{ "bcoid": "GLY_000507", "title": "Human Cancer Mutation LOG and GOG effect", "description": "", "filename": "human_protein_mutation_cancer_glycoeffect.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Protein", "tags": "Somatic Cancer Mutations LOG-GOG", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q9NYU1-1...", "1398..." ], [ "A6NJZ7-1...", "1273..." ] ], "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": "mim_id" }, { "type": "string", "label": "somatic_status" }, { "type": "string", "label": "minor_allelic_frequency" }, { "type": "string", "label": "is_known_glycoprotein" }, { "type": "string", "label": "motif_start" }, { "type": "string", "label": "ref_motif" }, { "type": "string", "label": "alt_motif" }, { "type": "string", "label": "effect" } ], [ "Q9NYU1-1", "1398", "K", "N", "13", "95853633", "95853633", "C", "G", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q9NYU1", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "1398", "K", "N", "o-glyco-site-loss" ], [ "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).", "", "1", "", "no", "1273", "S", "G", "o-glyco-site-loss" ], [ "P05787-1", "37", "S", "C", "12", "52904873", "52904873", "T", "A", "0", "0", "0.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "P05787", "Somatic mutation passed 1 out of 6 filters: o-glyco-site-loss (S->C).", "", "1", "", "yes", "37", "S", "C", "o-glyco-site-loss" ], [ "Q8WXI7-1", "12100", "N", "I", "19", "8922962", "8922962", "T", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q8WXI7", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-loss (NAT->IAT).", "", "1", "", "yes", "12100", "NAT", "IAT", "n-glyco-sequon-loss" ], [ "P21796-1", "78", "D", "N", "5", "133991040", "133991040", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P21796", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DNT->NNT).", "", "1", "", "yes", "78", "DNT", "NNT", "n-glyco-sequon-gain" ], [ "P17655-1", "68", "S", "G", "1", "223712842", "223712842", "A", "G", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "P17655", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "68", "S", "G", "o-glyco-site-loss" ], [ "Q9Y458-1", "268", "T", "M", "X", "80027260", "80027260", "C", "T", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q9Y458", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "268", "T", "M", "o-glyco-site-loss" ], [ "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).", "", "1", "", "yes", "355", "K", "N", "o-glyco-site-loss" ], [ "P48307-1", "33", "A", "T", "7", "93890311", "93890311", "C", "T", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "P48307", "Somatic mutation passed 2 out of 6 filters: num. of cancers (3); n-glyco-sequon-gain (NNA->NNT).", "", "1", "", "yes", "31", "NNA", "NNT", "n-glyco-sequon-gain" ], [ "P04637-1", "241", "S", "C", "17", "7674241", "7674241", "G", "C", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P04637", "Somatic mutation passed 1 out of 6 filters: num. of cancers (19). 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In dbSNP: rs28934573.", "", "1", "", "yes", "241", "S", "C", "o-glyco-site-loss" ], [ "Q92752-1", "465", "D", "N", "1", "175391402", "175391402", "C", "T", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q92752", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DVT->NVT).", "", "1", "", "yes", "465", "DVT", "NVT", "n-glyco-sequon-gain" ], [ "Q9HC56-1", "714", "K", "N", "13", "67226299", "67226299", "C", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9HC56", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KYT->NYT).", "", "1", "", "yes", "714", "KYT", "NYT", "n-glyco-sequon-gain" ], [ "Q9HC56-1", "714", "K", "N", "13", "67226299", "67226299", "C", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9HC56", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KYT->NYT).", "", "1", "", "yes", "714", "K", "N", 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"protein_xref_biomuta", "Q9UPA5", "Somatic mutation passed 1 out of 6 filters: o-glyco-site-loss (T->I).", "", "1", "", "yes", "1987", "T", "I", "o-glyco-site-loss" ], [ "Q9ULM3-1", "880", "S", "L", "3", "183777603", "183777603", "C", "T", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q9ULM3", "Somatic mutation passed 1 out of 6 filters: o-glyco-site-loss (S->L).", "", "1", "", "yes", "880", "S", "L", "o-glyco-site-loss" ], [ "Q6S8J3-1", "173", "K", "N", "2", "131218921", "131218921", "G", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q6S8J3", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KRT->NRT).", "", "1", "", "yes", "173", "KRT", "NRT", "n-glyco-sequon-gain" ], [ "Q6S8J3-1", "173", "K", "N", "2", "131218921", "131218921", "G", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q6S8J3", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KRT->NRT).", "", "1", "", "yes", "173", "K", "N", "o-glyco-site-loss" ], [ "P13727-1", "23", "T", "N", "11", "57389308", "57389308", "G", "T", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "P13727", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (TST->NST); o-glyco-site-loss (T->N).", "", "1", "", "yes", "23", "TST", "NST", "n-glyco-sequon-gain" ], [ "P13727-1", "23", "T", "N", "11", "57389308", "57389308", "G", "T", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "P13727", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (TST->NST); o-glyco-site-loss (T->N).", "", "1", "", "yes", "23", "T", "N", "o-glyco-site-loss" ], [ "Q9P0L2-1", "648", "T", "M", "1", "220653307", "220653307", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9P0L2", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "648", "T", "M", "o-glyco-site-loss" ], [ "Q96RV3-1", "702", "N", "K", "14", "70978443", "70978443", "T", "G", "0", "0", "0.0", "icgc", "11934", "DOID:11934 / head and neck cancer", "protein_xref_biomuta", "Q96RV3", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-loss (NDS->KDS).", "", "1", "", "yes", "702", "NDS", "KDS", "n-glyco-sequon-loss" ], [ "O75628-1", "142", "D", "N", "20", "31482287", "31482287", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "O75628", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DKS->NKS).", "", "1", "", "yes", "142", "DKS", "NKS", "n-glyco-sequon-gain" ], [ "Q7LBE3-1", "324", "S", "L", "1", "205928032", "205928032", "G", "A", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q7LBE3", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "324", "S", "L", "o-glyco-site-loss" ], [ "O95171-1", "383", "N", "S", "13", "77604406", "77604406", "A", "G", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "O95171", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NKN->NKS).", "", "1", "", "yes", "383", "NIT", "SIT", "n-glyco-sequon-loss" ], [ "O95171-1", "383", "N", "S", "13", "77604406", "77604406", "A", "G", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "O95171", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NKN->NKS).", "", "1", "", "yes", "381", "NKN", "NKS", "n-glyco-sequon-gain" ], [ "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 (5).", "", "1", "", "yes", "1274", "T", "M", "o-glyco-site-loss" ], [ "Q86SQ4-1", "70", "T", "M", "6", "142367674", "142367674", "C", "T", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q86SQ4", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "70", "T", "M", "o-glyco-site-loss" ], [ "Q5T752-1", "107", "S", "G", "1", "152798113", "152798113", "A", "G", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q5T752", "Somatic mutation passed 1 out of 6 filters: num. of cancers (6).", "", "1", "", "no", "107", "S", "G", "o-glyco-site-loss" ], [ "Q9Y4C5-1", "227", "D", "N", "3", "143121495", "143121495", "G", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9Y4C5", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DLS->NLS).", "", "1", "", "yes", "227", "DLS", "NLS", "n-glyco-sequon-gain" ], [ "Q9UBL0-1", "56", "S", "F", "3", "35682885", "35682885", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9UBL0", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "56", "S", "F", "o-glyco-site-loss" ], [ "Q9BQ31-1", "307", "S", "L", "2", "17931928", "17931928", "C", "T", "0", "0", "0.0", "icgc", "11934", "DOID:11934 / head and neck cancer", "protein_xref_biomuta", "Q9BQ31", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "no", "307", "S", "L", "o-glyco-site-loss" ], [ "Q96RN5-1", "73", "K", "T", "22", "20553154", "20553154", "A", "C", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q96RN5", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NKK->NKT).", "", "1", "", "yes", "71", "NKK", "NKT", "n-glyco-sequon-gain" ], [ "P36776-1", "80", "S", "L", "19", "5719894", "5719894", "G", "A", "0", "0", "0.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "P36776", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "80", "S", 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"protein_xref_biomuta", "P29401", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KIS->NIS).", "", "1", "", "yes", "102", "K", "N", "o-glyco-site-loss" ], [ "Q8N2S1-1", "1028", "S", "P", "19", "40616957", "40616957", "T", "C", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q8N2S1", "Somatic mutation passed 1 out of 6 filters: o-glyco-site-loss (S->P).", "", "1", "", "yes", "1028", "S", "P", "o-glyco-site-loss" ], [ "Q9UEF7-1", "919", "D", "N", "13", "33063902", "33063902", "G", "A", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q9UEF7", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DRT->NRT).", "", "1", "", "yes", "919", "DRT", "NRT", "n-glyco-sequon-gain" ], [ "P25311-1", "298", "S", "R", "7", "99967006", "99967006", "G", "T", "0", "0", "0.0", "icgc", "11934", "DOID:11934 / head and neck cancer", "protein_xref_biomuta", "P25311", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "298", "S", "R", "o-glyco-site-loss" ], [ "A6NHR9-1", "1709", "S", "L", "18", "2772323", "2772323", "C", "T", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "A6NHR9", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "1709", "S", "L", "o-glyco-site-loss" ], [ "P35663-1", "159", "D", "N", "X", "83873183", "83873183", "G", "A", "0", "0", "0.0", "icgc", "4362", "DOID:4362 / cervical cancer", "protein_xref_biomuta", "P35663", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DKT->NKT).", "", "1", "", "yes", "159", "DKT", "NKT", "n-glyco-sequon-gain" ], [ "Q8WYK1-1", "287", "K", "N", "2", "124446880", "124446880", "G", "T", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q8WYK1", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KHT->NHT).", "", "1", "", "yes", "287", "KHT", "NHT", "n-glyco-sequon-gain" ], [ "Q8WYK1-1", "287", "K", "N", "2", "124446880", "124446880", "G", "T", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q8WYK1", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KHT->NHT).", "", "1", "", "yes", "287", "K", "N", "o-glyco-site-loss" ], [ "Q9Y5I1-1", "725", "T", "M", "5", "140871277", "140871277", "C", "T", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q9Y5I1", "Somatic mutation passed 1 out of 6 filters: num. of cancers (8).", "", "1", "", "yes", "725", "T", "M", "o-glyco-site-loss" ], [ "Q9Y5H3-1", "627", "T", "M", "5", "141415055", "141415055", "C", "T", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q9Y5H3", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "627", "T", "M", "o-glyco-site-loss" ], [ "P22459-1", "111", "S", "N", "11", "30012347", "30012347", "C", "T", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "P22459", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (SGS->NGS).", "", "1", "", "yes", "111", "SGS", "NGS", "n-glyco-sequon-gain" ], [ "P22459-1", "111", "S", "N", "11", "30012347", "30012347", "C", "T", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "P22459", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (SGS->NGS).", "", "1", "", "yes", "111", "S", "N", "o-glyco-site-loss" ], [ "Q9H4M9-1", "201", "S", "L", "11", "64860237", "64860237", "G", "A", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q9H4M9", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "201", "S", "L", "o-glyco-site-loss" ], [ "Q9H306-1", "145", "K", "N", "11", "102703025", "102703025", "T", "G", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q9H306", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KFT->NFT).", "", "1", "", "yes", "145", "KFT", "NFT", "n-glyco-sequon-gain" ], [ "Q9H306-1", "145", "K", "N", "11", "102703025", "102703025", "T", "G", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q9H306", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KFT->NFT).", "", "1", "", "yes", "145", "K", "N", "o-glyco-site-loss" ], [ "P62079-1", "49", "N", "H", "4", "98486872", "98486872", "T", "G", "0", "0", "0.0", "icgc", "11934", "DOID:11934 / head and neck cancer", "protein_xref_biomuta", "P62079", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-loss (NIS->HIS).", "", "1", "", "yes", "49", "NIS", "HIS", "n-glyco-sequon-loss" ], [ "O60741-1", "642", "P", "S", "5", "45262670", "45262670", "G", "A", "0", "0", "0.0", "icgc", "11934", "DOID:11934 / head and neck cancer", "protein_xref_biomuta", "O60741", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NYP->NYS).", "", "1", "", "yes", "640", "NYP", "NYS", "n-glyco-sequon-gain" ], [ "Q9GZW8-1", "162", "S", "L", "11", "60389535", "60389535", "C", "T", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q9GZW8", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "162", "S", "L", "o-glyco-site-loss" ], [ "Q13509-1", "149", "T", "M", "16", "89934897", "89934897", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q13509", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "149", "T", "M", "o-glyco-site-loss" ], [ "A8MTB9-1", "114", "T", "I", "19", "51480621", "51480621", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "A8MTB9", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-loss (NYT->NYI).", "", "1", "", "yes", "112", "NYT", "NYI", "n-glyco-sequon-loss" ], [ "A8MTB9-1", "114", "T", "I", "19", "51480621", "51480621", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "A8MTB9", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-loss (NYT->NYI).", "", "1", "", "yes", "114", "T", "I", "o-glyco-site-loss" ], [ "Q86TC9-1", "691", "S", "N", "10", "68174164", "68174164", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q86TC9", "Somatic mutation passed 2 out of 6 filters: num. of cancers (3); n-glyco-sequon-gain (SMT->NMT); o-glyco-site-loss (S->N).", "", "1", "", "yes", "691", "SMT", "NMT", "n-glyco-sequon-gain" ], [ "Q86TC9-1", "691", "S", "N", "10", "68174164", "68174164", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q86TC9", "Somatic mutation passed 2 out of 6 filters: num. of cancers (3); n-glyco-sequon-gain (SMT->NMT); o-glyco-site-loss (S->N).", "", "1", "", "yes", "691", "S", "N", "o-glyco-site-loss" ], [ "Q8WZ42-1", "29191", "D", "N", "2", "178549132", "178549132", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q8WZ42", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DTS->NTS).", "", "1", "", "yes", "29191", "DTS", "NTS", "n-glyco-sequon-gain" ], [ "P49790-1", "1003", "S", "Y", "6", "17629191", "17629191", "G", "T", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "P49790", "Somatic mutation passed 1 out of 6 filters: o-glyco-site-loss (S->Y).", "", "1", "", "yes", "1003", "S", "Y", "o-glyco-site-loss" ], [ "Q9P232-1", "975", "K", "N", "3", "74266542", "74266542", "C", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q9P232", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KAT->NAT).", "", "1", "", "yes", "975", "KAT", "NAT", "n-glyco-sequon-gain" ], [ "Q9P232-1", "975", "K", "N", "3", "74266542", "74266542", "C", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q9P232", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KAT->NAT).", "", "1", "", "yes", "975", "K", "N", "o-glyco-site-loss" ], [ "Q96HI0-1", "124", "K", "N", "3", "196885553", "196885553", "G", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q96HI0", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KNS->NNS).", "", "1", "", "yes", "124", "KNS", "NNS", "n-glyco-sequon-gain" ], [ "Q96HI0-1", "124", "K", "N", "3", "196885553", "196885553", "G", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q96HI0", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KNS->NNS).", "", "1", "", "yes", "124", "K", "N", "o-glyco-site-loss" ], [ "Q969N4-1", "6", "S", "F", "6", "132552709", "132552709", "C", "T", "1", "470", "0.2", "tcga", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q969N4", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-loss (NFS->NFF).", "", "1", "", "yes", "4", "NFS", "NFF", "n-glyco-sequon-loss" ], [ "Q969N4-1", "6", "S", "F", "6", "132552709", "132552709", "C", "T", "1", "470", "0.2", "tcga", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q969N4", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-loss (NFS->NFF).", "", "1", "", "yes", "6", "S", "F", "o-glyco-site-loss" ], [ "Q8IVF2-1", "3095", "T", "M", "14", "104946167", "104946167", "G", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q8IVF2", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "3095", "T", "M", "o-glyco-site-loss" ], [ "Q9UQ52-1", "419", "S", "Y", "3", "1329827", "1329827", "C", "A", "0", "0", "0.0", "icgc", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "Q9UQ52", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "419", "S", "Y", "o-glyco-site-loss" ], [ "Q5T9G4-1", "164", "T", "M", "6", "35747307", "35747307", "C", "T", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q5T9G4", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "164", "T", "M", "o-glyco-site-loss" ], [ "P16422-1", "232", "D", "N", "2", "47379805", "47379805", "G", "A", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "P16422", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DLT->NLT).", "", "1", "", "yes", "232", "DLT", "NLT", "n-glyco-sequon-gain" ], [ "P19099-1", "173", "K", "R", "8", "142915123", "142915123", "T", "C", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "P19099", "Somatic mutation passed 1 out of 6 filters: num. of cancers (7).", "", "1", "", "no", "173", "K", "R", "o-glyco-site-loss" ], [ "O95477-1", "824", "S", "L", "9", "104825754", "104825754", "G", "A", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "O95477", "Somatic mutation passed 1 out of 6 filters: num. of cancers (5).", "", "1", "", "yes", "824", "S", "L", "o-glyco-site-loss" ], [ "Q14162-1", "273", "P", "S", "17", "1640641", "1640641", "G", "A", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q14162", "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NEP->NES).", "", "1", "", "yes", "271", "NEP", "NES", "n-glyco-sequon-gain" ] ] }, "readme": "Name\n - Human Cancer Mutation LOG and GOG effect\n\nVersion\n - v-2.0.3\n\nCreated on\n - 2020-06-25T13:28:50.371628\n\nModified on\n - 2022-09-26T09:08:12.504427\n\nCreated by\n - [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nExecution Domain\n Scripts\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-2.0.3/reviewed/glycan_masterlist.csv\n Name: human_protein_mutation_cancer.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_protein_mutation_cancer.csv\n Name: human_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_glyconnect.csv\n Name: human_proteoform_glycosylation_sites_gptwiki.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_gptwiki.csv\n Name: human_proteoform_glycosylation_sites_harvard.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_harvard.csv\n Name: human_proteoform_glycosylation_sites_literature.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_literature.csv\n Name: human_proteoform_glycosylation_sites_literature_mining.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_literature_mining.csv\n Name: human_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_literature_mining_manually_verified.csv\n Name: human_proteoform_glycosylation_sites_oglcnac_atlas.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_oglcnac_atlas.csv\n Name: human_proteoform_glycosylation_sites_oglcnac_mcw.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_oglcnac_mcw.csv\n Name: human_proteoform_glycosylation_sites_o_gluc.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_o_gluc.csv\n Name: human_proteoform_glycosylation_sites_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_pdb.csv\n Name: human_proteoform_glycosylation_sites_tyr_o_linked.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_tyr_o_linked.csv\n Name: human_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_unicarbkb.csv\n Name: human_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv\n Name: human_proteoform_glycosylation_sites_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_proteoform_glycosylation_sites_uniprotkb.csv\n Name: aadict.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/misc/aadict.csv\n Output Subdomain\n Name: human_protein_mutation_cancer_glycoeffect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_protein_mutation_cancer_glycoeffect.csv\n Name: human_protein_mutation_cancer_glycoeffect.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_protein_mutation_cancer_glycoeffect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"8078\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"3240\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"18\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"20\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"25\"\n Name: \"chr_start_pos\"\n Description: \"\"\n Unique Values: \"25039\"\n Name: \"chr_end_pos\"\n Description: \"\"\n Unique Values: \"25039\"\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: \"3\"\n Name: \"patients_tested\"\n Description: \"The total number of patients tested for the given cancer mutation\"\n Unique Values: \"29\"\n Name: \"mut_freq\"\n Description: \"Frequency count of mutations across datasets\"\n Unique Values: \"15\"\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: \"25\"\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: \"8078\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"1793\"\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\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"2\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"3307\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"530\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"536\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"", "downloadurl": "/ln2data/releases/data/v-2.0.3/reviewed/human_protein_mutation_cancer_glycoeffect.csv" }