTTTCACAATTGGTGGCGATGGTTTTCTCCTTCCATTTATCTTTCTAGGTCATCCCCTTCTAAATGCCCATCATTAGATGATAGGTGGTACATGCACAGTTGCTCTGGGAGTCTTCAGAATAGAAACTACCCATCTCAAGAGGAGCTCATTAAGGTTGTTGATGTGGAGGAGCAACAGCTGGAAGAGTCTGGGCCACACGATTTGACGGAAACATCTTACTTGCCAAGGCAAGATCTAGGTAATATTTCATCTGCTGTATTGGAACAAACACTTTGATTTTACTCTGAATCCTACATAAAGATATTCTGGTTAACCAACTTTTAGATGTACTAGTCTATCATGGACACTTTTGTTATACTTAATTAAGCCCACTTTAGAAAAATAGCTCAAGTGTTAATCAAGGTTTACTTGAAAATTATTGAAACTGTTAATCCATCTATATTTTAATTAATGGTTTAACTAATGATTTTGAGGATGAGGGAGTCTTGGTGTACTCTAAATGTATTATTTCAGGCCAGGCATAGTGGCTCACGCCTGTAATCCCAGTACTCCAGGAGGCCGAGGCAGGTGGATCAGCTGAGGTCAGGAGTTCAAGACCTGTCTGGCCAACATGGTGAAACCCTGTCTCTACTAAAAATACAAAAAAATTAACTGGGTGTGCTAGTGCATGCCCGTAATCCTAGCTACTCTGGAGGCTGAGGCAGCAGAATCACTTGAACCCGGGAGGCGGAGGTTGCGGTGAGCCAAGATCACACCACTGCACTCCAGTCTGGGTGACAGAGCAAGACTCCATCTCAAAAAATATATATATATATATATACACACATATATTTTATTTCAACTGTTAGACAAGAGTCCAAAGGCCAAAGAATAAAGTTTTAGGCCAGTCCTTTATTAGAAAATGAGTCAAATCCCAAAGCAAGTTTTTTTTATGAGTTAATGAATATAAATGACTACATATTTTATGCCTTAAAAATCACTTTTAATGAATGGTGTTTTATGGCTTGTAAATCAGAGTTTTAATCAGTAAAGAAAGTTTTTAATCCTCAAAAACACGTTATCATAAAAGACACTGTTTGGCATCAAATGTGGTATTTGGCCATGTTCATTAGGGTCATTTTAGGAATCTCATACATTCTACTTAGCTATGCTTAATTCCTGATACCATGGCATTTTCTGAAATGTTTCAAGGATGACATCTCTGCTGTTTTTAATTTGGTAATGATATCTGCTGATTTATTAAGTGAAAAAAGTAATGGTGTCATTACCTTGGATGAAGAAACAAAAATAAAGCATTTGCCACATTTTTCAACTTTTTTTTCCTTTCTTACAAAATTGCTATAAGCTCATTGCCCCCAAATTGGACAATATAGGGAATAAAAAAGATAATTTGGGGTGGGGTTAGACACGGGTCTTGTTATGTTGCCGAGGCTGGTCTCTAACTCCTGGCCTCATGCAATCTTCCTACCTTGGCCTCCCAAAGTGCTGGGATTATAGGTGTGAGCCACTTCACCAAGCTGAGATGCCACCTCTTAAAAGATAAAATAAGGACAGATTACAGCCACTGCTCATGCCTGTAATCTCAGTACTTTGGGAGGCCAAGGTGGGAGAATTGCTCGAGGCCAAGAGTTCAAGACCAGCCTGGGCAATGTAGCGAGACCTGATCTCTATAAAAAGTAAAAAAAAAAAAAAACTAGCTGGGGCCAGGCGTGGTGGGTGGCTTACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCAGATCACCTGAGGGCAGGAGTTCAGGACCAACCTGACCAATATGGAGAAACCCTGTCTCTACTAAAAATACAAAATTAGCCAGGCTTGGTGGCTTATGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCAGAGGTTTCAGTGAGCTGAGATCGCGCCATTGCACTCTAGCCTGGGCAACAAGAATGAAACTCCATCTCAAAAAAAAAAAAAATCAGCTGGAAGGTGGCAAACACCTGTGGTCCCAGCTACTCAGGAGGCTGAGACAGGAAGATCACTTGAGTCCAGGAGGTCAAGGCTGCAGGTGAGCCATGTTTGTGCCACTGCACTGCAGCCTGGATGACAGACCGAGACCCTTCTCAAAAAAAAAAATATTACCCGTACTCTTTTTTGAGACGGAGTTTCACTCTTGTTGCCCAGGCTGGAGTGCAATGGCGCAATCTCGGCTCAGCGCAACCTCCGCCTCCTGGGTTCGAGCGATTCTCCTGCTTCAGCCTCCCCAGTAGCTGGGATTACAGGCATGCACCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACAGGGTTTCTCCATGTTGGTCAGACTGGTCTCGACCTCTTGACCTCAGGTGATCCGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCCTGAGCCACCGCACCCGGCCTGTACTCTTATTCTTTAATAATAAAATATTTCTGTGTTTCTTTAGTCATTTTACATAAACTTTTATTTATTTATTTATTTTTATTTATTTATTTTTTTGAGACGGAGTCTCGCTCTGTTGCCCAGGCTGGAATGCAATGGCTCAATCTCAGCTCACTGCAAGCTCTGCCTCCCGGGTACACGCCATTCCCCTGCCTCAGCCTCCCTAGTAGCCGGGACTACAGGCGCCCGCCACCACGCCCAGCTAATTTTTTTTTTTGTATTTTCAGTAGAGACAGGGTTTCACTGTGTTAGCCAGGATGGTCTTGATCTCCTGACCTCGTGATCCACCCGTCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGTGCTCGGCCCATAAACTTTTATTTTTAAAATAATGTCATGATAAATAATATTGCTTAGGTGTCTTTAATATATTAGTAACATTTCTGTTTTATTGTACATCAACATTTATATTCAAATTAATGGGTGAAGAGTACTCCATTGGACTAGGTATATCGTAATTTAATCTCCTATTATTGGACAACTACATTGTTTCTAAAATTATACTATTCCTATGACTAAACCTTTGCATATATCTTTTATCTCCCTAGGATATATTTCTAAAACTAGCATTGTTGACTGAAAGTGTAAATACGTGTTAAGGTGTTTGCTACATAATGCCATATTTCCTTTTTAGGAAACTAAGCTACTTTGGATTTCCACCAACACTGTATTCATGTACCCATTTTTCTCTTAACCTAACTTTATTGGTCTTTTTAATTCTTAACAGAGACCAGAACTTTGTAATTCAACATTCATCGTTGTGTAAATTAAACTTCTCCCATTCCTTTCAGAGGGAACCCCTTACCTGGAATCTGGAATCAGCCTCTTCTCTGATGACCCTGAATCTGATCCTTCTGAAGACAGAGCCCCAGAGTCAGCTCGTGTTGGCAACATACCATCTTCAACCTCTGCATTGAAAGTTCCCCAATTGAAAGTTGCAGAATCTGCCCAGAGTCCAGCTGCTGCTCATACTACTGATACTGCTGGGTATAATGCAATGGAAGAAAGTGTGAGCAGGGAGAAGCCAGAATTGACAGCTTCAACAGAAAGGGTCAACAAAAGAATGTCCATGGTGGTGTCTGGCCTGACCCCAGAAGAATTTGTGAGTGTATCCATATGTATCTCCCTAATGACTAAGACTTAACAACATTCTGGAAAGAGTTTTATGTAGGTATTGTCAATTAATAACCTAGAGGAAGAAATCTAGAAAACAATCACAGTTCTGTGTAATTTAATTTCGATTACTAATTTCTGAAAATTTAGATCTAGATAAAGCTATAGTGTGGATTATTTTATGTATATTTACTTGAGAAAATAATTATTAAATATTAGTGGAAAAGCTATACTTTGGGTATGATATAGGACTTTCGAATTGGAATTTTCCTTTCTATCTGTAAAAGCAAGTAGGTATAGTTTTATTCCCCAGAAGGCATCTTTTTCTCCCCCTTGTCTCACATGGGTGAATTTACCAGCATATTTAACTAAATTCAGACTGGTTCCAAATGTACTGCCAGATAGTAGCATTTCTCTAGTGTTTGTTTTCATCCTGGCTTGTAAGAATGCCCTGCCACTTCTGCCCTGCAATATCCCTTGCTATTAGGATTTTGGCATCACCTTGGGTCCTTAATGCCAGAAATGGGAATTGCTTCATACTGTGGAAAAATACCCATTAAAATATTAAGACCAGTAAAACCTCGTTTCTGCTTGGGCTATTTGTGGATTTCAGACATCCTGAGAAGTTTACCACCCCTGTAATTAATTGTCATTGTCATCACTTCATAATAAAAATAATTGCATGGCCGGGCATGGTGGCTCAAGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGTCAGATCACCTAAGGTCAGGAGATCAAGACCAGCCTGACCAACATGAAGAAACCCCATCTTTACTAAAAATACACAATTAGCCGGGCGTGGTGGCGCATGCCTATAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGAGGCGGAGGTTGCGGTGAGCCGAGATTGCACCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCTGTCTCAATAATAAGAAGAAGAATTGCGTGAATATTTCTTTAAAACTATGATGAGATAACATACCAGATTATCAAATGGATTCAGTAGTGGGTGTGCCATTTATTGCACACTGAGAGATGACCAAGTCATTCTGAAATATCTTTATTAATATATCCTTCCTAGGATTTTTCATCCTAACTTCTCCATAGGTAGTTACTTAGCATAACATCTCTGTGGCCAGATGTATCCCACTACTAAAAGGGCAAAGTAAGCTGTGGCTGCCCTGGTAGATACAATGAGTAAGTGCACAGTGATGGCTATAAATGTTTTCATCTCATAATCCCATGTCCAGACCAGCAATTTGCTCTGAAAGCTCTTACCTGTGTCTGTTTCAATGGCTCTTGATCACTTGCCTGCACGTCCAGAATTCCTTATTTATTCATTGAAAATTAGCGTTCTTTATCCCTTTGTTTTGCAAGTTCAGCTTTTTAGAGATGGCTAAAATGGTCTAATCTTTCTTGGCAAAGGCAATTCTGAGCTGCAGATTAGACTACAAGTGGCTTGGGTACATGTTGTCTTTAAACAAGCGAAGAGGAAAACTTTGAGCTCTATTCAGACTTGGTGAAGTGTGGTAAATTTATGATGAAAGCTACTGACTGTATTACACATGATTAATTCTGAAGCCCATATTAAGATGATCTTTTCAGCAGTTCAGCATTGCTCTTCTAACTGAACAGTTTCAAGGCTGGGATTTCAGCAATTAATCAGTTCAGAATTGCTAATGATCCTGGCGGAGGGTGGTAGCAAAAGGGGGAGGATGTCATTAGCTTCTCTAGCCTGCCTTTTTTCAGTGCCCTGTGGCAGTATGGAGTGAGGCAACATGAAAGAAAGATGGCCTGACCTTCATGGCAGTATTGTGCAACACGTAAATACTGGTGTGAGTGGCTGTGGCTATGGCTAGTAAATGATGGCCCTTGGTAAACAAAGTTATTTATCAGACAATACCTACCAGCTAGGTCAACTGTGCCCATAATTGATCTGGTTAATTTCTTTTGCTGCCTATTGATTTTTATTTGGTTGATAGATAATAGCTAGAGGACTCTAAATTTCTTTGGGGAAGAACATGAACCCCTTCTAAGCCTTCTTACGAGAGAATTGATCGCTTTTGCACTGACCTTTAGTAACATCCTGATTTCAGTGTTTTGTAACTATCAGAGGGTTGAGTCTTGGTTTTAAGCCATGTATATCTGTAGCATAACTTTCTGTGTAGGCTAGTTACCTCTCAGCTTATAAAGTGTAGGCTGATAAATTTATAGTACAGTAGAGTGTCACTATGCAAAGAAACGATCTTAGGGAATCGAATGATATCTGCTATTAAAGCAAAATTAATATATATTTTTTCTTTTTACTTTTTTTTTTTTTTAAAGACATGAAATCTCACTGTATTGCCCAGGCTGGTCTTGGTCTCAGACTCTTGAGCTCAAGCAGTCCTCCCACCTCAGCTTCCCAAAGTGCTGGGATTATAGGCATGAGCTGCCGTGTCTGGCCCAGTATATATTTTTTAAGTTTTAAGTTTTGTGGTACGTAGTAGGTTTATAATATTATTTTGAATCCTTAGTTGTAATTTTATGTCTGCTGATGTGTACATAATTTTTATTAAACTATTTATTTGAGACTTCAGGTATCTTTTTTTTTTTTTTGAGACGGAGTCTCGCACTCTCGCCCAGGCTAGAGTGCAGTGGCGCCATCTCGGCTTACTGCAAGCTCTGCTTCCTGGGTTCACGCCATTCTCCTGCCTCAGCCTCCTGAGTAGCTGAGACTACAGGTGCCCGCCACCACGCCTGGCTAATTTTTTGTATTTTTAGTAGAGACAGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTTGTGATCTGCCCGCCTCAGCCTCCCAAAGTGCTGAGATTACAGGCGTGAGCCACCGCGCCCAGCCGAGACTTCAGGTGTCTTAGAATTTTTTAAATGTACCCTTTCTGAGAAAAACAGAGACTTAAAGCTAGGATAACTGGTATTCTATTTTTTTTTTTTTTTTTTTTTTACCTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTAAAAAAAAAAAAAAAAAAATTCACTTTAAATAGTTCCAGGACACGTGTAGAACGTGCAGGATTGCTACATAGGTAAACATATGCCATGGTGGAATAACTAGTATTCTGAGCTGTGTGCTAGAGGTAACTCATGATAATGGAATATTTGATTTAATTTCAGATGCTCGTGTACAAGTTTGCCAGAAAACACCACATCACTTTAACTAATCTAATTACTGAAGAGACTACTCATGTTGTTATGAAAACAGGTATACCAAGAACCTTTACAGAATACCTTGCATCTGCTGCATAAAACCACATGAGGCGAGGCACGGTGGCGCATGCCTGTAATCGCAGCACTTTGGGAGGCCGAGGCGGGCAGATCACGAGATTAGGAGATCGAGACCATCCTGGCCAGCATGGTGAAACCCCGTCTCTACTAAAAAATAAAAAAATTAGCTGGGTGTGGTCGCGTGCGCCTGTAGTCCCAGCTACTCGTGAGGCTGAGGCAGGAGAATCACTTGAACCGGGGAGATGGAGGTTGCAGTGAGCCGAGATCATGCCACTGCATTCCAGCCTGGCGACAGAGCAAGGCTCCGTCTCAAAAAAAAAAAAAAAAAACGTGAAAAAATAAGAATATTTGTTGAGCATAGCATGGATGATAGTCTTCTAATAGTCAATCAATTACTTTATGAAAGACAAATAATAGTTTTGCTGCTTCCTTACCTCCTTTTGTTTTGGGTTAAGATTTGGAGTGTGGGCCAGGCACGGTGGCTCACACCTGTAATCTCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACGTGTTGAAACCCCGTCTCTACTAAAAATATAAAAATTAGGTGGGCGTGGTGGCAGGCACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGCAGAATCGCTTGAACCCAGGAGGTGGAGGTTGCAGTGACCCAAGATCGCACCATTGCACTCCAGCCTGGGGACAAGAGCGAGATTCTTGTCTCAAAAAAAAAAAAAAAAAAAAAAGGTTTGGAGGGTGGTGAGCTGAGATAGTCAACTATTAACTCCTATCTACCTGCTGGGACTACACTGGTGAGGTGGAGCCTAAGTCCTAAAACAACAAGTGAGGCAGCTGGACGCGGTGGCTCGCATCAGTAATCCCAGCACTTTGGGAGCCTGAGGCGGGCAGATCACAAGGTCAGGAGTTCGAGACCAGCCTGGCCAATATGGTAAAACCCAGTCTCTACTAAAAATACATAAATTGGCTGGGCGTGGTGGTGTGCACCTGTAATCCCAGCTACTTGGGAGGCTGACACAGAAGAATTGCTTGAACTCTGGAGGCTGAGGTTGCAGTCAGCTGAGATCCTGCCACTGCACTCCAGCCTGGCGACAGAGTGAGACTCTGTCTCAACAACAACAAAAGAAAGAACAAGTGAGGCAAAACCTGGAGACCCCAGCTTCATGTAACACCTAGTTTGAGTATTGTTGAGAGTTTTTCAGGAAAAAAGTCTGATAACAGCTCCGAGATAGTCTTAACATATGAAAAAGCAAAAAAGGGAGGAGACAGATCATTTGTCCTATACCTTTCTCTTTTAAGGTTTTAATTATAACTTGTGTAATACAGGAGACCTCTGGGTGTTTTTAGTTGACTATAAACTAAATCTGAGTACACATTTCAGGGCTGCTAAAAATGCTTATTTGAAACTGGGCCGTATTAACACAAGCAGAGGCTCTGGAGCAAGTGAAGTACAGATCCAGAGCCCCACTGTATTCTCCAATGGAGTGATTGCCTGAAAGATGATGTCAGTTTTAAGCACCGTGCTTGGTTTTTAACATGGTCACTGACAAATTGGAGAGTGTTTATCCAGAGGTAGATGGTAAAGATACATAAAAGTAACTTGAAATACTGTCTTTTGAAGAAGAAATGAGAAGATTTAAGGAAATAAGACACTGTCTTCAAGTATCTGAAGAACCGTTACCCGGAAGAGAACTGTTATCTGGAACAGGATTAAGACTCACTCATGGGGCTCCAGAAAGCAGACGAGTGCATGGAGGACGCAGAAGATGCAGATTGTGTGGCTCAACTCTAAAATCTTTCTAACAAAATTAGTTCTCTGGATGTGTTCCAGTTCACTTGATGATGATTCTTTTGTTTTTGTTTTTGTTTTTGAGGTGTAGTTTTTCACTCTTGTTGCCCAGGCTGCTGGAGTGCAATGGCACGATCTTGGCTTGCTGCAACCTCCCCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGAATGCACCACCATACCTAATTTTGTATTTTTAGTAGAGACAGGGTTTTTCCATGTCAGTCAGGCTGGTCTTGGACTCCCGACCTCAGGTGATCCACCTACCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCATCGCGCCTAGCCTATGATGATTCTTTTCACAGAGATACAGGCACTTAAGGAGAGGATCTAAACCCCTTGGACACATTGCCGTTGAACTTCTAAGATCTTAGGTTTCCACTTACTCATGAAAATTATACCACAGGGTCAGAGGGTAGTGTTCATTGGAGCCAGGTGCCAGAACAAGTTATTACAAACTACTATTTTAGAGAAAAATGTCATTAAAGTTTAAGATACCTTAAGCTATAGGTTTGCATCAAAGTTAATGAAAGGTAAAAAGATGCCAAGCGTGGTGGCTCAGGCCTGTAATCCCAGCGCTTTGGGGGGCCAAGGCGGGCAGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTAGTAAAAATACAAAAAATTAGCCGGGCATGGTGGCGGGCATCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATGGCATGAACCCAGGAGGCAGAGCTTGCCGTGAGCTGAGATCCAGCCACTGCACTCCAGCCTGGCTGACAGAGCAAGACTGCATCTCAAAAAAAAAAAAAAAAAAAAATGCAAATCAAATCTAAAGTAGTTCAGTCTTTAAACTCAAAGCCAATACATTTGCTTTGAACTACAAATGAACTGAAGTTTTTAAGTGTAATAAATGTTACTAAATCGGCTTTTGTAGCAGTTAAACAAAAAACTTCAAAAATTGTAAGGATTCTGTGAGGGAGCATGGCTGCTGCTGCTGCTGCTGCTTGCAGATAGCCTGCTGTGTTTAGGATTTAGTTAAATACATTTCTCCTGTTTAAAACTAAATGGTCTTTCCTTAGTTTGCTTAGTTCTTCAGAAGGGCCTTTGAAACACTGGGAAATAAACAAGTGATTCTTTAGCTACTGCTTTCTGAAATACTTATATAAAAGCTCTGCACTGTATTCTCCCATCCCTCTCAGGGGAATATTAGAGGGTTAGGACTCCCCAGGTAGACATTCTAGGGGTGAAAATTTGTCATTACATTGACATTTCAGATTTAGGTTTTCAACAATACTGTTTTCTTCTTTCACATATTGCCATCTAGTAATATAGATGTTCTCCGTCCACATTAATCAAAACTATTGACATGGATAATTCCTAATTCCTTGAACACTATAATGGAGATCTATAGCTAGCCTTGGCGTCTAGAAGATGGGTGTTGAGAAGAGGGAGTGGACAGATATTTCCTCTGGTCTTAACTTCATATCAGCCTCCCCTAGACTTCCAAATATCCATACCTGCTGGTTATAATTAGTGGTGTTTTCAGCCTCTGATTCTGTCACCAGGGGTTTTAGAATCATAAATCCAGATTGATCTTGGGAGTGTAAAAAACTGAGGCTCTTTAGCTTCTTAGGACAGCACTTCCTGATTTTGTTTTCAACTTCTAATCCTTTGAGTGTTTTTCATTCTGCAGATGCTGAGTTTGTGTGTGAACGGACACTGAAATATTTTCTAGGAATTGCGGGAGGAAAATGGGTAGTTAGCTATTTCTGTAAGTATAATACTATTTCTCCCCTCCTCCCTTTAACACCTCAGAATTGCATTTTTACACCTAACGTTTAACACCTAAGGTTTTTGCTGATGCTGAGTCTGAGTTACCAAAAGGTCTTTAATTGTAATACTAAACTACTTTTATCTTTAATATCACTTTGTTCAGATAAGCTGGTGATGCTGGGAAAATGGGTCTCTTTTATAACTAATAGGACCTAATCTGCTCCTAGCAATGTTAGCATATGAGCTAGGGATTTATTTAATAGTCGGCAGGAATCCATGTGCAGCAGGCAAACTTATAATGTTTAAATTAAACATCAACTCTGTCTCCAGAAGGAAACTGCTGCTACAAGCCTTATTAAAGGGCTGTGGCTTTAGAGGGAAGGACCTCTCCTCTGTCATTCTTCCTGTGCTCTTTTGTGAATCGCTGACCTCTCTATCTCCGTGAAAAGAGCACGTTCTTCTGCTGTATGTAACCTGTCTTTTCTATGATCTCTTTAGGGGTGACCCAGTCTATTAAAGAAAGAAAAATGCTGAATGAGGTAAGTACTTGATGTTACAAACTAACCAGAGATATTCATTCAGTCATATAGTTAAAAATGTATTTGCTTCCTTCCATCAATGCACCACTTTCCTTAACAATGCACAAATTTTCCATGATAATGAGGATCATCAAGAATTATGCAGGCCTGCACTGTGGCTCATACCTATAATCCCAGCGCTTTGGGAGGCTGAGGCGCTTGGATCACCTGATGTCGGGAGTTCAAGACCAGCCTGACCAACATGGAGAAACCCCGTTTCTACTAAAAATACAAAATTAGCCGGGCTTGGTGGCACTTGCCTGTAATTCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGCGGGGGTTGCAGTGAGCTGAGATCGCATCATTGCACTCTAACCTGGGCAACAAGAGCAAAACTCCATCAAAAGAAAAAAAAAATCGGGTGCAGTGGCTCATGCCTGTAATCCTAACACTGTGGGAGGCCAAGACAGGCAGATTGCCTGAGCTCAGGAGTTCGAGATCAGCCTGGGCAACATGGTGAAACCCTGTCTCTACTAAAATACAAAAAATTACTCAGCGTGGTGGCATGCGCCTTTAGTTCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCTCTTGAACCCGGGAGGTGGAGGTTGCAATGAGCCAAGATCGTGCCACTGCACTCCAACCTGGCAACAGAGCGAGACTCCGTCTTAAAAAAAAAAAAAATTTTGCAGCGCAAACCAGGATATCCTCTGTTCTCATTTGTTCTAGATTTCAAAAGAAACAGTCCTTTCTTTGGGGAAAAGAGAAAGGAAAAGGAGTTTTATAAAAGGAAAGAAAAGATTCATAAGAACAAGAAGTGGGCCCACTTGCATATACCTTTGTAGAAAACTGTTCACTGTTGTTGAAGAAAAGCTCTTCATATTAATATGCAGTCCAGATGCAGTGGCTCACACTTATAATCTCAGCCCTTTGGGAGGCTGAGACAGGAAGATTACTTGAGGCCAGGAGTTTGAAACCAGCCTGGGCAACATAGTGAGACTCTGTCTCCACAAAATTTTTTTTTAATTAGCCGGGCATGGCAGTGTGCTTCTGTAGTCTTAGCTACTGAGGAAGCTAAGCCAGAAGAATCACTTGAGCCCAGGAGTTCAAGGCTGCAGTGAGCTATGATCATACCATTGCACTCTTGCACTTGCACAGAGCAAGACCCTGTCTCTTAAAAAAAAAAAAGTGTGTGTGTGCATATGCATATATACATATATATACATGCAAATGTATCTGTTTATAATTCAGATTGCTTCAAAAAGATGTTGCACTTTATGATACTGAGAACAGTGAGAAGTAAATAAGATAGAGTGTAGGAGGAGGAATAATTTCAGAACAGCCATCTGAGAACTTCTGTGACAACAGATCAGGCAAAATGAAATGTGAAAGTAATTTTATAGGCCAGGCGTGGTGGCTCATGCCTATAATCCCAGCACTTTGAGTGGCCAAGGCAGGTGGATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGTCAACATGGTGAAACCTTGTCTCTACTAAAAACACAAAAAAATTAGTCGAGCGTGGTGGCATGTGCCTGTAATCCTAGCTGCTGGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCTAGATTGCACCACTGCACTCCAGCCTGTGAGACAGAATGAGACCCTGTCTTAAAAAAAAAAAAAAAGTAATTTTATAAACTATTGTGCACAATTCGATGTATTCATAATTAATTAAATGATTATTTTTGTTGGTTTTAACTTTTATTCAGTGGCTATTTATTGGGAGCCTACTGTGTTCTGGGCACTAGGAATGCAACAGTAAATAAGACTAACTAAGTCCCTGGTAGGATTCAGGTTCTGTCGAGGGGAGATACACAATAAAGATGAATTTAAGATAACAATAAATGCTATGGAGAAATATACAGAACAGTGGAATAGTATTAGCTGTCAAAGGTTGTTGATTACTTTCGTTTAAGGAGGCCAGGGAAAGCCTTTCTGAAAAAATTGAGCTGAGACCTAAATAACAAGAAATAATTGTCCTTGAAAAATGAAGGGAATGCATCTTATAGGCAGAGGAATAGCAAACATAAAGGTCTTGAGGTAATAATGAGTGTGGTTTTTTGATTTCTGTATTTTGGTTTTTTTGAGATGGTGTCTCCCTCTATCCCCCAGGCTGGAGTGCAGTGGCACAATCTTGGCTCACTGCAAACTCTGTCTCCTGGGTTCAAGCAATTCTCCTGCCTTGGCCTCCTGAGTAGCTGGTATTACAGGCACGCGTGCTACCACACCCGACTAGTTTTTATTTTTAGTAGAGATGGGGTTTTACCACGTTGGTCAGGCTGGTCTCAAACTCCTGAACTCAAGTGATCCAACCACCTCAACCTCCCAAAGTGCTGGGATCACAGGTGTGAGCCACTGTGCCCGGCCAGAGCTTGGTTTATTTTTTAAAAGATAGGCCAATGTTGGTCGTGTGTGGTGGCTCGTGCCTATAATCCCAGCACTTTGGGAAGCCAAGGCAGGCAAATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAAACTAGCATGGTGTGGTGGTGTGTGCCTGTAATCCCAGTGCCTGTAATCCCAGCTACTCCAGAGGCTGAGGCAGGAGAATCACTTGAACCGAAAGGTAGGAGTTACAGTGAGCCAAGATCGCATCACTGCACTCCAGCCTGAACGACAGAGCAAGACTCCTGTCTCAAGAAATAATAATGATAAAAGGTTCGGGCACAGTGGCTCACACCTGTAATTCCAGCACTCTAGGAGGCCGAGGCAGGCAGATCCCCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACGTGGCAAAACCCCATCTCTACTAAAAAATGCAAAAATTAGCTGGGCACGGCTGGGTGTGGTGGCTCATTCCTGTAATCCCAGCACTTTGGGAGGTCAAGGCGGACAGATCACTGAGGTAGAAACCCTGTCTCTACTAAAAATACAAAAATTTGCCCAGCGTGGTGGCGCGTGCCTCTAATCCCAGCTACACGGGAGGCTGAGACAAGAGAATCACTTCATCAACCCGGGAGGTGGAGGTTGTGGTGAGCTGAGATCGCACCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAACAAAAAAAAATTAGCTGGGAATGGTGGCATGTGCCTGTAATCACAGCTACTTGGGAGGCTGGGGCAGGAGAATCGCTTGAACCCAGGAGGCGGAGATTGCAGTGAGCTGAGATTGCGCCACTGCACTCCAGGCTGGGCGAAAGAGCAAGACTCCGTCTCAAAAATAATAATAATAATAATAATAGGCCAGTGTAGCTGGAGTAATTTGCAAATTATGTGTGGAGGCAGAGATTACACAAGGAATGGGAGAAGGTCATAGATGAGGGCCAGATCACATAGTATTTGGTGGTAAGGAATTCAGATTTTATCCTTGTGGTAATTGGTGGTGTGGAGATGGTTAAAAACAAGGTTGGTTTGGGATGGGTTTGAAGAGAGGACTTGCTAATGGATTAAATTTGGAGGATAAGGTAAAGAGAAATTGAAGGAGTGACACTTGGGTTTTGGCTTGAACAATAGATCTTGTTAGTAATATTAAATTAGATGAAGAAGGCATGGTAGGGAATATGGGGGAGTGGGAAAGGCAGGAAGCAGGAATGGAACCAGGAACTCTGTTTTAGATGTGAGAATTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTGACAGCATCTCGTTCTGTTGCCCAGGCTAGAGTGCATGGAGTGCGGTAGCACGATCTCAGCTCACTCCAACCTCCGCCTCCCGGTTCAAGTGATTTTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCACCTGCCACAATGCCTGGCTAATACTTGTATTTTTAGTAGAGATGGGGTTTTACCATGTTGGCCAGGCTGGTCTTAAACTCCTGACCTCAGGTAATCCACCCACCTCGGCCTCCCAAAGTGCTGGGATTGCAGGTGTGAGCCACTGTGCCCGGCCAGATGCATGAATTTTGAGATGTATACTAGACTTCTGGATAGAGAAGTTAAGTAGGCAGTTGGACACATTGTATGAAGCTCAGGGGTACAAGGAGGACTATGAACATGGGAGTCTTCTGACAAATTTATCACTAGACTCCTCATTCAAGTAACTAGGAAATGTCAGATATTCTTCCCCTAGTAATAGCCAGTGGTTATACTCTTGCCTTTAGTTTTCTTCACAATACTCTTGGCAACACATAAGGCCTTCCCTACAATCTGAGTTTCAGTCAGAATTGTTTCTGAGCGTTCTTCCTCAAATTTCTCCCCAGTCTCATTATTCTTTATTCTCATGTCCATGACCAGTCATAATAGTAATTATGAAAAACCTCTAACTTTCTTTAGTGCATTGAATGTATATTTTATCATTTTGGTTGTGTTAACTGTAAATCTCTCAGTGGAAATCTGAAAAGCCTTTATTTCCTTAGATGATAATATACAATTGATTTAGGAGATAGGGAATTTTTCAGTTACCTTTATAACAGCACAGTATTAGCAGTCTAATCTAAATGCTAAGTGAATGTTTTGAGAGGAGATAGATGTTGAAAATTAAAATACATTAAGTCCCAGTGAGGTGAAAAGCCGATTGTTAAGTTCTGCACACAAAAGATTTGCTTCAGTGAATTGATTTCAACAGCTGAGATCCTAGTCATTTCACCTGGTCTACCAAAAAGAATGATTTTACTTGCTTTTGGTCAAATCTCTGCCCAGCAATTCTTTTTCTTTCTTTCTTTTTTTTGTTTTATGTGTGTGTGTGTGTGTGTTTTTTTTTAGCAGAGTCTCACTTTGTCACCCAGGCGGGAGTGTGGTGGTATGATCACAGTTCACTGCAGCCTCCAACTCCTGGGCTCAAGTGATCCTCCAGCTTCAGCTTTTCAAGAAATTGGGACTGCAGGCACATGCAACTATGCCTGGCTGAGGTTTTATGTATCTTTTTTCTAGAGAAGGGGTCTCACTGTGTTGCCCAGCTGGGTCTCCAGCTCCTGGTCTCAAGCTGTCCTCCTGCCTCAGCCTCCCAAAGTGCCAAAGTGCTAGGGTTATAGGTGTGAGCCATTGGTGCCCAGCTACTGCCTGCCTGGCAATTCTGAATGCCTTAAATTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTTTCACTCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCGTGGCTCACAGCAACCTCTGCCTCCTGGATTCCAGCAATTCTCATGCCTCAGCTTCCCGAGTAGCTGGGACTACAGGTGCATGCCACCACGCCCAGCTAATTTTTGGTTTTTTTGTTTGTTTGTTTGTTTGTTTTGAGACGGAGTCTCGCTCAGTTGCCCAGGCTGGAGTGCAGTGGCGTGATCTCCGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACTACACCCGGCTAATTTTTTTGTATTTTAAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCTGTCTCGGCCTCCCAAAGTCCTGGGATTACAGGCGTGAGCCACCACACCCGGCCTAATTTTTTTTTTTTTAATTTTATTTTTAATTTTTTGAGATGCGAGATGGAGTCTCGCTCTGTTACCCAGGCTGGAGTGCAGTGGCACCATCTCAGCTCACTGCAACCTCCACCTCCTGCATTCAAAAGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGTGCCTGCCACCACGCCCAACTAATTTTTTGTATTTTTAGTAGAGATGAGGTTTCACCATGTTGGTCAGACTGGTGTCGAACTCCTGACCTCAAGTGATCTGCCTGCCTCAGTCTCCCAAAGTGCTAGGATTACAGGGGTGAGCCACTGCGCCTGGCCTGAATGCCTTAAATATGACGTGTCTGCTCCACTTCCATTGAAGGAAGCTTCTCTTTCTCTTATCCTGATGGGTTGTGTTTGGTTTCTTTCAGCATGATTTTGAAGTCAGAGGAGATGTGGTCAATGGAAGAAACCACCAAGGTCCAAAGCGAGCAAGAGAATCCCAGGACAGAAAGGTAAAGCTCCCTCCCTCAAGTTGACAAAAATCTCACCCCACCACTCTGTATTCCACTCCCCTTTGCAGAGATGGGCCGCTTCATTTTGTAAGACTTATTACATACATACACAGTGCTAGATACTTTCACACAGGTTCTTTTTTCACTCTTCCATCCCAACCACATAAATAAGTATTGTCTCTACTTTATGAATGATAAAACTAAGAGATTTAGAGAGGCTGTGTAATTTGGATTCCCGTCTCGGGTTCAGATCTTAGCTGATAAGTGGAAGAGCTGGGACTTTAAGCAGATGAGAATCTAAAGACTTTGCTCTTTTCACTTCACTGGGGTGTCTTTCTCTCTCTCTCTCTTGCTCTCTCTCTCTCTTTTTTTTTTTCCCAAGACGGAGTCTCACTCCATTGCCCAGGCCAGAGTGCAGTGGTGCGATCTCAGCTCACTGAAAACTCATCTTGCCCAGGCTGGTCTTGAACCCCTGACCTTGTGATCCTCCCGCCTTGGCCTCCCCAAGTGCTGGGATAGGCGTGAGCCACCGTGCCCAGCCAATAATAGCTAAAATTTATATAATGTTCACTGGGCCAGGCACAGCGGCTCGTTCCTGTTATCCCAGCACTTTGGGAAGCTGAGGCAGGCAGATCGCTTGAGCCAAGGAGTTCGATACCAGCCTGGGCAACATGGCAAAACCCCATCTCTACCAAAAAAAATATACAAAAATTAGCCAGGCGTGGTGGCATGTACTTGTAGTTCCAGCTACTCGGAAGGCTGAGTTGAGAGTATCTCTTGAGCCCAAGAAGAGGGGACTACAGTGAACGGAGATTGCGCCACTGCACTCCAGCCTAGACGACAGACAGAAGATCTCAAAAGAAAAAAAAAAAAAAAAGATCACTTTATGCTGGGACTGCTCTAAAGGCCCAACCATGTTTTAACTAATTAACAATTTTATGACAACTCTATGAGCTATGTACTGTAATTATGCCTATATTACAGATGTGAAAATTGAGGCTCAGAGAGGTTGAATAAGTTGCTCAAAGTCACACAGGTAATAAGTGATGGAACTAGAAGTTGAACTCAGGAAGTCTAGCTCCAAGTCTAAATTCTTTGTTAATTTATTTTTCGGGCCAGAGTCTTACTCTGTCACCCAGGCTGGAGTGCAGTGCCACTATCTCTGCTCACTGCAACCTTCACCTCCCAAGTTCAAACCTTGTTCAATTCTTGTGCCTTGGCCTCCCAAGTGGCTAGGATTACAGGCATGTGCCACAACAACTAGCTAATTTTTTGTCTGATTCTGTTGGCCAGTCTGGAGTGCAGTGGCGCAATCTCAGCTCACTGCAGTCTCCAGCTCCCAGGTTCAAGTGATTCTCGTGCCTTAGCCTCCCAAATAGCTGGGATTACAGGCACGTGCCACCACACCGAGATAGTTTTTTGTATTTTTAATAGAAACAAGGTTTCAACATGTTGGCCAGGCTGGTCTCAAATTCCAGACCTCAGATCATCTGCCCGCCTCAGGCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCACCCGGCCTTAATTTTTATATTTTTATTAGAGATGGGGTTTTGCCATGTTGGCCAGGCTGGCCTTGATCTCCTGGCCTCCAGTGATCCACCCGCCTTGGCTTCCCAAAGTGCTGGGATTACAAGCATGAGCCACTGCACCCGGCCTCCAATTCTAAACTCTTAACAACAATACTATAGTTTCTTGAAAAGTTGTTGAAGGCTTCACGGAGGGAAAAAAAATGGAGCATTCTAACAACTTTGCAGATGAGACCCAAGAAGACTCAATGACTTTCTCCTGATCATATTGTAGCAGATGACTTAGCCAGAACTCTGACTTCCTCACAGGGAGAAAGTCTGCAAGATTTCACACTTACCTGTCAGGCCTGAGCTGGCTGCTTTCTCAGCTCCCTAAGTGCTATGTTCCCAGTCTGCTTTTCTTCCTTTTTCAAGTGTGCACTACCAGGCATTTCAGAACATCCCAGGCTGGTCGCGGTGGCTCACACCTGTGATCCCAGCACTTTGGGAGCCCAAGGCGGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAGTTAACTGGGCGTGGTGGTAGGCACCTGTAATCCTAGCTCAGGATTACTCGGGAGGCTGAGGCTAGAGAATCGGTTGAACCCAGGAGGCGGAGGTTGCAGTGAGCCAAGATTGCGCCACTGCACTCTAGCCTGGGGACAAGAGGGAGACTTCATCTCAAAAAAAAAAAAAAAATCCCAGCTGGGCACAGCGGCTCACTTCTGTAATCCCAGCACTTTAGGAGGCCAAGGCAGGAGGATCACTTGAGCCCAGGAGTTCAAGACTAGCCTGGGCAACATAGTAAGACCCTGTCTCTACAAAAAAATTTAAAAATTAATTGGGTGTCGTAGCACACTCTTGTATTCCCAGCTACTCAGGAGGCTGAGGTGAGAAGAATGCTTGAGTCTGGGAGGTCGAGGCTGCAGTGAGCCATGATGGTGCTACTGCACTCCAGCCTGGCCAACATTGTGAGACCTTGTCTCAAAACAAAACAAAACATCCTTCTACTGAGCACTTTCTGTCCCTTTATAGAAACTTAAGAGGGAACCAGTAGAGGTAATTTCCTAAGGAAAACTGCTTTGGGACATGATCACAAATGAAGCCTGGAGTTTTGAACTGCTGAGGTCAGCCTGTTTTTACCTTCTGAGCCTATCAAGTAATTGTTCCAGATGCCAAGAAAAGCTGCTGGCCTTATTTCTGCTTCTGCCTTTACCACAGGGGAGCGCCATGTGAGCCAGTCCTCTGTTTTTCCTCCACTGTATGCTAGGCAGTATTAGCACCAGATTCTTCCCCTCTTTAAAAAGAAATTCTAGTGCTTTGGATTTTTTCCTCCATGCAGAATAGCAATGATGGAAAGTATGTGGTCAAAGTAATGACATTCTGAAAATACTAAATGTCACCATAGTATTTTTCTCTGGAAGAGAAATGTATATGTAGAGGTGAAACTTCAAATTTCTTTTTTTTTTTTTTTAAGACGAAGCTTTGCTCTTCTTGCCCAGGCTGAAGTACAATGGCGTGATCTTGGCTCACCGCAATCTCTGCCTCCAGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCTAAGTAGCTAGGATTACAGGCATGTGCCACCACGCCCAGCTGATTTTGTATTTTTAGTAGAGATGGGGTTTCTCCATGTTGGTCACGCTGGTCTTGAACTCCCGACCCCAAGTGATCCACCCACCTCGGCCTCCCAAAGTGCTAGGATTACAGGCCACCGCGCCCGGCCTGAAACTTCAAATTTCTTTTTTTTTTTGAGACAGAGTCTCGCTATGTCACCCAGGCTGGAGTGCAGTGGCGCCGTCTCGGCTCACTACCAGCTCCACTCCACCTCCTGGGTTCACACCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGCCCGCCACCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAGACGGGTTTTCACTGTGTTAGACGGGATGGTCTCCATCTCTTGACCTCGTGATCCGCCTGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTACGCCAAGCCCGAAACTTCAAATTTCTTATCTCATAACTAGGCATCCTCATCACTGAGTGTTAGCCTGGATATAAACATTCCTAATCTTTTGTACTTTTCATGTCAGCATTTGGCTCCACTTGGCTGCCTGGGGAGAACTTCTAGCATTATGAGCATGCAGGTCCTATCAACAGGTTGGGGGTGCGGTTTATTCATACAGGTAGTGAGAGTGGCACAGATGGATGCTGTCCCTTAAAACAAACAGACTTGTCTTTGGGAGCCTGAGGCGGGTGGATCATGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATAGTGAAACCCCGTTTCTACTAAAAATACAAAAAATTAGCCGGGTGTGGTGGTGTGCACCTGTAATCCCAGCTACTAGGGAGGCTGAGGCAGGAGAATCACTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCGAGATGGCACCATTGCACTCCAGCCCAGGCGACAGTGCAAGACTGCGTCTCAAAAAAAAAAAAAAAACACACAGACTTGTCCTACTGCCATTTCTTTTCACTCTGGCGGTAAAGTAAGAGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTCTGTCCGTCTGTCTGTCAAGGGGGAGGGTGACCACTTTCTAAAAGGCCATCCGTGTATTTTTAGCTTCCTGATTTTTTTCTCTATCGCAGTCTCTTTGAAGCCAGGTGAATTTTAGGCCTTGGCAATTTTCTTTTTATTGCAATGGGAAGGTCAAGACACTGAGAGTCACCCAAAACATATCCATCCAAAATGATACAATTTTAGGGTTTATTTTTAAGTGATACCCAAGTTATTTGCTAAGAACCTATGCCAGTGTGTTTATGAGAATTTGCACTGTCCCACACTGTTGCCACCAGCCACATGGGACTGTTTAAATTTAAATTTTACAAATTAGCCAGTCATGGTGGTGTGCACTTGTAGTCCCAGCTACTTAGGAGGCTGAGGCAAGAGGATTGCTTGAGCCCAGAAGTTCAATACTGCAGCAAGCTATGATCGTGCCACTGTACTCCAGCCTGAGTGACAGAATGAGACCTCATCTCTTCAAAAAAAAAGAAAAAAATTAAAATATGAAGTTTAGTTCTTCATTCACCCTAACCACATCTCCAGTGCTCAATAACTATATGTGACTCATGGCTACCTTATTAGCATAGATATAGAACATTGTGACTATCACAGAAAGTTGTTTTGAACAGTGTTGCCAAGCCCTGTAAGTGGAAGAGGCAGTGCAGTGTGATCTGTGTCTTCAGGAAACCAGGTAGTCAGACTAGTTCAATGAGGAGAGGCAGAACCTGGCTTCACTTCTAGATTAAAAACTGCTTAGGTGGCCTAAAGATACAATGGCCATTCTCAGAGTAGTGAGAAGGAAGGAACAGATGTTTAGGGGGCTAGAAGAAAGTCAGAGAGGGCCGGGCGCAGTGGCTTATGCCTGTAATCCCAGCACTTTGGAAGGCCAAGACAGGCAGATCACGAGGTCAGGAGTTCGAGACCAGCCTGACCAACATGGTGAAACCCTGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGTGCGCGCCTGTAATCCCAGCTACTCAGGAGGCTAAGGCAGGAGAATCGCTTGAACCCTGGAGGCAGAGGTTGCAGTGAGCCCAGATCGCACCACTACGCTCCAGCCTAGGTGACAGAGAGAGACTCCGTCTCAAAAAAAAAAAAAAAAGTCAGAGGAGACAAGGAGCATGTACACCTAAAATCAACATAGACCCCTCTGTTGATGGGGTCATAGTGAGTACTTGAGGTACCAAGTCTGGATAAACATCAAACTTCAGCCAATAACTTTGAGTTTCTAGCCATCCAAGCCTCTTATTAAACATACAGAAGGACCTTTTTTCCCTTGCATCTAACAAGTTAAAGCACCTGCAGAGATCATTAGGGAGGAGCCTTGGCCTGATTGGTGACAAAAGTGAGATGCTCAGTCCTTGAATGACAAAGAATGCCTGTAGAGTGCAGGTCAACTACATATGCACTTCAAGAAGATCTTCTGAAATCCAGTAGTGTTCTGGACATTGGACTGCTTGTCCCTGGGAAGTAGCAGCAGAAATCATCAGGTGGTGAACAGAAGAAAAAGAAAAGCTCTTCCTTTTTGAAAGTCTGTTTTTTGAATAAAAGCCAATATTCTTTTATAACTAGATTTTCCTTCTCTCCATTCCCCTGTCCCTCTCTCTTCCTCTCTTCTTCCAGATCTTCAGGGGGCTAGAAATCTGTTGCTATGGGCCCTTCACCAACATGCCCACAGGTAAGAGCCTGGGAGAACCCCAGAGTTCCAGCACCAGCCTTTGTCTTACATAGTGGAGTATTATAAGCAAGATCCCACGATGGGGGTTCCTCAGATTGCTGAAATGTTCTAGAGGCTATTCTATTTCTCTACCACTCTCCAAACAAAACAGCACCTAAATGTTATCCTATGGCAAAAAAAAACTATACCTTGTCCCCCTTCTCAAGAGCATGAAGGTGGTTAATAGTTAGGATTCAGTATGTTATGTGTTCAGATGGCGTTGAGCTGCTGTTAGTGCCAACATGTTAGTGAGAAAATATCTTTGGATAGGTAAAAATCAAGGAGGAGTTCTCCTCTTCCTAAACCATCTTAATTTACTTACATAGAAGAAAGCACAGCAGCTGGCCCACCACGGACGGGCCCAGAGCAGGGGAAGATTCTCGGTGAACATTTCTTTTTTTTTTTCTTTTTTTTTGAGGTCGAGTCTCTGTTGCCCAGGCCAGAGTGCAATGGCGCGATCTCGGCTCACTGCAACCTCCACCTCCCGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAAATAGCTGAGACTACAGGCGTGTGCCACCACGCCCGACTAATTTTTTGTATTTTTTTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAATATGGTCCCGATCTCCTGACCTCGTGATCCACCCGCCTCAGCCTCCCAAAGTGCTAGGATTACAGGCATGAGCCACTGTGCCCAGCCCTCTCCATGAACATTTTCTAATTAAACTTGACACTTAATACAATGTTATGCTTAGGACTGCTATAAAGCTTACCTCTGGAGTTGCGCAGCACAAAGGCCTTGGTGTGTGTATAAATTTGGTTTGTTCTTTTCACAGCAAAAGCTACCCACCTTTGCCTCCTGTGCCTGCTTCTGCCCAGGGACTTAGGTCCTCTTACACCTTAGAGAAAGGCCTTAGCATCTGGTCACAGGCAGATGAGTGACAGCAAGAAAACCTGGCTGCAATGTAATTTTGTTTCCATCCTCTTTATTAGTTATCAATTGGATTTTTATGAAATTTCCAAGTTCCACTCAAGGATTTCTCAGTGTTTTTTTACTTTGGTATAGTGGAAACCAGGGTTGCCAGAAAGTATTATTTTGGGGGTGAGTTAGTCAACCTTCGTTCAGTCAGACAGACAGGAGCACCTCAGCAATTCCCAGAAACGGGCTGATGGGAAAGAGCAACATACATGAATGTCTTGAAGAACACAGCCAACAGAGCCCATTGGGCAGTTCTGATTTTCCAGGTACACAGCATCTCCACAGTCTCTTCTGATTTTTATTCCCCTGAGTATATGGATTCCAGCTCAGCATGTAGCCTTTCCCTGCTGAGTCTCTAACCAGGATAACATGTATTTTTTTGACTGGATGAATTATCTTCCCATCTCTTGACATTTACAGTAATTACCACCAAGTATGGTATTTTCAGTGGCCGTGATTATCAGTTACCAACACAGAATTAGGATGAAGGGAGGAAGGGAGGGAAGGAAGGTGGGTGTTTTTTCACACAGTGTCTTAGCCAGCAATTTAGCAAATTAATGGAAATTAGATCTTTGATTTTTTTTTCTTTCAAGCATTTTATTTGAGAGACTATCAAACCTTATACCAAGTGGCCTTATGGAGACTGATAACCAGAGTACATGGCATATCAGTGGCAAATTGACTTAAAATCCATACCCCTACTATTTTAAGACCATTGTCCTTTGGAGCAGAGAGACAGACTCTCCCATTGAGAGGTCTTGCTATAAGCCTTCATCCGGAGAGTGTAGGGTAGAGGGCCTGGGTTAAGTATGCAGATTACTGCAGTGATTTTACATCTAAATGTCCATTTTAGATCAACTGGAATGGATGGTACAGCTGTGTGGTGCTTCTGTGGTGAAGGAGCTTTCATCATTCACCCTTGGCACAGTAAGTATTGGGTGCCCTGTCAGAGAGGGAGGACACAATATTCTCTCCTGTGAGCAAGACTGGCACCTGTCAGTCCCTATGGATGCCCCTACTGTAGCCTCAGAAGTCTTCTCTGCCCACATACCTGTGCCAAAAGACTCCATCTGTAAGGGATGGGTAAGGATTTGAGAACTGCACATATTAAATATACTGAGGGAAGACTTTTTCCCTCTAACTCTTTTTCCCATATGTCCCTCCCCCTCCTCTCTGTGACTGCCCCAGCATACTGTGTTTCAACAAATCATCAAGAAATGATGGGCTGGAGGCTGGGCATGGTGGCTCATGTCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGTGGATCACTTGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCCATCTGTACTAAAAAAAAAAAAACAAAAAGTAGCCAGGCCTGGTGGAGCATGCCTGTAATGCCAGCTATTTGGGAAGTTGAGGTGTGAGCATCGCTTGAACGTGGGAGGCAGAGGTTGCAGTGAGCCAAGATTGCACCACTGCACTCCAGACTGGGTGACAGAGTGAGACTTTGTCTAAAAAAAAAAAAAAAGAGAGAGAGAGAAAAGCTAGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCAGATCACGAGGTCAAGAGATCGAGACCATCCTGGCCAACCAACATGGCGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCTGGGCGTAGGGGCGCACGCCTGTAGTCCCAGCTACTTGAGGGGCTGGGGCAGGAGAATCGCTTGAACCCCGGAGGCGGAGGTTGCAGTGAGCCAAGATCGCGCCACTGCACTCCAGCCCGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAGAGAGAGAGAGAAATGATGGGCTGGGCCAGTGCCCCACCCCTGTAATCACAACACTGGGAGGCCAAGGTGGGAGAATCGCTTGAGCCTGGGAGCTGAAGACCAGCCTGGGCAATACAGTAGGACCTCATGTCTACAAAAAAATTATTAAAAATTAGCCAAGGCTGGGTGCGGTGGCTCATGCCTATAATCCCGGGGGTGAAGTTGAGCCCAGGAGTTTGAGACCAGCCTGGGCAACATGGCAAAACCCTGTCTCTACCAAAAATACAAAAAAATTAGCCAGGGGTGGTGGTACGTGTCTGTAGTTCCAGCTACTTAGGAGGCTGAGATGGAAGGATTGCTTGAGCCCAGGAGGCAGAGGTGGCAGTGAGCTGAGATCACACCACTGCACTCCAGCCTGGGTGACAGAGCAAGACCCTGTCTCAAAAACAAACAAAAAAAATGATGAAGTGACAGTTCCAGTAGTCCTACTTTGACACTTTGAATGCTCTTTCCTTCCTGGGGATCCAGGGTGTCCACCCAATTGTGGTTGTGCAGCCAGATGCCTGGACAGAGGACAATGGCTTCCATGGTAAGGTGCCTGCATGTACCTGTGCTATATGGGGTCCTTTTGCATGGGTTTGGTTTATCACTCATTACCTGGTGCTTGAGTAGCACAGTTCTTGGCACATTTTAAATATTTGTTGAATGAATGGCTAAAATGTCTTTTTGATGTTTTTATTGTTATTTGTTTTATATTGTAAAAGTAATACATGAACTGTTTCCATGGGGTGGGAGTAAGATATGAATGTTCATCACAAAAACATAAATCAAGGCCGGGCATGGTGGCTCATGCCTATAATTCCAGCACTTTGGGAGGTCAAGATGGAGGTCAAGGTGGGAGCCTAGAAGTTCGAGACCAGCCTGGGCAACATAAGGAGACTTCATCTGTACAACAAATTTAAAAAGTAGCTGGGTGTGGTGGCAGATGCCTGTAGTCGCAGCTACTTGGGAAGCTGAGGTGGGAGGATCACTTGAGCTCAGGAGGTTGATGCTTCAGTGAGCCACGATCACACCACTGTACTCCAGCCTGGGCGACAGAGCGAGACCGTGTCTCAAAAAGAAAAAAGAAAGTATAAATTTACACAAAAACAATAAAATAATCCCAGTAATTCCACCACTTGGAGATGATCACCATAAAACTCCACCAGGCATATGTGCGTATATATACACGTGTATTTTATAAAATGTGATCATAATTACACTGTTTTGCTTTTTTCCTTAAGATATTACATACATTTTTCCACATCGTTAAATTACAGTGCTGTTTTCCTGGTGGCTTTCCTTTAACAGATTGAAGTTCATGTTAATACAGTTGCCAGAGGCTGTGGGCTTTCACTGTCACCAGGAGTCACTCCTAGGGCCTCTTCAGAGCAAGGCCTTATGTCCTGAAGCATTGCCTTTTTTTTTTTTTTTTGAGGTGGAGTCTCACTCTGTCACTTAGCAGGCTGGAGTGCAGTGGCCCAGTCTTGGCTCACTGCAACCTCCGCCTCCTGGGTTTAAATGATTCTCCTGCCTCAGCCTCAGGGCGGATCACCTGACATCAGGAGTTTGAGACCAGCCTGGCCAATATGGCGAAACCCCATCTCTACTAAAAATACTAAAAAAAATTAGCCAGGCATGGTGGCACGCACTTGTAGTCCCAGCTACTTGGGAGACTGAGGCAGGAGAATCGCTTGAACCCAGGATGTTGAGGTTGCAGTGAGCTGAGATCACACCATCACAATCCAGCCTGAGTGACAGAGTGAGACTCCATCTGAAAAAAAAGAAAAAACAATTAGCCTGGCATGGTGGCAGGCACCTGTAATCCCTGCTACTTGGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCTGAGATCGTGCCATTGCATTCCAGGCTGAGCAACAAGAGCAAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAGGCCAGGTGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGTGGATCACCTGAGGTCAGGAGTTCCAGAGCAGCCTGGCCAACATTGTGAAACCCCCGTCTCTACTAAAAATACAAAAATTAGCTGGGTGTGATGGCATGTGCCTGTAATTCCAGCTACTCAGGAGGCAGAGACAGGAGAATTGCTTGAACCCAGGAGGCGGAGGTTGAATGAGCCGAGATTGCGCCATCACACTCTAGCCTCGGCGACAGAGCAAGACTCCGTCTCAAAAAAAAAAAAAAAAAATTAGCTTCTACCTCATTAATCCTAAGAACTCATACAACCAGGACCCTGGAGTCGATTGATTAGAGCCTAGTCCAGGAGAATGAATTGACACTAATCTCTGCTTGTGTTCTCTGTCTCCAGCAATTGGGCAGATGTGTGAGGCACCTGTGGTGACCCGAGAGTGGGTGTTGGACAGTGTAGCACTCTACCAGTGCCAGGAGCTGGACACCTACCTGATA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-0-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_rep1",
            "score_rep2",
            "score_rna",
            "score_rna_rep1",
            "score_rna_rep2"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5_rep1",
            "count_day11_rep1",
            "count_day5_rep2",
            "count_day11_rep2",
            "count_rna_rep1",
            "count_rna_rep2"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-0-1",
        "variant_count": 3893,
        "experiment": "urn:mavedb:00000097-0",
        "is_meta_analysis": true,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-28",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-b-1",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "Each of the seven libraries was sequenced individually and analyzed separately using in-house Python scripts archived at https://github.com/elifesciences-publications/DMS-FastQ-processing.\r\n\r\nReads that had more than 20 base mismatches between forward and reverse reads were discarded. Merged reads with a posterior Q score of 10 were also discarded. Variants with an unexpectedly high error rate or mutations in more than one codon were also discarded.\r\n\r\nFitness scores were calculated as a ratio of frequency ratios:\r\n\r\n$$s_v = \\log_2\\left(\\frac{\\frac{f_{v, selected}}{f_{v, non-selected}}}{\\frac{f_{wt, selected}}{f_{wt, non-selected}}}\\right)$$\r\n\r\nThe mean fitness score of all synonymous variants in each library was subtracted from all variants in that library to normalize the scores between libraries.\r\n\r\nThe scores are the average of two replicates if the variant was scored in both replicates, otherwise the score given is the score from one replicate. Variants that were scored in both replicates have a standard deviation (SD) calculated from the two replicate scores.",
        "short_description": "Amino acid scores for deep mutational scan of VIM-2 metallo-β-lactamase at 16 µg/mL ampicillin at 25C",
        "title": "VIM-2 16 µg/mL AMP at 25C",
        "keywords": [
            {
                "text": "ampicillin"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "VIM-2 with p.Met1_Phe2insGly",
            "reference_sequence": {
                "sequence": "ATGGGATTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGCCCGCTCGCTTTTTCCGTAGATTCTAGCGGAGAATATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTTGAAGGACTTTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAATTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTTGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000073-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "SD"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000073-b-1",
        "variant_count": 5549,
        "experiment": "urn:mavedb:00000073-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-h-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 5, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 5 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 5 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 5",
            "reference_sequence": {
                "sequence": "TTAATTTCAGGAGCCTACAAGAAAGTACGAGATTTAGTCAACTTGTTGAAGAGCTATTGAAAATCATTTGTGCTTTTCAGCTTGACACAGGTTTGGAGTGTAAGTGTTG",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-h-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-h-1",
        "variant_count": 303,
        "experiment": "urn:mavedb:00000097-h",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-h-1",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "Samples are collected after 48h and sequenced by Illumina. The counts for each variant is first added by 1, then divided by total sequence counts at this time point to calculate variant frequency. The functional score equals the division of a variant frequency at this time point and its frequency in initial library. Further normalizing the functional scores by wild type scores will give the relative enrichment values. The score data includes scores from three replicates which are suffixed by: _rep1, _rep2 & _rep3. The final score is the median of them.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 48h",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "RAF",
            "reference_sequence": {
                "sequence": "TCTAAGACAAGCAACACTATCCGTGTTTTCTTGCCGAACAAGCAAAGAACAGTGGTCAATGTGCGAAATGGAATGAGCTTGCATGACTGCCTTATGAAAGCACTCAAGGTGAGGGGC",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 51,
                "identifier": "P04049",
                "url": "http://purl.uniprot.org/uniprot/P04049",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000061-h-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_rep1",
            "score_rep2",
            "score_rep3"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000061-h-1",
        "variant_count": 298,
        "experiment": "urn:mavedb:00000061-h",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-11-04",
        "modification_date": "2021-11-04",
        "urn": "urn:mavedb:00000086-f-1",
        "publish_date": "2021-11-04",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study examined the fitness effects of single amino acid mutations in TEM-1 β-lactamase in *Escherichia coli* under selection for ampicillin resistance or cefotaxime resistance.",
        "method_text": "Scores were calculated as the fitness value $F_i^a$ for an amino acid change $a$ at position $i$. The counts $N$ from either the selection condition or the unselected 0 μg/ml condition were used for the variant or wild-type TEM-1:\r\n\r\n$$F_i^a = \\log_{10} \\left( \\frac{N_i^{a,sel}}{N_i^{a,unsel}} \\right) -  \\log_{10} \\left( \\frac{N_i^{wt,sel}}{N_i^{wt,unsel}} \\right)$$",
        "short_description": "Effects of TEM-1 mutations on cefotaxime resistance at 0.15 μg/ml",
        "title": "TEM-1 0.15 μg/ml cefotaxime",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25723163",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25723163",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TEM-1 β-lactamase",
            "reference_sequence": {
                "sequence": "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P62593",
                "url": "http://purl.uniprot.org/uniprot/P62593",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000086-f-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000086-f-1",
        "variant_count": 4997,
        "experiment": "urn:mavedb:00000086-f",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-08-08",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000042-a-1",
        "publish_date": "2019-08-08",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This is a dataset demonstrating the use of landing pad cell lines to generate recombinant mammalian cells. The experiment measured the effect of mutating the start codon of an EGFP construct with an N-terminal ubiquitin fusion. Once the ubiquitin is removed by cellular DUBs, the protein exposes a new N-terminal amino acid, which may target the protein for degradation.",
        "method_text": "Read counts for each bin were converted into frequencies. Scores were calculated by multiplying the frequency in each of the four bins bin by the bin number (lowest abundance=1, highest abundance=4) and taking the sum. Scores for each of four replicates are reported individually, and the overall score is the mean of the four replicates.",
        "short_description": "Nucleotide scores for the start codon of EGFP and its effect on an N-terminal fusion.",
        "title": "EGFP N-terminal codon nucleotide scores",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "FACS"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "28335006",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28335006",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "EGFP",
            "reference_sequence": {
                "sequence": "ATG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "C5MKY7",
                "url": "http://purl.uniprot.org/uniprot/C5MKY7",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000042-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "e1_score",
            "e2_score",
            "e3_score",
            "e4_score",
            "sd",
            "sem",
            "lower_ci",
            "upper_ci"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000042-a-1",
        "variant_count": 65,
        "experiment": "urn:mavedb:00000042-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-08-16",
        "modification_date": "2021-08-16",
        "urn": "urn:mavedb:00000066-a-1",
        "publish_date": "2021-08-16",
        "created_by": "0000-0001-6465-5776",
        "modified_by": "0000-0001-6465-5776",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "GDI1  variant effect map score set (Short description - to be updated)",
        "title": "GDI1  variant effect map score set",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-6465-5776"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "GDI1",
            "reference_sequence": {
                "sequence": "ATGGACGAGGAATACGATGTGATCGTGCTGGGGACCGGTCTCACCGAATGCATCCTGTCGGGCATCATGTCTGTGAACGGGAAGAAGGTGCTGCACATGGACCGGAACCCCTACTACGGGGGCGAGAGCTCCTCCATCACACCCCTGGAGGAGCTGTATAAGCGTTTTCAGTTGCTGGAGGGGCCCCCTGAGTCGATGGGCCGAGGCCGAGACTGGAATGTTGACCTGATTCCCAAATTCCTCATGGCTAACGGGCAGCTGGTAAAGATGCTACTGTATACAGAGGTGACTCGCTACCTGGACTTCAAGGTGGTGGAGGGCAGCTTTGTCTACAAGGGGGGCAAGATCTACAAAGTGCCGTCCACTGAGACTGAGGCCTTGGCTTCCAATCTGATGGGCATGTTTGAGAAACGGCGCTTCCGCAAGTTCCTGGTGTTTGTGGCAAACTTCGATGAGAATGACCCCAAGACCTTTGAGGGCGTTGACCCCCAGACTACCAGCATGCGTGACGTCTACCGGAAGTTTGATCTGGGCCAGGATGTCATCGATTTCACTGGCCATGCCCTGGCGCTCTACCGCACTGATGACTACCTGGACCAGCCCTGCCTTGAGACCGTCAACCGCATCAAGTTGTACAGTGAGTCCCTGGCCCGGTATGGCAAGAGCCCATATTTATACCCGCTCTACGGCTTGGGCGAGCTGCCCCAGGGTTTTGCAAGATTGAGTGCCATCTATGGGGGGACATATATGCTGAACAAACCTGTGGATGACATCATCATGGAGAACGGCAAGGTGGTGGGCGTGAAGTCTGAGGGAGAGGTGGCCCGCTGCAAGCAGCTGATCTGTGACCCCAGCTACATCCCGGACCGTGTGCGGAAGGCTGGCCAGGTTATCCGCATCATCTGTATCCTTAGCCACCCCATCAAGAACACCAACGACGCCAACTCCTGCCAAATAATCATCCCCCAGAACCAGGTCAACAGGAAGTCAGACATCTACGTGTGCATGATCTCCTATGCACACAACGTGGCGGCCCAGGGCAAGTACATAGCTATTGCCAGCACTACTGTGGAGACCACGGACCCTGAAAAGGAGGTGGAGCCGGCTCTGGAGCTGTTGGAGCCCATTGACCAGAAGTTTGTGGCTATCAGTGACTTGTATGAGCCCATTGATGATGGTTGTGAGAGCCAGGTGTTCTGTTCCTGCTCCTACGATGCCACCACACACTTTGAGACAACCTGCAACGACATCAAAGACATCTACAAACGCATGGCTGGCACGGCCTTTGACTTTGAGAACATGAAGCGCAAACAGAACGACGTCTTTGGAGAAGCTGAGCAGTGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P31150",
                "url": "http://purl.uniprot.org/uniprot/P31150",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000066-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_sd",
            "quality_score",
            "num_replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000066-a-1",
        "variant_count": 5008,
        "experiment": "urn:mavedb:00000066-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000021-a-1",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {
            "chr": "6",
            "end": 396593,
            "start": 396143,
            "reference": "hg38"
        },
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "The effect of each variant was calculated using a multiple linear regression model based on the DNA counts and RNA counts. Each variant needed to have 10 unique barcode tags to be included in the downstream analyses.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>\r\n\r\nMetadata contains the genomic coordinates for the target sequence.\r\n\r\nColumn descriptions:\r\n\r\n- 'score' is the Log2 variant expression effect derived from the fit of the linear model (coefficient).\r\n- 'p-value' is the P-value of the coefficient.\r\n- 'unique_tags' is the number of unique tags associated with the variant.\r\n- 'dna_sequences' is the count of DNA sequences that contain the variant (used for fitting the linear model).\r\n- 'rna_sequences' is the count of RNA sequences that contain the variant (used for fitting the linear model).",
        "short_description": "Saturation mutagenesis MPRA of IRF4 enhancer in SK-MEL-28 cells.",
        "title": "Saturation mutagenesis MPRA of IRF4 enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "IRF4 enhancer",
            "reference_sequence": {
                "sequence": "GGCGTGTCCGCCTGTTGGAATATGCTTCTCAGGTCTTCTGGGAAACAGATGTTTTGTGGAAGTGGAAGATTTTGGAAGTAGTGCCTTATCATGTGAAACCACAGGGCAGCTGATCTCTTCAGGCTTTCTTGATGTGAATGACAGCTTTGTTTCATCCACTTTGGTGGGTAAAAGAAGGCAAATTCCCCTGTGGTACTTTTGGTGCCAGGTTTAGCCATATGACGAAGCTTTACATAAAACAGTACAAGTATCTCCATTGTCCTTTATGATCCTCCATGAGTGTTTTCACTTAGTCTGATGAAGGGTTCACTCCAGTCTTTTCGGATGATAAAATGCTTCGGCTGTCAGTCTAATAAGGGATTCCCTGAGGAGTTTGGAGGCTGTAAGAGCACCCCCCGTCTCAATGCCAGTGCTTCTTATCTCAGCCTCTCCTGCACTCCTTTACCCCCGT",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000021-a-1",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "p-value",
            "unique_tags",
            "dna_sequences",
            "rna_sequences"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000021-a-1",
        "variant_count": 1510,
        "experiment": "urn:mavedb:00000021-a",
        "is_meta_analysis": false,
        "data_usage_policy": "We are making our data available prior to publication in line with Fort Lauderdale principle, allowing others to use the data but allowing the data producers to make the first presentations and to publish the first paper with global analyses of the data. In addition, we also reserve the right to publish the first analysis of the differences seen in the TERT knock-down experiments and alternative cell-type experiments. Studies that do not overlap with these intentions may be submitted for publication at any time, but must appropriately cite the data source. After publication of the data, the first publication of the data producers should be cited for any use of these data."
    },
    {
        "creation_date": "2021-11-13",
        "modification_date": "2021-11-13",
        "urn": "urn:mavedb:00000088-a-1",
        "publish_date": "2021-11-13",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "A deep mutational scan of influenza nucleoprotein was performed to measure the fitness landscape, e.g. enumerate the mutants likely to produce viable viruses. Two homologs of nucleoprotein were scanned: one from H1N1 PR/1934 and one from H3N2 Aichi/1968. Because effects of single mutants in two highly similar (94% identical) sequence contexts were measured, small contrasts can be drawn between the score sets.",
        "method_text": "Overlapping paired-end read data was merged and aligned to the reference gene sequence. Sequence data were processed using the `mapmuts` package to calculate site preferences for each position.",
        "short_description": "Deep mutational scan of H1N1 PR/1934 nucleoprotein assaying for viral replication.",
        "title": "Influenza H1N1 PR/1934 nucleoprotein",
        "keywords": [
            {
                "text": "Influenza"
            },
            {
                "text": "Viral replication"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "26226986",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/26226986",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "NP, H1N1 PR/1934",
            "reference_sequence": {
                "sequence": "MASQGTKRSYEQMETDGERQNATEIRASVGKMIGGIGRFYIQMCTELKLSDYEGRLIQNSLTIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVNGKWMRELILYDKEEIRRIWRQANNGDDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELVRMIKRGINDRNFWRGENGRKTRIAYERMCNILKGKFQTAAQKAMMDQVRESRNPGNAEFEDLTFLARSALILRGSVAHKSCLPACVYGPAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVLSFIKGTKVLPRGKLSTRGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRASAGQISIQPTFSVQRNLPFDRTTIMAAFNGNTEGRTSDMRTEIIRMMESARPEDVSFQGRGVFELSDEKAASPIVPSFDMSNEGSYFFGDNAEEYDN",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P03466",
                "url": "http://purl.uniprot.org/uniprot/P03466",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000088-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000088-a-1",
        "variant_count": 9960,
        "experiment": "urn:mavedb:00000088-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-06-16",
        "modification_date": "2022-06-17",
        "urn": "urn:mavedb:00000094-a-15",
        "publish_date": "2022-06-17",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "13. Normalized currents of 62 KCNQ1 missense SNVs in the homozygous state.",
        "method_text": "",
        "short_description": "13. Normalized currents of 62 KCNQ1 missense SNVs in the homozygous state.",
        "title": "Normalized currents of 62 KCNQ1 missense SNVs in the homozygous state.",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ1",
            "reference_sequence": {
                "sequence": "MAAASSPPRAERKRWGWGRLPGARRGSAGLAKKCPFSLELAEGGPAGGALYAPIAPGAPGPAPPASPAAPAAPPVASDLGPRPPVSLDPRVSIYSTRRPVLARTHVQGRVYNFLERPTGWKCFVYHFAVFLIVLVCLIFSVLSTIEQYAALATGTLFWMEIVLVVFFGTEYVVRLWSAGCRSKYVGLWGRLRFARKPISIIDLIVVVASMVVLCVGSKGQVFATSAIRGIRFLQILRMLHVDRQGGTWRLLGSVVFIHRQELITTLYIGFLGLIFSSYFVYLAEKDAVNESGRVEFGSYADALWWGVVTVTTIGYGDKVPQTWVGKTIASCFSVFAISFFALPAGILGSGFALKVQQKQRQKHFNRQIPAAASLIQTAWRCYAAENPDSSTWKIYIRKAPRSHTLLSPSPKPKKSVVVKKKKFKLDKDNGVTPGEKMLTVPHITCDPPEERRLDHFSVDGYDSSVRKSPTLLEVSMPHFMRTNSFAEDLDLEGETLLTPITHISQLREHHRATIKVIRRMQYFVAKKKFQQARKPYDVRDVIEQYSQGHLNLMVRIKELQRRLDQSIGKPSLFISVSEKSKDRGSNTIGARLNRVEDKVTQLDQRLALITDMLHQLLSLHGGSTPGSGGPPREGGAHITQPCGSGGSVDPELFLPSNTLPTYEQLTVPRRGPDEGS",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-15",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": "urn:mavedb:00000094-a-14",
        "next_version": null,
        "current_version": "urn:mavedb:00000094-a-15",
        "variant_count": 62,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000031-a-1",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {
            "chr": "5",
            "end": 1295247,
            "start": 1294989,
            "reference": "hg38"
        },
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "The effect of each variant was calculated using a multiple linear regression model based on the DNA counts and RNA counts. Each variant needed to have 10 unique barcode tags to be included in the downstream analyses.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>\r\n\r\nMetadata contains the genomic coordinates for the target sequence.\r\n\r\nColumn descriptions:\r\n\r\n- 'score' is the Log2 variant expression effect derived from the fit of the linear model (coefficient).\r\n- 'p-value' is the P-value of the coefficient.\r\n- 'unique_tags' is the number of unique tags associated with the variant.\r\n- 'dna_sequences' is the count of DNA sequences that contain the variant (used for fitting the linear model).\r\n- 'rna_sequences' is the count of RNA sequences that contain the variant (used for fitting the linear model).",
        "short_description": "Saturation mutagenesis MPRA of TERT promoter in HEK293T cells.",
        "title": "Saturation mutagenesis MPRA of TERT promoter, HEK",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TERT promoter",
            "reference_sequence": {
                "sequence": "TCGCGGGGGTGGCCGGGGCCAGGGCTTCCCACGTGCGCAGCAGGACGCAGCGCTGCCTGAAACTCGCGCCGCGAGGAGAGGGCGGGGCCGCGGAAAGGAAGGGGAGGGGCTGGGAGGGCCCGGAGGGGGCTGGGCCGGGGACCCGGGAGGGGTCGGGACGGGGCGGGGTCCGCGCGGAGGAGGCGGAGCTGGAAGGTGAAGGGGCAGGACGGGTGCCCGGGTCCCCAGTCCCTCCGCCACGTGGGAAGCGCGGTCCTGG",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000031-a-1",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "p-value",
            "unique_tags",
            "dna_sequences",
            "rna_sequences"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000031-a-1",
        "variant_count": 975,
        "experiment": "urn:mavedb:00000031-a",
        "is_meta_analysis": false,
        "data_usage_policy": "We are making our data available prior to publication in line with Fort Lauderdale principle, allowing others to use the data but allowing the data producers to make the first presentations and to publish the first paper with global analyses of the data. In addition, we also reserve the right to publish the first analysis of the differences seen in the TERT knock-down experiments and alternative cell-type experiments. Studies that do not overlap with these intentions may be submitted for publication at any time, but must appropriately cite the data source. After publication of the data, the first publication of the data producers should be cited for any use of these data."
    },
    {
        "creation_date": "2022-02-22",
        "modification_date": "2022-05-15",
        "urn": "urn:mavedb:00000094-a-2",
        "publish_date": "2022-05-15",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "Normalized currents of 4,085 KCNQ4 missense SNVs in the homozygous state.",
        "method_text": "Normalized currents of 4,085 KCNQ4 missense SNVs in the homozygous state.",
        "short_description": "1. Normalized currents of 4,085 KCNQ4 missense SNVs in the homozygous state.",
        "title": "Normalized currents of 4,085 KCNQ4 missense SNVs in the homozygous state.",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ4",
            "reference_sequence": {
                "sequence": "MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGGGSPRRLGLLGSPLPPGAPLPGPGSGSGSACGQRSSAAHKRYRRLQNWVYNVLERPRGWAFVYHVFIFLLVFSCLVLSVLSTIQEHQELANECLLILEFVMIVVFGLEYIVRVWSAGCCCRYRGWQGRFRFARKPFCVIDFIVFVASVAVIAAGTQGNIFATSALRSMRFLQILRMVRMDRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLVYLAEKDANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAGILGSGFALKVQEQHRQKHFEKRRMPAANLIQAAWRLYSTDMSRAYLTATWYYYDSILPSFRELALLFEHVQRARNGGLRPLEVRRAPVPDGAPSRYPPVATCHRPGSTSFCPGESSRMGIKDRIRMGSSQRRTGPSKQHLAPPTMPTSPSSEQVGEATSPTKVQKSWSFNDRTRFRASLRLKPRTSAEDAPSEEVAEEKSYQCELTVDDIMPAVKTVIRSIRILKFLVAKRKFKETLRPYDVKDVIEQYSAGHLDMLGRIKSLQTRVDQIVGRGPGDRKAREKGDKGPSDAEVVDEISMMGRVVKVEKQVQSIEHKLDLLLGFYSRCLRSGTSASLGAVQVPLFDPDITSDYHSPVDHEDISVSAQTLSISRSVSTNMD",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000094-a-2",
        "variant_count": 4085,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-02-24",
        "modification_date": "2022-05-15",
        "urn": "urn:mavedb:00000094-a-4",
        "publish_date": "2022-05-15",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "Normalized currents of co-expressing 915  current-reduced variants with WT.",
        "method_text": "Normalized currents of co-expressing 915  current-reduced variants with WT.",
        "short_description": "3. Normalized currents of co-expressing 915  current-reduced variants with WT.",
        "title": "Normalized currents of co-expressing 915  current-reduced variants with WT",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ4",
            "reference_sequence": {
                "sequence": "MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGGGSPRRLGLLGSPLPPGAPLPGPGSGSGSACGQRSSAAHKRYRRLQNWVYNVLERPRGWAFVYHVFIFLLVFSCLVLSVLSTIQEHQELANECLLILEFVMIVVFGLEYIVRVWSAGCCCRYRGWQGRFRFARKPFCVIDFIVFVASVAVIAAGTQGNIFATSALRSMRFLQILRMVRMDRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLVYLAEKDANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAGILGSGFALKVQEQHRQKHFEKRRMPAANLIQAAWRLYSTDMSRAYLTATWYYYDSILPSFRELALLFEHVQRARNGGLRPLEVRRAPVPDGAPSRYPPVATCHRPGSTSFCPGESSRMGIKDRIRMGSSQRRTGPSKQHLAPPTMPTSPSSEQVGEATSPTKVQKSWSFNDRTRFRASLRLKPRTSAEDAPSEEVAEEKSYQCELTVDDIMPAVKTVIRSIRILKFLVAKRKFKETLRPYDVKDVIEQYSAGHLDMLGRIKSLQTRVDQIVGRGPGDRKAREKGDKGPSDAEVVDEISMMGRVVKVEKQVQSIEHKLDLLLGFYSRCLRSGTSASLGAVQVPLFDPDITSDYHSPVDHEDISVSAQTLSISRSVSTNMD",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-4",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000094-a-4",
        "variant_count": 915,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-08-07",
        "modification_date": "2021-01-18",
        "urn": "urn:mavedb:00000059-a-1",
        "publish_date": "2021-01-18",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "To comprehensively characterize the consequences of the p53 mutation spectrum, the author generated ~10,000 variants on the DNA-binding domain (DBD) of p53 variants in human cells and measured the relative growth rate of each mutant through selection.",
        "method_text": "The log (base 2) fold change for each mutation at each time point is first calculated. The values in each of the sub-library is normalized by all of the variants to make sure that the mean synonymous mutation values are the same across the sub-libraries. The relative fitness (RFS) score for each variant was calculated as the median of the enrichment/depletion ratio at each time point.",
        "short_description": "The impact of p53 variant is represented by the frequency change of cells harboring that mutation over several time point.",
        "title": "p53 variant effect measured by cell growth",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29979965",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29979965",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "p53",
            "reference_sequence": {
                "sequence": "ACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGGCATAGTGTGGTGGTGCCCTATGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATGGGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACTCCAGTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCGCAAGAAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 101,
                "identifier": "P04637",
                "url": "http://purl.uniprot.org/uniprot/P04637",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000059-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000059-a-1",
        "variant_count": 9273,
        "experiment": "urn:mavedb:00000059-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-04-26",
        "modification_date": "2022-04-26",
        "urn": "urn:mavedb:00000094-a-1",
        "publish_date": "2022-04-26",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "try_dataset_KCNQ4",
        "method_text": "try_dataset_KCNQ4",
        "short_description": "try_dataset_KCNQ4",
        "title": "try_dataset_KCNQ4",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ4",
            "reference_sequence": {
                "sequence": "MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGGGSPRRLGLLGSPLPPGAPLPGPGSGSGSACGQRSSAAHKRYRRLQNWVYNVLERPRGWAFVYHVFIFLLVFSCLVLSVLSTIQEHQELANECLLILEFVMIVVFGLEYIVRVWSAGCCCRYRGWQGRFRFARKPFCVIDFIVFVASVAVIAAGTQGNIFATSALRSMRFLQILRMVRMDRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLVYLAEKDANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAGILGSGFALKVQEQHRQKHFEKRRMPAANLIQAAWRLYSTDMSRAYLTATWYYYDSILPSFRELALLFEHVQRARNGGLRPLEVRRAPVPDGAPSRYPPVATCHRPGSTSFCPGESSRMGIKDRIRMGSSQRRTGPSKQHLAPPTMPTSPSSEQVGEATSPTKVQKSWSFNDRTRFRASLRLKPRTSAEDAPSEEVAEEKSYQCELTVDDIMPAVKTVIRSIRILKFLVAKRKFKETLRPYDVKDVIEQYSAGHLDMLGRIKSLQTRVDQIVGRGPGDRKAREKGDKGPSDAEVVDEISMMGRVVKVEKQVQSIEHKLDLLLGFYSRCLRSGTSASLGAVQVPLFDPDITSDYHSPVDHEDISVSAQTLSISRSVSTNMD",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000094-a-1",
        "variant_count": 1,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-i-1",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes the sequence for an AC-rich RNA-seq enhancer sequence.",
        "method_text": "Reads were filtered by accepting only those that had an unmutated 6nt stretch at the end of the read and had no mutations other than those that were designed. FASTQ quality scores were not used.\r\n\r\nThe sum of the reads in each of the two replicate transfections was used to calculate the scores, defined as the ratio of RNA read count to DNA read count (called the Enrichment Index, or EI).\r\n\r\nThe score reported here is the “LEIsc”, which is $log_2 EI$ re-scaled from -1 to +1 with the target sequence at 0, which enables easier comparison between the different 6-mers tested in the study.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, AC-rich RNA-seq enhancer sequence.",
        "title": "Exonic splicing for AC-rich enhancer",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Minigene exon - AC-rich enhancer",
            "reference_sequence": {
                "sequence": "AGTTACCACCGGGAGCTCCAGCACAGTGAAATGGACAGAAGGGCAGAGCAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000083-i-1",
            "type": "Other noncoding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "EI"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000083-i-1",
        "variant_count": 556,
        "experiment": "urn:mavedb:00000083-i",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-g-1",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\n\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Dopamine",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "alpha-synuclein",
            "reference_sequence": {
                "sequence": "ATGGATGTATTCATGAAAGGACTTTCAAAGGCCAAGGAGGGAGTTGTGGCTGCTGCTGAGAAAACCAAACAGGGTGTGGCAGAAGCAGCAGGAAAGACAAAAGAGGGTGTTCTCTATGTAGGCTCCAAAACCAAGGAGGGAGTGGTGCATGGTGTGGCAACAGTGGCTGAGAAGACCAAAGAGCAAGTGACAAATGTTGGAGGAGCAGTGGTGACGGGTGTGACAGCAGTAGCCCAGAAGACAGTGGAGGGAGCAGGGAGCATTGCAGCAGCCACTGGCTTTGTCAAAAAGGACCAGTTGGGCAAGAATGAAGAAGGAGCCCCACAGGAAGGAATTCTGGAAGATATGCCTGTGGATCCTGACAATGAGGCTTATGAAATGCCTTCTGAGGAAGGGTATCAAGACTACGAACCTGAAGCCTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P37840",
                "url": "http://purl.uniprot.org/uniprot/P37840",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg16",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.10",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000045-g-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000045-g-1",
        "variant_count": 2800,
        "experiment": "urn:mavedb:00000045-g",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-i-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 15, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 15 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 15 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 15",
            "reference_sequence": {
                "sequence": "AGTGTGAGCAGGGAGAAGCCAGAATTGACAGCTTCAACAGAAAGGGTCAACAAAAGAATGTCCATGGTGGTGTCTGGCCTGACCCCAGAAGAATTTGTGAGTGTAT",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-i-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-i-1",
        "variant_count": 306,
        "experiment": "urn:mavedb:00000097-i",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-17",
        "modification_date": "2019-07-28",
        "urn": "urn:mavedb:00000010-a-1",
        "publish_date": "2019-02-18",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the sequence-function relationships for variants in a common, eukaryotic RNA binding domain, the RRM2 domain of yeast Pab1. The results identified clusters of residues with similar mutational patterns as well as highly-conserved residues that are critical for stability and/or function.",
        "method_text": "Variant reads were filtered such that all bases had at least Q20 for all positions. Log ratio scores were calculated using the Enrich software package and normalized to the wild type score.",
        "short_description": "Deep mutational scan of the RRM2 domain of the Saccharomyces cerevisiae poly(A)-binding protein (Pab1). Data for single and double mutants only.",
        "title": "Deep mutational scan of Pab1 RRM domain",
        "keywords": [
            {
                "text": "RNA-binding"
            },
            {
                "text": "log ratios"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "22006916",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/22006916",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "24064791",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24064791",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "PAB1",
            "reference_sequence": {
                "sequence": "GGTAACATCTTTATCAAGAACTTGCACCCTGATATTGACAACAAGGCTTTGTATGACACTTTCTCTGTGTTTGGTGACATCTTGTCCAGCAAGATTGCCACCGACGAAAACGGAAAATCCAAGGGTTTTGGGTTTGTTCACTTCGAAGAAGAAGGTGCTGCCAAGGAAGCTATTGATGCTTTGAATGGTATGCTGTTGAACGGTCAAGAAATTTATGTTGCTCCT",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 125,
                "identifier": "P04147",
                "url": "http://purl.uniprot.org/uniprot/P04147",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000010-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000010-a-1",
        "variant_count": 40852,
        "experiment": "urn:mavedb:00000010-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-w-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 22, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 22 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 22 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 22",
            "reference_sequence": {
                "sequence": "TCCTGGGGATCCAGGGTGTCCACCCAATTGTGGTTGTGCAGCCAGATGCCTGGACAGAGGACAATGGCTTCCATGGTAAGGTGCCTGCATGTACCTGTGC",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-w-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-w-1",
        "variant_count": 288,
        "experiment": "urn:mavedb:00000097-w",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-20",
        "modification_date": "2021-09-20",
        "urn": "urn:mavedb:00000071-a-1",
        "publish_date": "2021-09-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Deep mutational scanning was used on a library of 1.9x10^7 *Streptococcus pyogenes* Cas9 (SpCas9) variants to infer the effects of each mutation and screen for functional changes. A selection system in *E. coli* was established to differentiate between active and inactive mutant variants of SpCas9. The biological system used positive and negative selection to assay SpCas9 nuclease function in order to gather information about amino acids that allow SpCas9 to cleave DNA.",
        "method_text": "Nucleotide counts were obtained using a modified version of dms_tools version 1.1.3 that included a nucleotide counting feature in dms_barcodedsubamplicons. The output of count files were combined with additional information about each mutation using custom R and Ruby scripts. \r\n\r\nTo assign scores for each variant, the  $log_2$ fold change was calculated for each mutation count after negative or positive selection.",
        "short_description": "Positive (on-target) selection of SpCas9 in a bacterial selection system.",
        "title": "SpCas9 positive selection",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29203891",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29203891",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "SpCas9 (Human Codon Optimized)",
            "reference_sequence": {
                "sequence": "ATGGATAAAAAATACTCAATCGGGCTGGACATCGGGACCAACTCAGTGGGCTGGGCAGTCATCACAGACGAATACAAAGTCCCAAGCAAGAAGTTCAAGGTGCTGGGGAACACCGATCGCCACAGTATCAAGAAAAATCTGATTGGGGCCCTGCTGTTCGACTCAGGAGAGACAGCTGAAGCAACTCGGCTGAAAAGAACAGCTCGGAGAAGGTATACTCGCCGAAAGAATCGGATCTGCTACCTGCAGGAGATTTTCAGCAACGAAATGGCCAAGGTGGACGATAGCTTCTTTCATAGACTGGAGGAATCCTTCCTGGTCGAGGAAGATAAGAAACACGAGAGGCATCCCATCTTTGGCAACATTGTGGACGAGGTCGCTTATCACGAAAAGTACCCTACTATCTATCATCTGCGGAAGAAACTGGTGGACTCTACCGATAAAGCAGACCTGAGACTGATCTATCTGGCCCTGGCTCACATGATTAAGTTCAGGGGACATTTTCTGATCGAGGGCGATCTGAACCCAGACAATAGCGATGTGGACAAGCTGTTCATCCAGCTGGTCCAGACATACAATCAGCTGTTTGAGGAAAACCCCATTAATGCATCAGGAGTGGACGCAAAAGCCATCCTGAGCGCCCGCCTGTCTAAGAGTCGGAGACTGGAGAACCTGATCGCTCAGCTGCCAGGCGAAAAGAAAAACGGACTGTTTGGCAATCTGATTGCACTGTCCCTGGGGCTGACACCCAACTTCAAGTCTAATTTTGATCTGGCCGAGGACGCTAAACTGCAGCTGTCTAAGGACACTTATGACGATGACCTGGATAACCTGCTGGCTCAGATCGGCGATCAGTACGCAGACCTGTTCCTGGCCGCTAAGAATCTGTCTGACGCCATCCTGCTGAGTGATATTCTGAGAGTGAACACCGAGATTACAAAAGCCCCCCTGAGCGCCAGCATGATCAAGCGGTACGACGAGCACCATCAGGATCTGACCCTGCTGAAGGCTCTGGTGCGGCAGCAGCTGCCTGAGAAGTACAAAGAAATCTTCTTTGATCAGAGCAAGAATGGGTACGCCGGATATATTGACGGCGGGGCTTCCCAGGAGGAATTCTACAAGTTTATCAAACCTATTCTGGAGAAGATGGACGGCACCGAGGAACTGCTGGTGAAACTGAATAGGGAAGACCTGCTGAGGAAGCAGCGCACATTTGATAACGGGAGCATCCCTCACCAGATTCATCTGGGAGAGCTGCACGCCATCCTGAGGCGCCAGGAAGACTTCTACCCATTTCTGAAGGATAACAGGGAGAAGATCGAAAAAATTCTGACCTTCCGCATTCCCTACTATGTGGGACCTCTGGCAAGAGGCAATAGTAGGTTTGCCTGGATGACAAGAAAATCAGAGGAAACAATCACTCCCTGGAACTTCGAGGAAGTGGTCGATAAGGGCGCTTCCGCACAGTCTTTCATTGAGAGGATGACAAACTTCGACAAGAACCTGCCAAACGAAAAAGTGCTGCCCAAGCACTCTCTGCTGTACGAGTATTTCACCGTCTATAACGAACTGACAAAGGTGAAATACGTCACTGAGGGCATGCGCAAGCCTGCCTTCCTGAGCGGGGAACAGAAGAAAGCTATCGTGGACCTGCTGTTTAAAACCAATCGGAAGGTGACAGTCAAGCAGCTGAAAGAGGACTATTTCAAGAAAATTGAATGTTTCGATTCTGTGGAGATCAGTGGAGTCGAAGACCGGTTCAACGCCAGCCTGGGCACCTACCACGATCTGCTGAAGATCATTAAGGATAAAGACTTCCTGGACAACGAGGAAAATGAGGATATCCTGGAAGACATTGTGCTGACCCTGACACTGTTTGAGGATAGGGAAATGATCGAGGAACGCCTGAAGACTTATGCCCATCTGTTCGATGACAAAGTGATGAAACAGCTGAAGCGACGGAGATACACCGGGTGGGGACGACTGTCCCGGAAGCTGATCAATGGCATTAGAGACAAACAGAGCGGGAAGACTATCCTGGACTTTCTGAAATCCGATGGCTTCGCCAACAGGAACTTCATGCAGCTGATTCACGATGACAGCCTGACCTTCAAAGAGGATATCCAGAAGGCACAGGTGTCCGGCCAGGGGGACTCTCTGCACGAGCATATCGCAAACCTGGCCGGATCCCCTGCCATCAAGAAAGGCATTCTGCAGACCGTGAAGGTGGTCGACGAGCTGGTGAAAGTCATGGGGCGCCATAAGCCAGAAAACATCGTGATTGAGATGGCCCGAGAAAATCAGACCACACAGAAAGGACAGAAGAACTCAAGGGAGCGCATGAAACGCATCGAGGAAGGGATTAAGGAACTGGGAAGCCAGATCCTGAAAGAGCACCCCGTGGAAAACACTCAGCTGCAGAATGAGAAGCTGTATCTGTACTATCTGCAGAATGGCAGGGATATGTACGTGGACCAGGAGCTGGATATTAACCGCCTGTCCGATTATGACGTGGATCATATCGTCCCACAGTCATTCCTGAAAGATGACAGCATTGACAATAAGGTGCTGACCCGCTCTGACAAAAACCGAGGGAAGAGTGATAATGTCCCCTCAGAGGAAGTGGTCAAGAAAATGAAGAACTACTGGCGGCAGCTGCTGAATGCCAAACTGATCACCCAGCGAAAGTTTGATAACCTGACAAAAGCTGAGCGGGGAGGCCTGAGTGAACTGGACAAAGCAGGCTTCATTAAGCGACAGCTGGTGGAGACCCGGCAGATCACAAAGCACGTCGCTCAGATTCTGGATAGCCGCATGAACACAAAGTACGATGAGAATGACAAACTGATCCGGGAAGTGAAGGTCATTACTCTGAAGTCAAAACTGGTGAGCGACTTTCGGAAAGATTTCCAGTTTTATAAGGTCAGAGAGATCAACAACTACCACCATGCTCATGACGCATACCTGAACGCAGTGGTCGGAACCGCCCTGATTAAGAAATACCCTAAACTGGAGAGCGAATTCGTGTACGGCGACTATAAGGTGTACGATGTCAGGAAAATGATCGCCAAGTCTGAGCAGGAAATTGGCAAAGCCACCGCTAAGTATTTCTTTTACAGTAACATCATGAATTTCTTTAAGACTGAGATCACCCTGGCAAATGGCGAAATCCGAAAGCGGCCACTGATTGAGACTAACGGCGAGACCGGGGAAATCGTGTGGGACAAAGGGAGAGATTTTGCTACCGTGAGGAAGGTCCTGAGCATGCCCCAAGTGAATATTGTCAAGAAAACAGAGGTGCAGACTGGGGGATTCAGTAAGGAATCAATTCTGCCTAAACGCAACTCCGATAAGCTGATCGCCCGAAAGAAAGACTGGGATCCTAAGAAATATGGCGGGTTCGACTCCCCAACAGTGGCTTACTCTGTCCTGGTGGTCGCAAAGGTGGAGAAGGGGAAAAGCAAGAAACTGAAATCCGTCAAGGAACTGCTGGGAATCACTATTATGGAGAGAAGCTCCTTCGAAAAGAATCCTATCGATTTTCTGGAGGCCAAAGGATATAAGGAAGTGAAGAAAGACCTGATCATCAAGCTGCCAAAGTACTCACTGTTTGAGCTGGAAAACGGCAGAAAGAGGATGCTGGCAAGCGCCGGCGAGCTGCAGAAAGGGAATGAACTGGCCCTGCCCTCCAAGTACGTGAACTTCCTGTATCTGGCTTCTCACTACGAGAAGCTGAAAGGCAGTCCTGAGGATAACGAACAGAAACAGCTGTTTGTGGAGCAGCACAAGCATTATCTGGACGAGATCATTGAACAGATTAGCGAGTTCTCCAAAAGAGTGATCCTGGCTGACGCAAATCTGGATAAGGTCCTGTCCGCATACAACAAACACCGGGATAAGCCAATCAGAGAGCAGGCCGAAAATATCATTCATCTGTTCACTCTGACCAACCTGGGAGCACCAGCAGCCTTCAAGTATTTTGACACTACCATCGATCGCAAACGATACACATCTACTAAGGAGGTGCTGGACGCTACCCTGATCCACCAGAGTATTACTGGACTGTACGAGACCAGAATCGACCTGAGTCAGCTGGGAGGCGATTCAAGGGCCGACCCTAAAAAGAAAAGAAAAGTCTGTACATATCCCTATGATGTCCCTGATTATGCCTAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000071-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000071-a-1",
        "variant_count": 2470,
        "experiment": "urn:mavedb:00000071-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-j-1",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\n\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Tunicamycin",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "alpha-synuclein",
            "reference_sequence": {
                "sequence": "ATGGATGTATTCATGAAAGGACTTTCAAAGGCCAAGGAGGGAGTTGTGGCTGCTGCTGAGAAAACCAAACAGGGTGTGGCAGAAGCAGCAGGAAAGACAAAAGAGGGTGTTCTCTATGTAGGCTCCAAAACCAAGGAGGGAGTGGTGCATGGTGTGGCAACAGTGGCTGAGAAGACCAAAGAGCAAGTGACAAATGTTGGAGGAGCAGTGGTGACGGGTGTGACAGCAGTAGCCCAGAAGACAGTGGAGGGAGCAGGGAGCATTGCAGCAGCCACTGGCTTTGTCAAAAAGGACCAGTTGGGCAAGAATGAAGAAGGAGCCCCACAGGAAGGAATTCTGGAAGATATGCCTGTGGATCCTGACAATGAGGCTTATGAAATGCCTTCTGAGGAAGGGTATCAAGACTACGAACCTGAAGCCTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P37840",
                "url": "http://purl.uniprot.org/uniprot/P37840",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg16",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.10",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000045-j-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000045-j-1",
        "variant_count": 2800,
        "experiment": "urn:mavedb:00000045-j",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-08-25",
        "modification_date": "2022-08-26",
        "urn": "urn:mavedb:00000103-b-1",
        "publish_date": "2022-08-26",
        "created_by": "0000-0001-6624-4698",
        "modified_by": "0000-0001-6624-4698",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "MAPK1 Induced with DOX",
        "title": "MAPK1 DOX",
        "keywords": [
            {
                "text": "resistance"
            },
            {
                "text": "complementation"
            },
            {
                "text": "MAPK1"
            },
            {
                "text": "ERK2"
            },
            {
                "text": "MITE"
            },
            {
                "text": "VRT-11E"
            },
            {
                "text": "SCH772984"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1016/j.celrep.2016.09.061",
                "url": "http://doi.org/10.1016/j.celrep.2016.09.061",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "27760319",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27760319",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0001-6624-4698"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MAPK1",
            "reference_sequence": {
                "sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": {
                "offset": 0,
                "identifier": "NP_002736.3",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_002736.3",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000103-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "DOX_REP_ A",
            "DOX_REP_B",
            "DOX_REP_C",
            "DOX_REP_D",
            "DOX_SD"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000103-b-1",
        "variant_count": 6810,
        "experiment": "urn:mavedb:00000103-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-08-24",
        "modification_date": "2020-12-10",
        "urn": "urn:mavedb:00000052-a-1",
        "publish_date": "2020-12-10",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study generated thousands of mutated sequence on Gcn4 activation domain which contains one or several amino acid substitutions. They used a high-throughput fluorescent reporter assay to identify the transcription ability of mutated Gcn4 sequences through cell sorting.",
        "method_text": "The variant abundance in each bin is determined by high-throughput sequencing to the barcodes in an Illumina platform. The reads are first normalized by the total reads in each bin. A weighted mean value is calculated through the median GFP/mCherry ratio in each bin. This mean value is further divided by wildtype median value and logarithm (base 2) transformed. The raw activity result for the two replicates are shown in the score data (\"Raw_Replicate_1\" & \"Raw_Replicate_2\"). The original paper only used the normalized result for the first replicate which becomes the \"score\" column and the normalized result for replicate two is also deposited as \"Norm_Replicate_2\". Count data includes 8 bins for experiments in complete media with 2 replicates and sorted on mCherry only.\r\n\r\nBecause each barcode was scored individually and reported in the supplement, there are multiple scores for each variant. Each of these is the score from one barcode.",
        "short_description": "Mutagenesis study of Gcn4 activation domain in complete media using fluorescent reporter assay.",
        "title": "Gcn4 activation domain activity",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29525204",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29525204",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Gcn4",
            "reference_sequence": {
                "sequence": "AGCACTGATTCAACTCCAATGTTTGAGTATGAAAACCTAGAAGACAACTCTAAAGAATGGACATCCTTGTTTGACAATGACATTCCAGTTACCACTGACGATGTTTCATTGGCTGATAAGGCAATTGAATCC",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 100,
                "identifier": "P03069",
                "url": "http://purl.uniprot.org/uniprot/P03069",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000052-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "Norm_Replicate_2",
            "Raw_Replicate_2",
            "Raw_Replicate_1"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000052-a-1",
        "variant_count": 6500,
        "experiment": "urn:mavedb:00000052-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-g-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 5, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 5 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 5 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 5",
            "reference_sequence": {
                "sequence": "TTAATTTCAGGAGCCTACAAGAAAGTACGAGATTTAGTCAACTTGTTGAAGAGCTATTGAAAATCATTTGTGCTTTTCAGCTTGACACAGGTTTGGAGTGTAAGTGTTG",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-g-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-g-1",
        "variant_count": 303,
        "experiment": "urn:mavedb:00000097-g",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000026-a-1",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {
            "chr": "8",
            "end": 127519732,
            "start": 127519270,
            "reference": "hg38"
        },
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "The effect of each variant was calculated using a multiple linear regression model based on the DNA counts and RNA counts. Each variant needed to have 10 unique barcode tags to be included in the downstream analyses.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>\r\n\r\nMetadata contains the genomic coordinates for the target sequence.\r\n\r\nColumn descriptions:\r\n\r\n- 'score' is the Log2 variant expression effect derived from the fit of the linear model (coefficient).\r\n- 'p-value' is the P-value of the coefficient.\r\n- 'unique_tags' is the number of unique tags associated with the variant.\r\n- 'dna_sequences' is the count of DNA sequences that contain the variant (used for fitting the linear model).\r\n- 'rna_sequences' is the count of RNA sequences that contain the variant (used for fitting the linear model).",
        "short_description": "Saturation mutagenesis MPRA of MYC enhancer (rs11986220) in LNCaP cells with 100nM DHT.",
        "title": "Saturation mutagenesis MPRA of MYC enhancer (rs11986220)",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MYC enhancer (rs11986220)",
            "reference_sequence": {
                "sequence": "GGTAAGTCAACATGAAATTATAAACCATGTTTAACTAACCCACAAGAAAAACAGAAAAAGAAAACAGATACATGAAAATCTGAGAGGAAAAAAAAAAAACAGAGAACACAATGGGAAGCTTCATTCAATGTAAGGGTACTAGAAGTTCTAGCCAGTGCAATTAAGAGGAAAAAAATAAATAAAAAGGCATATGTGTTGAAAGGAAGAAATTAAACTGTCTTTATTTGCAAATGACATGATTATCAGCACAGATAATCAAGATAAATATATAAAAAGATTTCTGAAACTAATAAGTTAGTTCAGTAAGGTCGTAAGCTATAAGACAAACAAAGGAAAATCAATTGTATTTGAATGTATCGACAGTAAACATATGGACATTAAAATTAACAATACAATATAATTTATATTTATTAAAAATATAAAATGCTTAGGCATAAATCTAACAAAACCCCCACAGTACTTG",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000026-a-1",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "p-value",
            "unique_tags",
            "dna_sequences",
            "rna_sequences"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000026-a-1",
        "variant_count": 1681,
        "experiment": "urn:mavedb:00000026-a",
        "is_meta_analysis": false,
        "data_usage_policy": "We are making our data available prior to publication in line with Fort Lauderdale principle, allowing others to use the data but allowing the data producers to make the first presentations and to publish the first paper with global analyses of the data. In addition, we also reserve the right to publish the first analysis of the differences seen in the TERT knock-down experiments and alternative cell-type experiments. Studies that do not overlap with these intentions may be submitted for publication at any time, but must appropriately cite the data source. After publication of the data, the first publication of the data producers should be cited for any use of these data."
    },
    {
        "creation_date": "2021-09-18",
        "modification_date": "2021-09-18",
        "urn": "urn:mavedb:00000070-a-2",
        "publish_date": "2021-09-18",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the experimental fitness of variants in the TEM-1 $\\beta$-lactamase gene in _Escherichia coli_. Fitness measurements were estimated based on growth under increasing concentrations of ampicillin using a band-pass selection system.",
        "method_text": "Variant reads were aligned to the template sequence and all codon substitution variants were mapped. Indels were assumed to be sequencing errors and ignored. Reads were removed if the average quality score was less than 30, if the read did not span the full sub-region, or if the read contained mutations in more than one codon.\r\n\r\nReads were counted for each of 13 concentrations of Amp used in the experiment. The raw fitness score $f$ of allele $i$ was calculated as:\r\n\r\n$$ f_i = \\frac{\\sum_{p=1}^{13} c_{i,p} \\log_2\\left(a_p\\right)}{\\sum_{p=1}^{13} c_{i,p}} $$\r\n\r\nVariants with five or fewer total counts were not assigned a fitness value. Additional measures were taken to calculate fitness values for variants with counts at many Amp concentrations (see manuscript SI for details).\r\n\r\nRaw fitness scores were normalized to wild type to get a normalized fitness $w_i$ using:\r\n\r\n$$ w_i = \\frac{2^{f_i}}{2^f_{wt}} $$\r\n\r\nThe wild type fitness score was calculated using the counts of all alleles with synonymous substitutions. Therefore a normalized fitness value of 1.0 is equivalent to wild type, greater than 1.0 is beneficial, and 0 to 1.0 is deleterious. Only the normalized scores were reported.\r\n\r\nThe score for a protein variant was calculated as the average fitness of all equivalent nucleotide variants.\r\n\r\nThe estimated error ('err' column) is based on the percent difference in fitness between the nucleotide variant fitness and the average fitness of the corresponding amino acid variant.\r\n\r\nThe 'ambler' column provides the [Ambler position](https://pubmed.ncbi.nlm.nih.gov/2039479/) of the amino acid .",
        "short_description": "Amino acid fitness scores for variants in the TEM-1 β-lactamase gene in the presence of ampicillin.",
        "title": "Amino acid fitness scores of TEM-1 β-lactamase",
        "keywords": [
            {
                "text": "normalized"
            },
            {
                "text": "band-pass selection"
            },
            {
                "text": "resistance"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24567513",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24567513",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TEM-1 β-lactamase",
            "reference_sequence": {
                "sequence": "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P62593",
                "url": "http://purl.uniprot.org/uniprot/P62593",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000070-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "err",
            "ambler"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000070-a-2",
        "variant_count": 5740,
        "experiment": "urn:mavedb:00000070-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-j-1",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes a pyrimidine sequence avoiding PPT pairing.",
        "method_text": "A custom synthesized 60-bp 1760,00 element microarray was purchased from Aligent. Variant minigenes were constructed using primer extension PCR. The microarray wild type clusters were present in a higher number to provide the denominator sufficient for later analysis. The 3’ end of the 60-mer was constant and the remaining 47 nucleotides were specified as wild type or variants of WT-1 exon 5. The full minigene library was constructed by three-fragment overlap extension PCR and transfected into HEK293 cells.\r\n\r\nTwo independent transfections were performed.\r\n \r\nInput DNA and reverse-transcribed RNA were amplified and prepared for sequencing. Sequencing was carried out using Illumina with 74 base pair reads.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, pyrimidine sequence avoiding PPT pairing.",
        "title": "Exonic splicing for pyrimidine sequence",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Minigene exon - pyrimidine sequence",
            "reference_sequence": {
                "sequence": "AGTTTCTTTTGGGAGCTCCAGCACAGTGAAATGGACAGAAGGGCAGAGCAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000083-j-1",
            "type": "Other noncoding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "EI"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000083-j-1",
        "variant_count": 556,
        "experiment": "urn:mavedb:00000083-j",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-27",
        "modification_date": "2020-11-20",
        "urn": "urn:mavedb:00000049-a-4",
        "publish_date": "2020-11-20",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "A deep mutational scan of human MTHFR via functional complementation in yeast at 12ug/ml folate in WT background",
        "title": "MTHFR at 12ug/ml folate in WT background",
        "keywords": [
            {
                "text": "imputation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1628-9390",
            "0000-0002-9219-4310",
            "0000-0002-2550-2141",
            "0000-0001-6465-5776"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MTHFR",
            "reference_sequence": {
                "sequence": "ATGGTGAACGAAGCCAGAGGAAACAGCAGCCTCAACCCCTGCTTGGAGGGCAGTGCCAGCAGTGGCAGTGAGAGCTCCAAAGATAGTTCGAGATGTTCCACCCCGGGCCTGGACCCCGAGCGGCATGAGAGACTCCGGGAGAAGATGAGGCGGCGATTGGAATCTGGTGACAAGTGGTTCTCCCTGGAATTCTTCCCTCCTCGAACTGCTGAGGGAGCTGTCAATCTCATCTCAAGGTTTGACCGGATGGCAGCAGGTGGCCCCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCCTGGCTCAGACAAGGAGACCTCCTCCATGATGATCGCCAGCACCGCCGTGAACTACTGTGGCCTGGAGACCATCCTGCACATGACCTGCTGCCGTCAGCGCCTGGAGGAGATCACGGGCCATCTGCACAAAGCTAAGCAGCTGGGCCTGAAGAACATCATGGCGCTGCGGGGAGACCCAATAGGTGACCAGTGGGAAGAGGAGGAGGGAGGCTTCAACTACGCAGTGGACCTGGTGAAGCACATCCGAAGTGAGTTTGGTGACTACTTTGACATCTGTGTGGCAGGTTACCCCAAAGGCCACCCCGAAGCAGGGAGCTTTGAGGCTGACCTGAAGCACTTGAAGGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGCTTTTCTTTGAGGCTGACACATTCTTCCGCTTTGTGAAGGCATGCACCGACATGGGCATCACTTGCCCCATCGTCCCCGGGATCTTTCCCATCCAGGGCTACCACTCCCTTCGGCAGCTTGTGAAGCTGTCCAAGCTGGAGGTGCCACAGGAGATCAAGGACGTGATTGAGCCAATCAAAGACAACGATGCTGCCATCCGCAACTATGGCATCGAGCTGGCCGTGAGCCTGTGCCAGGAGCTTCTGGCCAGTGGCTTGGTGCCAGGCCTCCACTTCTACACCCTCAACCGCGAGATGGCTACCACAGAGGTGCTGAAGCGCCTGGGGATGTGGACTGAGGACCCCAGGCGTCCCCTACCCTGGGCTCTCAGCGCCCACCCCAAGCGCCGAGAGGAAGATGTACGTCCCATCTTCTGGGCCTCCAGACCAAAGAGTTACATCTACCGTACCCAGGAGTGGGACGAGTTCCCTAACGGCCGCTGGGGCAATTCCTCTTCCCCTGCCTTTGGGGAGCTGAAGGACTACTACCTCTTCTACCTGAAGAGCAAGTCCCCCAAGGAGGAGCTGCTGAAGATGTGGGGGGAGGAGCTGACCAGTGAAGAAAGTGTCTTTGAAGTCTTCGTTCTTTACCTCTCGGGAGAACCAAACCGGAATGGTCACAAAGTGACTTGCCTGCCCTGGAACGATGAGCCCCTGGCGGCTGAGACCAGCCTGCTGAAGGAGGAGCTGCTGCGGGTGAACCGCCAGGGCATCCTCACCATCAACTCACAGCCCAACATCAACGGGAAGCCGTCCTCCGACCCCATCGTGGGCTGGGGCCCCAGCGGGGGCTATGTCTTCCAGAAGGCCTACTTAGAGTTTTTCACTTCCCGCGAGACAGCGGAAGCACTTCTGCAAGTGCTGAAGAAGTACGAGCTCCGGGTTAATTACCACCTTGTCAATGTGAAGGGTGAAAACATCACCAATGCCCCTGAACTGCAGCCGAATGCTGTCACTTGGGGCATCTTCCCTGGGCGAGAGATCATCCAGCCCACCGTAGTGGATCCCGTCAGCTTCATGTTCTGGAAGGACGAGGCCTTTGCCCTGTGGATTGAGCGGTGGGGAAAGCTGTATGAGGAGGAGTCCCCGTCCCGCACCATCATCCAGTACATCCACGACAACTACTTCCTGGTCAACCTGGTGGACAATGACTTCCCACTGGACAACTGCCTCTGGCAGGTGGTGGAAGACACATTGGAGCTTCTCAACAGGCCCACCCAGAATGCGAGAGAAACGGAGGCTCCATGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P42898",
                "url": "http://purl.uniprot.org/uniprot/P42898",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000177000",
                "url": "http://www.ensembl.org/id/ENSG00000177000",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 230,
                "identifier": "NM_005957",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_005957",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000049-a-4",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "se",
            "exp.score",
            "exp.se",
            "df",
            "pred.score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000049-a-4",
        "variant_count": 13704,
        "experiment": "urn:mavedb:00000049-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-e-1",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes a sequence similar to an hnRNP D binding site.",
        "method_text": "Reads were filtered by accepting only those that had an unmutated 6nt stretch at the end of the read and had no mutations other than those that were designed. FASTQ quality scores were not used.\r\n\r\nThe sum of the reads in each of the two replicate transfections was used to calculate the scores, defined as the ratio of RNA read count to DNA read count (called the Enrichment Index, or EI).\r\n\r\nThe score reported here is the “LEIsc”, which is $log_2 EI$ re-scaled from -1 to +1 with the target sequence at 0, which enables easier comparison between the different 6-mers tested in the study.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, similar to an hnRNP D binding site.",
        "title": "Exonic splicing for hnRNP D binding site",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Minigene exon - hnRNP D binding site",
            "reference_sequence": {
                "sequence": "AGTTATATATGGGAGCTCCAGCACAGTGAAATGGACAGAAGGGCAGAGCAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000083-e-1",
            "type": "Other noncoding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "EI"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000083-e-1",
        "variant_count": 556,
        "experiment": "urn:mavedb:00000083-e",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-07-29",
        "modification_date": "2019-07-29",
        "urn": "urn:mavedb:00000038-b-2",
        "publish_date": "2019-07-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment used the same library of ubiquitin variants as previously described in Roscoe et al. 2013. The ubiquitin variants were displayed as C-terminal fusions with Aga2-HA and reacted with E1. Bound cells were isolated using FACS and deep sequencing was used to quantify enrichment or depletion of cells in the bound population.\r\n\r\nThis entry describes the second of two regions assayed with excess E1, covering ubiquitin positions 68-76.",
        "method_text": "Scores were calculated using the EMPIRIC log ratios approach, using the ratio of E1-reactive cells to HA-displaying cells. Scores were normalized such that the average wild type synonymous variant was 1 and the average nonsense mutation was 0. The raw $log_2$ ratio is included as an extra column. The \"Std\" column lists the standard deviation calculated from multiple measurements of synonymous codons. This value is `nan` when only one codon was measured.",
        "short_description": "Amino acid scores for deep mutational scan of ubiquitin in a yeast display binding assay to E1 with excess E1. Region 2 (positions 68-76).",
        "title": "Ubiquitin-E1 yeast display amino acid scores, excess E1, region 2",
        "keywords": [
            {
                "text": "EMPIRIC"
            },
            {
                "text": "Binding"
            },
            {
                "text": "FACS"
            },
            {
                "text": "ubiquitin"
            },
            {
                "text": "E1"
            },
            {
                "text": "yeast display"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24862281",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24862281",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23376099",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23376099",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Ubiquitin",
            "reference_sequence": {
                "sequence": "CACTTGGTCTTGAGATTGAGAGGTGGT",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 67,
                "identifier": "P0CG63",
                "url": "http://purl.uniprot.org/uniprot/P0CG63",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000038-b-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "log2 (E1react/display)",
            "Std"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000038-b-2",
        "variant_count": 185,
        "experiment": "urn:mavedb:00000038-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000014-a-1",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {
            "chr": "2",
            "end": 60495539,
            "start": 60494940,
            "reference": "hg38"
        },
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://doi.org/10.1038/s41467-019-11526-w>",
        "method_text": "The effect of each variant was calculated using a multiple linear regression model based on the DNA counts and RNA counts. Each variant needed to have 10 unique barcode tags to be included in the downstream analyses.\r\n\r\nAs described by <https://doi.org/10.1038/s41467-019-11526-w>\r\n\r\nMetadata contains the genomic coordinates for the target sequence.\r\n\r\nColumn descriptions:\r\n\r\n- 'score' is the Log2 variant expression effect derived from the fit of the linear model (coefficient).\r\n- 'p-value' is the P-value of the coefficient.\r\n- 'unique_tags' is the number of unique tags associated with the variant.\r\n- 'dna_sequences' is the count of DNA sequences that contain the variant (used for fitting the linear model).\r\n- 'rna_sequences' is the count of RNA sequences that contain the variant (used for fitting the linear model).",
        "short_description": "Saturation mutagenesis MPRA of BCL11A enhancer in HEL 92.1.7 cells.",
        "title": "Saturation mutagenesis MPRA of BCL11A enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BCL11A enhancer",
            "reference_sequence": {
                "sequence": "CCTAACACAGTAGCTGGTACCTGATAGGTGCCTATATGTGATGGATGGGTGGACAGCCCGACAGATGAAAAATGGACAATTATGAGGAGGGGAGAGTGCAGACAGGGGAAGCTTCACCTCCTTTACAATTTTGGGAGTCCACACGGCATGGCATACAAATTATTTCATTCCCATTGAGAAATAAAATCCAATTCTCCATCACCAAGAGAGCCTTCCGAAAGAGGCCCCCCTGGGCAAACGGCCACCGATGGAGAGGTCTGCCAGTCCTCTTCTACCCCACCCACGCCCCCACCCTAATCAGAGGCCAAACCCTTCCTGGAGCCTGTGATAAAAGCAACTGTTAGCTTGCACTAGACTAGCTTCAAAGTTGTATTGACCCTGGTGTGTTATGTCTAAGAGTAGATGCCATATCTCTTTTCTGGCCTATGTTATTACCTGTATGGACTTTGCACTGGAATCAGCTATCTGCTCTTACTTATGCACACCTGGGGCATAGAGCCAGCCCTGTATCGCTTTTCAGCCATCTCACTACAGATAACTCCCAAGTCCTGTCTAGCTGCCTTCCTTATCACAGGAATAGCACCCAAGGTCCATCAGTAC",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000014-a-1",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "p-value",
            "unique_tags",
            "dna_sequences",
            "rna_sequences"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000014-a-1",
        "variant_count": 2062,
        "experiment": "urn:mavedb:00000014-a",
        "is_meta_analysis": false,
        "data_usage_policy": "We are making our data available prior to publication in line with Fort Lauderdale principle, allowing others to use the data but allowing the data producers to make the first presentations and to publish the first paper with global analyses of the data. In addition, we also reserve the right to publish the first analysis of the differences seen in the TERT knock-down experiments and alternative cell-type experiments. Studies that do not overlap with these intentions may be submitted for publication at any time, but must appropriately cite the data source. After publication of the data, the first publication of the data producers should be cited for any use of these data."
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000075-a-1",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study presents a neutralization based assay to assess mutations’ in the E protein in the viral envelope of Zika Virus (ZIKV). E protein genes were used to detect variant interactions’ effect on viral neutralization by monoclonal antibodies. DMS measured 9,576 possible amino acid mutations that contribute to 31,752 possible mutant codon sequences within the E protein. Variant infectivity was determined by a TCID50 assay.",
        "method_text": "Sequencing data was analyzed using dms_tools2 version 2.4.14 to calculate site preferences for each amino acid position for each biological replicate. The replicates were combined by averaging the preferences.",
        "short_description": "Site preference scores for deep mutational scan of the Zika Virus E protein.",
        "title": "Zika E protein DMS",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25990960",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25990960",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "31511387",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31511387",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Zika E protein MR766",
            "reference_sequence": {
                "sequence": "ATCAGGTGCATTGGAGTCAGCAATAGAGACTTCGTGGAGGGCATGTCAGGTGGGACCTGGGTTGATGTTGTCTTGGAACATGGAGGCTGCGTTACCGTGATGGCACAGGACAAGCCAACAGTTGACATAGAGTTGGTCACGACGACGGTTAGTAACATGGCCGAGGTAAGATCCTATTGCTACGAGGCATCGATATCGGACATGGCTTCGGACAGTCGTTGCCCAACACAAGGTGAGGCCTACCTTGACAAGCAATCAGACACTCAATATGTCTGCAAAAGAACATTAGTGGACAGAGGTTGGGGAAACGGTTGTGGACTTTTTGGCAAAGGGAGCTTGGTGACATGTGCCAAGTTTACGTGTTCTAAGAAGATGACCGGGAAGAGCATTCAACCGGAAAATCTGGAGTATCGGATAATGCTATCAGTGCATGGCTCCCAGCATAGCGGGATGATTGTCAATGATACAGGATATGAAACTGACGAAAATAGAGCGAAAGTCGAGGTTACGCCTAATTCACCAAGAGCGGAAGCAACCTTGGGAGGCTTTGGAAGCTTAGGACTTGACTGTGAACCAAGGACAGGCCTTGACTTTTCAGATCTGTATTACCTGACCATGAACAATAAGCATTGGTTGGTGCACAAAGAGTGGTTTCATGACATCCCATTGCCTTGGCATGCTGGGGCAGACACCGGAACTCCACACTGGAACAACAAAGAGGCATTGGTAGAATTCAAGGATGCCCACGCCAAGAGGCAAACCGTCGTCGTTCTGGGGAGCCAGGAAGGAGCCGTTCACACGGCTCTCGCTGGAGCTCTAGAGGCTGAGATGGATGGTGCAAAGGGAAAGCTGTTCTCTGGCCACTTGAAATGCCGCCTAAAAATGGACAAGCTTAGATTGAAGGGCGTGTCATATTCCTTGTGCACTGCGGCATTCACATTCACCAAGGTCCCAGCTGAAACACTGCATGGAACAGTCACAGTGGAGGTGCAGTATGCAGGGACAGATGGACCCTGCAAGATCCCAGTCCAGATGGCGGTGGACATGCAGACCCTGACCCCAGTTGGAAGGCTGATAACCGCCAACCCCGTGATTACTGAAAGCACTGAGAACTCAAAGATGATGTTGGAGCTTGACCCACCATTTGGGGATTCTTACATTGTCATAGGAGTTGGGGACAAGAAAATCACCCACCACTGGCATAGGAGTGGTAGCACCATCGGAAAGGCATTTGAGGCCACTGTGAGAGGCGCCAAGAGAATGGCAGTCCTGGGGGATACAGCCTGGGACTTCGGATCAGTCGGGGGTGTGTTCAACTCACTGGGTAAGGGCATTCACCAGATTTTTGGAGCAGCCTTCAAATCACTGTTTGGAGGAATGTCCTGGTTCTCACAGATCCTCATAGGCACGCTGCTAGTGTGGTTAGGTTTGAACACAAAGAATGGATCTATCTCCCTCACATGCTTGGCCCTGGGGGGAGTGATGATCTTCCTCTCCACGGCTGTTTCTGCT",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000075-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000075-a-1",
        "variant_count": 10080,
        "experiment": "urn:mavedb:00000075-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-b-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 2, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 2 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 2 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 2",
            "reference_sequence": {
                "sequence": "AAGTTCATTGGAACAGAAAGAAATGGATTTATCTGCTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-b-1",
        "variant_count": 312,
        "experiment": "urn:mavedb:00000097-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-k-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 16, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 16 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 16 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 16",
            "reference_sequence": {
                "sequence": "TTAATTTCAGATGCTCGTGTACAAGTTTGCCAGAAAACACCACATCACTTTAACTAATCTAATTACTGAAGAGACTACTCATGTTGTTATGAAAACAGGTATACCAAG",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-k-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-k-1",
        "variant_count": 311,
        "experiment": "urn:mavedb:00000097-k",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-08-25",
        "modification_date": "2022-08-25",
        "urn": "urn:mavedb:00000102-0-1",
        "publish_date": "2022-08-25",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment used massively parallel sequencing (VAMP-seq) to measure the abundance scores of new variants in the PTEN gene, as well as to validate abundance measurements for previously studied variants in the PTEN gene. The resulting PTEN abundance dataset demonstrates the ability of large-scale variant functional data paired with cancer genomics datasets and follow-up assays to understand how uncharacterized cancer-associated variants contribute to oncogenesis.",
        "method_text": "Abundance scores from the original and fill-in datasets were aggregated and a composite score was calculated by taking the mean of all 15 replicate scores (8 from the original, 7 for the fill-in).",
        "short_description": "Amino acid scores for variant abundance by massively parallel sequencing (VAMP-seq) applied to PTEN (combination of original and fill-in datasets).",
        "title": "PTEN VAMP-seq Combined",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "34649609",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/34649609",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-3537-3865"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "PTEN",
            "reference_sequence": {
                "sequence": "ATGACAGCCATCATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTGACCTATATTTATCCAAACATTATTGCTATGGGATTTCCTGCAGAAAGACTTGAAGGCGTATACAGGAACAATATTGATGATGTAGTAAGGTTTTTGGATTCAAAGCATAAAAACCATTACAAGATATACAATCTTTGTGCTGAAAGACATTATGACACCGCCAAATTTAATTGCAGAGTTGCACAATATCCTTTTGAAGACCATAACCCACCACAGCTAGAACTTATCAAACCCTTTTGTGAAGATCTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTGTAATGATATGTGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCCTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAGGGAGTAACTATTCCCAGTCAGAGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACTTGCAATCCTCAGTTTGTGGTCTGCCAGCTAAAGGTGAAGATATATTCCTCCAATTCAGGACCCACACGACGGGAAGACAAGTTCATGTACTTTGAGTTCCCTCAGCCGTTACCTGTGTGTGGTGATATCAAAGTAGAGTTCTTCCACAAACAGAACAAGATGCTAAAAAAGGACAAAATGTTTCACTTTTGGGTAAATACATTCTTCATACCAGGACCAGAGGAAACCTCAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATCGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAATATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACAAAGCCAACCGATACTTTTCTCCAAATTTTAAGGTGAAGCTGTACTTCACAAAAACAGTAGAGGAGCCGTCAAATCCAGAGGCTAGCAGTTCAACTTCTGTAACACCAGATGTTAGTGACAATGAACCTGATCATTATAGATATTCTGACACCACTGACTCTGATCCAGAGAATGAACCTTTTGATGAAGATCAGCATACACAAATTACAAAAGTCTGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P60484",
                "url": "http://purl.uniprot.org/uniprot/P60484",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000102-0-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "expts",
            "se",
            "lower_ci",
            "upper_ci",
            "score_PMID29785012",
            "score_PMID34649609",
            "score1",
            "score2",
            "score3",
            "score4",
            "score5",
            "score6",
            "score7",
            "score8",
            "score9",
            "score10",
            "score11",
            "score12",
            "score13",
            "score14",
            "score15"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000102-0-1",
        "variant_count": 5477,
        "experiment": "urn:mavedb:00000102-0",
        "is_meta_analysis": true,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-07-29",
        "modification_date": "2019-07-29",
        "urn": "urn:mavedb:00000038-b-1",
        "publish_date": "2019-07-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment used the same library of ubiquitin variants as previously described in Roscoe et al. 2013. The ubiquitin variants were displayed as C-terminal fusions with Aga2-HA and reacted with E1. Bound cells were isolated using FACS and deep sequencing was used to quantify enrichment or depletion of cells in the bound population.\r\n\r\nThis entry describes the first of two regions assayed with excess E1, covering ubiquitin positions 40-48.",
        "method_text": "Scores were calculated using the EMPIRIC log ratios approach, using the ratio of E1-reactive cells to HA-displaying cells. Scores were normalized such that the average wild type synonymous variant was 1 and the average nonsense mutation was 0. The raw $log_2$ ratio is included as an extra column. The \"Std\" column lists the standard deviation calculated from multiple measurements of synonymous codons. This value is `nan` when only one codon was measured.",
        "short_description": "Amino acid scores for deep mutational scan of ubiquitin in a yeast display binding assay to E1 with excess E1. Region 1 (positions 40-48).",
        "title": "Ubiquitin-E1 yeast display amino acid scores, excess E1, region 1",
        "keywords": [
            {
                "text": "EMPIRIC"
            },
            {
                "text": "Binding"
            },
            {
                "text": "FACS"
            },
            {
                "text": "ubiquitin"
            },
            {
                "text": "E1"
            },
            {
                "text": "yeast display"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24862281",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24862281",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23376099",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23376099",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Ubiquitin",
            "reference_sequence": {
                "sequence": "CAACAAAGATTGATCTTTGCTGGTAAG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 39,
                "identifier": "P0CG63",
                "url": "http://purl.uniprot.org/uniprot/P0CG63",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000038-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "log2 (E1react/display)",
            "Std"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000038-b-1",
        "variant_count": 188,
        "experiment": "urn:mavedb:00000038-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000076-b-1",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilized site directed mutagenesis to generate variants in the  carboxyl-terminal tail anchor (TA) on the Fis1p protein within yeast. All possible codons at 27 amino acid positions were assayed for their ability to target the mitochondrial membrane.",
        "method_text": "FASTQ paired end data were stripped of adapters and combined using PANDAseq assembler. Sequences not encoding the Fis1p tail anchor were removed.\r\n\r\nScores were calculated by taking the $\\log_2$ ratio of the variant count in the experimental condition to the variant count in the SC -Trp condition. If the variant count in the SC -Trp condition was 0, it was set to 1 to avoid a divide-by-zero error.",
        "short_description": "Amino acid scores for deep mutational scan of the yeast Fis1 tail anchor, SMM -Trp -His medium with 10mM 3-aminotriazole.",
        "title": "Fis1 tail anchor, SMM -Trp -His with 10mM 3-AT",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.5061/dryad.j14r5",
                "url": "http://doi.org/10.5061/dryad.j14r5",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "28007883",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28007883",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Fis1 tail anchor",
            "reference_sequence": {
                "sequence": "LKGVVVAGGVLAGAVAVASFFLRNKRR",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000076-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000076-b-1",
        "variant_count": 530,
        "experiment": "urn:mavedb:00000076-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2018-06-29",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-b-2",
        "publish_date": "2018-06-29",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957)",
        "method_text": "##Scoring procedure:\r\nDMS-TileSeq reads were processed using the [dmsPipeline](https://bitbucket.org/rothlabto/dmspipeline) software. Briefly, TileSeq read counts were used to establish relative allele frequencies in each condition. Non-mutagenized control counts were subtracted from counts (as estimates of sequencing error). log ratios of selection over non-selection counts were calculated. The resulting TileSeq fitness values were then normalized to 0-1 scale where 0 corresponds to the median nonsense score and 1 corresponds to the median synonymous score.\r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for more details.\r\n\r\n## Additional columns:\r\n* exp.score = experimental score from the joint DMS-BarSeq/DMS-TileSeq screens\r\n* exp.sd = standard deviation of the experimental score\r\n* df = degrees of freedom (number of replicates contributing to the experimental score)\r\n* pred.score = machine-learning predicted score",
        "short_description": "A Deep Mutational Scan of the human SUMO1 using functional complementation in yeast via DMS-TileSeq",
        "title": "SUMO1 DMS-TileSeq",
        "keywords": [
            {
                "text": "sumoylation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29269382",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29269382",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "SUMO1",
            "reference_sequence": {
                "sequence": "ATGTCTGACCAGGAGGCAAAACCTTCAACTGAGGACTTGGGGGATAAGAAGGAAGGTGAATATATTAAACTCAAAGTCATTGGACAGGATAGCAGTGAGATTCACTTCAAAGTGAAAATGACAACACATCTCAAGAAACTCAAAGAATCATACTGTCAAAGACAGGGTGTTCCAATGAATTCACTCAGGTTTCTCTTTGAGGGTCAGAGAATTGCTGATAATCATACTCCAAAAGAACTGGGAATGGAGGAAGAAGATGTGATTGAAGTTTATCAGGAACAAACGGGGGGTCATTCAACAGTTTAG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P63165",
                "url": "http://purl.uniprot.org/uniprot/P63165",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000116030",
                "url": "http://www.ensembl.org/id/ENSG00000116030",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 149,
                "identifier": "NM_001005781.1",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_001005781.1",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000001-b-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "se"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000001-b-2",
        "variant_count": 4698,
        "experiment": "urn:mavedb:00000001-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-01-24",
        "modification_date": "2019-07-26",
        "urn": "urn:mavedb:00000008-a-2",
        "publish_date": "2019-01-24",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {
            "chr": "7",
            "end": 29161744,
            "start": 29161443,
            "reference": "mm9"
        },
        "abstract_text": "This study described the functional consequence of over 100,000 enhancer variants *in vivo* in mouse liver. Two human enhancers (ALDOB, ECR11) and one mouse enhancer (LTV1) were known to be active in mouse liver and therefore variants in these enhancers should show a measurable difference in transcription. The results were broadly consistent with evolutionary data and transcription factor binding sites, but were not always concordant demonstrating the importance of measuring the effect of enhancer variants directly.\r\n\r\nThis MaveDB entry describes the LTV1 enhancer data. Datasets for other enhancers described in the same publication are also available: [ALDOB](https://www.mavedb.org/experiment/urn:mavedb:00000006-a/) [ECR11](https://www.mavedb.org/experiment/urn:mavedb:00000007-a/)",
        "method_text": "Scores were calculated using a trivariate linear regression model. A separate model was built for each position in the enhancer, with a predictor for each possible variant nucleotide at that position.\r\n\r\nBecause most enhancer haplotypes in the LTV1 dataset had multiple tags, the data were normalized by dividing the total number of counts for a given haplotype by the number of tags for that haplotype.\r\n\r\nThe scores presented are therefore a combination of the effects of each individual variant on diverse enhancer haplotype backgrounds.\r\n\r\nSee metadata (available via download button) for wild type genomic coordinates in JSON format.",
        "short_description": "Trivariate regression scores for each nucleotide change as described in Patwardhan et al. 2012.",
        "title": "Trivariate regression scores for LTV1 replicate 2 of 2",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "doped oligo synthesis"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "liver"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "22371081",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/22371081",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "LTV1 enhancer",
            "reference_sequence": {
                "sequence": "CTTTGGGTGACCCCTGACCCTGGCCGCCTGGGCTCGCCTTCCCGCACATTCCGTCCTCGCCGCCCCGCCCCACCCCGCCCTCCTTCCTTGGCCCTGTGGGGACGGAAACATCCCGTTCCTGCCCAAGCTGGGTCAAGAGCCGGAGGGACAGGACCAGAGCACCCCTTACGCCAGAACTAGCTCTCCTTGTTCCTACTGGGTGACCTCATCTCGCCACGCCTCCTCAGGTGAACACCCGGGCTGGTAACGTCACTTCCTGCCAGGTAAGCGCCCCCAGGCAGCACTGCTCACGGAAAGGTCTG",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "mm9",
                        "organism_name": "Mus musculus",
                        "assembly_identifier": {
                            "identifier": "GCF_000001635.18",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.18",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000008-a-2",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "pvalue"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000008-a-2",
        "variant_count": 906,
        "experiment": "urn:mavedb:00000008-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-28",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-i-1",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "Each of the seven libraries was sequenced individually and analyzed separately using in-house Python scripts archived at https://github.com/elifesciences-publications/DMS-FastQ-processing.\r\n\r\nReads that had more than 20 base mismatches between forward and reverse reads were discarded. Merged reads with a posterior Q score of 10 were also discarded. Variants with an unexpectedly high error rate or mutations in more than one codon were also discarded.\r\n\r\nFitness scores were calculated as a ratio of frequency ratios:\r\n\r\n$$s_v = \\log_2\\left(\\frac{\\frac{f_{v, selected}}{f_{v, non-selected}}}{\\frac{f_{wt, selected}}{f_{wt, non-selected}}}\\right)$$\r\n\r\nThe mean fitness score of all synonymous variants in each library was subtracted from all variants in that library to normalize the scores between libraries.\r\n\r\nThe scores are the average of two replicates if the variant was scored in both replicates, otherwise the score given is the score from one replicate. Variants that were scored in both replicates have a standard deviation (SD) calculated from the two replicate scores.",
        "short_description": "Amino acid scores for deep mutational scan of VIM-2 metallo-β-lactamase at 2 µg/mL ampicillin at 37C",
        "title": "VIM-2 2 µg/mL AMP at 37C",
        "keywords": [
            {
                "text": "ampicillin"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "VIM-2 with p.Met1_Phe2insGly",
            "reference_sequence": {
                "sequence": "ATGGGATTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGCCCGCTCGCTTTTTCCGTAGATTCTAGCGGAGAATATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTTGAAGGACTTTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAATTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTTGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000073-i-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "SD"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000073-i-1",
        "variant_count": 5549,
        "experiment": "urn:mavedb:00000073-i",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-02-24",
        "modification_date": "2022-05-15",
        "urn": "urn:mavedb:00000094-a-3",
        "publish_date": "2022-05-15",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "V1/2 of 3,319 KCNQ4 missense SNVs in the homozygous state.",
        "method_text": "V1/2 of 3,319 KCNQ4 missense SNVs in the homozygous state.",
        "short_description": "2. V1/2 of 3,319 KCNQ4 missense SNVs in the homozygous state.",
        "title": "V1/2 of 3,319 KCNQ4 missense SNVs in the homozygous state",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ4",
            "reference_sequence": {
                "sequence": "MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGGGSPRRLGLLGSPLPPGAPLPGPGSGSGSACGQRSSAAHKRYRRLQNWVYNVLERPRGWAFVYHVFIFLLVFSCLVLSVLSTIQEHQELANECLLILEFVMIVVFGLEYIVRVWSAGCCCRYRGWQGRFRFARKPFCVIDFIVFVASVAVIAAGTQGNIFATSALRSMRFLQILRMVRMDRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLVYLAEKDANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAGILGSGFALKVQEQHRQKHFEKRRMPAANLIQAAWRLYSTDMSRAYLTATWYYYDSILPSFRELALLFEHVQRARNGGLRPLEVRRAPVPDGAPSRYPPVATCHRPGSTSFCPGESSRMGIKDRIRMGSSQRRTGPSKQHLAPPTMPTSPSSEQVGEATSPTKVQKSWSFNDRTRFRASLRLKPRTSAEDAPSEEVAEEKSYQCELTVDDIMPAVKTVIRSIRILKFLVAKRKFKETLRPYDVKDVIEQYSAGHLDMLGRIKSLQTRVDQIVGRGPGDRKAREKGDKGPSDAEVVDEISMMGRVVKVEKQVQSIEHKLDLLLGFYSRCLRSGTSASLGAVQVPLFDPDITSDYHSPVDHEDISVSAQTLSISRSVSTNMD",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-3",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000094-a-3",
        "variant_count": 3319,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-g-1",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "Samples are collected after 24h and sequenced by Illumina. The counts for each variant is first added by 1, then divided by total sequence counts at this time point to calculate variant frequency. The functional score equals the division of a variant frequency at this time point and its frequency in initial library. Further normalizing the functional scores by wild type scores will give the relative enrichment values. The score data includes scores from three replicates which are suffixed by: _rep1, _rep2 & _rep3. The final score is the median of them.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 24h",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "RAF",
            "reference_sequence": {
                "sequence": "TCTAAGACAAGCAACACTATCCGTGTTTTCTTGCCGAACAAGCAAAGAACAGTGGTCAATGTGCGAAATGGAATGAGCTTGCATGACTGCCTTATGAAAGCACTCAAGGTGAGGGGC",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 51,
                "identifier": "P04049",
                "url": "http://purl.uniprot.org/uniprot/P04049",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000061-g-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_rep1",
            "score_rep2",
            "score_rep3"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000061-g-1",
        "variant_count": 298,
        "experiment": "urn:mavedb:00000061-g",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2018-06-29",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-d-1",
        "publish_date": "2018-06-29",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957)",
        "method_text": "##Scoring procedure:\r\nDMS-TileSeq reads were processed using the [dmsPipeline](https://bitbucket.org/rothlabto/dmspipeline) software. Briefly, TileSeq read counts were used to establish relative allele frequencies in each condition. Non-mutagenized control counts were subtracted from counts (as estimates of sequencing error). log ratios of selection over non-selection counts were calculated. The resulting TileSeq fitness values were then normalized to 0-1 scale where 0 corresponds to the median nonsense score and 1 corresponds to the median synonymous score. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for more details.",
        "short_description": "A Deep Mutational Scan of human TPK1 using functional complementation in yeast via DMS-TileSeq.",
        "title": "TPK1 DMS-TileSeq",
        "keywords": [
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29269382",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29269382",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TPK1",
            "reference_sequence": {
                "sequence": "ATGGAGCATGCCTTTACCCCGTTGGAGCCCCTGCTTTCCACTGGGAATTTGAAGTACTGCCTTGTAATTCTTAATCAGCCTTTGGACAACTATTTTCGTCATCTTTGGAACAAAGCTCTTTTAAGAGCCTGTGCCGATGGAGGTGCCAACCGCTTATATGATATCACCGAAGGAGAGAGAGAAAGCTTTTTGCCTGAATTCATCAATGGAGACTTTGATTCTATTAGGCCTGAAGTCAGAGAATACTATGCTACTAAGGGATGTGAGCTCATTTCAACTCCTGATCAAGACCACACTGACTTTACTAAGTGCCTTAAAATGCTCCAAAAGAAGATAGAAGAAAAAGACTTAAAGGGAAAGCACAGGTTGCATGTAGACACTGGAATGGAGGGTGATTGGTGTGGCCTTATTCCTGTTGGACAGCCTTGTATGCAGGTTACAACCACAGGCCTCAAGTGGAACCTCACAAATGATGTGCTTGCTTTTGGAACATTGGTCAGTACTTCCAATACCTACGACGGGTCTGGTGTTGTGACTGTGGAAACTGACCACCCACTCCTCTGGACCATGGCCATCAAAAGCTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "Q9H3S4",
                "url": "http://purl.uniprot.org/uniprot/Q9H3S4",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000196511",
                "url": "http://www.ensembl.org/id/ENSG00000196511",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 104,
                "identifier": "NM_022445.3",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_022445.3",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000001-d-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "se"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000001-d-1",
        "variant_count": 9542,
        "experiment": "urn:mavedb:00000001-d",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-p-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 18, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 18 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 18 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 18",
            "reference_sequence": {
                "sequence": "TGTAACCTGTCTTTTCTATGATCTCTTTAGGGGTGACCCAGTCTATTAAAGAAAGAAAAATGCTGAATGAGGTAAGTACTTGATGTTACAAACTAACCAGA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-p-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-p-1",
        "variant_count": 294,
        "experiment": "urn:mavedb:00000097-p",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-x-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 22, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 22 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 22 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 22",
            "reference_sequence": {
                "sequence": "TCCTGGGGATCCAGGGTGTCCACCCAATTGTGGTTGTGCAGCCAGATGCCTGGACAGAGGACAATGGCTTCCATGGTAAGGTGCCTGCATGTACCTGTGC",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-x-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-x-1",
        "variant_count": 288,
        "experiment": "urn:mavedb:00000097-x",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-01-12",
        "modification_date": "2021-01-12",
        "urn": "urn:mavedb:00000055-a-1",
        "publish_date": "2021-01-12",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment identified candidate pharmacogenomic variants in NUDT15 that could contribute to thiopurine toxicity. Two functional assays were performed on the same variant library, one for NUDT15 activity and one for protein stability.",
        "method_text": "Barcode-variant counts were converted to variant counts and transformed to scores using a weighted average of counts in FACS bins as described by Matreyek et al. 2018.\r\n\r\nReported are the non-normalized average score and standard deviation for each missense change, but the nature of the averaging (e.g. distinct codons with synonymous consequences or replicate assays) was not specified.",
        "short_description": "NUDT15 protein stability scores measured by VAMP-seq.",
        "title": "NUDT15 protein stability scores",
        "keywords": [
            {
                "text": "VAMP-seq"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29785012",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29785012",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "32094176",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32094176",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "NUDT15",
            "reference_sequence": {
                "sequence": "ATGACGGCCAGCGCACAGCCGCGCGGGCGGCGGCCAGGAGTCGGAGTCGGAGTCGTGGTGACCAGCTGCAAGCATCCGCGTTGCGTCCTCCTGGGGAAGAGGAAAGGCTCGGTTGGAGCTGGCAGTTTCCAACTCCCTGGAGGTCATCTGGAGTTCGGTGAAACCTGGGAAGAATGTGCTCAAAGGGAAACCTGGGAAGAAGCAGCTCTTCACCTGAAAAATGTTCACTTTGCCTCAGTTGTGAATTCTTTCATTGAGAAGGAGAATTACCATTATGTTACTATATTAATGAAAGGAGAAGTGGATGTGACTCATGATTCAGAACCAAAGAATGTAGAGCCTGAAAAAAATGAAAGTTGGGAGTGGGTTCCTTGGGAAGAACTACCTCCCCTGGACCAGCTTTTCTGGGGACTGCGTTGTTTAAAAGAACAAGGCTATGATCCATTTAAAGAAGATCTGAACCATCTGGTGGGATACAAAGGAAATCATCTCTAG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "Q9NV35",
                "url": "http://purl.uniprot.org/uniprot/Q9NV35",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000055-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000055-a-1",
        "variant_count": 3100,
        "experiment": "urn:mavedb:00000055-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-06-19",
        "modification_date": "2020-06-19",
        "urn": "urn:mavedb:00000044-b-2",
        "publish_date": "2020-06-19",
        "created_by": "0000-0001-6713-6904",
        "modified_by": "0000-0001-6713-6904",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "Full methods provided in the [preprint](https://www.biorxiv.org/content/10.1101/2020.06.17.157982v1) and full analysis provided in the [GitHub repo](https://github.com/jbloomlab/SARS-CoV-2-RBD_DMS).\r\n\r\n`score` column is the change in log<sub>10</sub>(_K_<sub>D,app</sub>) relative to the average wildtype binding, polarized such that a positive score indicates improved binding, and negative indicates reduced binding affinity. The `library` column indicates which of our two duplicate mutant libraries a measurement is from. The `average` column is the average mutation effect from the duplicate libraries. The values in the `average` column were used in the paper analysis.",
        "short_description": "RBD mutation and expression score for each amino acid mutation",
        "title": "per-single-mutant expression score",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-6713-6904",
            "0000-0001-9278-3644",
            "0000-0003-1267-3408"
        ],
        "licence": {
            "long_name": "Other - See Data Usage Guidelines",
            "short_name": "Other - See Data Usage Guidelines",
            "link": "",
            "version": "1.0"
        },
        "target": {
            "name": "SARS-CoV-2 receptor binding domain",
            "reference_sequence": {
                "sequence": "AATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACT",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000044-b-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "average",
            "library"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000044-b-2",
        "variant_count": 8040,
        "experiment": "urn:mavedb:00000044-b",
        "is_meta_analysis": false,
        "data_usage_policy": "See licence from GitHub: https://github.com/jbloomlab/SARS-CoV-2-RBD_DMS/blob/master/LICENSE.md\r\n\r\nBSD 3-Clause License\r\n\r\nCopyright (c) 2020, Tyler N. Starr, Allison J. Greaney, and Jesse D. Bloom\r\nAll rights reserved.\r\n\r\nRedistribution and use in source and binary forms, with or without\r\nmodification, are permitted provided that the following conditions are met:\r\n\r\n1. Redistributions of source code must retain the above copyright notice, this\r\n   list of conditions and the following disclaimer.\r\n\r\n2. Redistributions in binary form must reproduce the above copyright notice,\r\n   this list of conditions and the following disclaimer in the documentation\r\n   and/or other materials provided with the distribution.\r\n\r\n3. Neither the name of the copyright holder nor the names of its\r\n   contributors may be used to endorse or promote products derived from\r\n   this software without specific prior written permission."
    },
    {
        "creation_date": "2022-02-24",
        "modification_date": "2022-05-15",
        "urn": "urn:mavedb:00000094-a-10",
        "publish_date": "2022-05-15",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "Normalized currents of co-expressing 76  variants (normal currents and large leftward shifts in V1/2 in the homozygous state) with WT.",
        "method_text": "Normalized currents of co-expressing 76  variants (normal currents and large leftward shifts in V1/2 in the homozygous state) with WT.",
        "short_description": "9. Normalized currents of co-expressing 76  variants (normal currents and large leftward shifts in V1/2 in the homozygous state) with WT.",
        "title": "Normalized currents of co-expressing 76  variants (normal currents and large leftward shifts in V1/2 in the homozygous state) with WT",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ4",
            "reference_sequence": {
                "sequence": "MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGGGSPRRLGLLGSPLPPGAPLPGPGSGSGSACGQRSSAAHKRYRRLQNWVYNVLERPRGWAFVYHVFIFLLVFSCLVLSVLSTIQEHQELANECLLILEFVMIVVFGLEYIVRVWSAGCCCRYRGWQGRFRFARKPFCVIDFIVFVASVAVIAAGTQGNIFATSALRSMRFLQILRMVRMDRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLVYLAEKDANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAGILGSGFALKVQEQHRQKHFEKRRMPAANLIQAAWRLYSTDMSRAYLTATWYYYDSILPSFRELALLFEHVQRARNGGLRPLEVRRAPVPDGAPSRYPPVATCHRPGSTSFCPGESSRMGIKDRIRMGSSQRRTGPSKQHLAPPTMPTSPSSEQVGEATSPTKVQKSWSFNDRTRFRASLRLKPRTSAEDAPSEEVAEEKSYQCELTVDDIMPAVKTVIRSIRILKFLVAKRKFKETLRPYDVKDVIEQYSAGHLDMLGRIKSLQTRVDQIVGRGPGDRKAREKGDKGPSDAEVVDEISMMGRVVKVEKQVQSIEHKLDLLLGFYSRCLRSGTSASLGAVQVPLFDPDITSDYHSPVDHEDISVSAQTLSISRSVSTNMD",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-10",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000094-a-10",
        "variant_count": 76,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-11-02",
        "modification_date": "2021-11-02",
        "urn": "urn:mavedb:00000085-a-1",
        "publish_date": "2021-11-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the experimental fitness of variants in the TEM-1 β-lactamase gene in *Escherichia coli* on different backgrounds. Fitness measurements were estimated based on growth under increasing concentrations of ampicillin using a band-pass selection system.",
        "method_text": "Variant reads were aligned to the template sequence and all codon substitution variants were mapped. Indels were assumed to be sequencing errors and ignored. Reads were removed if the average quality score was less than 30, if the read did not span the full sub-region, or if the read contained mutations in more than one codon.\r\n\r\nReads were counted for each of 13 concentrations of Amp used in the experiment. The raw fitness score $f$ of allele $i$ was calculated as:\r\n\r\n$$ f_i = \\frac{\\sum_{p=1}^{13} c_{i,p} \\log_2\\left(a_p\\right)}{\\sum_{p=1}^{13} c_{i,p}} $$\r\n\r\nAdditional measures were taken to calculate fitness values for variants with counts at many Amp concentrations (see manuscript SI for details).\r\n\r\nRaw fitness scores were normalized to wild type to get a normalized fitness $w_i$ using:\r\n\r\n$$ w_i = \\frac{2^{f_i}}{2^f_{wt}} $$\r\n\r\nThe wild type fitness score was calculated using the counts of all alleles with synonymous substitutions. Therefore a normalized fitness value of 1.0 is equivalent to wild type, greater than 1.0 is beneficial, and 0 to 1.0 is deleterious. Only the normalized scores are reported.\r\n\r\nThe score for a protein variant was calculated as the average fitness of all equivalent nucleotide variants.\r\n\r\nThe estimated error (‘err’ column) is based on the percent difference in fitness between the nucleotide variant fitness and the average fitness of the corresponding amino acid variant.\r\n\r\nThe ‘ambler’ column provides the [Ambler position](https://pubmed.ncbi.nlm.nih.gov/2039479/) of the amino acid .",
        "short_description": "Amino acid scores for TEM-19 (TEM-1 variant) fitness on Amp.",
        "title": "TEM-19 Amp scores",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23284860",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23284860",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "24567513",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24567513",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "19502423",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/19502423",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "27173379",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27173379",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TEM-19 β-lactamase",
            "reference_sequence": {
                "sequence": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000085-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "ambler",
            "err"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "ambler",
            "c_0.25",
            "c_0.5",
            "c_1",
            "c_2",
            "c_4",
            "c_8",
            "c_16",
            "c_32",
            "c_64",
            "c_128",
            "c_256",
            "c_512",
            "c_1024"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000085-a-1",
        "variant_count": 3623,
        "experiment": "urn:mavedb:00000085-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-i-1",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\n\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Rapamycin",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "alpha-synuclein",
            "reference_sequence": {
                "sequence": "ATGGATGTATTCATGAAAGGACTTTCAAAGGCCAAGGAGGGAGTTGTGGCTGCTGCTGAGAAAACCAAACAGGGTGTGGCAGAAGCAGCAGGAAAGACAAAAGAGGGTGTTCTCTATGTAGGCTCCAAAACCAAGGAGGGAGTGGTGCATGGTGTGGCAACAGTGGCTGAGAAGACCAAAGAGCAAGTGACAAATGTTGGAGGAGCAGTGGTGACGGGTGTGACAGCAGTAGCCCAGAAGACAGTGGAGGGAGCAGGGAGCATTGCAGCAGCCACTGGCTTTGTCAAAAAGGACCAGTTGGGCAAGAATGAAGAAGGAGCCCCACAGGAAGGAATTCTGGAAGATATGCCTGTGGATCCTGACAATGAGGCTTATGAAATGCCTTCTGAGGAAGGGTATCAAGACTACGAACCTGAAGCCTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P37840",
                "url": "http://purl.uniprot.org/uniprot/P37840",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg16",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.10",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000045-i-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000045-i-1",
        "variant_count": 2800,
        "experiment": "urn:mavedb:00000045-i",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-20",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000032-a-1",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {
            "chr": "2",
            "end": 161238998,
            "start": 161238408,
            "reference": "hg38"
        },
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "The effect of each variant was calculated using a multiple linear regression model based on the DNA counts and RNA counts. Each variant needed to have 10 unique barcode tags to be included in the downstream analyses.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>\r\n\r\nMetadata contains the genomic coordinates for the target sequence.\r\n\r\nColumn descriptions:\r\n\r\n- 'score' is the Log2 variant expression effect derived from the fit of the linear model (coefficient).\r\n- 'p-value' is the P-value of the coefficient.\r\n- 'unique_tags' is the number of unique tags associated with the variant.\r\n- 'dna_sequences' is the count of DNA sequences that contain the variant (used for fitting the linear model).\r\n- 'rna_sequences' is the count of RNA sequences that contain the variant (used for fitting the linear model).",
        "short_description": "Saturation mutagenesis MPRA of UC88 (ultraconserved element) enhancer in Neuro-2a cells.",
        "title": "Saturation mutagenesis MPRA of UC88 enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "UC88 enhancer",
            "reference_sequence": {
                "sequence": "ATACAGATAAATGCACACATGTATACGCGAAAGGTTAACTCGGCGGAGGACTCGCCCAAATAAGCACCGGGATTGCATTTAAAATAATAATAATAAATAAATAAATAAACTAGGAAGGAAAGCGGGGGGAGGGAAGCAGAAGTCGGGAAGAAAAGAGAAAAGCAGCAGGCTGATTACGAGGTGTCAAAACTGCCAGGAGCAAGAAGGTGATAGCAATCAGGGGTGAGAAGAGTGCGGCATTCGTGCGGGGCAACTAATTATCCGTCTCATTTGAGAAGAGCAGCATTTGAGGCAGCAGCGTTCGCCTGCTGAACGGTGACAGATTGGCGCGGAGGAGAGGGGAGGTGTTAAAACAATGGAGCCGGGCGCGCGAGCGCTGCTGCATGCTAATCAGCCCTCCCTCCGCCTGCCTGCCGCGCTCCCTCCTTCCTCCCGGCCTCCCTCCTCCGCGCTCCCTCCTCCCGCCTGCGGCGCTCCCTCCTTTCCAGCGGGCCCCGCGCCGCCGCCGCCACCCGCTTCCTGCTCCCTCGCTTTCCCGCGCGTCCTTCCCGCCGCTGGCGAGTGGAACCCAGCCACCGCCACCGAGTCCCA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000032-a-1",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "p-value",
            "unique_tags",
            "dna_sequences",
            "rna_sequences"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000032-a-1",
        "variant_count": 1964,
        "experiment": "urn:mavedb:00000032-a",
        "is_meta_analysis": false,
        "data_usage_policy": "We are making our data available prior to publication in line with Fort Lauderdale principle, allowing others to use the data but allowing the data producers to make the first presentations and to publish the first paper with global analyses of the data. In addition, we also reserve the right to publish the first analysis of the differences seen in the TERT knock-down experiments and alternative cell-type experiments. Studies that do not overlap with these intentions may be submitted for publication at any time, but must appropriately cite the data source. After publication of the data, the first publication of the data producers should be cited for any use of these data."
    },
    {
        "creation_date": "2021-09-28",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-a-1",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "Each of the seven libraries was sequenced individually and analyzed separately using in-house Python scripts archived at https://github.com/elifesciences-publications/DMS-FastQ-processing.\r\n\r\nReads that had more than 20 base mismatches between forward and reverse reads were discarded. Merged reads with a posterior Q score of 10 were also discarded. Variants with an unexpectedly high error rate or mutations in more than one codon were also discarded.\r\n\r\nFitness scores were calculated as a ratio of frequency ratios:\r\n\r\n$$s_v = \\log_2\\left(\\frac{\\frac{f_{v, selected}}{f_{v, non-selected}}}{\\frac{f_{wt, selected}}{f_{wt, non-selected}}}\\right)$$\r\n\r\nThe mean fitness score of all synonymous variants in each library was subtracted from all variants in that library to normalize the scores between libraries.\r\n\r\nThe scores are the average of two replicates if the variant was scored in both replicates, otherwise the score given is the score from one replicate. Variants that were scored in both replicates have a standard deviation (SD) calculated from the two replicate scores.",
        "short_description": "Amino acid scores for deep mutational scan of VIM-2 metallo-β-lactamase at 128 µg/mL ampicillin at 25C",
        "title": "VIM-2 128 µg/mL AMP at 25C",
        "keywords": [
            {
                "text": "ampicillin"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "VIM-2 with p.Met1_Phe2insGly",
            "reference_sequence": {
                "sequence": "ATGGGATTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGCCCGCTCGCTTTTTCCGTAGATTCTAGCGGAGAATATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTTGAAGGACTTTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAATTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTTGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000073-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "SD"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000073-a-1",
        "variant_count": 5549,
        "experiment": "urn:mavedb:00000073-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-10-06",
        "modification_date": "2022-08-16",
        "urn": "urn:mavedb:00000070-a-3",
        "publish_date": "2022-08-16",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the experimental fitness of variants in the TEM-1 $\\beta$-lactamase gene in _Escherichia coli_. Fitness measurements were estimated based on growth under increasing concentrations of ampicillin using a band-pass selection system.",
        "method_text": "Variant reads were aligned to the template sequence and all codon substitution variants were mapped. Indels were assumed to be sequencing errors and ignored. Reads were removed if the average quality score was less than 30, if the read did not span the full sub-region, or if the read contained mutations in more than one codon.\r\n\r\nReads were counted for each of 13 concentrations of Amp used in the experiment. The raw fitness score $f$ of allele $i$ was calculated as:\r\n\r\n$$ f_i = \\frac{\\sum_{p=1}^{13} c_{i,p} \\log_2\\left(a_p\\right)}{\\sum_{p=1}^{13} c_{i,p}} $$\r\n\r\nVariants with five or fewer total counts were not assigned a fitness value. Additional measures were taken to calculate fitness values for variants with counts at many Amp concentrations (see manuscript SI for details).\r\n\r\nRaw fitness scores were normalized to wild type to get a normalized fitness $w_i$ using:\r\n\r\n$$ w_i = \\frac{2^{f_i}}{2^f_{wt}} $$\r\n\r\nThe wild type fitness score was calculated using the counts of all alleles with synonymous substitutions. Therefore a normalized fitness value of 1.0 is equivalent to wild type, greater than 1.0 is beneficial, and 0 to 1.0 is deleterious. Only the normalized scores were reported.\r\n\r\nThe score for a protein variant was calculated as the average fitness of all equivalent nucleotide variants.\r\n\r\nThe estimated error ('err' column) is based on the percent difference in fitness between the nucleotide variant fitness and the average fitness of the corresponding amino acid variant.\r\n\r\nThe 'ambler' column provides the [Ambler position](https://pubmed.ncbi.nlm.nih.gov/2039479/) of the amino acid .",
        "short_description": "Nucleotide fitness scores for variants in the TEM-1 β-lactamase gene in the presence of ampicillin.",
        "title": "Nucleotide fitness scores of TEM-1 β-lactamase",
        "keywords": [
            {
                "text": "normalized"
            },
            {
                "text": "band-pass selection"
            },
            {
                "text": "resistance"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24567513",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24567513",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TEM-1 β-lactamase",
            "reference_sequence": {
                "sequence": "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P62593",
                "url": "http://purl.uniprot.org/uniprot/P62593",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000070-a-3",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "err",
            "ambler"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "c_0.25",
            "c_0.5",
            "c_1",
            "c_2",
            "c_4",
            "c_8",
            "c_16",
            "c_32",
            "c_64",
            "c_128",
            "c_256",
            "c_512",
            "c_1024",
            "c_total",
            "ambler"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000070-a-3",
        "variant_count": 18081,
        "experiment": "urn:mavedb:00000070-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-08-07",
        "modification_date": "2019-08-07",
        "urn": "urn:mavedb:00000039-a-3",
        "publish_date": "2019-08-07",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effects of yeast HSP90 variants under the control of different promoters to explore the relationship between protein sequence and expression level. The results showed that reduced expression level (compared to wild-type expression) revealed new partial loss of function mutations.",
        "method_text": "Growth rates were calculated for each variant and converted into selection coefficients. The selection coefficient for each variant under control of this promoter/UTR combination is reported as the score. For variants with multiple synonymous codons, the reported coefficient is the average of all synonymous variant's selection coefficients.\r\n\r\nVariants annotated as \"null-like\" have a score of -1.",
        "short_description": "Deep mutational scan of all single mutants in a nine-amino acid region of Hsp90 (Hsp82) in Saccharomyces cerevisiae under the control of the CYC promoter with CYC 3'UTR.",
        "title": "Deep mutational scan of HSP90, CYC construct",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "promoter"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23825969",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23825969",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "HSP90",
            "reference_sequence": {
                "sequence": "CAATTTGGTTGGTCTGCTAATATGGAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 581,
                "identifier": "P02829",
                "url": "http://purl.uniprot.org/uniprot/P02829",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000039-a-3",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000039-a-3",
        "variant_count": 189,
        "experiment": "urn:mavedb:00000039-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-07-29",
        "modification_date": "2019-07-29",
        "urn": "urn:mavedb:00000038-a-1",
        "publish_date": "2019-07-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effect of single amino acid changes in ubiquitin on binding to E1 (Uba1). Combined with work from a previous study on the effect of ubiquitin mutations on yeast growth rate, this showed that ubiquitin-E1 binding was not linearly related to growth rate and that mutations in ubiquitin are likely to affect multiple function that modulate growth rate.\r\n\r\nThis experiment was performed in limiting E1 conditions (as opposed to excess E1).",
        "method_text": "Scores were calculated using the EMPIRIC log ratios approach, using the ratio of E1-reactive cells to HA-displaying cells. Scores were normalized such that the average wild type synonymous variant was 1 and the average nonsense mutation was 0. The raw $log_2$ ratio is included as an extra column. The \"Std\" column lists the standard deviation calculated from multiple measurements of synonymous codons. This value is `nan` when only one codon was measured.",
        "short_description": "Amino acid scores for deep mutational scan of ubiquitin in a yeast display binding assay to E1 with limiting E1.",
        "title": "Ubiquitin-E1 yeast display amino acid scores, limiting E1",
        "keywords": [
            {
                "text": "EMPIRIC"
            },
            {
                "text": "Binding"
            },
            {
                "text": "FACS"
            },
            {
                "text": "ubiquitin"
            },
            {
                "text": "E1"
            },
            {
                "text": "yeast display"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24862281",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24862281",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23376099",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23376099",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Ubiquitin",
            "reference_sequence": {
                "sequence": "CAAATTTTCGTCAAGACTTTAACCGGTAAGACTATTACCCTGGAAGTTGAATCTTCTGACACTATTGACAATGTCAAGTCCAAGATCCAAGACAAGGAAGGTATTCCACCTGACCAACAAAGATTGATCTTTGCTGGTAAGCAATTGGAAGATGGTAGAACTTTGTCCGACTACAACATCCAAAAGGAATCTACTCTACACTTGGTCTTGAGATTGAGAGGTGGT",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 1,
                "identifier": "P0CG63",
                "url": "http://purl.uniprot.org/uniprot/P0CG63",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000038-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "log2 (E1react/display)",
            "Std"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000038-a-1",
        "variant_count": 1528,
        "experiment": "urn:mavedb:00000038-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-08-25",
        "modification_date": "2022-08-25",
        "urn": "urn:mavedb:00000101-a-1",
        "publish_date": "2022-08-25",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment used massively parallel sequencing (VAMP-seq) to measure the abundance scores of new variants in the PTEN gene, as well as to validate abundance measurements for previously studied variants in the PTEN gene. The resulting PTEN abundance dataset demonstrates the ability of large-scale variant functional data paired with cancer genomics datasets and follow-up assays to understand how uncharacterized cancer-associated variants contribute to oncogenesis.",
        "method_text": "Sequencing reads were converted to FASTQ format with bcl2fastq. Barcode paired sequencing reads were joined using the fastq- join tool within the ea-utils package using the default parameters. Barcodes for each bin were counted and associated with variant sequences using Enrich2. Scores were calculated based on the frequency of each variant in each bin using a weighted average such that increased abundance in high-signal bins gives a higher score. Abundance scores were calculated based on a min-max normalization using wild type (score of 1) and the average nonsense variant score (score of 0). The scores reported are the average of the seven fill-in replicate scores. Confidence intervals and variance estimates are based on the replicate scores.",
        "short_description": "Amino acid scores for variant abundance by massively parallel sequencing (VAMP-seq) applied to PTEN (fill-in dataset).",
        "title": "PTEN VAMP-seq Fill-in",
        "keywords": [
            {
                "text": "VAMP-seq"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "34649609",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/34649609",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-3537-3865"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "PTEN",
            "reference_sequence": {
                "sequence": "ATGACAGCCATCATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTGACCTATATTTATCCAAACATTATTGCTATGGGATTTCCTGCAGAAAGACTTGAAGGCGTATACAGGAACAATATTGATGATGTAGTAAGGTTTTTGGATTCAAAGCATAAAAACCATTACAAGATATACAATCTTTGTGCTGAAAGACATTATGACACCGCCAAATTTAATTGCAGAGTTGCACAATATCCTTTTGAAGACCATAACCCACCACAGCTAGAACTTATCAAACCCTTTTGTGAAGATCTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTGTAATGATATGTGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCCTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAGGGAGTAACTATTCCCAGTCAGAGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACTTGCAATCCTCAGTTTGTGGTCTGCCAGCTAAAGGTGAAGATATATTCCTCCAATTCAGGACCCACACGACGGGAAGACAAGTTCATGTACTTTGAGTTCCCTCAGCCGTTACCTGTGTGTGGTGATATCAAAGTAGAGTTCTTCCACAAACAGAACAAGATGCTAAAAAAGGACAAAATGTTTCACTTTTGGGTAAATACATTCTTCATACCAGGACCAGAGGAAACCTCAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATCGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAATATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACAAAGCCAACCGATACTTTTCTCCAAATTTTAAGGTGAAGCTGTACTTCACAAAAACAGTAGAGGAGCCGTCAAATCCAGAGGCTAGCAGTTCAACTTCTGTAACACCAGATGTTAGTGACAATGAACCTGATCATTATAGATATTCTGACACCACTGACTCTGATCCAGAGAATGAACCTTTTGATGAAGATCAGCATACACAAATTACAAAAGTCTGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P60484",
                "url": "http://purl.uniprot.org/uniprot/P60484",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000101-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "expts",
            "se",
            "lower_ci",
            "upper_ci",
            "score9",
            "score10",
            "score11",
            "score12",
            "score13",
            "score14",
            "score15"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000101-a-1",
        "variant_count": 4514,
        "experiment": "urn:mavedb:00000101-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-12-14",
        "modification_date": "2020-12-20",
        "urn": "urn:mavedb:00000053-a-1",
        "publish_date": "2020-12-20",
        "created_by": "0000-0002-2866-3880",
        "modified_by": "0000-0002-2866-3880",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "This contains the double mutations found in the dataset",
        "title": "Pairwise mutations in PSD95 PDZ3",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2866-3880"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "PSD95 PDZ3",
            "reference_sequence": {
                "sequence": "CCACGCCGCATCGTCATCCACCGTGGGTCAACGGGGTTAGGCTTCAATATCGTCGGTGGAGAGGATGGTGAGGGAATCTTCATCTCATTCATTCTGGCGGGAGGACCGGCCGATTTAAGCGGAGAACTTCGCAAAGGTGACCAGATCCTTTCGGTGAATGGCGTAGATTTGCGCAACGCATCACACGAACAGGCGGCCATCGCATTAAAGAACGCCGGCCAGACCGTTACGATTATCGCGCAGTATAAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 309,
                "identifier": "P78352",
                "url": "http://purl.uniprot.org/uniprot/P78352",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000053-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sigma"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "base_1",
            "base_2",
            "base_3",
            "base_4",
            "base_5",
            "base_6",
            "chlor_1",
            "chlor_2",
            "chlor_3",
            "chlor_4",
            "chlor_5",
            "chlor_6"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000053-a-1",
        "variant_count": 648022,
        "experiment": "urn:mavedb:00000053-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-11-02",
        "modification_date": "2021-11-02",
        "urn": "urn:mavedb:00000085-b-1",
        "publish_date": "2021-11-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the experimental fitness of variants in the TEM-1 β-lactamase gene in *Escherichia coli* on different backgrounds. Fitness measurements were estimated based on growth under increasing concentrations of ampicillin using a band-pass selection system.",
        "method_text": "Variant reads were aligned to the template sequence and all codon substitution variants were mapped. Indels were assumed to be sequencing errors and ignored. Reads were removed if the average quality score was less than 30, if the read did not span the full sub-region, or if the read contained mutations in more than one codon.\r\n\r\nReads were counted for each of 13 concentrations of Amp used in the experiment. The raw fitness score $f$ of allele $i$ was calculated as:\r\n\r\n$$ f_i = \\frac{\\sum_{p=1}^{13} c_{i,p} \\log_2\\left(a_p\\right)}{\\sum_{p=1}^{13} c_{i,p}} $$\r\n\r\nAdditional measures were taken to calculate fitness values for variants with counts at many Amp concentrations (see manuscript SI for details).\r\n\r\nRaw fitness scores were normalized to wild type to get a normalized fitness $w_i$ using:\r\n\r\n$$ w_i = \\frac{2^{f_i}}{2^f_{wt}} $$\r\n\r\nThe wild type fitness score was calculated using the counts of all alleles with synonymous substitutions. Therefore a normalized fitness value of 1.0 is equivalent to wild type, greater than 1.0 is beneficial, and 0 to 1.0 is deleterious. Only the normalized scores are reported.\r\n\r\nThe score for a protein variant was calculated as the average fitness of all equivalent nucleotide variants.\r\n\r\nThe estimated error (‘err’ column) is based on the percent difference in fitness between the nucleotide variant fitness and the average fitness of the corresponding amino acid variant.\r\n\r\nThe ‘ambler’ column provides the [Ambler position](https://pubmed.ncbi.nlm.nih.gov/2039479/) of the amino acid .",
        "short_description": "Amino acid scores for TEM-17 (TEM-1 variant) fitness on Amp.",
        "title": "TEM-17 Amp scores",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23284860",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23284860",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "24567513",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24567513",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "19502423",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/19502423",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "27173379",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27173379",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TEM-17 β-lactamase",
            "reference_sequence": {
                "sequence": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000085-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "ambler",
            "err"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "ambler",
            "c_0.25",
            "c_0.5",
            "c_1",
            "c_2",
            "c_4",
            "c_8",
            "c_16",
            "c_32",
            "c_64",
            "c_128",
            "c_256",
            "c_512",
            "c_1024"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000085-b-1",
        "variant_count": 3317,
        "experiment": "urn:mavedb:00000085-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-v-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 21, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 21 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 21 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 21",
            "reference_sequence": {
                "sequence": "ATGTCCATTTTAGATCAACTGGAATGGATGGTACAGCTGTGTGGTGCTTCTGTGGTGAAGGAGCTTTCATCATTCACCCTTGGCACAGTAAGTATTGGGTGCCCT",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-v-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-v-1",
        "variant_count": 305,
        "experiment": "urn:mavedb:00000097-v",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-11-13",
        "modification_date": "2021-11-13",
        "urn": "urn:mavedb:00000091-a-1",
        "publish_date": "2021-11-13",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "To search for possible secondary mutations that that can confer drug resistance in the context of BRAF V600E, the authors performed a deep mutation scan of human BRAF, selecting for enrichment in B3/F cells surviving vemurafenib treatment.",
        "method_text": "Log enrichments for the two replicates were calculated and the median enrichment for each amino acid (across all synonymous codons) are reported here.\r\n\r\nOnly a small subset of variants were reported.",
        "short_description": "Deep mutational scan of the BRAF V600E allele for resistance to the cancer drug vemurafenib.",
        "title": "BRAF resistance to vemurafenib",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24112705",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24112705",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRAF",
            "reference_sequence": {
                "sequence": "HGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDF",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 476,
                "identifier": "P15056",
                "url": "http://purl.uniprot.org/uniprot/P15056",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000091-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000091-a-1",
        "variant_count": 73,
        "experiment": "urn:mavedb:00000091-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-11-11",
        "modification_date": "2020-11-11",
        "urn": "urn:mavedb:00000048-c-1",
        "publish_date": "2020-11-11",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilised site-saturation mutagenesis (SSM) to measure the functional consequences of mutations in the human chemokine receptor, CXCR4 and to map ligand interaction sites. Cells were selected for binding to Ab 12G5.",
        "method_text": "Data obtained from selecting cells for Ab 12G5 binding was analysed using Enrich (version unspecified). Log~2~ enrichment ratios were calculated and normalised by subtracting the frequency of the WT sequence. Log~2~ enrichment ratios for two replicates were averaged to obtain variant scores. Note that the scores here were not reported in the manuscript tables, but were calculated from the replicate enrichment ratios that were reported.",
        "short_description": "Deep mutational scan selecting for CXCR4 binding to Ab 12G5 in Expi293F cells.",
        "title": "CXCR4 Ab 12G5 binding",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29678950",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29678950",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23827138",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23827138",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-6681-7994"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "CXCR4",
            "reference_sequence": {
                "sequence": "GAGGGGATCAGTATATACACTTCAGATAACTACACCGAGGAAATGGGCTCAGGGGACTATGACTCCATGAAGGAACCCTGTTTCCGTGAAGAAAATGCTAATTTCAATAAAATCTTCCTGCCCACCATCTACTCCATCATCTTCTTAACTGGCATTGTGGGCAATGGATTGGTCATCCTGGTCATGGGTTACCAGAAGAAACTGAGAAGCATGACGGACAAGTACAGGCTGCACCTGTCAGTGGCCGACCTCCTCTTTGTCATCACGCTTCCCTTCTGGGCAGTTGATGCCGTGGCAAACTGGTACTTTGGGAACTTCCTATGCAAGGCAGTCCATGTCATCTACACAGTCAACCTCTACAGCAGTGTCCTCATCCTGGCCTTCATCAGTCTGGACCGCTACCTGGCCATCGTCCACGCCACCAACAGTCAGAGGCCAAGGAAGCTGTTGGCTGAAAAGGTGGTCTATGTTGGCGTCTGGATCCCTGCCCTCCTGCTGACTATTCCCGACTTCATCTTTGCCAACGTCAGTGAGGCAGATGACAGATATATCTGTGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATCATGGTTGGCCTTATCCTGCCTGGTATTGTCATCCTGTCCTGCTATTGCATTATCATCTCCAAGCTGTCACACTCCAAGGGCCACCAGAAGCGCAAGGCCCTCAAGACCACAGTCATCCTCATCCTGGCTTTCTTCGCCTGTTGGCTGCCTTACTACATTGGGATCAGCATCGACTCCTTCATCCTCCTGGAAATCATCAAGCAAGGGTGTGAGTTTGAGAACACTGTGCACAAGTGGATTTCCATCACCGAGGCCCTAGCTTTCTTCCACTGTTGTCTGAACCCCATCCTCTATGCTTTCCTTGGAGCCAAATTTAAAACCTCTGCCCAGCACGCACTCACCTCTGTGAGCAGAGGGTCCAGCCTCAAGATCCTCTCCAAAGGAAAGCGAGGTGGACATTCATCTGTTTCCACTGAGTCTGAGTCTTCAAGTTTTCACTCCAGC",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 1,
                "identifier": "P61073",
                "url": "http://purl.uniprot.org/uniprot/P61073",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000048-c-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "rep1",
            "rep2"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000048-c-1",
        "variant_count": 7021,
        "experiment": "urn:mavedb:00000048-c",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-20",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000031-c-1",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {
            "chr": "5",
            "end": 1295247,
            "start": 1294989,
            "reference": "hg38"
        },
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "The effect of each variant was calculated using a multiple linear regression model based on the DNA counts and RNA counts. Each variant needed to have 10 unique barcode tags to be included in the downstream analyses.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>\r\n\r\nMetadata contains the genomic coordinates for the target sequence.\r\n\r\nColumn descriptions:\r\n\r\n- 'score' is the Log2 variant expression effect derived from the fit of the linear model (coefficient).\r\n- 'p-value' is the P-value of the coefficient.\r\n- 'unique_tags' is the number of unique tags associated with the variant.\r\n- 'dna_sequences' is the count of DNA sequences that contain the variant (used for fitting the linear model).\r\n- 'rna_sequences' is the count of RNA sequences that contain the variant (used for fitting the linear model).",
        "short_description": "Saturation mutagenesis MPRA of TERT promoter in glioblastoma SF7996 (GBM) cells, siRNA knockdown of GABPA.",
        "title": "Saturation mutagenesis MPRA of TERT promoter, GBM siRNA knockdown",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TERT promoter",
            "reference_sequence": {
                "sequence": "TCGCGGGGGTGGCCGGGGCCAGGGCTTCCCACGTGCGCAGCAGGACGCAGCGCTGCCTGAAACTCGCGCCGCGAGGAGAGGGCGGGGCCGCGGAAAGGAAGGGGAGGGGCTGGGAGGGCCCGGAGGGGGCTGGGCCGGGGACCCGGGAGGGGTCGGGACGGGGCGGGGTCCGCGCGGAGGAGGCGGAGCTGGAAGGTGAAGGGGCAGGACGGGTGCCCGGGTCCCCAGTCCCTCCGCCACGTGGGAAGCGCGGTCCTGG",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000031-c-1",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "p-value",
            "unique_tags",
            "dna_sequences",
            "rna_sequences"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000031-c-1",
        "variant_count": 974,
        "experiment": "urn:mavedb:00000031-c",
        "is_meta_analysis": false,
        "data_usage_policy": "We are making our data available prior to publication in line with Fort Lauderdale principle, allowing others to use the data but allowing the data producers to make the first presentations and to publish the first paper with global analyses of the data. In addition, we also reserve the right to publish the first analysis of the differences seen in the TERT knock-down experiments and alternative cell-type experiments. Studies that do not overlap with these intentions may be submitted for publication at any time, but must appropriately cite the data source. After publication of the data, the first publication of the data producers should be cited for any use of these data."
    },
    {
        "creation_date": "2020-08-23",
        "modification_date": "2020-12-10",
        "urn": "urn:mavedb:00000051-b-1",
        "publish_date": "2020-12-10",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study mutated the residues on ErbB2 helix region of the bacterial inner membrane. The experiment links the insertion and self-association property of the tested region to the survive of bacteria and studied the membrane-protein energetics landscape of missense mutations of the target.",
        "method_text": "The helix region of ErbB2 is used as the membrane-spanning segment for dsT$\\beta$L in this experiment. The frequency of the count of each mutant relative to wild-type in the selected and reference pools was computed. Variants with <100 counts in the reference population were removed. The selection coefficients were calculated as the ratio of variant relative frequency in the selected and reference pool. The selection coeffcients were then transformed to apparent changes in free energy due to each single-point substitution through the Gibbs free-energy equation: \r\n\r\n$$ \\Delta\\Delta G^{app} = -RT\\ln(s) $$\r\n\r\nwhere R is the gas constant and T is the absolute temperature (310K). The count data table includes the count of each variant in the reference and selected pool.",
        "short_description": "A deep mutational scanning experiment targeting ErbB2 helix region on the bacterial inner membrane.",
        "title": "Helix region of ErbB2",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.7554/eLife.12125",
                "url": "https://doi.org/10.7554/eLife.12125",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "26824389",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/26824389",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "ErbB2",
            "reference_sequence": {
                "sequence": "CTGACGTCTATCATCTCTGCGGTGGTTGGCATTCTGCTGGTCGTGGTCTTGGGCGTGGTCTTTGGCATCCTG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 650,
                "identifier": "P04626",
                "url": "http://purl.uniprot.org/uniprot/P04626",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000051-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "frequency_ref",
            "frequency_sel",
            "ratio"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_reference",
            "count_selected"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000051-b-1",
        "variant_count": 480,
        "experiment": "urn:mavedb:00000051-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-08-07",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000040-a-1",
        "publish_date": "2019-08-07",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effect of variants in yeast HSP90 under different combinations of temperature (30C or 36C) and presence/absence of salt (0.5 M NaCl). The results explore the adaptive potential of this essential gene.",
        "method_text": "Sequencing reads were filtered based on a minimum Phred quality score of 20 across all 36 bases. For each time point, the log2 ratio of each variant's count to the wild type count was calculated. The score of each variant was calculated as the slope of these log ratios to time in wild type generations. Scores of -0.5 are considered null-like.",
        "short_description": "Deep mutational scan of all single mutants in a nine-amino acid region of Hsp90 (Hsp82) in Saccharomyces cerevisiae at 30C without addition of NaCl.",
        "title": "Deep mutational scan of HSP90, 30C no salt",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24299404",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24299404",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "HSP90",
            "reference_sequence": {
                "sequence": "CAATTTGGTTGGTCTGCTAATATGGAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 581,
                "identifier": "P02829",
                "url": "http://purl.uniprot.org/uniprot/P02829",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000040-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000040-a-1",
        "variant_count": 189,
        "experiment": "urn:mavedb:00000040-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-m-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 17, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 17 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 17 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 17",
            "reference_sequence": {
                "sequence": "CATTCTGCAGATGCTGAGTTTGTGTGTGAACGGACACTGAAATATTTTCTAGGAATTGCGGGAGGAAAATGGGTAGTTAGCTATTTCTGTAAGTATAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-m-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-m-1",
        "variant_count": 287,
        "experiment": "urn:mavedb:00000097-m",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2018-06-29",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-b-1",
        "publish_date": "2018-06-29",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957)",
        "method_text": "##Scoring procedure:\r\nDMS-TileSeq reads were processed using the [dmsPipeline](https://bitbucket.org/rothlabto/dmspipeline) software. Briefly, TileSeq read counts were used to establish relative allele frequencies in each condition. Non-mutagenized control counts were subtracted from counts (as estimates of sequencing error). log ratios of selection over non-selection counts were calculated. The resulting TileSeq fitness values were then normalized to 0-1 scale where 0 corresponds to the median nonsense score and 1 corresponds to the median synonymous score. Random-Forest-based machine learning was used to impute missing values and refine low-confidence measurements, based on intrinsic, structural, and biochemical features.\r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for more details.\r\n\r\n## Additional columns:\r\n* exp.score = experimental score from the joint DMS-BarSeq/DMS-TileSeq screens\r\n* exp.sd = standard deviation of the experimental score\r\n* df = degrees of freedom (number of replicates contributing to the experimental score)\r\n* pred.score = machine-learning predicted score",
        "short_description": "A machine-learning imputed and refined Deep Mutational Scan of the human SUMO1 using functional complementation in yeast.",
        "title": "SUMO1 imputed and refined",
        "keywords": [
            {
                "text": "sumoylation"
            },
            {
                "text": "imputation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29269382",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29269382",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "SUMO1",
            "reference_sequence": {
                "sequence": "ATGTCTGACCAGGAGGCAAAACCTTCAACTGAGGACTTGGGGGATAAGAAGGAAGGTGAATATATTAAACTCAAAGTCATTGGACAGGATAGCAGTGAGATTCACTTCAAAGTGAAAATGACAACACATCTCAAGAAACTCAAAGAATCATACTGTCAAAGACAGGGTGTTCCAATGAATTCACTCAGGTTTCTCTTTGAGGGTCAGAGAATTGCTGATAATCATACTCCAAAAGAACTGGGAATGGAGGAAGAAGATGTGATTGAAGTTTATCAGGAACAAACGGGGGGTCATTCAACAGTTTAG",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P63165",
                "url": "http://purl.uniprot.org/uniprot/P63165",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000116030",
                "url": "http://www.ensembl.org/id/ENSG00000116030",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 149,
                "identifier": "NM_001005781.1",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_001005781.1",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000001-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "se",
            "exp.score",
            "exp.sd",
            "df",
            "pred.score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000001-b-1",
        "variant_count": 2020,
        "experiment": "urn:mavedb:00000001-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-08-23",
        "modification_date": "2022-08-23",
        "urn": "urn:mavedb:00000100-a-1",
        "publish_date": "2022-08-23",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study characterized the effect of single-codon insertion and deletion events on the function of TEM-1 beta-lactamase in the presence of varying concentrations of ampicillin.",
        "method_text": "Reads were analyzed using custom MATLAB scripts. MiSeq  paired-end reads were trimmed and merged. Reads were aligned to TEM-1 using Smith-Waterman with gap open penalty of 1 and gap extension penalty of 0.1. Reads with an alignment score below 100 and reads containing multiple insertions or deletions were removed from the analysis. Synonymous codons were grouped by summing the counts for each nucleotide variant. Variants with fewer than 20 counts were excluded. Fitness values were calculated by calculating a midpoint ampicillin concentration for resistance, and then normalized to the wild-type value.",
        "short_description": "Effect of single-codon insertions on TEM-1 fitness",
        "title": "TEM-1 single-codon insertions",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "31034887",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31034887",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "TEM-1 β-lactamase",
            "reference_sequence": {
                "sequence": "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P62593",
                "url": "http://purl.uniprot.org/uniprot/P62593",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000100-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "error",
            "ambler"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "c_0.25",
            "c_0.5",
            "c_1",
            "c_2",
            "c_4",
            "c_8",
            "c_16",
            "c_32",
            "c_64",
            "c_128",
            "c_256",
            "c_512",
            "c_1024",
            "ambler"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000100-a-1",
        "variant_count": 4780,
        "experiment": "urn:mavedb:00000100-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-06-19",
        "modification_date": "2020-06-19",
        "urn": "urn:mavedb:00000044-a-1",
        "publish_date": "2020-06-19",
        "created_by": "0000-0001-6713-6904",
        "modified_by": "0000-0001-6713-6904",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "Full methods provided in the [preprint](https://www.biorxiv.org/content/10.1101/2020.06.17.157982v1) and full analysis provided in the [GitHub repo](https://github.com/jbloomlab/SARS-CoV-2-RBD_DMS).\r\n\r\n`score` column is the change in log<sub>10</sub>(_K_<sub>D,app</sub>) relative to the average wildtype binding, polarized such that a positive score indicates improved binding, and negative indicates reduced binding affinity. The `library` column indicates which of our two duplicate mutant libraries a measurement is from. The `average` column is the average mutation effect from the duplicate libraries. The values in the `average` column were used in the paper analysis.",
        "short_description": "RBD mutation and binding score for each amino acid mutation",
        "title": "per-single-mutant binding score",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-6713-6904",
            "0000-0001-9278-3644",
            "0000-0003-1267-3408"
        ],
        "licence": {
            "long_name": "Other - See Data Usage Guidelines",
            "short_name": "Other - See Data Usage Guidelines",
            "link": "",
            "version": "1.0"
        },
        "target": {
            "name": "SARS-CoV-2 receptor binding domain",
            "reference_sequence": {
                "sequence": "AATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACT",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000044-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "average",
            "library"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000044-a-1",
        "variant_count": 8040,
        "experiment": "urn:mavedb:00000044-a",
        "is_meta_analysis": false,
        "data_usage_policy": "See licence from GitHub: https://github.com/jbloomlab/SARS-CoV-2-RBD_DMS/blob/master/LICENSE.md\r\n\r\nBSD 3-Clause License\r\n\r\nCopyright (c) 2020, Tyler N. Starr, Allison J. Greaney, and Jesse D. Bloom\r\nAll rights reserved.\r\n\r\nRedistribution and use in source and binary forms, with or without\r\nmodification, are permitted provided that the following conditions are met:\r\n\r\n1. Redistributions of source code must retain the above copyright notice, this\r\n   list of conditions and the following disclaimer.\r\n\r\n2. Redistributions in binary form must reproduce the above copyright notice,\r\n   this list of conditions and the following disclaimer in the documentation\r\n   and/or other materials provided with the distribution.\r\n\r\n3. Neither the name of the copyright holder nor the names of its\r\n   contributors may be used to endorse or promote products derived from\r\n   this software without specific prior written permission."
    },
    {
        "creation_date": "2021-09-29",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-e-1",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "Each of the seven libraries was sequenced individually and analyzed separately using in-house Python scripts archived at https://github.com/elifesciences-publications/DMS-FastQ-processing.\r\n\r\nReads that had more than 20 base mismatches between forward and reverse reads were discarded. Merged reads with a posterior Q score of 10 were also discarded. Variants with an unexpectedly high error rate or mutations in more than one codon were also discarded.\r\n\r\nFitness scores were calculated as a ratio of frequency ratios:\r\n\r\n$$s_v = \\log_2\\left(\\frac{\\frac{f_{v, selected}}{f_{v, non-selected}}}{\\frac{f_{wt, selected}}{f_{wt, non-selected}}}\\right)$$\r\n\r\nThe mean fitness score of all synonymous variants in each library was subtracted from all variants in that library to normalize the scores between libraries.\r\n\r\nThe scores are the average of two replicates if the variant was scored in both replicates, otherwise the score given is the score from one replicate. Variants that were scored in both replicates have a standard deviation (SD) calculated from the two replicate scores.",
        "short_description": "Amino acid scores for deep mutational scan of VIM-2 metallo-β-lactamase at 2 µg/mL ampicillin at 25C",
        "title": "VIM-2 2 µg/mL AMP at 25C",
        "keywords": [
            {
                "text": "ampicillin"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "VIM-2 with p.Met1_Phe2insGly",
            "reference_sequence": {
                "sequence": "ATGGGATTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGCCCGCTCGCTTTTTCCGTAGATTCTAGCGGAGAATATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTTGAAGGACTTTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAATTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTTGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000073-e-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "SD"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000073-e-1",
        "variant_count": 5549,
        "experiment": "urn:mavedb:00000073-e",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-08-25",
        "modification_date": "2022-08-26",
        "urn": "urn:mavedb:00000103-a-1",
        "publish_date": "2022-08-26",
        "created_by": "0000-0001-6624-4698",
        "modified_by": "0000-0001-6624-4698",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "Average mutant sequencing reads for all replicates of the reference early time point (ETP)",
        "title": "MAP1K ETP",
        "keywords": [
            {
                "text": "resistance"
            },
            {
                "text": "complementation"
            },
            {
                "text": "MAPK1"
            },
            {
                "text": "ERK2"
            },
            {
                "text": "MITE"
            },
            {
                "text": "VRT-11E"
            },
            {
                "text": "SCH772984"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1016/j.celrep.2016.09.061",
                "url": "http://doi.org/10.1016/j.celrep.2016.09.061",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "27760319",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27760319",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0001-6624-4698"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MAPK1",
            "reference_sequence": {
                "sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000103-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "ETP_SD",
            "ETP_REP_A",
            "ETP_REP_B",
            "ETP_REP_C",
            "ETP_REP_D"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000103-a-1",
        "variant_count": 6810,
        "experiment": "urn:mavedb:00000103-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-f-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 4, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 4 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 4 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 4",
            "reference_sequence": {
                "sequence": "TATAATTTATAGATTTTGCATGCTGAAACTTCTCAACCAGAAGAAAGGGCCTTCACAGTGTCCTTTATGTAAGAATGATATAACCAAAAGGTATATAATT",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-f-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-f-1",
        "variant_count": 293,
        "experiment": "urn:mavedb:00000097-f",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-01-24",
        "modification_date": "2019-07-26",
        "urn": "urn:mavedb:00000008-a-1",
        "publish_date": "2019-01-24",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {
            "chr": "7",
            "end": 29161744,
            "start": 29161443,
            "reference": "mm9"
        },
        "abstract_text": "This study described the functional consequence of over 100,000 enhancer variants *in vivo* in mouse liver. Two human enhancers (ALDOB, ECR11) and one mouse enhancer (LTV1) were known to be active in mouse liver and therefore variants in these enhancers should show a measurable difference in transcription. The results were broadly consistent with evolutionary data and transcription factor binding sites, but were not always concordant demonstrating the importance of measuring the effect of enhancer variants directly.\r\n\r\nThis MaveDB entry describes the LTV1 enhancer data. Datasets for other enhancers described in the same publication are also available: [ALDOB](https://www.mavedb.org/experiment/urn:mavedb:00000006-a/) [ECR11](https://www.mavedb.org/experiment/urn:mavedb:00000007-a/)",
        "method_text": "Scores were calculated using a trivariate linear regression model. A separate model was built for each position in the enhancer, with a predictor for each possible variant nucleotide at that position.\r\n\r\nBecause most enhancer haplotypes in the LTV1 dataset had multiple tags, the data were normalized by dividing the total number of counts for a given haplotype by the number of tags for that haplotype.\r\n\r\nThe scores presented are therefore a combination of the effects of each individual variant on diverse enhancer haplotype backgrounds.\r\n\r\nSee metadata (available via download button) for wild type genomic coordinates in JSON format.",
        "short_description": "Trivariate regression scores for each nucleotide change as described in Patwardhan et al. 2012.",
        "title": "Trivariate regression scores for LTV1 replicate 1 of 2",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "doped oligo synthesis"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "liver"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "22371081",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/22371081",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "LTV1 enhancer",
            "reference_sequence": {
                "sequence": "CTTTGGGTGACCCCTGACCCTGGCCGCCTGGGCTCGCCTTCCCGCACATTCCGTCCTCGCCGCCCCGCCCCACCCCGCCCTCCTTCCTTGGCCCTGTGGGGACGGAAACATCCCGTTCCTGCCCAAGCTGGGTCAAGAGCCGGAGGGACAGGACCAGAGCACCCCTTACGCCAGAACTAGCTCTCCTTGTTCCTACTGGGTGACCTCATCTCGCCACGCCTCCTCAGGTGAACACCCGGGCTGGTAACGTCACTTCCTGCCAGGTAAGCGCCCCCAGGCAGCACTGCTCACGGAAAGGTCTG",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "mm9",
                        "organism_name": "Mus musculus",
                        "assembly_identifier": {
                            "identifier": "GCF_000001635.18",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.18",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000008-a-1",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "pvalue"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000008-a-1",
        "variant_count": 906,
        "experiment": "urn:mavedb:00000008-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-01-17",
        "urn": "urn:mavedb:00000057-b-1",
        "publish_date": "2021-01-17",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors used saturation mutagenesis to study the variant effect of Ras, with the regulation of GTPase activating protein (GAP) but in the absence of guanine nucleotide exchange factor (GEF). The variants were selected by bacterial two-hybrid strategy.",
        "method_text": "The frequency of each mutant was determined through sequencing. The natural logarithm of the frequency ratio for each mutant after and before selection was calculated. These values were then normalized by dividing the wild type values which were calculated the same way.",
        "short_description": "Selection result of Ras mutants expressed in the presence of the GAP, but without the GEF",
        "title": "Attenuated-Ras",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "28686159",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28686159",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Ras",
            "reference_sequence": {
                "sequence": "ACGGAATATAAGCTGGTGGTGGTGGGCGCCGGCGGTGTGGGCAAGAGTGCGCTGACCATCCAGCTGATCCAGAACCATTTTGTGGACGAATACGACCCCACTATAGAGGATTCCTACCGGAAGCAGGTGGTCATTGATGGGGAGACGTGCCTGTTGGACATCCTGGATACCGCCGGCCAGGAGGAGTACAGCGCCATGCGGGACCAGTACATGCGCACCGGGGAGGGCTTCCTGTGTGTGTTTGCCATCAACAACACCAAGTCTTTTGAGGACATCCACCAGTACAGGGAGCAGATCAAACGGGTGAAGGACTCGGATGACGTGCCCATGGTGCTGGTGGGGAACAAGTGTGACCTGGCTGCACGCACTGTGGAATCTCGGCAGGCTCAGGACCTCGCCCGAAGCTACGGCATCCCCTACATCGAGACCTCGGCCAAGACCCGGCAGGGAGTGGAGGATGCCTTCTACACGTTGGTGCGTGAGATCCGGCAGCAC",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 1,
                "identifier": "P01112",
                "url": "http://purl.uniprot.org/uniprot/P01112",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000057-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000057-b-1",
        "variant_count": 3300,
        "experiment": "urn:mavedb:00000057-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-02",
        "modification_date": "2021-10-02",
        "urn": "urn:mavedb:00000079-a-1",
        "publish_date": "2021-10-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the variant effects of pyrrolidine ketide synthase (PyKS) whose wildtype has low protein stability. The PyKS single mutation library is generated with the fluorescent protein GFP fused and selected by FACS. Mutants with high protein stability will have higher fluorescence intensity.",
        "method_text": "Sequencing data was processed using Enrich and custom scripts. The solubility score $\\zeta_i$ for FACS data is described in Kowalsky et al. 2015 and as follows. $\\epsilon_i$ is the enrichment ratio of variant $i$, $\\epsilon_{wt}$ is the wild-type enrichment ratio, $\\sigma$ is the standard deviation of the population and $\\phi$ is the percentage of cells collected in the gating population.\r\n\r\n$$\\zeta_i = \\log_2 (e) \\sqrt{2} \\sigma^{\\prime} [erf ^{-1} (1 - \\phi 2^{(\\epsilon_{wt} + 1)} - erf ^{-1} (1 - \\phi 2^{(\\epsilon_{i} + 1)}]$$\r\n\r\nThe solubility score is listed as the score, and the raw $\\log_2$ ratios are also included.\r\n\r\nNote that the wild-type counts and ratios were not reported by the authors and that the tile containing positions 157-234 was also not included in the supplemental data.",
        "short_description": "Selecting on pyrrolidine ketide synthase (PyKS) with higher protein stability by GFP fusing.",
        "title": "Stability selection of PyKS",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25790064",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25790064",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "30721031",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30721031",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "PyKS",
            "reference_sequence": {
                "sequence": "KFGRVHERAEGPAKILAIGTATPFHWVDQSSYPDYYFRVTNSDHLVDLKEKFRRICNRTMISKRHMFLTEEILQKNPNLCSHNEPSFDVRQDILVSEIPKLGKEAVLMAIDEWAQPKSKITHLVFCTRSGVDMPGADYQLIKLLGLSPSVQRVMMYQQGCFAGGTMLRLAKDLAENNKGARVLVVCAESSAIGFRGPSEDHPDNLIAQALFGDGAAALIIGSDPKMGLERPIFEIVTTAQTFVPNGDCHLALHLREMGLTFHCTKDVPPTIAKNVESCLIKAFEPLGISDWNSIFWILHPGGNAIVDQVESTLGLEPNKLQATRNILREYGNLSSACVLFILDEIRKKSGREGLKTSGDGLDLGVLLSFGPGLTIETVVLR",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 7,
                "identifier": "A0A3G4RHW3_ATRBE",
                "url": "http://purl.uniprot.org/uniprot/A0A3G4RHW3_ATRBE",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000079-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "log2_ratio"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000079-a-1",
        "variant_count": 5746,
        "experiment": "urn:mavedb:00000079-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-03-14",
        "modification_date": "2021-04-15",
        "urn": "urn:mavedb:00000063-b-1",
        "publish_date": "2021-04-15",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the variant effects of <i>E.coli</i> dihydrofolate reductase (DHFR) whose function is necessary for the survival of the bacteria. The study cultured the bacteria in an early Log phase growth period without the control of Lon protease and determined the variant frequency change after cultivation, indicating the impact of DHFR variants.",
        "method_text": "This variant library consists of four sub-libraries which cover different positions in the target protein (40 residues each). Each mutant library is generated by parallel inverse PCR reactions. The libraries are transformed to E.coli with deficient Lon gene by electroporation, and the selection experiments take 2 libraries at a time. Samples after 0, 2, 4, 6, 8, 12, 16 and 18 hours of cultivation are collected and sequenced by Illumina NextSeq. <br>\r\nThe results with less than four timepoints reported and larger standard error from regression are discarded. The rest are analyzed by Enrich2 and normalized. Each sub-library is tested three times and the final scores are the average of them. The results are discarded when there are less than two replicates available or the standard deviation is larger than the threshold.<br>\r\nThe count data records the counts result from transformation rescue medium, overnight outgrowth and each timepoint outgrowth. Each library is tested three times and two of the four libraries are tested at the same time which gives the six repeats in the count data.",
        "short_description": "Growth rate of E.coli with mutated dihydrofolate reductase (DHFR) with deficient Lon protease",
        "title": "Growth rate of mutated DHFR with deficient Lon",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.7554/eLife.53476",
                "url": "https://doi.org/10.7554/eLife.53476",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32701056",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32701056",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "DHFR",
            "reference_sequence": {
                "sequence": "ATGATCAGTCTGATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCCGTGGAACCTGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATGGGCCGCCATACCTGGGAATCAATCGGTCGTCCGTTGCCAGGACGCAAAAATATTATCCTCAGCAGTCAACCGGGTACGGACGATCGCGTAACGTGGGTGAAGTCGGTGGATGAAGCCATCGCGGCGTGTGGTGACGTACCAGAAATCATGGTGATTGGCGGCGGTCGCGTTTATGAACAGTTCTTGCCAAAAGCGCAAAAACTGTATCTGACGCATATCGACGCAGAAGTGGAAGGCGACACCCATTTCCCGGATTACGAGCCGGATGACTGGGAATCGGTATTCAGCGAATTCCACGATGCTGATGCGCAGAACTCTCACAGCTATTGCTTTGAGATTCTGGAGCGGCGGTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P0ABQ4",
                "url": "http://purl.uniprot.org/uniprot/P0ABQ4",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000063-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "standard deviation",
            "standard error"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "Repeat1_library_transformation",
            "Repeat1_outgrowth",
            "Repeat1_t_00hrs",
            "Repeat1_t_02hrs",
            "Repeat1_t_04hrs",
            "Repeat1_t_06hrs",
            "Repeat1_t_08hrs",
            "Repeat1_t_12hrs",
            "Repeat1_t_16hrs",
            "Repeat1_t_18hrs",
            "Repeat2_library_transformation",
            "Repeat2_outgrowth",
            "Repeat2_t_00hrs",
            "Repeat2_t_02hrs",
            "Repeat2_t_04hrs",
            "Repeat2_t_06hrs",
            "Repeat2_t_08hrs",
            "Repeat2_t_12hrs",
            "Repeat2_t_16hrs",
            "Repeat2_t_18hrs",
            "Repeat3_library_transformation",
            "Repeat3_outgrowth",
            "Repeat3_t_00hrs",
            "Repeat3_t_02hrs",
            "Repeat3_t_04hrs",
            "Repeat3_t_06hrs",
            "Repeat3_t_08hrs",
            "Repeat3_t_12hrs",
            "Repeat3_t_16hrs",
            "Repeat3_t_18hrs",
            "Repeat4_library_transformation",
            "Repeat4_outgrowth",
            "Repeat4_t_00hrs",
            "Repeat4_t_02hrs",
            "Repeat4_t_04hrs",
            "Repeat4_t_06hrs",
            "Repeat4_t_08hrs",
            "Repeat4_t_12hrs",
            "Repeat4_t_16hrs",
            "Repeat4_t_18hrs",
            "Repeat5_library_transformation",
            "Repeat5_outgrowth",
            "Repeat5_t_00hrs",
            "Repeat5_t_02hrs",
            "Repeat5_t_04hrs",
            "Repeat5_t_06hrs",
            "Repeat5_t_08hrs",
            "Repeat5_t_12hrs",
            "Repeat5_t_16hrs",
            "Repeat5_t_18hrs",
            "Repeat6_library_transformation",
            "Repeat6_outgrowth",
            "Repeat6_t_00hrs",
            "Repeat6_t_02hrs",
            "Repeat6_t_04hrs",
            "Repeat6_t_06hrs",
            "Repeat6_t_08hrs",
            "Repeat6_t_12hrs",
            "Repeat6_t_16hrs",
            "Repeat6_t_18hrs"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000063-b-1",
        "variant_count": 3171,
        "experiment": "urn:mavedb:00000063-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-a-1",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes the sequence present at wild-type Wilms’ tumor gene 1 exon 5.",
        "method_text": "Reads were filtered by accepting only those that had an unmutated 6nt stretch at the end of the read and had no mutations other than those that were designed. FASTQ quality scores were not used.\r\n\r\nThe sum of the reads in each of the two replicate transfections was used to calculate the scores, defined as the ratio of RNA read count to DNA read count (called the Enrichment Index, or EI).\r\n\r\nThe score reported here is the “LEIsc”, which is $log_2 EI$ re-scaled from -1 to +1 with the target sequence at 0, which enables easier comparison between the different 6-mers tested in the study.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, Wilms’ tumor gene 1 exon 5.",
        "title": "Exonic splicing for Wilms’ tumor gene",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Minigene exon - Wilms’ tumor gene",
            "reference_sequence": {
                "sequence": "AGTTGCTGCTGGGAGCTCCAGCACAGTGAAATGGACAGAAGGGCAGAGCAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000083-a-1",
            "type": "Other noncoding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "EI"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000083-a-1",
        "variant_count": 556,
        "experiment": "urn:mavedb:00000083-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-s-1",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 20, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Illumina bcl2fastq v2.16 was used to call bases and demultiplex samples. Sample quality was assessed using fastqc v0.11.3. SeqPrep was used to trim adapters and merge overlapping read pairs. Reads containing “N” bases wer eremoved. Reads were aligned to the BRCA1 gDNA using Needleman-Wunsch in EMBOSS v6.4.0. Reads were counted if an HDR marker edit was observed. All counts received a pseudocount of 1.\r\n\r\nThe `score_raw` is the log2-transformed ratio of frequencies of the variant at day 11 over the input. The `score_day5` is the log2-transformed ratio of frequencies of the variant at day 5 over the input. The day 5 scores were used to perform a LOESS regression to normalize based on genomic position. This model was fit on the day 5 data and the model’s output was subtracted from the day 11 log ratios, producing the `score` here. The `score_rna` is the day 5 cDNA frequency over the gDNA frequency.",
        "short_description": "BRCA1 SGE exon 20 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 20 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "BRCA1 Exon 20",
            "reference_sequence": {
                "sequence": "CTCTCTTCCTCTCTTCTTCCAGATCTTCAGGGGGCTAGAAATCTGTTGCTATGGGCCCTTCACCAACATGCCCACAGGTAAGAGCCTGGGAGAACCCCAG",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000097-s-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_raw",
            "score_day5",
            "score_rna"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "count_negative_control",
            "count_library",
            "count_day5",
            "count_day11",
            "count_rna"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000097-s-1",
        "variant_count": 287,
        "experiment": "urn:mavedb:00000097-s",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000024-a-1",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {
            "chr": "10",
            "end": 46046834,
            "start": 46046244,
            "reference": "hg38"
        },
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "The effect of each variant was calculated using a multiple linear regression model based on the DNA counts and RNA counts. Each variant needed to have 10 unique barcode tags to be included in the downstream analyses.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>\r\n\r\nMetadata contains the genomic coordinates for the target sequence.\r\n\r\nColumn descriptions:\r\n\r\n- 'score' is the Log2 variant expression effect derived from the fit of the linear model (coefficient).\r\n- 'p-value' is the P-value of the coefficient.\r\n- 'unique_tags' is the number of unique tags associated with the variant.\r\n- 'dna_sequences' is the count of DNA sequences that contain the variant (used for fitting the linear model).\r\n- 'rna_sequences' is the count of RNA sequences that contain the variant (used for fitting the linear model).",
        "short_description": "Saturation mutagenesis MPRA of MSMB promoter in HEK293T cells.",
        "title": "Saturation mutagenesis MPRA of MSMB promoter",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MSMB promoter",
            "reference_sequence": {
                "sequence": "AAGCAGGACTCCTTATAGACAGGTACATCCAGGCAAAGCTGCATCAAACTTTTATACTGGAGAGGGCAACCACGCATTCGACATCATTGGGAATGATAACAAGGTGAGAACACATTGAGTGTTTACAGAGGGTTGACTATCAAAAGGAAAGTATGGTTTCAGATGATTTATGAGTTATTAATCAATCACATCTCCACCCAAGTTATGTGTTTACCTTGTCCCCACCCCGATCTGCATTTGCTGCTGACCTAAAAGAGCAGAGGAGGAGAGAACTTCTCTTTGCTGAGCCTTCGCCCTATGCTGGTGGATTGCTAGCACGTGATGTGTCCTTATTCGATTTTATACACAAAGAAACAGCCTCAGCGATGCCAGTCACAACAGCCAGGTGGTAAAGGTGGGTTTCCTGAAGGCATAAGAATAGCCCACAGGTCAGCCCACCAGGCCCACCGGGCCTGGGTCTGTGGCCCAGATGACCCTGCCCTTAGGGTCTGACATGAGAACAGAAATGGGTCAAGCCATCCTGCAGGGCACAGGAGAGCAAGAACTACATACAGCTCGGGGTTCCCTGACAAGCTGAATTGCTGGACCTTT",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000024-a-1",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "p-value",
            "unique_tags",
            "dna_sequences",
            "rna_sequences"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000024-a-1",
        "variant_count": 2019,
        "experiment": "urn:mavedb:00000024-a",
        "is_meta_analysis": false,
        "data_usage_policy": "We are making our data available prior to publication in line with Fort Lauderdale principle, allowing others to use the data but allowing the data producers to make the first presentations and to publish the first paper with global analyses of the data. In addition, we also reserve the right to publish the first analysis of the differences seen in the TERT knock-down experiments and alternative cell-type experiments. Studies that do not overlap with these intentions may be submitted for publication at any time, but must appropriately cite the data source. After publication of the data, the first publication of the data producers should be cited for any use of these data."
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000076-e-1",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilized site directed mutagenesis to generate variants in the  carboxyl-terminal tail anchor (TA) on the Fis1p protein within yeast. All possible codons at 27 amino acid positions were assayed for their ability to target the mitochondrial membrane.",
        "method_text": "FASTQ paired end data were stripped of adapters and combined using PANDAseq assembler. Sequences not encoding the Fis1p tail anchor were removed.\r\n\r\nScores were calculated by taking the $\\log_2$ ratio of the variant count in the experimental condition to the variant count in the SC -Trp condition. If the variant count in the SC -Trp condition was 0, it was set to 1 to avoid a divide-by-zero error.",
        "short_description": "Amino acid scores for deep mutational scan of the yeast Fis1 tail anchor, SC -Ura medium.",
        "title": "Fis1 tail anchor, SC -Ura",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.5061/dryad.j14r5",
                "url": "http://doi.org/10.5061/dryad.j14r5",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "28007883",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28007883",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Fis1 tail anchor",
            "reference_sequence": {
                "sequence": "LKGVVVAGGVLAGAVAVASFFLRNKRR",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 128,
                "identifier": "P40515",
                "url": "http://purl.uniprot.org/uniprot/P40515",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000076-e-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000076-e-1",
        "variant_count": 525,
        "experiment": "urn:mavedb:00000076-e",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-06-19",
        "modification_date": "2020-06-19",
        "urn": "urn:mavedb:00000044-b-1",
        "publish_date": "2020-06-19",
        "created_by": "0000-0001-6713-6904",
        "modified_by": "0000-0001-6713-6904",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "Full methods provided in the [preprint](https://www.biorxiv.org/content/10.1101/2020.06.17.157982v1) and full analysis provided in the [GitHub repo](https://github.com/jbloomlab/SARS-CoV-2-RBD_DMS).\r\n\r\n`score` column is the change in log(MFI) relative to the average wildtype expression, polarized such that a positive score indicates improved expression and negative indicates reduced expression. The `library` column indicates which of our two duplicate mutant libraries a measurement is from.",
        "short_description": "RBD genotype and expression score for each unique barcoded variant in the mutant library",
        "title": "per-barcode expression score",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-6713-6904",
            "0000-0001-9278-3644",
            "0000-0003-1267-3408"
        ],
        "licence": {
            "long_name": "Other - See Data Usage Guidelines",
            "short_name": "Other - See Data Usage Guidelines",
            "link": "",
            "version": "1.0"
        },
        "target": {
            "name": "SARS-CoV-2 receptor binding domain",
            "reference_sequence": {
                "sequence": "AATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACT",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000044-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "count",
            "library"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000044-b-1",
        "variant_count": 195081,
        "experiment": "urn:mavedb:00000044-b",
        "is_meta_analysis": false,
        "data_usage_policy": "See licence from GitHub: https://github.com/jbloomlab/SARS-CoV-2-RBD_DMS/blob/master/LICENSE.md\r\n\r\nBSD 3-Clause License\r\n\r\nCopyright (c) 2020, Tyler N. Starr, Allison J. Greaney, and Jesse D. Bloom\r\nAll rights reserved.\r\n\r\nRedistribution and use in source and binary forms, with or without\r\nmodification, are permitted provided that the following conditions are met:\r\n\r\n1. Redistributions of source code must retain the above copyright notice, this\r\n   list of conditions and the following disclaimer.\r\n\r\n2. Redistributions in binary form must reproduce the above copyright notice,\r\n   this list of conditions and the following disclaimer in the documentation\r\n   and/or other materials provided with the distribution.\r\n\r\n3. Neither the name of the copyright holder nor the names of its\r\n   contributors may be used to endorse or promote products derived from\r\n   this software without specific prior written permission."
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-f-1",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\n\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Spermidine",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "alpha-synuclein",
            "reference_sequence": {
                "sequence": "ATGGATGTATTCATGAAAGGACTTTCAAAGGCCAAGGAGGGAGTTGTGGCTGCTGCTGAGAAAACCAAACAGGGTGTGGCAGAAGCAGCAGGAAAGACAAAAGAGGGTGTTCTCTATGTAGGCTCCAAAACCAAGGAGGGAGTGGTGCATGGTGTGGCAACAGTGGCTGAGAAGACCAAAGAGCAAGTGACAAATGTTGGAGGAGCAGTGGTGACGGGTGTGACAGCAGTAGCCCAGAAGACAGTGGAGGGAGCAGGGAGCATTGCAGCAGCCACTGGCTTTGTCAAAAAGGACCAGTTGGGCAAGAATGAAGAAGGAGCCCCACAGGAAGGAATTCTGGAAGATATGCCTGTGGATCCTGACAATGAGGCTTATGAAATGCCTTCTGAGGAAGGGTATCAAGACTACGAACCTGAAGCCTAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P37840",
                "url": "http://purl.uniprot.org/uniprot/P37840",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg16",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.10",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000045-f-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000045-f-1",
        "variant_count": 2800,
        "experiment": "urn:mavedb:00000045-f",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-09-25",
        "modification_date": "2021-09-25",
        "urn": "urn:mavedb:00000072-a-1",
        "publish_date": "2021-09-25",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "A deep mutational scan of the CH3 domain of human IgG1 was performed to measure the effect of mutants on stability. Stability selected for by a proxy, binding to either CD64 or an antibody against human CH2 domain. This was performed at 79C under the premise that less stable mutants would be denatured at that temperature and therefore unable to bind.",
        "method_text": "Reads sequenced in the experiments for binding to CD64 or CH2 were pooled for analysis.\r\n\r\nReads with a quality score <20 were removed from the dataset. Remaining high-quality reads were filtered such that only those that spanned the entire CH2 or CH3 domain were retained. Reads that did not match the expected length after trimming the ends or that contained frameshifts were also removed.\r\n\r\nThe quality-filtered sequences were compared to the target sequence and the scores for each position were calculated independently as a “change in mutation rate” (or ratio of ratios) where the mutation rate at position $x$ to residue $y$ is calculated as:\r\n$$r_{x,y} = \\frac{n_{x,y}}{n_{total}}$$\r\nThe scores were reported as the “change in mutation rate” $c_{x,y}$ calculated as:\r\n$$c_{x,y} = \\frac{r_{x,y,selected}}{r_{x,y,input}}$$",
        "short_description": "Deep mutational scan of human IgG1 (CH3 domain) binding by CD64 and anti-human CH2, under 79C heat stress as a proxy for stability.",
        "title": "Human IgG1 Fc stability",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "22846908",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/22846908",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-8037-6045"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "IGHG1",
            "reference_sequence": {
                "sequence": "GQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPG",
                "sequence_type": "protein"
            },
            "uniprot": {
                "offset": 223,
                "identifier": "P01857",
                "url": "http://purl.uniprot.org/uniprot/P01857",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000072-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000072-a-1",
        "variant_count": 698,
        "experiment": "urn:mavedb:00000072-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-02",
        "modification_date": "2021-10-02",
        "urn": "urn:mavedb:00000080-a-2",
        "publish_date": "2021-10-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured fluorescence levels of mutants of the Aequorea victoria GFP (avGFP) using error-prone PCR, FACS, and a probability model developed using the observed fluorescence levels. Epistasis of mutations was also discussed, using a model of sequence divergence.",
        "method_text": "Genotypes containing insertions, deletions, or stop codons were excluded from analysis. The final dataset consisted of 56,086 unique nucleotide genotypes and 51,715 unique amino acid genotypes.\r\n\r\nBarcode distributions were fit to Gaussian distributions using actual values of logarithms of sorting gates boundaries and used the observed fluorescence signal to calculate a probability of a given mutation being neutral.\r\n\r\nThe median brightness of all unique barcodes for a variant is reported as the score.",
        "short_description": "Deep mutational scan evaluating the effect of mutations on fluorescence of Aequorea victoria GFP, amino acid variants.",
        "title": "GFP mutations and fluorescence levels, amino acid variants",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.6084/m9.figshare.3102154",
                "url": "http://doi.org/10.6084/m9.figshare.3102154",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "27193686",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27193686",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2072-3436"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "avGFP",
            "reference_sequence": {
                "sequence": "AGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGTCATACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACACTAGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCACGGCATGGACGAGCTGTACAAGTGA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "Other",
                        "organism_name": "Other - genome not listed",
                        "assembly_identifier": null
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000080-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "std",
            "uniqueBarcodes"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000080-a-2",
        "variant_count": 54025,
        "experiment": "urn:mavedb:00000080-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-06-08",
        "modification_date": "2022-06-08",
        "urn": "urn:mavedb:00000095-b-1",
        "publish_date": "2022-06-08",
        "created_by": "0000-0002-0730-2576",
        "modified_by": "0000-0002-0730-2576",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "This study measured the functional consequences of mutations in CYP2C9, as measured by two different assays, one using Variant Abundance by Massively Parallel sequencing (VAMP-seq) in HEK293T cells, and one using a yeast activity-based protein profiling assay (Click-seq). This entry contains amino acid scores from the abundance assay using VAMP-seq in HEK293T cells.",
        "title": "CYP2C9 abundance scores as measured by VAMP-seq",
        "keywords": [
            {
                "text": "NNK mutagenesis"
            },
            {
                "text": "FACS"
            },
            {
                "text": "VAMP-seq"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "34314704",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/34314704",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "29785012",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29785012",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0002-0730-2576"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "CYP2C9",
            "reference_sequence": {
                "sequence": "ATGGATTCTCTTGTGGTCCTTGTGCTCTGTCTCTCATGTTTGCTTCTCCTTTCACTCTGGAGACAGAGCTCTGGGAGAGGAAAACTCCCTCCTGGCCCCACTCCTCTCCCAGTGATTGGAAATATCCTACAGATAGGTATTAAGGACATCAGCAAATCCTTAACCAATCTCTCAAAGGTCTATGGCCCTGTGTTCACTCTGTATTTTGGCCTGAAACCCATAGTGGTGCTGCATGGATATGAAGCAGTGAAGGAAGCCCTGATTGATCTTGGAGAGGAGTTTTCTGGAAGAGGCATTTTCCCACTGGCTGAAAGAGCTAACAGAGGATTTGGAATTGTTTTCAGCAATGGAAAGAAATGGAAGGAGATCCGGCGTTTCTCCCTCATGACGCTGCGGAATTTTGGGATGGGGAAGAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCCCGCTGCCTTGTGGAGGAGTTGAGAAAAACCAAGGCCTCACCCTGTGATCCCACTTTCATCCTGGGCTGTGCTCCCTGCAATGTGATCTGTAGTATCATATTTCACAAGCGGTTCGACTATAAGGACCAGCAATTCTTGAACCTTATGGAGAAACTGAATGAGAATATCAAAATTCTCTCAAGTCCGTGGATTCAGATTTGCAACAACTTTAGTCCCATTATTGATTATTTTCCGGGAACACACAACAAATTGCTGAAAAATGTAGCTTTTATGAAAAGTTACATTCTCGAGAAAGTCAAAGAGCATCAAGAGTCAATGGATATGAACAATCCTCAAGACTTCATTGATTGCTTCTTGATGAAAATGGAAAAGGAGAAACACAACCAACCATCTGAGTTCACAATCGAGTCACTGGAAAACACGGCCGTAGATCTCTTTGGTGCGGGGACGGAGACAACGAGTACGACTCTTAGATACGCGCTCCTTTTGTTGCTGAAGCACCCAGAAGTCACCGCGAAGGTGCAAGAAGAAATCGAGCGGGTAATCGGACGAAACAGATCCCCTTGTATGCAGGATAGAAGTCACATGCCCTACACAGATGCTGTGGTGCACGAGGTCCAGAGATACATTGACCTTCTCCCCACCAGCCTGCCCCATGCAGTGACCTGTGACATTAAATTCAGAAACTATCTCATTCCCAAGGGCACAACCATATTAATTTCCCTGACTTCTGTGCTACATGACAACAAAGAATTTCCCAACCCAGAGATGTTTGACCCTCATCACTTTCTGGATGAAGGTGGCAATTTCAAGAAGAGCAAGTATTTCATGCCTTTCTCAGCAGGAAAACGGATTTGTGTGGGAGAAGCCCTGGCCGGCATGGAGCTGTTTTTATTCCTGACCTCCATTTTACAGAACTTTAACCTGAAATCTCTGGTTGACCCAAAGAACCTTGACACCACTCCAGTTGTCAATGGATTTGCCTCTGTGCCGCCCTTCTACCAGCTGTGCTTCATTCCTGTC",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P11712",
                "url": "http://purl.uniprot.org/uniprot/P11712",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000095-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "expts",
            "se",
            "lower_ci",
            "upper_ci",
            "score2",
            "score3",
            "score6",
            "exp2_w_ave",
            "exp3_w_ave",
            "exp6_w_ave"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000095-b-1",
        "variant_count": 6821,
        "experiment": "urn:mavedb:00000095-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2018-06-26",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-a-1",
        "publish_date": "2018-06-26",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957)",
        "method_text": "##Scoring procedure:\r\nDMS-BarSeq and DMS-TileSeq reads were processed using the [dmsPipeline](https://bitbucket.org/rothlabto/dmspipeline) software. Briefly, Barseq read counts were used to establish relative frequencies of each strain at each timepoint and converted to estimates of absolute frequencies using OD measurement data. Absolute counts were used to establish growth curves from which fitness parameters were estimated and then normalized to 0-1 scale where 0 corresponds to null controls and 1 corresponds to WT controls. Meanwhile, TileSeq read counts were used to establish relative allele frequencies in each condition. Non-mutagenized control counts were subtracted from counts (as estimates of sequencing error). log ratios of selection over non-selection counts were calculated. The resulting TileSeq fitness values were then rescaled to the distribution of the BarSeq fitness scores. Fitness scores were joined using confidence-weighted averages. Random-Forest base machine learning was used to impute missing values and refine low-confidence measurements, based on intrinsic, structural, and biochemical features.\r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for more details.\r\n\r\n## Additional columns:\r\n* exp.score = experimental score from the joint DMS-BarSeq/DMS-TileSeq screens\r\n* exp.sd = standard deviation of the experimental score\r\n* df = degrees of freedom (number of replicates contributing to the experimental score)\r\n* pred.score = machine-learning predicted score",
        "short_description": "A joint Deep Mutational Scan of the human SUMO E2 conjugase UBE2I using functional complementation in yeast, combining DMS-BarSeq and DMS-TileSeq data, followed by machine-learning-based imputation and refinement.",
        "title": "UBE2I imputed & refined",
        "keywords": [
            {
                "text": "DMS-BarSeq"
            },
            {
                "text": "E2"
            },
            {
                "text": "sumoylation"
            },
            {
                "text": "imputation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29269382",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29269382",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "UBE2I",
            "reference_sequence": {
                "sequence": "ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCATGGAGGAAAGACCACCCATTTGGTTTCGTGGCTGTCCCAACAAAAAATCCCGATGGCACGATGAACCTCATGAACTGGGAGTGCGCCATTCCAGGAAAGAAAGGGACTCCGTGGGAAGGAGGCTTGTTTAAACTACGGATGCTTTTCAAAGATGATTATCCATCTTCGCCACCAAAATGTAAATTCGAACCACCATTATTTCACCCGAATGTGTACCCTTCGGGGACAGTGTGCCTGTCCATCTTAGAGGAGGACAAGGACTGGAGGCCAGCCATCACAATCAAACAGATCCTATTAGGAATACAGGAACTTCTAAATGAACCAAATATCCAAGACCCAGCTCAAGCAGAGGCCTACACGATTTACTGCCAAAACAGAGTGGAGTACGAGAAAAGGGTCCGAGCACAAGCCAAGAAGTTTGCGCCCTCATAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P63279",
                "url": "http://purl.uniprot.org/uniprot/P63279",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000103275",
                "url": "http://www.ensembl.org/id/ENSG00000103275",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 159,
                "identifier": "NM_003345",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_003345",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000001-a-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "se",
            "exp.score",
            "exp.sd",
            "df",
            "pred.score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000001-a-1",
        "variant_count": 3180,
        "experiment": "urn:mavedb:00000001-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-08-07",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000040-a-4",
        "publish_date": "2019-08-07",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effect of variants in yeast HSP90 under different combinations of temperature (30C or 36C) and presence/absence of salt (0.5 M NaCl). The results explore the adaptive potential of this essential gene.",
        "method_text": "Sequencing reads were filtered based on a minimum Phred quality score of 20 across all 36 bases. For each time point, the log2 ratio of each variant's count to the wild type count was calculated. The score of each variant was calculated as the slope of these log ratios to time in wild type generations. Scores of -0.5 are considered null-like.",
        "short_description": "Deep mutational scan of all single mutants in a nine-amino acid region of Hsp90 (Hsp82) in Saccharomyces cerevisiae at 36C with 0.5 M NaCl.",
        "title": "Deep mutational scan of HSP90, 36C with salt",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24299404",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24299404",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "HSP90",
            "reference_sequence": {
                "sequence": "CAATTTGGTTGGTCTGCTAATATGGAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 581,
                "identifier": "P02829",
                "url": "http://purl.uniprot.org/uniprot/P02829",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000040-a-4",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000040-a-4",
        "variant_count": 189,
        "experiment": "urn:mavedb:00000040-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000023-a-1",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {
            "chr": "19",
            "end": 11089548,
            "start": 11089231,
            "reference": "hg38"
        },
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "The effect of each variant was calculated using a multiple linear regression model based on the DNA counts and RNA counts. Each variant needed to have 10 unique barcode tags to be included in the downstream analyses.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>\r\n\r\nMetadata contains the genomic coordinates for the target sequence.\r\n\r\nColumn descriptions:\r\n\r\n- 'score' is the Log2 variant expression effect derived from the fit of the linear model (coefficient).\r\n- 'p-value' is the P-value of the coefficient.\r\n- 'unique_tags' is the number of unique tags associated with the variant.\r\n- 'dna_sequences' is the count of DNA sequences that contain the variant (used for fitting the linear model).\r\n- 'rna_sequences' is the count of RNA sequences that contain the variant (used for fitting the linear model).",
        "short_description": "Saturation mutagenesis MPRA of LDLR promoter in HepG2 cells. Biological replicate 1 of 2.",
        "title": "Saturation mutagenesis MPRA of LDLR promoter, replicate 1",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "LDLR promoter",
            "reference_sequence": {
                "sequence": "AGCTCTTCACCGGAGACCCAAATACAACAAATCAAGTCGCCTGCCCTGGCGACACTTTCGAAGGACTGGAGTGGGAATCAGAGCTTCACGGGTTAAAAAGCCGATGTCACATCGGCCGTTCGAAACTCCTCCTCTTGCAGTGAGGTGAAGACATTTGAAAATCACCCCACTGCAAACTCCTCCCCCTGCTAGAAACCTCACATTGAAATGCTGTAAATGACGTGGGCCCCGAGTGCAATCGCGGGAAGCCAGGGTTTCCAGCTAGGACACAGCAGGTCGTGATCCGGGTCGGGACACTGCCTGGCAGAGGCTGCGAGC",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000023-a-1",
            "type": "Regulatory"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "p-value",
            "unique_tags",
            "dna_sequences",
            "rna_sequences"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000023-a-1",
        "variant_count": 1083,
        "experiment": "urn:mavedb:00000023-a",
        "is_meta_analysis": false,
        "data_usage_policy": "We are making our data available prior to publication in line with Fort Lauderdale principle, allowing others to use the data but allowing the data producers to make the first presentations and to publish the first paper with global analyses of the data. In addition, we also reserve the right to publish the first analysis of the differences seen in the TERT knock-down experiments and alternative cell-type experiments. Studies that do not overlap with these intentions may be submitted for publication at any time, but must appropriately cite the data source. After publication of the data, the first publication of the data producers should be cited for any use of these data."
    },
    {
        "creation_date": "2019-02-27",
        "modification_date": "2020-11-20",
        "urn": "urn:mavedb:00000049-a-2",
        "publish_date": "2020-11-20",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "A deep mutational scan of human MTHFR via functional complementation in yeast at 25ug/ml folate in A222V background",
        "title": "MTHFR at 25ug/ml folate in A222V background",
        "keywords": [
            {
                "text": "imputation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "homocystinuria"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1628-9390",
            "0000-0002-9219-4310",
            "0000-0002-2550-2141",
            "0000-0001-6465-5776"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "MTHFR",
            "reference_sequence": {
                "sequence": "ATGGTGAACGAAGCCAGAGGAAACAGCAGCCTCAACCCCTGCTTGGAGGGCAGTGCCAGCAGTGGCAGTGAGAGCTCCAAAGATAGTTCGAGATGTTCCACCCCGGGCCTGGACCCCGAGCGGCATGAGAGACTCCGGGAGAAGATGAGGCGGCGATTGGAATCTGGTGACAAGTGGTTCTCCCTGGAATTCTTCCCTCCTCGAACTGCTGAGGGAGCTGTCAATCTCATCTCAAGGTTTGACCGGATGGCAGCAGGTGGCCCCCTCTACATAGACGTGACCTGGCACCCAGCAGGTGACCCTGGCTCAGACAAGGAGACCTCCTCCATGATGATCGCCAGCACCGCCGTGAACTACTGTGGCCTGGAGACCATCCTGCACATGACCTGCTGCCGTCAGCGCCTGGAGGAGATCACGGGCCATCTGCACAAAGCTAAGCAGCTGGGCCTGAAGAACATCATGGCGCTGCGGGGAGACCCAATAGGTGACCAGTGGGAAGAGGAGGAGGGAGGCTTCAACTACGCAGTGGACCTGGTGAAGCACATCCGAAGTGAGTTTGGTGACTACTTTGACATCTGTGTGGCAGGTTACCCCAAAGGCCACCCCGAAGCAGGGAGCTTTGAGGCTGACCTGAAGCACTTGAAGGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGCTTTTCTTTGAGGCTGACACATTCTTCCGCTTTGTGAAGGCATGCACCGACATGGGCATCACTTGCCCCATCGTCCCCGGGATCTTTCCCATCCAGGGCTACCACTCCCTTCGGCAGCTTGTGAAGCTGTCCAAGCTGGAGGTGCCACAGGAGATCAAGGACGTGATTGAGCCAATCAAAGACAACGATGCTGCCATCCGCAACTATGGCATCGAGCTGGCCGTGAGCCTGTGCCAGGAGCTTCTGGCCAGTGGCTTGGTGCCAGGCCTCCACTTCTACACCCTCAACCGCGAGATGGCTACCACAGAGGTGCTGAAGCGCCTGGGGATGTGGACTGAGGACCCCAGGCGTCCCCTACCCTGGGCTCTCAGCGCCCACCCCAAGCGCCGAGAGGAAGATGTACGTCCCATCTTCTGGGCCTCCAGACCAAAGAGTTACATCTACCGTACCCAGGAGTGGGACGAGTTCCCTAACGGCCGCTGGGGCAATTCCTCTTCCCCTGCCTTTGGGGAGCTGAAGGACTACTACCTCTTCTACCTGAAGAGCAAGTCCCCCAAGGAGGAGCTGCTGAAGATGTGGGGGGAGGAGCTGACCAGTGAAGAAAGTGTCTTTGAAGTCTTCGTTCTTTACCTCTCGGGAGAACCAAACCGGAATGGTCACAAAGTGACTTGCCTGCCCTGGAACGATGAGCCCCTGGCGGCTGAGACCAGCCTGCTGAAGGAGGAGCTGCTGCGGGTGAACCGCCAGGGCATCCTCACCATCAACTCACAGCCCAACATCAACGGGAAGCCGTCCTCCGACCCCATCGTGGGCTGGGGCCCCAGCGGGGGCTATGTCTTCCAGAAGGCCTACTTAGAGTTTTTCACTTCCCGCGAGACAGCGGAAGCACTTCTGCAAGTGCTGAAGAAGTACGAGCTCCGGGTTAATTACCACCTTGTCAATGTGAAGGGTGAAAACATCACCAATGCCCCTGAACTGCAGCCGAATGCTGTCACTTGGGGCATCTTCCCTGGGCGAGAGATCATCCAGCCCACCGTAGTGGATCCCGTCAGCTTCATGTTCTGGAAGGACGAGGCCTTTGCCCTGTGGATTGAGCGGTGGGGAAAGCTGTATGAGGAGGAGTCCCCGTCCCGCACCATCATCCAGTACATCCACGACAACTACTTCCTGGTCAACCTGGTGGACAATGACTTCCCACTGGACAACTGCCTCTGGCAGGTGGTGGAAGACACATTGGAGCTTCTCAACAGGCCCACCCAGAATGCGAGAGAAACGGAGGCTCCATGA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P42898",
                "url": "http://purl.uniprot.org/uniprot/P42898",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000177000",
                "url": "http://www.ensembl.org/id/ENSG00000177000",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 230,
                "identifier": "NM_005957",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_005957",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000049-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "se",
            "exp.score",
            "exp.se",
            "df",
            "pred.score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000049-a-2",
        "variant_count": 13690,
        "experiment": "urn:mavedb:00000049-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-03-10",
        "modification_date": "2021-04-15",
        "urn": "urn:mavedb:00000062-b-1",
        "publish_date": "2021-04-15",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the impact of CYP2C19 variants on the abundance of this protein in HEK293T. The authors fused the target protein with green fluorescent protein (GFP) and used the intensity of GPF as the indicator of target protein abundance.",
        "method_text": "After 5 days' growth, the cells were sorted to 4 bins by FACS according to the relative intensity of GFP and mCherry. The gate for each bin was set by the values of wildtype and known target protein variants, for example bin 1 represented protein expression less than 25%. Sorted cells for each bin were sequenced by Illumina and the frequency of each variant in the bin was determined. The protein abundance score for a variant was calculated as: the sum of weighted variant frequency in each bin (weight: 0.25, 0.5, 0.75 & 1 for bin1 to bin4) and divided by the sum of the un-weighted variant frequency in each bin.\r\nThe experiment was repeated 4 times and the final score was the mean of them.",
        "short_description": "This study tested the protein abundance of CYP2C19 variants by fusing green fluorescent protein.",
        "title": "Abundance of CYP2C19 variants",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.1111/cts.12758",
                "url": "https://doi.org/10.1111/cts.12758",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32004414",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32004414",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "CYP2C19",
            "reference_sequence": {
                "sequence": "CTCTGTCTCTCATGTTTGCTTCTCCTTTCAATCTGGAGACAGAGCTCTGGGAGAGGAAAACTCCCTCCTGGCCCCACTCCTCTCCCAGTGATTGGAAATATCCTACAGATAGATATTAAGGATGTCAGCAAATCCTTAACCAATCTCTCAAAAATCTATGGCCCTGTGTTCACTCTGTATTTTGGCCTGGAACGCATGGTGGTGCTGCATGGATATGAAGTGGTGAAGGAAGCCCTGATTGATCTTGGAGAGGAGTTTTCTGGAAGAGGCCATTTCCCACTGGCTGAAAGAGCTAACAGAGGATTTGGAATCGTTTTCAGCAATGGAAAGAGATGGAAGGAGATCCGGCGTTTCTCCCTCATGACGCTGCGGAATTTTGGGATGGGGAAGAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCCCGCTGCCTTGTGGAGGAGTTGAGAAAAACCAAGGCTTCACCCTGTGATCCCACTTTCATCCTGGGCTGTGCTCCCTGCAATGTGATCTGCTCCATTATTTTCCAGAAACGTTTCGATTATAAAGATCAGCAATTTCTTAACTTGATGGAAAAATTGAATGAAAACATCAGGATTGTAAGCACCCCCTGGATCCAGATATGCAATAATTTTCCCACTATCATTGATTATTTCCCGGGAACCCATAACAAATTACTTAAAAACCTTGCTTTTATGGAAAGTGATATTTTGGAGAAAGTAAAAGAACACCAAGAATCGATGGACATCAACAACCCTCGGGACTTTATTGATTGCTTCCTGATCAAAATGGAGAAGGAAAAGCAAAACCAACAGTCTGAATTCACTATTGAAAACTTGGTAATCACTGCAGCTGACTTACTTGGAGCTGGGACAGAGACAACAAGCACAACCCTGAGATATGCTCTCCTTCTCCTGCTGAAGCACCCAGAGGTCACAGCTAAAGTCCAGGAAGAGATTGAACGTGTCATTGGCAGAAACCGGAGCCCCTGCATGCAGGACAGGGGCCACATGCCCTACACAGATGCTGTGGTGCACGAGGTCCAGAGATACATCGACCTCATCCCCACCAGCCTGCCCCATGCAGTGACCTGTGACGTTAAATTCAGAAACTACCTCATTCCCAAGGGCACAACCATATTAACTTCCCTCACTTCTGTGCTACATGACAACAAAGAATTTCCCAACCCAGAGATGTTTGACCCTCGTCACTTTCTGGATGAAGGTGGAAATTTTAAGAAAAGTAACTACTTCATGCCTTTCTCAGCAGGAAAACGGATTTGTGTGGGAGAGGGCCTGGCCCGCATGGAGCTGTTTTTATTCCTGACCTTCATTTTACAGAACTTTAACCTGAAATCTCTGATTGACCCAAAGGACCTTGACACAACTCCTGTTGTCAATGGATTTGCTTCTGTCCCGCCCTTCTATCAGCTGTGCTTCATTCCT",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 8,
                "identifier": "P33261",
                "url": "http://purl.uniprot.org/uniprot/P33261",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000062-b-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "e1_score",
            "e2_score",
            "e3_score",
            "e4_score",
            "sd",
            "se",
            "lower_ci",
            "upper_ci"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000062-b-1",
        "variant_count": 121,
        "experiment": "urn:mavedb:00000062-b",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-06-16",
        "modification_date": "2022-06-16",
        "urn": "urn:mavedb:00000094-a-12",
        "publish_date": "2022-06-16",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "12. V1/2 properties of 29 synonymous variants expressed alone.",
        "method_text": "",
        "short_description": "12. V1/2 properties of 29 synonymous variants expressed alone.",
        "title": "V1/2 properties of 29 synonymous variants expressed alone",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ4",
            "reference_sequence": {
                "sequence": "MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGGGSPRRLGLLGSPLPPGAPLPGPGSGSGSACGQRSSAAHKRYRRLQNWVYNVLERPRGWAFVYHVFIFLLVFSCLVLSVLSTIQEHQELANECLLILEFVMIVVFGLEYIVRVWSAGCCCRYRGWQGRFRFARKPFCVIDFIVFVASVAVIAAGTQGNIFATSALRSMRFLQILRMVRMDRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLVYLAEKDANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAGILGSGFALKVQEQHRQKHFEKRRMPAANLIQAAWRLYSTDMSRAYLTATWYYYDSILPSFRELALLFEHVQRARNGGLRPLEVRRAPVPDGAPSRYPPVATCHRPGSTSFCPGESSRMGIKDRIRMGSSQRRTGPSKQHLAPPTMPTSPSSEQVGEATSPTKVQKSWSFNDRTRFRASLRLKPRTSAEDAPSEEVAEEKSYQCELTVDDIMPAVKTVIRSIRILKFLVAKRKFKETLRPYDVKDVIEQYSAGHLDMLGRIKSLQTRVDQIVGRGPGDRKAREKGDKGPSDAEVVDEISMMGRVVKVEKQVQSIEHKLDLLLGFYSRCLRSGTSASLGAVQVPLFDPDITSDYHSPVDHEDISVSAQTLSISRSVSTNMD",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-12",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000094-a-12",
        "variant_count": 29,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-01-17",
        "urn": "urn:mavedb:00000057-c-1",
        "publish_date": "2021-01-17",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors used saturation mutagenesis to study the variant effect of Ras, with the regulation of GTPase activating protein (GAP) and guanine nucleotide exchange factor (GEF). The variants were selected by bacterial two-hybrid strategy.",
        "method_text": "The frequency of each mutant was determined through sequencing. The natural logarithm of the frequency ratio for each mutant after and before selection was calculated. These values were then normalized by dividing the wild type values which were calculated the same way.",
        "short_description": "In the presence of a GAP and a GEF, selection result on the mutated H-Ras.",
        "title": "Regulated-Ras",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "28686159",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28686159",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Ras",
            "reference_sequence": {
                "sequence": "ACGGAATATAAGCTGGTGGTGGTGGGCGCCGGCGGTGTGGGCAAGAGTGCGCTGACCATCCAGCTGATCCAGAACCATTTTGTGGACGAATACGACCCCACTATAGAGGATTCCTACCGGAAGCAGGTGGTCATTGATGGGGAGACGTGCCTGTTGGACATCCTGGATACCGCCGGCCAGGAGGAGTACAGCGCCATGCGGGACCAGTACATGCGCACCGGGGAGGGCTTCCTGTGTGTGTTTGCCATCAACAACACCAAGTCTTTTGAGGACATCCACCAGTACAGGGAGCAGATCAAACGGGTGAAGGACTCGGATGACGTGCCCATGGTGCTGGTGGGGAACAAGTGTGACCTGGCTGCACGCACTGTGGAATCTCGGCAGGCTCAGGACCTCGCCCGAAGCTACGGCATCCCCTACATCGAGACCTCGGCCAAGACCCGGCAGGGAGTGGAGGATGCCTTCTACACGTTGGTGCGTGAGATCCGGCAGCAC",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 1,
                "identifier": "P01112",
                "url": "http://purl.uniprot.org/uniprot/P01112",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000057-c-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000057-c-1",
        "variant_count": 3300,
        "experiment": "urn:mavedb:00000057-c",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2022-02-24",
        "modification_date": "2022-05-15",
        "urn": "urn:mavedb:00000094-a-7",
        "publish_date": "2022-05-15",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "V1/2 of co-expressing 153 variants (normal currents and large rightward shifts in V1/2 in the homozygous state) with WT.",
        "method_text": "V1/2 of co-expressing 153 variants (normal currents and large rightward shifts in V1/2 in the homozygous state) with WT.",
        "short_description": "6. V1/2 of co-expressing 153 variants (normal currents and large rightward shifts in V1/2 in the homozygous state) with WT.",
        "title": "V1/2 of co-expressing 153 variants (normal currents and large rightward shifts in V1/2 in the homozygous state) with WT",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "KCNQ4",
            "reference_sequence": {
                "sequence": "MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGGGSPRRLGLLGSPLPPGAPLPGPGSGSGSACGQRSSAAHKRYRRLQNWVYNVLERPRGWAFVYHVFIFLLVFSCLVLSVLSTIQEHQELANECLLILEFVMIVVFGLEYIVRVWSAGCCCRYRGWQGRFRFARKPFCVIDFIVFVASVAVIAAGTQGNIFATSALRSMRFLQILRMVRMDRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLVYLAEKDANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAGILGSGFALKVQEQHRQKHFEKRRMPAANLIQAAWRLYSTDMSRAYLTATWYYYDSILPSFRELALLFEHVQRARNGGLRPLEVRRAPVPDGAPSRYPPVATCHRPGSTSFCPGESSRMGIKDRIRMGSSQRRTGPSKQHLAPPTMPTSPSSEQVGEATSPTKVQKSWSFNDRTRFRASLRLKPRTSAEDAPSEEVAEEKSYQCELTVDDIMPAVKTVIRSIRILKFLVAKRKFKETLRPYDVKDVIEQYSAGHLDMLGRIKSLQTRVDQIVGRGPGDRKAREKGDKGPSDAEVVDEISMMGRVVKVEKQVQSIEHKLDLLLGFYSRCLRSGTSASLGAVQVPLFDPDITSDYHSPVDHEDISVSAQTLSISRSVSTNMD",
                "sequence_type": "protein"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000094-a-7",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "replicates"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000094-a-7",
        "variant_count": 153,
        "experiment": "urn:mavedb:00000094-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-f-1",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "Samples are collected after 12h and sequenced by Illumina. The counts for each variant is first added by 1, then divided by total sequence counts at this time point to calculate variant frequency. The functional score equals the division of a variant frequency at this time point and its frequency in initial library. Further normalizing the functional scores by wild type scores will give the relative enrichment values. The score data includes scores from three replicates which are suffixed by: _rep1, _rep2 & _rep3. The final score is the median of them.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 12h",
        "keywords": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "RAF",
            "reference_sequence": {
                "sequence": "TCTAAGACAAGCAACACTATCCGTGTTTTCTTGCCGAACAAGCAAAGAACAGTGGTCAATGTGCGAAATGGAATGAGCTTGCATGACTGCCTTATGAAAGCACTCAAGGTGAGGGGC",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 51,
                "identifier": "P04049",
                "url": "http://purl.uniprot.org/uniprot/P04049",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000061-f-1",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "score_rep1",
            "score_rep2",
            "score_rep3"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000061-f-1",
        "variant_count": 298,
        "experiment": "urn:mavedb:00000061-f",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2019-08-07",
        "modification_date": "2019-08-07",
        "urn": "urn:mavedb:00000039-a-5",
        "publish_date": "2019-08-07",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effects of yeast HSP90 variants under the control of different promoters to explore the relationship between protein sequence and expression level. The results showed that reduced expression level (compared to wild-type expression) revealed new partial loss of function mutations.",
        "method_text": "Growth rates were calculated for each variant and converted into selection coefficients. The selection coefficient for each variant under control of this promoter/UTR combination is reported as the score. For variants with multiple synonymous codons, the reported coefficient is the average of all synonymous variant's selection coefficients.\r\n\r\nVariants annotated as \"null-like\" have a score of -1.",
        "short_description": "Deep mutational scan of all single mutants in a nine-amino acid region of Hsp90 (Hsp82) in Saccharomyces cerevisiae under the control of the GPD promoter with CYC 3'UTR.",
        "title": "Deep mutational scan of HSP90, GPD construct",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "promoter"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23825969",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23825969",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "HSP90",
            "reference_sequence": {
                "sequence": "CAATTTGGTTGGTCTGCTAATATGGAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 581,
                "identifier": "P02829",
                "url": "http://purl.uniprot.org/uniprot/P02829",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "sacCer3/R64",
                        "organism_name": "Saccharomyces cerevisiae",
                        "assembly_identifier": {
                            "identifier": "GCF_000146045.2",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000039-a-5",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000039-a-5",
        "variant_count": 182,
        "experiment": "urn:mavedb:00000039-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2018-06-26",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-a-2",
        "publish_date": "2018-06-29",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957)",
        "method_text": "##Scoring procedure:\r\nDMS-BarSeq and reads were processed using the [dmsPipeline](https://bitbucket.org/rothlabto/dmspipeline) software. Briefly, Barseq read counts were used to establish relative frequencies of each strain at each timepoint and converted to estimates of absolute frequencies using OD measurement data. Absolute counts were used to establish growth curves from which fitness parameters were estimated and then normalized to 0-1 scale where 0 corresponds to null controls and 1 corresponds to WT controls. \r\n\r\nSee [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for more details.",
        "short_description": "A Deep Mutational Scan of the human SUMO E2 conjugase UBE2I using functional complementation in yeast via DMS-BarSeq",
        "title": "UBE2I DMS-BarSeq",
        "keywords": [
            {
                "text": "DMS-BarSeq"
            },
            {
                "text": "E2"
            },
            {
                "text": "sumoylation"
            },
            {
                "text": "complementation"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29269382",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29269382",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "licence": {
            "long_name": "CC BY 4.0 (Attribution)",
            "short_name": "CC BY 4.0",
            "link": "https://creativecommons.org/licenses/by/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "UBE2I",
            "reference_sequence": {
                "sequence": "ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCATGGAGGAAAGACCACCCATTTGGTTTCGTGGCTGTCCCAACAAAAAATCCCGATGGCACGATGAACCTCATGAACTGGGAGTGCGCCATTCCAGGAAAGAAAGGGACTCCGTGGGAAGGAGGCTTGTTTAAACTACGGATGCTTTTCAAAGATGATTATCCATCTTCGCCACCAAAATGTAAATTCGAACCACCATTATTTCACCCGAATGTGTACCCTTCGGGGACAGTGTGCCTGTCCATCTTAGAGGAGGACAAGGACTGGAGGCCAGCCATCACAATCAAACAGATCCTATTAGGAATACAGGAACTTCTAAATGAACCAAATATCCAAGACCCAGCTCAAGCAGAGGCCTACACGATTTACTGCCAAAACAGAGTGGAGTACGAGAAAAGGGTCCGAGCACAAGCCAAGAAGTTTGCGCCCTCATAA",
                "sequence_type": "dna"
            },
            "uniprot": {
                "offset": 0,
                "identifier": "P63279",
                "url": "http://purl.uniprot.org/uniprot/P63279",
                "dbversion": null,
                "dbname": "UniProt"
            },
            "ensembl": {
                "offset": 0,
                "identifier": "ENSG00000103275",
                "url": "http://www.ensembl.org/id/ENSG00000103275",
                "dbversion": null,
                "dbname": "Ensembl"
            },
            "refseq": {
                "offset": 159,
                "identifier": "NM_003345",
                "url": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_003345",
                "dbversion": null,
                "dbname": "RefSeq"
            },
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg38",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.26",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000001-a-2",
            "type": "Protein coding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "sd",
            "se"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000001-a-2",
        "variant_count": 3418,
        "experiment": "urn:mavedb:00000001-a",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-d-1",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes the sequence for an hnRNPA1 binding site (with upstream T).",
        "method_text": "Reads were filtered by accepting only those that had an unmutated 6nt stretch at the end of the read and had no mutations other than those that were designed. FASTQ quality scores were not used.\r\n\r\nThe sum of the reads in each of the two replicate transfections was used to calculate the scores, defined as the ratio of RNA read count to DNA read count (called the Enrichment Index, or EI).\r\n\r\nThe score reported here is the “LEIsc”, which is $log_2 EI$ re-scaled from -1 to +1 with the target sequence at 0, which enables easier comparison between the different 6-mers tested in the study.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, hnRNPA1 binding site (with upstream T).",
        "title": "Exonic splicing for hnRNPA1 binding site",
        "keywords": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",
            "short_name": "CC BY-NC-SA 4.0",
            "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
            "version": "4.0"
        },
        "target": {
            "name": "Minigene exon - hnRNPA1 binding site",
            "reference_sequence": {
                "sequence": "AGTTAGGGATGGGAGCTCCAGCACAGTGAAATGGACAGAAGGGCAGAGCAA",
                "sequence_type": "dna"
            },
            "uniprot": null,
            "ensembl": null,
            "refseq": null,
            "reference_maps": [
                {
                    "genome": {
                        "short_name": "hg19",
                        "organism_name": "Homo sapiens",
                        "assembly_identifier": {
                            "identifier": "GCF_000001405.13",
                            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13",
                            "dbversion": null,
                            "dbname": "GenomeAssembly"
                        }
                    }
                }
            ],
            "scoreset": "urn:mavedb:00000083-d-1",
            "type": "Other noncoding"
        },
        "score_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro",
            "score",
            "EI"
        ],
        "count_columns": [
            "hgvs_nt",
            "hgvs_splice",
            "hgvs_pro"
        ],
        "previous_version": null,
        "next_version": null,
        "current_version": "urn:mavedb:00000083-d-1",
        "variant_count": 556,
        "experiment": "urn:mavedb:00000083-d",
        "is_meta_analysis": false,
        "data_usage_policy": ""
    },
    {
        "creation_date": "2018-07-10",
        "modification_date": "2019-07-28",
        "urn": "urn:mavedb:00000003-b-2",
        "publish_date": "2018-07-10",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "These experiments measured the functional consequences of mutations in the BRCA1 RING domain, where most clinically-relevant single nucleotide variants reside. One goal of the study was to create a \"look-up table\" of single nucleotide variants for clinical use, by prospectively measuring the impact of all possible variants that are likely to appear in patients. The study combines two different assays - one based on E3 ubiquitin ligase activity and one based on BRCA1-BARD1 heterodimer formation - and makes one of the first attempts to combine data from different MAVEs on the same target.\r\n\r\nThis entry contains scores from the yeast two-hybrid assay, which tested the BRCA1-BARD1 heterodimer formation in BRCA1 variants.\r\n\r\nNote that this score set does not describe the scores presented in the original publication. It is a reanalysis of the raw data that was produced as part of testing and development for Enrich2.",
        "method_text": "Scores were calculated using the Enrich2 weighted least squares regression scoring model. Replicate scores were combined using the Enrich2 random-effects model. Counts for each variant were calculated as the sum of counts for all barcodes associated with a variant with the same amino acid sequence.\r\n\r\nThe scores and standard errors calculated for each of replicate appear as additional columns.\r\n\r\nCount columns are named using the format `<replicate>_c_<timepoint>`. The 0 time point is the input (unselected). Time points are given in hours.",
        "short_description": "Amino acid variant scores for deep mutational scan of the BRCA1 RING domain using yeast two-hybrid calculated by Enrich2.",
        "title": "Enrich2 amino acid variant scores for BRCA1 Y2H",
        "keywords": [
            {
                "text": "Yeast two-hybrid"
            },
            {
                "text": "ubiquitin"
            },
            {
                "text": "regression"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "28784151",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28784151",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "licence": {
            "long_name": "CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike)",