{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004043181,0.00007250075,0.00007732371,0.00009844839,0.00007488935,0.00005863164,0.00007289911,0.0001012468,0.00002063807],"category_scores_gemma":[0.0001082812,0.00005315836,0.00002472626,0.00006041303,0.0001440972,0.0000362072,0.00005249089,0.00005567113,0.000007124931],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002053184,"about_ca_system_score_gemma":0.00004264351,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000007934569,"about_ca_topic_score_gemma":0.000003160415,"domain_scores_codex":[0.9993005,0.00009087247,0.000149988,0.0001345981,0.0001702563,0.0001537734],"domain_scores_gemma":[0.9996096,0.00004109596,0.00004932845,0.0001522855,0.0001018856,0.00004577444],"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":[0.00008756778,0.00001253139,0.008077643,0.00004936795,0.0000111393,9.799155e-8,0.0001450971,0.000003030493,0.9848578,0.0003077663,0.00002784972,0.006420088],"study_design_scores_gemma":[0.001304578,0.0004873685,0.04852469,0.00006219982,0.000009353096,0.000002855652,0.0002079043,0.0006921668,0.9459044,0.000553067,0.002079548,0.0001718379],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9879037,0.00004336463,0.01143522,0.0001059951,0.00002531502,0.0001509376,0.0002212513,0.000004290775,0.0001099105],"genre_scores_gemma":[0.9991319,0.0001908567,0.0003455704,0.00001142821,0.00001999312,0.000005852997,0.0001117056,0.000009253137,0.000173461],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04044705,"threshold_uncertainty_score":0.2167735,"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."}}