{"id":"W2029201460","doi":"10.1371/journal.pcbi.1003214","title":"The Next Generation of Transcription Factor Binding Site Prediction","year":2013,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":217,"is_retracted":false,"has_abstract":true,"ca_institutions":"Child and Family Research Institute; University of British Columbia","funders":"National Institute of General Medical Sciences; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; National Institutes of Health","keywords":"DNA binding site; ENCODE; Computational biology; Transcription factor; Binding site; Computer science; DNA microarray; DNA; Data mining; Genetics; Biology; Gene; Gene expression; Promoter","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":[0.00118986,0.001139617,0.001349495,0.001605149,0.000393484,0.001057981,0.001451134,0.001729801,0.007815334],"category_scores_gemma":[0.003941257,0.0007035966,0.001833961,0.001360712,0.0003787765,0.001101601,0.0009095164,0.001811216,0.00468761],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006446661,"about_ca_system_score_gemma":0.00096937,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00496258,"about_ca_topic_score_gemma":0.005403165,"domain_scores_codex":[0.9994426,0.000127473,0.00002421961,0.0001894974,0.0001661752,0.00005003199],"domain_scores_gemma":[0.9988236,0.0005886761,0.00008275169,0.0001941791,0.0002362181,0.00007454641],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.001450098,0.0003609011,0.01365213,0.001665489,0.0007005411,0.0006694294,0.0001258417,0.1170075,0.0754621,0.01727696,0.078511,0.693118],"study_design_scores_gemma":[0.0001485063,0.0002098563,0.00329082,0.000131352,0.0002139311,0.0003218192,0.0000276823,0.9042385,0.01674892,0.03243625,0.04214501,0.0000873859],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.03747473,0.0160982,0.8890516,0.001845147,0.001181684,0.0001969928,0.02380878,0.02443079,0.005912111],"genre_scores_gemma":[0.2039565,0.007428317,0.7116361,0.002134316,0.0003694282,0.0008871288,0.06517428,0.00162618,0.006787643],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.007815334,"threshold_uncertainty_score":0.02614486,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03361436893284375,"score_gpt":0.2293162488155568,"score_spread":0.1957018798827131,"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."}}