{"id":"W2014323284","doi":"10.1038/ncomms4644","title":"Processed pseudogenes acquired somatically during cancer development","year":2014,"lang":"en","type":"article","venue":"Nature Communications","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":112,"is_retracted":false,"has_abstract":true,"ca_institutions":"SickKids Foundation; Hospital for Sick Children; BC Cancer Agency; University of Toronto","funders":"National Research Council Canada; Rosetrees Trust; University College London Hospitals NHS Foundation Trust; European Commission; Wellcome Trust; Academy of Medical Sciences; Kay Kendall Leukaemia Fund; National Institute for Health and Care Research; National Cancer Institute; National Institutes of Health; Cancer Research UK","keywords":"Pseudogene; Biology; Retrotransposon; Genetics; Germline; Gene; Germline mutation; Exon; Intron; Context (archaeology); Mutation; Somatic cell; Cancer; Genome; Transposable element","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":[0.00009013508,0.000101846,0.00008974344,0.00002709049,0.0002350253,0.00003639385,0.0006233595,0.0001833911,0.00001009383],"category_scores_gemma":[0.0001997328,0.0001010901,0.00003555978,0.00008180783,0.00006209099,0.000003171252,0.0003392654,0.0001099868,0.000008899146],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000271831,"about_ca_system_score_gemma":0.0001700802,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000815953,"about_ca_topic_score_gemma":0.0009070328,"domain_scores_codex":[0.999403,0.00003119844,0.0001649079,0.000171927,0.00008084252,0.0001480977],"domain_scores_gemma":[0.9987695,0.0000360573,0.00006461692,0.0009206695,0.0001469539,0.00006218622],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00004842764,0.0002354829,0.01417449,0.00008588436,0.0001420557,3.472496e-7,0.0002843255,0.0001709079,0.9635768,0.00356481,0.003808037,0.01390842],"study_design_scores_gemma":[0.00070929,0.00003946356,0.05419676,0.00004887062,0.0000350075,0.000006431087,0.00006948377,0.0003520476,0.4427604,0.0001698707,0.5012226,0.0003898345],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9860355,0.008875823,0.0006589888,0.002001494,0.0001435472,0.0001873521,0.00001489921,0.00002751983,0.002054903],"genre_scores_gemma":[0.9865368,0.001464193,0.01078036,0.0006376573,0.000138673,0.0001308286,0.0001391892,0.00001862117,0.0001536491],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5208164,"threshold_uncertainty_score":0.4122335,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01159716898897905,"score_gpt":0.2817251476966157,"score_spread":0.2701279787076366,"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."}}