{"id":"W3158383713","doi":"10.1186/s13059-021-02318-x","title":"Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes","year":2021,"lang":"en","type":"article","venue":"Genome biology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":20,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Ontario Institute for Cancer Research","funders":"Terry Fox Research Institute; University of Toronto; Ontario Institute for Cancer Research; Government of Ontario; Canadian Institutes of Health Research; Cancer Research Society","keywords":"Biology; CTCF; Genetics; Chromatin; Mutagenesis; ChIA-PET; Genome; Mutation rate; Computational biology; Mutation; Gene; DNA binding site; Transcription factor; Chromatin remodeling; Enhancer; Promoter; 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":[0.0002117887,0.00008173571,0.0001711203,0.00003456321,0.00001637645,0.000001982762,0.00005895595,0.0001114029,0.00004382106],"category_scores_gemma":[0.00003852466,0.00008483988,0.00003261615,0.0000567861,0.00009708403,0.000001247953,0.00009471682,0.00002979779,3.947741e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001697427,"about_ca_system_score_gemma":0.000137018,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003517499,"about_ca_topic_score_gemma":0.0002879531,"domain_scores_codex":[0.9991499,0.0001182073,0.0003283085,0.0002479434,0.00003005724,0.0001255897],"domain_scores_gemma":[0.9995329,0.00001601867,0.0001487865,0.0001847696,0.00009227805,0.00002527593],"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":[0.00002162424,0.00002834715,0.3213129,0.00003319321,0.00002407849,0.000001470121,0.00002259913,0.0001318155,0.6718395,0.00002951315,0.000001419544,0.006553552],"study_design_scores_gemma":[0.0004174235,0.00008755852,0.9024333,0.000004373522,0.00001245785,0.000009141868,0.00002735217,0.0003230474,0.09577269,0.0006067847,0.0002244614,0.00008138215],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9968839,0.002486675,0.0003189273,0.00001383622,0.00009044643,0.00008356316,0.00008858048,0.000001134215,0.00003292355],"genre_scores_gemma":[0.997824,0.0007576497,0.001153886,0.00003073817,0.00003488278,0.00001341272,0.0001293859,0.000007284395,0.00004873284],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5811204,"threshold_uncertainty_score":0.345967,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007421506937675702,"score_gpt":0.2429057315056108,"score_spread":0.2354842245679351,"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."}}