{ "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": [ [ "Q08AF3-1...", "468..." ], [ "P0C862-1...", "67..." ] ], "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": "chromosome_id" }, { "type": "string", "label": "chr_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" } ], [ "Q08AF3-1", "468", "M", "L", "17", "33591465", "A", "T", "1", "50", "2.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q08AF3", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "P0C862-1", "67", "D", "N", "13", "24892988", "G", "A", "1", "820", "0.1", "tcga", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "P0C862", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DGT->NGT).", "glycancount:0, pmidcount:0" ], [ "O95907-1", "69", "Y", "*", "22", "38478674", "G", "T", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "O95907", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q8IZV5-1", "47", "G", "D", "8", "74207664", "G", "A", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q8IZV5", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q5T5N4-1", "212", "A", "T", "6", "165715177", "C", "T", "1", "456", "0.2", "tcga", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q5T5N4", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "O14646-1", "462", "R", "M", "5", "98233005", "C", "A", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "O14646", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "O60291-1", "78", "H", "Q", "16", "4701990", "C", "G", "1", "66", "1.5", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "O60291", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.5%).", "glycancount:0, pmidcount:0" ], [ "Q9UPZ3-1", "223", "F", "V", "11", "18327839", "A", "C", "1", "103", "1.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q9UPZ3", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.0%).", "glycancount:0, pmidcount:0" ], [ "O60486-1", "1175", "V", "E", "12", "94658928", "T", "A", "1", "25", "4.0", "icgc", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "O60486", "Somatic mutation passed 1 out of 6 filters: patient freq. (4.0%).", "glycancount:0, pmidcount:0" ], [ "Q96RT1-1", "264", "S", "P", "5", "65320251", "T", "C", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q96RT1", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "O00160-1", "644", "R", "W", "19", "8601249", "G", "A", "1", "558", "0.2", "tcga", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "O00160", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "A6NJZ7-1", "1273", "S", "G", "22", "21901449", "T", "C", "1", "103", "1.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "A6NJZ7", "Somatic mutation passed 2 out of 6 filters: patient freq. (1.0%); num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q6PIZ9-1", "179", "R", "H", "3", "108572699", "G", "A", "1", "162", "0.6", "tcga", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q6PIZ9", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0" ], [ "P05787-1", "37", "S", "C", "12", "53298657", "T", "A", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "P05787", "Somatic mutation passed 1 out of 6 filters: patient freq. 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(2.1%).", "glycancount:0, pmidcount:0" ], [ "Q9Y5I1-1", "620", "P", "T", "5", "140250546", "C", "A", "1", "72", "1.4", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q9Y5I1", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.4%).", "glycancount:0, pmidcount:0" ], [ "Q5T1V6-1", "111", "C", "W", "1", "200635536", "A", "C", "1", "94", "1.1", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q5T1V6", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.1%).", "glycancount:0, pmidcount:0" ], [ "Q86XP6-1", "83", "I", "M", "2", "69174345", "G", "C", "1", "103", "1.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q86XP6", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.0%).", "glycancount:0, pmidcount:0" ], [ "Q13233-1", "1383", "R", "K", "5", "56183238", "G", "A", "1", "25", "4.0", "icgc", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "Q13233", "Somatic mutation passed 1 out of 6 filters: patient freq. (4.0%).", "glycancount:0, pmidcount:0" ], [ "P23526-1", "68", "V", "I", "20", "32883218", "C", "T", "1", "456", "0.2", "tcga", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "P23526", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q14194-1", "16", "R", "*", "4", "5868477", "G", "A", "1", "48", "2.1", "tcga", "2531", "DOID:2531 / hematologic cancer", "protein_xref_biomuta", "Q14194", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.1%).", "glycancount:0, pmidcount:0" ], [ "P0C7Q6-1", "105", "Y", "C", "17", "7385617", "A", "G", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "P0C7Q6", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q6ZQQ6-1", "2141", "R", "W", "19", "38377773", "G", "A", "1", "254", "0.4", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q6ZQQ6", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q66K14-1", "939", "S", "*", "5", "179294825", "G", "T", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q66K14", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q8N7X1-1", "52", "A", "T", "X", "114424158", "G", "A", "1", "558", "0.2", "tcga", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q8N7X1", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q8NGE9-1", "248", "V", "I", "11", "57958704", "G", "A", "1", "1514", "0.1", "tcga", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q8NGE9", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q86SZ2-1", "100", "R", "H", "14", "39623467", "C", "T", "1", "1118", "0.1", "tcga", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "Q86SZ2", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q96LP2-1", "368", "Q", "E", "5", "94784045", "C", "G", "1", "1514", "0.1", "tcga", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q96LP2", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q9Y4F9-1", "233", "R", "W", "6", "24850926", "G", "A", "1", "678", "0.1", "tcga", "1319", "DOID:1319 / brain cancer", "protein_xref_biomuta", "Q9Y4F9", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q7LGC8-1", "189", "R", "H", "10", "73767355", "G", "A", "1", "72", "1.4", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q7LGC8", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.4%).", "glycancount:0, pmidcount:0" ], [ "Q6DHY5-1", "507", "A", "T", "17", "34797617", "C", "T", "1", "103", "1.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q6DHY5", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.0%).", "glycancount:0, pmidcount:0" ], [ "Q9H5Z1-1", "554", "A", "S", "20", "37652399", "G", "T", "1", "66", "1.5", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q9H5Z1", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.5%).", "glycancount:0, pmidcount:0" ], [ "Q05639-1", "418", "Y", "S", "20", "62120282", "T", "G", "1", "350", "0.3", "tcga", "4362", "DOID:4362 / cervical cancer", "protein_xref_biomuta", "Q05639", "Somatic mutation passed 1 out of 6 filters: num. of cancers (10).", "glycancount:0, pmidcount:0" ], [ "P06331-1", "5", "H", "L", "14", "106830032", "T", "A", "1", "38", "2.6", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "P06331", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.6%).", "glycancount:0, pmidcount:0" ], [ "P12882-1", "1568", "E", "A", "17", "10399820", "T", "G", "2", "191", "1.0", "tcga", "5041", "DOID:5041 / esophageal cancer", "protein_xref_biomuta", "P12882", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.0%).", "glycancount:0, pmidcount:0" ], [ "O14495-1", "153", "R", "C", "1", "56990067", "G", "A", "1", "399", "0.3", "tcga", "1793", "DOID:1793 / pancreatic cancer", "protein_xref_biomuta", "O14495", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "P35222-1", "41", "T", "A", "3", "41266124", "A", "G", "3", "1118", "0.3", "tcga", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "P35222", "Somatic mutation passed 1 out of 6 filters: num. of cancers (10). In dbSNP: rs121913412.", "glycancount:0, pmidcount:0" ], [ "Q9H6A9-1", "167", "R", "W", "11", "65385099", "C", "T", "1", "93", "1.1", "icgc", "2394", "DOID:2394 / ovarian cancer", "protein_xref_biomuta", "Q9H6A9", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.1%).", "glycancount:0, pmidcount:0" ], [ "Q2M3G0-4", "1196", "H", "N", "7", "20795059", "C", "A", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q2M3G0", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q969V6-1", "277", "Q", "H", "22", "40816901", "C", "G", "2", "820", "0.2", "tcga", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q969V6", "Somatic mutation passed 1 out of 6 filters: num. of cancers (6).", "glycancount:0, pmidcount:0" ], [ "Q9BZF9-1", "104", "A", "D", "15", "70983693", "G", "T", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q9BZF9", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q9Y6Y1-1", "1636", "Q", "*", "1", "7812541", "C", "T", "1", "103", "1.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q9Y6Y1", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.0%).", "glycancount:0, pmidcount:0" ], [ "Q14190-1", "280", "A", "T", "21", "38103440", "G", "A", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q14190", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q9HCD5-1", "538", "P", "S", "20", "44691067", "G", "A", "1", "820", "0.1", "tcga", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q9HCD5", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NPS->NSS).", "glycancount:0, pmidcount:0" ], [ "O60347-1", "732", "S", "L", "10", "96291153", "C", "T", "1", "742", "0.1", "tcga", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "O60347", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q96MG8-1", "162", "R", "Q", "8", "52746175", "C", "T", "1", "1144", "0.1", "tcga", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q96MG8", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0" ], [ "Q9NQG6-1", "410", "Q", "L", "22", "39910165", "A", "T", "1", "103", "1.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q9NQG6", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.0%).", "glycancount:0, pmidcount:0" ], [ "Q13620-2", "369", "R", "Q", "X", "119678367", "C", "T", "1", "1144", "0.1", "tcga", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q13620", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0" ], [ "P43354-1", "100", "Y", "N", "2", "157186401", "A", "T", "2", "150", "1.3", "tcga", "2531", "DOID:2531 / hematologic cancer", "protein_xref_biomuta", "P43354", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.3%).", "glycancount:0, pmidcount:0" ], [ "Q9UPV9-1", "139", "K", "N", "3", "42226230", "G", "T", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q9UPV9", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "P50391-1", "135", "V", "M", "10", "47087186", "G", "A", "1", "678", "0.1", "tcga", "1319", "DOID:1319 / brain cancer", "protein_xref_biomuta", "P50391", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "P14867-1", "421", "R", "*", "5", "161324318", "C", "T", "4", "678", "0.6", "tcga", "1319", "DOID:1319 / brain cancer", "protein_xref_biomuta", "P14867", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q14318-1", "279", "A", "E", "19", "18648517", "G", "T", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q14318", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "P01111-1", "61", "Q", "K", "1", "115256530", "G", "T", "1", "93", "1.1", "icgc", "2394", "DOID:2394 / ovarian cancer", "protein_xref_biomuta", "P01111", "Somatic mutation passed 2 out of 6 filters: patient freq. (1.1%); num. of cancers (14).", "glycancount:0, pmidcount:0" ], [ "Q13515-1", "218", "L", "F", "3", "133167414", "G", "T", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q13515", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q7Z6G8-1", "26", "R", "W", "12", "100377940", "T", "A", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q7Z6G8", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q9UBU7-1", "462", "L", "F", "7", "87536837", "C", "T", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q9UBU7", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "P38432-1", "115", "Q", "*", "17", "55028260", "G", "A", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "P38432", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q8N0X2-1", "437", "R", "C", "2", "214794778", "C", "T", "1", "742", "0.1", "tcga", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q8N0X2", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q5QP82-1", "8", "S", "R", "9", "37800887", "C", "A", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q5QP82", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "O43405-1", "91", "R", "Q", "14", "31348049", "G", "A", "1", "980", "0.1", "tcga", "11934", "DOID:11934 / head and neck cancer", "protein_xref_biomuta", "O43405", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "O95477-1", "136", "K", "N", "9", "107645333", "C", "A", "1", "456", "0.2", "tcga", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "O95477", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KKS->NKS).", "glycancount:0, pmidcount:0" ], [ "P08922-1", "1737", "E", "*", "6", "117658374", "C", "A", "1", "558", "0.2", "tcga", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P08922", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q9UPA5-1", "2031", "R", "C", "3", "49693080", "C", "T", "1", "125", "0.8", "icgc", "2531", "DOID:2531 / hematologic cancer", "protein_xref_biomuta", "Q9UPA5", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q92731-1", "501", "R", "C", "14", "64699947", "G", "A", "30", "1514", "2.0", "tcga", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q92731", "Somatic mutation passed 2 out of 6 filters: patient freq. (2.0%); patient count (30/1514).", "glycancount:0, pmidcount:0" ], [ "P17213-1", "425", "G", "S", "20", "36959481", "G", "A", "1", "820", "0.1", "tcga", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "P17213", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NIG->NIS).", "glycancount:0, pmidcount:0" ], [ "Q9UBN7-1", "506", "R", "H", "X", "48674571", "G", "A", "1", "558", "0.2", "tcga", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9UBN7", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "A1KZ92-1", "251", "V", "I", "8", "52384808", "C", "T", "1", "1144", "0.1", "tcga", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "A1KZ92", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q9UBE0-1", "78", "A", "T", "19", "47653480", "G", "A", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q9UBE0", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q15878-1", "802", "A", "V", "1", "181701627", "C", "T", "1", "558", "0.2", "tcga", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q15878", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0" ], [ "Q6UXN9-1", "71", "Y", "H", "3", "52304776", "A", "G", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q6UXN9", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q5TC12-1", "191", "A", "T", "1", "47118270", "C", "T", "1", "66", "1.5", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q5TC12", "Somatic mutation passed 1 out of 6 filters: patient freq. (1.5%).", "glycancount:0, pmidcount:0" ], [ "O95238-1", "197", "L", "P", "6", "34508805", "A", "G", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "O95238", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q8NHY0-1", "510", "V", "A", "17", "47246918", "T", "C", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q8NHY0", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q9H7T0-1", "155", "R", "*", "14", "92174488", "G", "A", "1", "215", "0.5", "icgc", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "Q9H7T0", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "glycancount:0, pmidcount:0" ], [ "Q8IX15-1", "539", "D", "E", "14", "23744820", "A", "T", "1", "66", "1.5", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q8IX15", "Somatic mutation passed 2 out of 6 filters: patient freq. (1.5%); num. of cancers (5).", "glycancount:0, pmidcount:0" ], [ "Q9H114-1", "66", "R", "K", "20", "23421101", "G", "A", "1", "50", "2.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q9H114", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "Q6IPR3-1", "174", "A", "E", "1", "75218070", "C", "A", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q6IPR3", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0" ], [ "O60481-1", "102", "P", "A", "X", "136649154", "C", "G", "1", "38", "2.6", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "O60481", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.6%).", "glycancount:0, pmidcount:0" ] ] }, "readme": "Name\n - Human Cancer Mutation\n\nVersion\n - 1.5.30\n\nCreated on\n - 2019-01-23T17:21:05.891293\n\nModified on\n - 2020-04-10T11:26:06.487519\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - \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\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/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: mutid-map.final.csv\n URI: https://data.glygen.org/ln2wwwdata/source/mutid-map.final.csv\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_masterlist.csv\n Name: human_cancer_mutation_literature.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_cancer_mutation_literature.csv\n Name: human_cancer_mutation_somatic.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_cancer_mutation_somatic.csv\n Name: human_cancer_mutation_literature.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_cancer_mutation_literature.csv\n Output Subdomain\n Name: human_protein_mutation_cancer.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_mutation_cancer.csv\n Name: human_protein_mutation_cancer.stat.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_mutation_cancer.stat.csv\n\nFields\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"21\"\n Name: \"glyco_annotation\"\n Description: \"\"\n Unique Values: \"54\"\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"17141\"\n Name: \"data_source\"\n Description: \"The source database for the data\"\n Unique Values: \"2\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"4\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"3482\"\n Name: \"xref_id\"\n Description: \"\"\n Unique Values: \"17141\"\n Name: \"patients_positive\"\n Description: \"The number of the patients having the cancer mutation\"\n Unique Values: \"61\"\n Name: \"chromosome_id\"\n Description: \"Chromosome number identifier\"\n Unique Values: \"24\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"136294\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"4908\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"21\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"20\"\n Name: \"mut_freq\"\n Description: \"Frequency count of mutations across datasets\"\n Unique Values: \"100\"\n Name: \"do_name\"\n Description: \"Disease Ontology term or name for the disease assigned to the Disease Ontology identifier\"\n Unique Values: \"21\"\n Name: \"patients_tested\"\n Description: \"The total number of patients tested for the given cancer mutation\"\n Unique Values: \"128\"\n Name: \"xref_key\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.5.30/reviewed/human_protein_mutation_cancer.csv" }