{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001840789,0.0001777114,0.0002964569,0.001154288,0.0001799492,0.0003669649,0.0001496561,0.0001856446,0.001221247],"category_scores_gemma":[0.0003724015,0.0001088622,0.0003246076,0.001020202,0.0001547917,0.0001054831,0.0002813809,0.0001835501,0.0002598451],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001372377,"about_ca_system_score_gemma":0.0001334051,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005630396,"about_ca_topic_score_gemma":0.0009613856,"domain_scores_codex":[0.9997815,0.00002209497,0.00001811941,0.00008070604,0.00005145883,0.00004605206],"domain_scores_gemma":[0.9997554,0.00008332661,0.00007697975,0.00003147586,0.00002479339,0.00002800007],"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":[0.0008685196,0.00004850472,0.3274183,0.0002303385,0.0004410414,0.0006147328,0.0001394263,0.0008971613,0.6433277,0.0001593369,0.0005476922,0.02530724],"study_design_scores_gemma":[0.00001202614,0.0001092545,0.9592563,0.00001040048,0.0002136928,0.001508059,0.0001043635,0.001042327,0.0348881,0.0001894156,0.002656198,0.000009815187],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9927353,0.001091533,0.0009732966,0.00003212113,0.000004358007,0.00001035997,0.004648356,0.00005172875,0.0004528702],"genre_scores_gemma":[0.9884695,0.0006045087,0.001329318,0.00003871441,0.000008445764,0.00002201366,0.009118713,0.00002894544,0.0003798315],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001221247,"threshold_uncertainty_score":0.004085481,"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."}}