{"id":"W2043748764","doi":"10.1186/gb-2012-13-3-r24","title":"The Transcription Factor Encyclopedia","year":2012,"lang":"en","type":"article","venue":"Genome biology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":160,"is_retracted":false,"has_abstract":true,"ca_institutions":"Health Sciences Centre; Sunnybrook Health Science Centre; McMaster University; Queen's University; Fraser Health; Provincial Health Services Authority; Institute for Research in Immunology and Cancer; Child and Family Research Institute; BC Cancer Agency; University of Toronto; Western University; Université de Montréal; University of British Columbia","funders":"National Institute of Environmental Health Sciences; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; National Eye Institute; National Human Genome Research Institute; National Institute of Mental Health; National Health and Medical Research Council; British Heart Foundation; Ministerio de Economía y Competitividad; Natural Sciences and Engineering Research Council of Canada; Leukaemia and Lymphoma Research; Fakultet Medicinskih Nauka, Univerziteta U Kragujevcu; Institut Universitaire de France; Université de Montréal; Centre National de la Recherche Scientifique; Flight Attendant Medical Research Institute; Simon Fraser University; Ministero dell’Istruzione, dell’Università e della Ricerca; ZonMw; National Cancer Institute; University Hospitals Coventry and Warwickshire NHS Trust; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; Agence Nationale de la Recherche; New York State Stem Cell Science; Deutsche Forschungsgemeinschaft; Université Paris Diderot; Ministerio de Ciencia e Innovación; Alexander and Margaret Stewart Trust; Action Medical Research; European Commission; European Foundation for the Study of Diabetes; Heart and Stroke Foundation of Canada; Newcastle University; Fondation pour la Recherche Médicale; National Institute of Neurological Disorders and Stroke; Leukemia and Lymphoma Society; Genome British Columbia; National Heart, Lung, and Blood Institute; Biotechnology and Biological Sciences Research Council; Cancer Research UK; Wellcome Trust; Institut National de la Santé et de la Recherche Médicale; Child and Family Research Institute; Medical Research Council; Diana Helis Henry Medical Research Foundation; Eunice Kennedy Shriver National Institute of Child Health and Human Development; GlaxoSmithKline; Cancer Research Society; Canadian Institutes of Health Research; Breast Cancer Campaign; U.S. Public Health Service; Associazione Italiana per la Ricerca sul Cancro; Genome Canada; University of British Columbia; Michael Smith Health Research BC; National Institutes of Health; Faculty of Medical Sciences, Newcastle University; Leukemia and Lymphoma Society of Canada; National Science Foundation","keywords":"Biology; Encyclopedia; Genome Biology; Human genetics; Computational biology; Evolutionary biology; Transcription factor; Genetics; Computational genomics; Genomics; Genome; Library science; Gene; Computer science","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":[0.0001327394,0.0001038512,0.00007466854,0.00001306405,0.0001437572,0.00001111307,0.0001885208,0.0001378374,0.00003006436],"category_scores_gemma":[0.00001918878,0.00007290248,0.00006481718,0.00003030029,0.0000787448,0.000001768341,0.00005224093,0.00005766123,0.0000537206],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001280803,"about_ca_system_score_gemma":0.00002285622,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004956636,"about_ca_topic_score_gemma":0.00001706469,"domain_scores_codex":[0.9992869,0.00005027826,0.0001397525,0.0001454889,0.00002970352,0.0003478226],"domain_scores_gemma":[0.9995958,0.000009845089,0.00004711725,0.0002514401,0.00002410133,0.00007167658],"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":[0.00001578169,0.00002125414,0.007220119,0.000002716564,0.00003117874,7.796621e-8,0.00009358463,0.000002720298,0.9850334,0.001260187,0.0001819304,0.006137053],"study_design_scores_gemma":[0.0001768128,0.000128396,0.05149846,4.622849e-7,0.000008154713,0.00001116767,0.00006018005,0.00001057886,0.005119927,0.0002405888,0.9425896,0.0001556524],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9898108,0.004399024,0.001256098,0.0001370214,0.0006673283,0.0001138287,0.00004439419,0.000009767642,0.0035617],"genre_scores_gemma":[0.9960876,0.001709785,0.0002740773,0.000147791,0.0006366328,0.00001834683,0.0001687225,0.0000138675,0.0009432368],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9799135,"threshold_uncertainty_score":0.2972877,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008572019895068093,"score_gpt":0.2255841287272206,"score_spread":0.2170121088321525,"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."}}