{ "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": "chr_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" }, { "type": "string", "label": "mim_id" }, { "type": "string", "label": "somatic_status" }, { "type": "string", "label": "minor_allelic_frequency" } ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "P30711-1", "188", "R", "P", "22", "24376583", "C", "G", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "P30711", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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). In dbSNP: rs201539458.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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). In dbSNP: rs1337913321.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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). In dbSNP: rs79029897.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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 2 out of 6 filters: patient freq. (2.0%); o-glyco-site-loss (S->C).", "glycancount:1, pmidcount:7", "", "1", "" ], [ "Q96AQ1-1", "122", "G", "R", "2", "132288220", "G", "A", "1", "820", "0.1", "tcga", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q96AQ1", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P01588-1", "166", "R", "H", "7", "100320671", "G", "A", "1", "399", "0.3", "tcga", "1793", "DOID:1793 / pancreatic cancer", "protein_xref_biomuta", "P01588", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q8N5T2-1", "100", "S", "I", "4", "26638837", "G", "T", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q8N5T2", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q96C55-1", "28", "P", "H", "19", "56113561", "C", "A", "1", "50", "2.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "Q96C55", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.0%).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "P17017-1", "603", "R", "*", "19", "19822283", "G", "A", "3", "558", "0.5", "tcga", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P17017", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3). In dbSNP: rs757216310.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "Q96M86-3", "1772", "R", "Q", "11", "6567484", "G", "A", "1", "48", "2.1", "tcga", "2531", "DOID:2531 / hematologic cancer", "protein_xref_biomuta", "Q96M86", "Somatic mutation passed 1 out of 6 filters: patient freq. (2.1%).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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%). In dbSNP: rs1001718385.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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). In dbSNP: rs199533546.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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). In dbSNP: rs746060364.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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). In dbSNP: rs763991701.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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). In dbSNP: rs753095324.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "P33241-1", "310", "K", "N", "11", "1908544", "G", "T", "1", "456", "0.2", "tcga", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "P33241", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KST->NST).", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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). In dbSNP: rs749957963.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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 2 out of 6 filters: num. of cancers (10); o-glyco-site-loss (T->A). In dbSNP: rs121913412.", "glycancount:1, pmidcount:15", "", "1", "" ], [ "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%). In dbSNP: rs989472796.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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). In dbSNP: rs121913254.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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). In dbSNP: rs142357329.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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). In dbSNP: rs528840784.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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). In dbSNP: rs782393826.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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). In dbSNP: rs776904737.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ], [ "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). In dbSNP: rs779893104.", "glycancount:0, pmidcount:0", "", "1", "" ], [ "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", "", "1", "" ], [ "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", "", "1", "" ] ] }, "readme": "Name\n - Human Cancer Mutation\n\nVersion\n - 1.8.25\n\nCreated on\n - 2019-01-23T17:21:05.891293\n\nModified on\n - 2021-03-24T15:39:40.641123\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 (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/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/ln2data/releases/data/v-1.8.25/source/mutid-map.final.csv\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_protein_masterlist.csv\n Name: human_cancer_mutation_literature.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_cancer_mutation_literature.csv\n Name: human_cancer_mutation_somatic.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_cancer_mutation_somatic.csv\n Name: human_cancer_mutation_literature.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_cancer_mutation_literature.csv\n Output Subdomain\n Name: human_protein_mutation_cancer.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_protein_mutation_cancer.csv\n Name: human_protein_mutation_cancer.stat.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_protein_mutation_cancer.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.25/reviewed/human_protein_mutation_cancer.csv" }