{ "bcoid": "GLY_000024", "title": "Human Cancer Mutation", "description": "The Human Cancer Mutation dataset contains human [taxid:9606] mutation data from BioMuta database (https://hive.biochemistry.gwu.edu/biomuta). ", "filename": "human_protein_mutation_cancer.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Protein" ], "tags": [ "Somatic Cancer Mutations" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P13535-1...", "1139..." ], [ "O60502-1...", "550..." ] ], "headers": [ "uniprotkb_ca...", "aa_pos..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "aa_pos" }, { "type": "string", "label": "ref_aa" }, { "type": "string", "label": "alt_aa" }, { "type": "string", "label": "chr_id" }, { "type": "string", "label": "chr_start_pos" }, { "type": "string", "label": "chr_end_pos" }, { "type": "string", "label": "ref_nt" }, { "type": "string", "label": "alt_nt" }, { "type": "string", "label": "patients_positive" }, { "type": "string", "label": "patients_tested" }, { "type": "string", "label": "mut_freq" }, { "type": "string", "label": "data_source" }, { "type": "string", "label": "do_id" }, { "type": "string", "label": "do_name" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "filter_flags" }, { "type": "string", "label": "glyco_annotation" }, { "type": "string", "label": "mim_id" }, { "type": "string", "label": "somatic_status" }, { "type": "string", "label": "minor_allelic_frequency" } ], [ "P13535-1", "1139", "R", "H", "17", "10400709", "10400709", "C", "T", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "P13535", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "O60502-1", "550", "A", "V", "10", "101799002", "101799002", "G", "A", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "O60502", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "A6NJZ7-1", "1273", "S", "G", "22", "21547160", "21547160", "T", "C", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "A6NJZ7", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9UBR1-1", "326", "R", "Q", "22", "24523679", "24523679", "G", "A", "0", "0", "0.0", "icgc", "2531", "DOID:2531 / hematologic cancer", "protein_xref_biomuta", "Q9UBR1", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P02708-2", "238", "V", "I", "2", "174753569", "174753569", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P02708", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P56373-1", "266", "D", "N", "11", "57350852", "57350852", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "P56373", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q92786-1", "415", "V", "I", "1", "213997778", "213997778", "G", "A", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q92786", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P19823-1", "159", "A", "T", "10", "7717633", "7717633", "G", "A", "0", "0", "0.0", "icgc", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "P19823", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "A3KFT3-1", "261", "R", "W", "1", "248145928", "248145928", "C", "T", "0", "0", "0.0", "icgc", "4362", "DOID:4362 / cervical cancer", "protein_xref_biomuta", "A3KFT3", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P48066-1", "258", "A", "V", "3", "10874977", "10874977", "C", "T", "0", "0", "0.0", "icgc", "3571", "DOID:3571 / liver cancer", "protein_xref_biomuta", "P48066", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q5HY64-1", "31", "A", "T", "X", "37008501", "37008501", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q5HY64", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P14867-1", "355", "K", "N", "5", "161897116", "161897116", "G", "T", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "P14867", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P50148-1", "96", "T", "S", "9", "77922196", "77922196", "T", "A", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "P50148", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8N434-1", "426", "T", "M", "7", "138621122", "138621122", "G", "A", "0", "0", "0.0", "icgc", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "Q8N434", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "O95402-1", "30", "A", "V", "19", "16578393", "16578393", "G", "A", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "O95402", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P01111-1", "61", "Q", "K", "1", "114713909", "114713909", "G", "T", "0", "0", "0.0", "icgc", "2394", "DOID:2394 / ovarian cancer", "protein_xref_biomuta", "P01111", "Somatic mutation passed 1 out of 6 filters: num. of cancers (12). In dbSNP: rs121913254.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q7Z401-1", "965", "V", "I", "15", "65696423", "65696423", "C", "T", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q7Z401", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q5GH72-1", "383", "R", "H", "20", "31996865", "31996865", "G", "A", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q5GH72", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q15750-1", "260", "A", "T", "22", "39421828", "39421828", "G", "A", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q15750", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9H115-1", "22", "K", "R", "20", "23421338", "23421338", "T", "C", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q9H115", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8N307-1", "595", "A", "T", "3", "195726386", "195726386", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q8N307", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8NGQ4-1", "280", "A", "T", "11", "58228038", "58228038", "C", "T", "0", "0", "0.0", "icgc", "2394", "DOID:2394 / ovarian cancer", "protein_xref_biomuta", "Q8NGQ4", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9P273-1", "6", "R", "H", "4", "182324037", "182324037", "G", "A", "0", "0", "0.0", "icgc", "1115", "DOID:1115 / sarcoma", "protein_xref_biomuta", "Q9P273", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8NFC6-1", "3049", "A", "V", "4", "13570021", "13570021", "G", "A", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q8NFC6", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8IV42-1", "80", "R", "Q", "10", "122982755", "122982755", "G", "A", "0", "0", "0.0", "icgc", "4362", "DOID:4362 / cervical cancer", "protein_xref_biomuta", "Q8IV42", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q13634-1", "50", "R", "C", "5", "19838839", "19838839", "G", "A", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q13634", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9H5Z6-1", "152", "A", "T", "2", "224401315", "224401315", "C", "T", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q9H5Z6", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P04637-1", "234", "Y", "C", "17", "7674262", "7674262", "T", "C", "0", "0", "0.0", "icgc", "1319", "DOID:1319 / brain cancer", "protein_xref_biomuta", "P04637", "Somatic mutation passed 1 out of 6 filters: num. of cancers (9). In dbSNP: rs587780073.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q6ZTA4-3", "606", "D", "N", "1", "231206787", "231206787", "G", "A", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q6ZTA4", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3). In dbSNP: rs372935882.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9Y5H4-1", "293", "R", "C", "5", "141331561", "141331561", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9Y5H4", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q86VR7-1", "592", "R", "Q", "19", "51338163", "51338163", "C", "T", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q86VR7", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9NYD6-1", "5", "R", "C", "12", "53985272", "53985272", "C", "T", "0", "0", "0.0", "icgc", "1319", "DOID:1319 / brain cancer", "protein_xref_biomuta", "Q9NYD6", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P20936-1", "802", "M", "I", "5", "87378457", "87378457", "G", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P20936", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P42336-1", "81", "E", "K", "3", "179199066", "179199066", "G", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P42336", "Somatic mutation passed 1 out of 6 filters: num. of cancers (8).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8TF62-1", "953", "R", "H", "15", "49876447", "49876447", "C", "T", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q8TF62", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q6NUI2-1", "692", "R", "C", "2", "96023181", "96023181", "G", "A", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q6NUI2", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P35712-1", "122", "R", "C", "11", "16318527", "16318527", "G", "A", "0", "0", "0.0", "icgc", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "P35712", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3). In dbSNP: rs769385306.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q86TI0-1", "125", "R", "W", "4", "37902468", "37902468", "C", "T", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q86TI0", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9UBR1-1", "326", "R", "Q", "22", "24523679", "24523679", "G", "A", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q9UBR1", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P08559-1", "378", "R", "C", "X", "19359612", "19359612", "C", "T", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "P08559", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9NZJ5-1", "436", "H", "Y", "2", "88588761", "88588761", "G", "A", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q9NZJ5", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9HCJ2-1", "284", "H", "Y", "11", "40115443", "40115443", "G", "A", "0", "0", "0.0", "icgc", "5041", "DOID:5041 / esophageal cancer", "protein_xref_biomuta", "Q9HCJ2", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q5HYA8-1", "906", "L", "I", "8", "93809839", "93809839", "C", "A", "0", "0", "0.0", "icgc", "4362", "DOID:4362 / cervical cancer", "protein_xref_biomuta", "Q5HYA8", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9Y5G6-1", "516", "A", "T", "5", "141384445", "141384445", "G", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9Y5G6", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8TE73-1", "78", "R", "Q", "5", "13928138", "13928138", "C", "T", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q8TE73", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P60484-1", "101", "I", "T", "10", "87933061", "87933061", "T", "C", "0", "0", "0.0", "icgc", "1319", "DOID:1319 / brain cancer", "protein_xref_biomuta", "P60484", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q92736-1", "266", "A", "T", "1", "237417071", "237417071", "G", "A", "0", "0", "0.0", "icgc", "2394", "DOID:2394 / ovarian cancer", "protein_xref_biomuta", "Q92736", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P42336-1", "1047", "H", "Y", "3", "179234296", "179234296", "C", "T", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "P42336", "Somatic mutation passed 1 out of 6 filters: num. of cancers (6). In dbSNP: rs121913281.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q6Q759-1", "1274", "T", "M", "1", "118025326", "118025326", "G", "A", "0", "0", "0.0", "icgc", "2531", "DOID:2531 / hematologic cancer", "protein_xref_biomuta", "Q6Q759", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P10071-1", "312", "T", "M", "7", "42040131", "42040131", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "P10071", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9BYG8-1", "412", "D", "N", "8", "129749505", "129749505", "C", "T", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q9BYG8", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P04637-1", "249", "R", "S", "17", "7674216", "7674216", "C", "A", "0", "0", "0.0", "icgc", "3571", "DOID:3571 / liver cancer", "protein_xref_biomuta", "P04637", "Somatic mutation passed 2 out of 6 filters: num. of cancers (7); Lit. mined (10). In dbSNP: rs28934571.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q6Y288-1", "337", "R", "H", "13", "31286765", "31286765", "G", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q6Y288", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8TF46-1", "614", "D", "G", "15", "66326004", "66326004", "A", "G", "0", "0", "0.0", "icgc", "2531", "DOID:2531 / hematologic cancer", "protein_xref_biomuta", "Q8TF46", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P04637-1", "126", "Y", "C", "17", "7675235", "7675235", "T", "C", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "P04637", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9Y297-1", "237", "S", "Y", "10", "101526166", "101526166", "C", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9Y297", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8N3A8-1", "844", "L", "I", "5", "50842033", "50842033", "C", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q8N3A8", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q93088-1", "57", "R", "C", "5", "79119261", "79119261", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q93088", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q96J87-1", "473", "R", "W", "15", "72287294", "72287294", "G", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q96J87", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9P2F8-1", "321", "R", "H", "1", "232514378", "232514378", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9P2F8", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q07157-1", "450", "V", "I", "15", "29737323", "29737323", "C", "T", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q07157", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P38398-1", "1613", "S", "G", "17", "43071077", "43071077", "T", "C", "0", "0", "0.0", "icgc", "2531", "DOID:2531 / hematologic cancer", "protein_xref_biomuta", "P38398", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9Y5H7-1", "44", "V", "I", "5", "140821905", "140821905", "G", "A", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q9Y5H7", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q96L73-1", "614", "V", "L", "5", "177210239", "177210239", "G", "T", "0", "0", "0.0", "icgc", "5041", "DOID:5041 / esophageal cancer", "protein_xref_biomuta", "Q96L73", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "O43374-1", "141", "E", "G", "7", "102605864", "102605864", "T", "C", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "O43374", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q14964-1", "119", "R", "W", "11", "107962073", "107962073", "C", "T", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q14964", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8TBB1-1", "565", "E", "K", "4", "53476952", "53476952", "C", "T", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q8TBB1", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "O75159-1", "464", "S", "L", "2", "46759921", "46759921", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "O75159", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q96EV2-1", "799", "R", "H", "7", "155745019", "155745019", "G", "A", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q96EV2", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8WZ42-1", "6731", "R", "Q", "2", "178724116", "178724116", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q8WZ42", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9BWW8-1", "312", "E", "K", "22", "35659498", "35659498", "G", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9BWW8", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P60484-1", "246", "P", "L", "10", "87957955", "87957955", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P60484", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q9BXJ1-1", "222", "F", "S", "17", "79047907", "79047907", "T", "C", "1", "92", "1.1", "tcga", "3953", "DOID:3953 / adrenal gland cancer", "protein_xref_biomuta", "Q9BXJ1", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.1%).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P38435-1", "704", "R", "Q", "2", "85550100", "85550100", "C", "T", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "P38435", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P46019-1", "930", "R", "W", "X", "18906513", "18906513", "G", "A", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "P46019", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P12259-1", "345", "R", "W", "1", "169555267", "169555267", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "P12259", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q6IS24-1", "105", "P", "L", "7", "71335625", "71335625", "C", "T", "0", "0", "0.0", "icgc", "5041", "DOID:5041 / esophageal cancer", "protein_xref_biomuta", "Q6IS24", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "O75335-3", "488", "R", "H", "1", "203049707", "203049707", "G", "A", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "O75335", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8N5C1-1", "32", "R", "C", "6", "116511790", "116511790", "C", "T", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q8N5C1", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P10253-1", "816", "V", "I", "17", "80117714", "80117714", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "P10253", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q86U10-1", "364", "S", "L", "14", "104105368", "104105368", "C", "T", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q86U10", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q76N89-1", "1232", "R", "C", "7", "43507199", "43507199", "C", "T", "0", "0", "0.0", "icgc", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "Q76N89", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q86Y91-5", "503", "R", "H", "17", "44931611", "44931611", "C", "T", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q86Y91", "Somatic mutation passed 1 out of 6 filters: num. of cancers (5).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P29475-1", "572", "V", "M", "12", "117272510", "117272510", "C", "T", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "P29475", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0", "", "1", "" ] ] }, "readme": "Name\n - Human Cancer Mutation\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2019-01-23T17:21:05.891293\n\nModified on\n - 2022-09-26T08:48:18.834228\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - Not Applicable []\n\nChecksum\n - \n\nUsability Domain\n - The Human Cancer Mutation dataset contains human [taxid:9606] mutation data from BioMuta database (https://hive.biochemistry.gwu.edu/biomuta).\n - The current version of BioMuta contains only nonsynonymous single-nucleotide variations (nsSNVs) associated with cancer.\n - BioMuta is a single-nucleotide variation (SNV) and disease association database where variations are mapped to genomes and NCBI RefSeq nucleotide entries, and unified through UniProtKB/Swiss-Prot positional coordinates.\n - The dataset is imported and contributed by BioMuta and processed by GlyGen. If you use this dataset please provide proper attribution to BioMuta and GlyGen. \n - Note the mutation shown in GlyGen are annotated based on passing of one or more filter criterias.\n - Filter criteria 1 - Positive Patient's Frequency Ratio \u2265 1.0%\n - Filter criteria 2 - Presence of mutation in number of cancer types \u2265 3 cancer types\n - Filter criteria 3 - Positive Patient's count \u2265 10 patients\n - Filter criteria 4 - Mutation reported and annotated in number of databases\n - Filter criteria 5 - Mutation minned from the literature using literaure mining tools (human_protein_mutation_literature.csv)\n - If there is also a germline mutation reported in dbSNP, the rsid is also shown\n - These filter criteria annotations are shown on the front end under the column Annotation Name\n - Also if the same mutation in the same cancer type on a given protein is reported in ICGC and TCGA then mutations from TCGA are only shown.\n - When mutations from TCGA are not available but are present in ICGC for the same protein and cancer type, ICGC mutations are shown in GlyGen\n - Two different DO child terms are merged into one single entry showing the parent cancer DO term from the DO cancer slim.\n - On the GlyGen interface, in Mutations section the mutations that have passed highest number of filter criteria are displayed first irrespective of their amio acid positions. For eg. the mutation entry that has passed 5 filter criteria will be shown first.\n\nDescription Domain\n Keywords\n - single-nucleotide variations (nsSNVs)\n - cancer mutations\n - BioMuta\n - disease\n\n Pipeline Steps\n - Step-1: The script extracts the mutation data from the BioMuta and maps the UniProtKB accession to the UniProtKB canonical accessions as per the criterias\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: glycan_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/glycan_masterlist.csv\n Name: human_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/human_protein_masterlist.csv\n Name: human_protein_mutation_literature.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/human_protein_mutation_literature.csv\n Name: protein_disease_idmap.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/protein_disease_idmap.csv\n Name: aadict.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/misc/aadict.csv\n Name: biomuta.csv\n URI: /data/shared/glyds/downloads/biomuta/v-5.0/biomuta.csv\n Name: clinical_information.csv\n URI: /data/shared/glyds/downloads/biomuta/v-5.0/clinical_information.csv\n Name: dbSNP-homo-sapiens.tsv\n URI: /data/shared/glyds/downloads/ebi/2023_02/dbSNP-homo-sapiens.tsv\n Output Subdomain\n Name: human_protein_mutation_cancer.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/human_protein_mutation_cancer.csv\n Name: human_protein_mutation_cancer.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/human_protein_mutation_cancer.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"6558\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"2108\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"20\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"21\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"24\"\n Name: \"chr_start_pos\"\n Description: \"\"\n Unique Values: \"12731\"\n Name: \"chr_end_pos\"\n Description: \"\"\n Unique Values: \"12731\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"4\"\n Name: \"patients_positive\"\n Description: \"The number of the patients having the cancer mutation\"\n Unique Values: \"10\"\n Name: \"patients_tested\"\n Description: \"The total number of patients tested for the given cancer mutation\"\n Unique Values: \"28\"\n Name: \"mut_freq\"\n Description: \"Frequency count of mutations across datasets\"\n Unique Values: \"23\"\n Name: \"data_source\"\n Description: \"The source database for the data\"\n Unique Values: \"3\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"24\"\n Name: \"do_name\"\n Description: \"Disease Ontology term or name for the disease assigned to the Disease Ontology identifier\"\n Unique Values: \"25\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"6558\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"768\"\n Name: \"glyco_annotation\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"1\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/human_protein_mutation_cancer.csv" }