{"id":"W2487234017","doi":"10.1016/j.celrep.2016.07.028","title":"Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer","year":2016,"lang":"en","type":"article","venue":"Cell Reports","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":45,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Cancer Agency; Hospital for Sick Children","funders":"National Research Council Canada; European Commission; Francis Crick Institute; Wellcome Trust","keywords":"Biology; Genetics; Nonsense mutation; Exon; Transcriptome; Somatic cell; Gene; Nonsense-mediated decay; Transcription (linguistics); Polyadenylation; Germline mutation; Mutation; Gene expression; RNA; Missense mutation; RNA splicing","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":[0.0003107121,0.0001768345,0.0002570741,0.0004841995,0.0001786487,0.0005101697,0.0001014519,0.0001522537,0.000371782],"category_scores_gemma":[0.0007330051,0.000138585,0.0002141753,0.0005247386,0.0002196996,0.0001914548,0.0002279107,0.0002068822,0.0001938502],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002391491,"about_ca_system_score_gemma":0.0002428832,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000533037,"about_ca_topic_score_gemma":0.001191492,"domain_scores_codex":[0.9997811,0.00003204876,0.00001850293,0.00006662988,0.00007474735,0.00002705151],"domain_scores_gemma":[0.9997107,0.0001126977,0.00007758455,0.00004364397,0.00003250247,0.00002276835],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001285657,0.0000136974,0.04153015,0.00007140644,0.00002626413,0.0002345042,0.0001017938,0.001316407,0.9459784,0.0003002885,0.000059061,0.0102395],"study_design_scores_gemma":[0.00001010093,0.0001901931,0.354719,0.00002063803,0.000116841,0.001664944,0.0002126728,0.01384717,0.6245898,0.002210983,0.002392887,0.00002478237],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9928036,0.0004483568,0.005387128,0.00002531862,0.000003902947,0.000009701617,0.0007691867,0.0001422247,0.0004105623],"genre_scores_gemma":[0.9932052,0.0003959774,0.005002848,0.00002965381,0.000003365356,0.000009811718,0.00112677,0.00003640267,0.0001900448],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.000533037,"threshold_uncertainty_score":0.001735151,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007491551931609585,"score_gpt":0.2307038143082761,"score_spread":0.2232122623766665,"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."}}