{"id":"W3105006481","doi":"10.1101/183889","title":"Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types","year":2017,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":25,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Ontario Institute for Cancer Research","funders":"Ludwig Center at Harvard; University of North Carolina at Chapel Hill; University of Texas MD Anderson Cancer Center; Swiss Institute of Bioinformatics; Universitätsspital Zürich; University of California, San Francisco; Peking University; Genome Institute of Singapore; University of Tokyo; Memorial Sloan-Kettering Cancer Center; University of Glasgow; Karolinska Institutet; University of Toronto; University College London; Eidgenössische Technische Hochschule Zürich; National University of Singapore; National Cancer Centre of Singapore; Universität Ulm; European Molecular Biology Laboratory; Duke-NUS Medical School","keywords":"Biology; Gene; Genetics; Somatic cell; Genome; Transcriptome; RNA; Germline; RNA splicing; Intron; Germline mutation; DNA; Gene expression; Computational biology; Mutation","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002430506,0.0004019777,0.0005396906,0.0001103563,0.0001998851,0.0001479721,0.0006494148,0.0004421237,0.00002291466],"category_scores_gemma":[0.0003296974,0.000450692,0.0002740281,0.00007431038,0.0001377027,0.000006803041,0.0003314069,0.0001883892,0.000006417315],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001264444,"about_ca_system_score_gemma":0.0009523592,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002415994,"about_ca_topic_score_gemma":0.00003986232,"domain_scores_codex":[0.9981602,0.00004204564,0.0004899791,0.000803459,0.0001395214,0.0003647995],"domain_scores_gemma":[0.9971107,0.0000399874,0.0006680446,0.001430534,0.0005842386,0.0001664687],"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":[0.00005360836,0.00006967683,0.00223297,0.0002289049,0.0004421555,0.000001382033,0.000003548049,0.000618181,0.991657,0.00003058313,0.004659045,0.000003006124],"study_design_scores_gemma":[0.0004892885,0.000101536,0.01178597,0.0001293294,0.0003805123,6.382292e-9,0.000001119861,0.00008646021,0.9197083,0.000003408708,0.06674077,0.0005732795],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9585316,0.01908723,0.003513148,0.0003608514,0.001179521,0.0009184207,0.01635962,0.00002856142,0.00002106643],"genre_scores_gemma":[0.9904081,0.005428048,0.002488274,0.0001921701,0.0009121157,0.0003652456,0.00002803451,0.0001118058,0.00006624505],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.07194863,"threshold_uncertainty_score":0.9997945,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02399406321317742,"score_gpt":0.2824851740869714,"score_spread":0.258491110873794,"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."}}