{ "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": [ [ "A6NJZ7-1...", "1273..." ], [ "P14867-1...", "355..." ] ], "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" } ], [ "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" ], [ "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" ], [ "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).", "", "1", "", "no", "426", "T", "M", "o-glyco-site-loss" ], [ "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).", "", "1", "", "no", "22", "K", "R", "o-glyco-site-loss" ], [ "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.", "", "1", "", "yes", "234", "Y", "C", "o-glyco-site-loss" ], [ "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).", "", "1", "", "yes", "1274", "T", "M", "o-glyco-site-loss" ], [ "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).", "", "1", "", "yes", "312", "T", "M", "o-glyco-site-loss" ], [ "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.", "", "1", "", "yes", "247", "NRR", "NRS", "n-glyco-sequon-gain" ], [ "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).", "", "1", "", "yes", "126", "Y", "C", "o-glyco-site-loss" ], [ "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).", "", "1", "", "no", "237", "S", "Y", "o-glyco-site-loss" ], [ "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).", "", "1", "", "yes", "1613", "S", "G", "o-glyco-site-loss" ], [ "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).", "", "1", "", "no", "464", "S", "L", "o-glyco-site-loss" ], [ "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).", "", "1", "", "no", "364", "S", "L", "o-glyco-site-loss" ], [ "P12872-1", "23", "T", "M", "6", "33801096", "33801096", "G", "A", "0", "0", "0.0", "icgc", "11934", "DOID:11934 / head and neck cancer", "protein_xref_biomuta", "P12872", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "23", "T", "M", "o-glyco-site-loss" ], [ "Q13901-1", "127", "S", "P", "2", "68042936", "68042936", "A", "G", "0", "0", "0.0", "icgc", "2531", "DOID:2531 / hematologic cancer", "protein_xref_biomuta", "Q13901", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "127", "S", "P", "o-glyco-site-loss" ], [ "Q92752-1", "200", "S", "L", "1", "175403517", "175403517", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q92752", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "198", "NCS", "NCL", "n-glyco-sequon-loss" ], [ "Q92752-1", "200", "S", "L", "1", "175403517", "175403517", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q92752", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "200", "S", "L", "o-glyco-site-loss" ], [ "P50748-1", "2209", "S", "L", "12", "122626224", "122626224", "C", "T", "0", "0", "0.0", "icgc", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "P50748", "Somatic mutation passed 1 out of 6 filters: DB annot. (1).", "", "1", "", "no", "2209", "S", "L", "o-glyco-site-loss" ], [ "Q6NUN0-1", "500", "S", "L", "16", "20437330", "20437330", "C", "T", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q6NUN0", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "500", "S", "L", "o-glyco-site-loss" ], [ "Q0GE19-2", "261", "S", "L", "4", "146283257", "146283257", "G", "A", "0", "0", "0.0", "icgc", "4362", "DOID:4362 / cervical cancer", "protein_xref_biomuta", "Q0GE19", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "259", "NNS", "NNL", "n-glyco-sequon-loss" ], [ "Q0GE19-2", "261", "S", "L", "4", "146283257", "146283257", "G", "A", "0", "0", "0.0", "icgc", "4362", "DOID:4362 / cervical cancer", "protein_xref_biomuta", "Q0GE19", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "261", "S", "L", "o-glyco-site-loss" ], [ "P0DPH7-1", "104", "A", "T", "13", "19178311", "19178311", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P0DPH7", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "102", "NYA", "NYT", "n-glyco-sequon-gain" ], [ "P04626-1", "310", "S", "Y", "17", "39711955", "39711955", "C", "A", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "P04626", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "310", "S", "Y", "o-glyco-site-loss" ], [ "P47755-1", "91", "K", "N", "7", "116904230", "116904230", "G", "T", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "P47755", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "91", "K", "N", "o-glyco-site-loss" ], [ "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 (4).", "", "1", "", "no", "173", "K", "R", "o-glyco-site-loss" ], [ "P04637-1", "132", "K", "N", "17", "7675216", "7675216", "C", "G", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "P04637", "Somatic mutation passed 2 out of 6 filters: num. of cancers (9); DB annot. (1).", "", "1", "", "yes", "132", "K", "N", "o-glyco-site-loss" ], [ "P31997-1", "327", "S", "Y", "19", "42583316", "42583316", "G", "T", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "P31997", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "327", "S", "Y", "o-glyco-site-loss" ], [ "P55259-1", "41", "S", "L", "16", "20324229", "20324229", "G", "A", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "P55259", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "41", "S", "L", "o-glyco-site-loss" ], [ "P21817-1", "4882", "T", "M", "19", "38580503", "38580503", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P21817", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "4882", "T", "M", "o-glyco-site-loss" ], [ "P13535-1", "1420", "T", "M", "17", "10396906", "10396906", "G", "A", "0", "0", "0.0", "icgc", "1319", "DOID:1319 / brain cancer", "protein_xref_biomuta", "P13535", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "1420", "T", "M", "o-glyco-site-loss" ], [ "Q5FWF5-1", "221", "T", "M", "18", "21574182", "21574182", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q5FWF5", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "221", "T", "M", "o-glyco-site-loss" ], [ "O95477-1", "824", "S", "L", "9", "104825754", "104825754", "G", "A", "0", "0", "0.0", "icgc", "4362", "DOID:4362 / cervical 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" ], [ "Q8N137-1", "710", "K", "N", "17", "7947707", "7947707", "G", "T", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q8N137", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "710", "K", "N", "o-glyco-site-loss" ], [ "P04637-1", "234", "Y", "C", "17", "7674262", "7674262", "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 (9). In dbSNP: rs587780073.", "", "1", "", "yes", "234", "Y", "C", "o-glyco-site-loss" ], [ "Q6ZV29-1", "922", "T", "M", "9", "137478076", "137478076", "G", "A", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q6ZV29", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "922", "T", "M", "o-glyco-site-loss" ], [ "Q8N8A6-1", "355", "D", "N", "12", "132141539", "132141539", "C", "T", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q8N8A6", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "355", "DQT", "NQT", "n-glyco-sequon-gain" ], [ "Q9HC73-1", "128", "S", "L", "X", "1202502", "1202502", "G", "A", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q9HC73", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "128", "S", "L", "o-glyco-site-loss" ], [ "Q9Y618-1", "2014", "S", "L", "12", "124336827", "124336827", "G", "A", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q9Y618", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "2014", "S", "L", "o-glyco-site-loss" ], [ "O95521-1", "316", "Y", "F", "1", "12795518", "12795518", "A", "T", "0", "0", "0.0", "icgc", "2531", "DOID:2531 / hematologic cancer", "protein_xref_biomuta", "O95521", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "316", "Y", "F", "o-glyco-site-loss" ], [ "O15266-1", "11", "S", "Y", "X", "630929", "630929", "C", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "O15266", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "11", "S", "Y", "o-glyco-site-loss" ], [ "A1KZ92-1", "1137", "S", "L", "8", "51408214", "51408214", "G", "A", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "A1KZ92", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "1137", "S", "L", "o-glyco-site-loss" ], [ "P56715-1", "1796", "T", "M", "8", "54629269", "54629269", "C", "T", "0", "0", "0.0", "icgc", "1319", "DOID:1319 / brain cancer", "protein_xref_biomuta", "P56715", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "1796", "T", "M", "o-glyco-site-loss" ], [ "O60810-1", "431", "S", "N", "1", "12879689", "12879689", "C", "T", "0", "0", "0.0", "icgc", "2531", "DOID:2531 / hematologic cancer", "protein_xref_biomuta", "O60810", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "431", "S", "N", "o-glyco-site-loss" ], [ "O00716-1", "181", "T", "M", "6", "20481242", "20481242", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "O00716", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "181", "T", "M", "o-glyco-site-loss" ], [ "O60312-1", "226", "T", "M", "15", "25736119", "25736119", "G", "A", "0", "0", "0.0", "icgc", "1781", "DOID:1781 / thyroid cancer", "protein_xref_biomuta", "O60312", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "226", "T", "M", "o-glyco-site-loss" ], [ "Q7Z3H0-2", "12", "S", "F", "12", "51888221", "51888221", "C", "T", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q7Z3H0", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "12", "S", "F", "o-glyco-site-loss" ], [ "Q49AJ0-1", "11", "S", "L", "8", "138367952", "138367952", "G", "A", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q49AJ0", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "11", "S", "L", "o-glyco-site-loss" ], [ "Q6ZMN7-1", "252", "S", "L", "12", "41194100", "41194100", "C", "T", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "Q6ZMN7", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "252", "S", "L", "o-glyco-site-loss" ], [ "Q8TF63-1", "75", "T", "P", "5", "135446886", "135446886", "T", "G", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q8TF63", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "73", "NKT", "NKP", "n-glyco-sequon-loss" ], [ "Q8TF63-1", "75", "T", "P", "5", "135446886", "135446886", "T", "G", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q8TF63", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "75", "T", "P", "o-glyco-site-loss" ], [ "Q8IUH8-1", "105", "T", "M", "17", "45845220", "45845220", "C", "T", "1", "185", "0.5", "tcga", "5041", "DOID:5041 / esophageal cancer", "protein_xref_biomuta", "Q8IUH8", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3). In dbSNP: rs139470538.", "", "1", "", "yes", "105", "T", "M", "o-glyco-site-loss" ], [ "Q16281-1", "565", "T", "M", "2", "98396864", "98396864", "C", "T", "0", "0", "0.0", "icgc", "2394", "DOID:2394 / ovarian cancer", "protein_xref_biomuta", "Q16281", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "565", "T", "M", "o-glyco-site-loss" ], [ "P63151-1", "289", "S", "L", "8", "26363784", "26363784", "C", "T", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "P63151", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "289", "S", "L", "o-glyco-site-loss" ], [ "Q13003-1", "646", "T", "M", "1", "36817214", "36817214", "G", "A", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q13003", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "646", "T", "M", "o-glyco-site-loss" ], [ "Q8WV92-1", "76", "K", "N", "2", "99173940", "99173940", "C", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q8WV92", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "76", "K", "N", "o-glyco-site-loss" ], [ "Q8TCU5-1", "171", "S", "L", "9", "101737468", "101737468", "G", "A", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q8TCU5", "Somatic mutation passed 1 out of 6 filters: num. of cancers (5).", "", "1", "", "yes", "171", "S", "L", "o-glyco-site-loss" ], [ "P28222-1", "243", "T", "M", "6", "77462676", "77462676", "G", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "P28222", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "243", "T", "M", "o-glyco-site-loss" ], [ "Q9P104-1", "87", "D", "N", "20", "54588567", "54588567", "G", "A", "0", "0", "0.0", "icgc", "263", "DOID:263 / kidney cancer", "protein_xref_biomuta", "Q9P104", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "no", "87", "DTS", "NTS", "n-glyco-sequon-gain" ], [ "Q9Y4I1-1", "397", "T", "I", "15", "52397330", "52397330", "G", "A", "0", "0", "0.0", "icgc", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "Q9Y4I1", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "397", "T", "I", "o-glyco-site-loss" ], [ "O75443-1", "815", "T", "M", "11", "121129714", "121129714", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "O75443", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "813", "NST", "NSM", "n-glyco-sequon-loss" ], [ "O75443-1", "815", "T", "M", "11", "121129714", "121129714", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "O75443", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "815", "T", "M", "o-glyco-site-loss" ], [ "Q7Z4V0-1", "813", "T", "M", "10", "30845010", "30845010", "G", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q7Z4V0", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "813", "T", "M", "o-glyco-site-loss" ], [ "P42261-1", "663", "T", "M", "5", "153764598", "153764598", "C", "T", "0", "0", "0.0", "icgc", "10283", "DOID:10283 / prostate cancer", "protein_xref_biomuta", "P42261", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "663", "T", "M", "o-glyco-site-loss" ], [ "P08F94-1", "830", "N", "S", "6", "52046107", "52046107", "T", "C", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "P08F94", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "830", "NAS", "SAS", "n-glyco-sequon-loss" ], [ "Q9UK32-1", "661", "S", "F", "X", "84065101", "84065101", "G", "A", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q9UK32", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "661", "S", "F", "o-glyco-site-loss" ], [ "Q9UQ05-1", "254", "D", "N", "17", "42176123", "42176123", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9UQ05", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "254", "DDT", "NDT", "n-glyco-sequon-gain" ], [ "P10515-1", "202", "S", "L", "11", "112028890", "112028890", "C", "T", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "P10515", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "no", "202", "S", "L", "o-glyco-site-loss" ], [ "Q3SY77-1", "469", "T", "M", "5", "36035864", "36035864", "G", "A", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q3SY77", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "469", "T", "M", "o-glyco-site-loss" ], [ "Q3SY77-1", "469", "T", "M", "5", "36035864", "36035864", "G", "A", "0", "0", "0.0", "icgc", "1319", "DOID:1319 / brain cancer", "protein_xref_biomuta", "Q3SY77", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "469", "T", "M", "o-glyco-site-loss" ], [ "Q658L1-1", "19", "S", "L", "15", "82271605", "82271605", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q658L1", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "19", "S", "L", "o-glyco-site-loss" ], [ "Q9P2N2-1", "594", "T", "M", "18", "6890476", "6890476", "C", "T", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q9P2N2", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "594", "T", "M", "o-glyco-site-loss" ], [ "P33032-1", "239", "T", "I", "18", "13826481", "13826481", "C", "T", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "P33032", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "239", "T", "I", "o-glyco-site-loss" ], [ "P14780-1", "466", "T", "M", "20", "46013321", "46013321", "C", "T", "0", "0", "0.0", "icgc", "4362", "DOID:4362 / cervical cancer", "protein_xref_biomuta", "P14780", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "466", "T", "M", "o-glyco-site-loss" ], [ "Q58EX2-1", "259", "S", "L", "17", "73438104", "73438104", "G", "A", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q58EX2", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "259", "S", "L", "o-glyco-site-loss" ], [ "Q92628-1", "852", "S", "L", "4", "6862937", "6862937", "C", "T", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "Q92628", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "852", "S", "L", "o-glyco-site-loss" ], [ "Q8NA92-1", "112", "K", "R", "19", "36039660", "36039660", "T", "C", "0", "0", "0.0", "icgc", "1612", "DOID:1612 / breast cancer", "protein_xref_biomuta", "Q8NA92", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "112", "K", "R", "o-glyco-site-loss" ], [ "P05305-1", "198", "K", "N", "6", "12296022", "12296022", "G", "T", "0", "0", "0.0", "icgc", "11054", "DOID:11054 / urinary bladder cancer", "protein_xref_biomuta", "P05305", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "198", "K", "N", "o-glyco-site-loss" ], [ "P28907-1", "264", "S", "L", "4", "15840490", "15840490", "C", "T", "0", "0", "0.0", "icgc", "9256", "DOID:9256 / colorectal cancer", "protein_xref_biomuta", "P28907", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "264", "S", "L", "o-glyco-site-loss" ], [ "Q9NR82-1", "693", "T", "M", "6", "73194693", "73194693", "C", "T", "0", "0", "0.0", "icgc", "10534", "DOID:10534 / stomach cancer", "protein_xref_biomuta", "Q9NR82", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "693", "T", "M", "o-glyco-site-loss" ], [ "Q6KF10-1", "405", "T", "M", "8", "96144717", "96144717", "G", "A", "0", "0", "0.0", "icgc", "363", "DOID:363 / uterine cancer", "protein_xref_biomuta", "Q6KF10", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "405", "T", "M", "o-glyco-site-loss" ], [ "Q96JF0-1", "346", "S", "L", "2", "106834053", "106834053", "G", "A", "0", "0", "0.0", "icgc", "1319", "DOID:1319 / brain cancer", "protein_xref_biomuta", "Q96JF0", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "346", "S", "L", "o-glyco-site-loss" ], [ "Q92543-1", "407", "S", "G", "11", "130914721", "130914721", "T", "C", "0", "0", "0.0", "icgc", "1324", "DOID:1324 / lung cancer", "protein_xref_biomuta", "Q92543", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "yes", "407", "S", "G", "o-glyco-site-loss" ], [ "Q8NEB9-1", "433", "S", "Y", "18", "42013569", "42013569", "C", "A", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q8NEB9", "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "", "1", "", "no", "433", "S", "Y", "o-glyco-site-loss" ], [ "Q9C0I4-1", "305", "S", "L", "2", "137057194", "137057194", "C", "T", "0", "0", "0.0", "icgc", "4159", "DOID:4159 / skin cancer", "protein_xref_biomuta", "Q9C0I4", "Somatic mutation passed 1 out of 6 filters: num. of cancers (4).", "", "1", "", "yes", "305", "S", "L", "o-glyco-site-loss" ] ] }, "readme": "Name\n - Human Cancer Mutation LOG and GOG effect\n\nVersion\n - v-2.1.1\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], Jingyue Wu [jingyue.wu@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-2.1.1/reviewed/glycan_masterlist.csv\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_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/human_proteoform_glycosylation_sites_glyconnect.csv\n Name: human_proteoform_glycosylation_sites_gptwiki.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/human_proteoform_glycosylation_sites_gptwiki.csv\n Name: human_proteoform_glycosylation_sites_harvard.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/human_proteoform_glycosylation_sites_harvard.csv\n Name: human_proteoform_glycosylation_sites_literature.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/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-2.1.1/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-2.1.1/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-2.1.1/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-2.1.1/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-2.1.1/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-2.1.1/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-2.1.1/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-2.1.1/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-2.1.1/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-2.1.1/reviewed/human_proteoform_glycosylation_sites_uniprotkb.csv\n Name: aadict.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/misc/aadict.csv\n Output Subdomain\n Name: human_protein_mutation_cancer_glycoeffect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/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-2.1.1/reviewed/human_protein_mutation_cancer_glycoeffect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1489\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"957\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"14\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"20\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"chr_start_pos\"\n Description: \"\"\n Unique Values: \"1793\"\n Name: \"chr_end_pos\"\n Description: \"\"\n Unique Values: \"1793\"\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: \"19\"\n Name: \"mut_freq\"\n Description: \"Frequency count of mutations across datasets\"\n Unique Values: \"12\"\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: \"23\"\n Name: \"do_name\"\n Description: \"Disease Ontology term or name for the disease assigned to the Disease Ontology identifier\"\n Unique Values: \"23\"\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: \"1489\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"135\"\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: \"971\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"92\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"99\"\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-2.1.1/reviewed/human_protein_mutation_cancer_glycoeffect.csv" }