{"id":"W953912505","doi":"10.1038/nmeth.3440","title":"Pathway and network analysis of cancer genomes","year":2015,"lang":"en","type":"article","venue":"Nature Methods","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":358,"is_retracted":false,"has_abstract":false,"ca_institutions":"Ontario Institute for Cancer Research; University of Toronto","funders":"National Institute of General Medical Sciences; National Cancer Institute; National Human Genome Research Institute; Canadian Institutes of Health Research","keywords":"Genome; Computational biology; Gene; Biology; Cancer; Genetics; Pathway analysis; Genomics; Gene expression","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005824418,0.0004111963,0.0003294855,0.002418707,0.0004903453,0.0009218688,0.0005199416,0.0002655197,0.003630265],"category_scores_gemma":[0.001816998,0.0001921868,0.001097926,0.00206993,0.0002519483,0.0006218849,0.0006913092,0.0006016776,0.0005066879],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006563209,"about_ca_system_score_gemma":0.0009983501,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004060434,"about_ca_topic_score_gemma":0.006191393,"domain_scores_codex":[0.9997069,0.00010334,0.00001440264,0.00008696186,0.00005472521,0.00003360935],"domain_scores_gemma":[0.9995307,0.000238579,0.00005403248,0.0000732027,0.00005964435,0.000043933],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001774493,0.0004428765,0.08229706,0.002903518,0.001769519,0.0006763363,0.0005791641,0.2875235,0.1073138,0.1421091,0.01684034,0.3557702],"study_design_scores_gemma":[0.0001030536,0.0001589172,0.05907978,0.0001302609,0.0005948841,0.000535216,0.0003681211,0.6814682,0.02181315,0.1938413,0.0418432,0.00006391551],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.5323746,0.005108402,0.3945103,0.001837075,0.0001465841,0.0002708484,0.05223992,0.003530673,0.00998156],"genre_scores_gemma":[0.8102046,0.002688699,0.1609381,0.0001080218,0.00003710146,0.0002094348,0.02280576,0.0002265599,0.002781672],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.004060434,"threshold_uncertainty_score":0.01214439,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01404375712307823,"score_gpt":0.3479617190518691,"score_spread":0.3339179619287909,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}