{"id":"W4291674330","doi":"10.1371/journal.pcbi.1010393","title":"Chromatin accessibility of primary human cancers ties regional mutational processes and signatures with tissues of origin","year":2022,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Ontario Institute for Cancer Research","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Government of Ontario; Terry Fox Research Institute; Ontario Institute for Cancer Research","keywords":"Biology; Epigenome; Carcinogenesis; Chromatin; Genetics; Cancer; Computational biology; Insertional mutagenesis; Mutagenesis; Mutation; Genome; Germline mutation; Gene; DNA methylation; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0000690539,0.00008542924,0.0001588606,0.00004656355,0.00009047759,0.000004352878,0.0001121072,0.0000400778,0.00003716262],"category_scores_gemma":[0.00003891427,0.00007875181,0.00001984213,0.00008204674,0.0002679435,0.000003363509,0.0001067675,0.00005582275,8.801187e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003375765,"about_ca_system_score_gemma":0.0005423884,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007180903,"about_ca_topic_score_gemma":0.0000524633,"domain_scores_codex":[0.999331,0.00004734227,0.0001949309,0.0002211957,0.0001229947,0.00008255733],"domain_scores_gemma":[0.9993986,0.000119548,0.000185365,0.00007491341,0.0001970628,0.00002449551],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.001388595,0.0007101511,0.1645886,0.001071897,0.000705482,0.000005977495,0.000920451,0.1338986,0.6757163,0.0168005,0.002347967,0.001845515],"study_design_scores_gemma":[0.008208369,0.01252775,0.6409878,0.0001914551,0.000303438,0.0001657348,0.001417728,0.00354976,0.2291223,0.08682349,0.01492904,0.001773156],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9968956,0.001976796,0.0003572276,0.00009304767,0.00002312288,0.0001310217,0.0003451881,0.000004320038,0.000173707],"genre_scores_gemma":[0.9957111,0.00003595772,0.002576417,0.0001571331,0.00005239429,0.00004153748,0.001399018,0.000007736274,0.00001866886],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4763992,"threshold_uncertainty_score":0.3211406,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01935733266507461,"score_gpt":0.2767434887618712,"score_spread":0.2573861560967966,"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."}}