{"id":"W2557429489","doi":"10.1093/nar/gkw1036","title":"Discovery and validation of information theory-based transcription factor and cofactor binding site motifs","year":2016,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":31,"is_retracted":false,"has_abstract":true,"ca_institutions":"Cytodiagnostics (Canada); Western University","funders":"Compute Canada","keywords":"Biology; Computational biology; ENCODE; Binding site; Genetics; Transcription factor; DNA binding site; Gene; Promoter; Gene expression","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":[0.003720014,0.0006055033,0.0005122005,0.002470713,0.0003068337,0.0006632351,0.0008044511,0.0005094227,0.0005980973],"category_scores_gemma":[0.01652732,0.0003136218,0.0006678066,0.001121395,0.000708125,0.0007356296,0.0006232674,0.0007084828,0.000264638],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005914408,"about_ca_system_score_gemma":0.0008261935,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001350451,"about_ca_topic_score_gemma":0.001851447,"domain_scores_codex":[0.9986115,0.0004623029,0.0001195617,0.0003423786,0.0003778555,0.00008642194],"domain_scores_gemma":[0.9924143,0.005524428,0.0007061317,0.0006277037,0.0005692118,0.0001582127],"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":[0.001170957,0.0004079816,0.1159721,0.0008389358,0.0007469538,0.0003222673,0.0003994531,0.2279891,0.4781497,0.01260613,0.000675933,0.1607206],"study_design_scores_gemma":[0.00005074732,0.000231894,0.03496285,0.00003137246,0.0001110158,0.0002107156,0.00005256203,0.8340339,0.1236363,0.005877942,0.0007488028,0.00005190178],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7216024,0.0003001348,0.2754148,0.00005357391,0.000009450875,0.00006504179,0.001229798,0.000672546,0.0006523801],"genre_scores_gemma":[0.8824338,0.00007408349,0.1151897,0.00002614755,0.000008542361,0.00006549615,0.002013857,0.00006255971,0.0001257782],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003720014,"threshold_uncertainty_score":0.01967359,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01797400744801315,"score_gpt":0.2746292853486504,"score_spread":0.2566552779006373,"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."}}