{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003232093,0.0002467485,0.0003002434,0.0003985667,0.0001410128,0.0004437391,0.0002680276,0.0002171014,0.001840125],"category_scores_gemma":[0.001171988,0.0002091392,0.0007124973,0.0004415925,0.0002604207,0.0001937166,0.0002902668,0.0002737102,0.0002521774],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003466952,"about_ca_system_score_gemma":0.0003969971,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006125527,"about_ca_topic_score_gemma":0.008402776,"domain_scores_codex":[0.99988,0.00003050316,0.000004775015,0.00006132414,0.00001205917,0.00001143348],"domain_scores_gemma":[0.9996415,0.0002206085,0.00004041101,0.00005505255,0.00002478962,0.00001757117],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"observational","study_design_scores_codex":[0.0004786233,0.00006053644,0.1536873,0.0002832678,0.0005248035,0.0001635187,0.0001607949,0.7759103,0.0281947,0.003319294,0.002081427,0.03513544],"study_design_scores_gemma":[0.00003638554,0.000118427,0.1326063,0.00001599669,0.0001402541,0.0002746859,0.00005928919,0.8493046,0.006093604,0.007789751,0.003533107,0.00002773343],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9315475,0.0004999877,0.05689162,0.0001561837,0.00001182019,0.00002995763,0.00849768,0.0006478342,0.001717557],"genre_scores_gemma":[0.9808522,0.0002343643,0.01095823,0.0000553661,0.00000588404,0.00003493762,0.007232612,0.00005301988,0.0005734342],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006125527,"threshold_uncertainty_score":0.01217979,"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."}}