{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00007847003,0.000054027,0.00007951591,0.00002332542,0.00001005222,0.000003476025,0.00002910905,0.00004277791,0.00005978586],"category_scores_gemma":[0.00002357213,0.00004124471,0.00003595604,0.00003140347,0.00006601162,0.000002039038,0.000008645216,0.00001182993,8.017647e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001761175,"about_ca_system_score_gemma":0.0001614028,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001499471,"about_ca_topic_score_gemma":0.0001185548,"domain_scores_codex":[0.9994937,0.00001121789,0.0002031119,0.000147345,0.00006296357,0.00008168249],"domain_scores_gemma":[0.9996932,0.00001430603,0.0001048717,0.0001156074,0.00004565235,0.00002636518],"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":[0.00001633133,0.00002986449,0.03607228,0.00001839122,0.00000632619,0.00003182641,0.00002224873,0.00006972825,0.9619792,0.00001745868,0.0002386167,0.001497786],"study_design_scores_gemma":[0.0002499961,0.00003236354,0.05581137,0.00004899218,0.000009969905,0.0001008506,0.00001614391,0.00000323533,0.9409992,0.0003899614,0.002250754,0.00008723146],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9967147,0.0009184451,0.0001831183,0.0002265622,0.0001727114,0.00007275712,0.00004879548,0.000002338053,0.001660559],"genre_scores_gemma":[0.9989144,0.0006208357,0.00007356257,0.00004515611,0.00005271477,0.0000194057,0.00001522893,0.000006025346,0.000252679],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02098001,"threshold_uncertainty_score":0.168191,"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."}}