{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006203759,0.0001578039,0.0002497168,0.0007702076,0.0001646842,0.0003441194,0.0002836464,0.0003369192,0.0009625143],"category_scores_gemma":[0.002576391,0.0001452675,0.0003319166,0.0005748659,0.000359686,0.0002933289,0.000323984,0.0003077126,0.0001415413],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004149984,"about_ca_system_score_gemma":0.0001698844,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008850869,"about_ca_topic_score_gemma":0.000812011,"domain_scores_codex":[0.9997036,0.00006992598,0.00001534849,0.0001340579,0.0000495365,0.00002739681],"domain_scores_gemma":[0.9984749,0.0009924265,0.0002618274,0.0001147205,0.00007770183,0.00007832544],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0006407365,0.00008197971,0.4882575,0.0004542701,0.0003500061,0.0002833828,0.0004099619,0.1122356,0.3613619,0.004433174,0.0003066937,0.03118481],"study_design_scores_gemma":[0.00002183609,0.0002330846,0.708137,0.00001624348,0.0001250788,0.0009299531,0.0001640174,0.2390945,0.04455507,0.005308227,0.001359211,0.00005575633],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9870639,0.0001557437,0.01206662,0.00001884117,0.000001219108,0.000007985557,0.000318331,0.0001072784,0.0002602199],"genre_scores_gemma":[0.9969181,0.0000378985,0.002529126,0.000005746585,0.000001834923,0.00001506913,0.000392356,0.00002347091,0.00007638482],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0009625143,"threshold_uncertainty_score":0.003280938,"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."}}