{"id":"W1900337607","doi":"10.1093/nar/gkv1176","title":"JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles","year":2015,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1059,"is_retracted":false,"has_abstract":true,"ca_institutions":"Child and Family Research Institute; University of British Columbia","funders":"Medical Research Council; Novo Nordisk Fonden; Natural Sciences and Engineering Research Council of Canada; Universität Zürich; BC Children's Hospital; Children's Hospital Foundation; Agence Nationale de la Recherche; Child and Family Research Institute; Canadian Institutes of Health Research; China Scholarship Council; Genome Canada","keywords":"Biology; Transcription factor; Database; DNA binding site; Computational biology; Genetics; Computer science; 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":[0.0005691759,0.00008477609,0.0001374314,0.0000548714,0.0001018686,0.00004783542,0.000699533,0.00006738627,0.0000191358],"category_scores_gemma":[0.0001139394,0.00005875721,0.00003240298,0.0001483087,0.0002598085,0.000005367664,0.001331474,0.00009354225,0.000001636748],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00000959099,"about_ca_system_score_gemma":0.0001499405,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002169241,"about_ca_topic_score_gemma":0.00004488668,"domain_scores_codex":[0.9989904,0.0001478121,0.0001751263,0.0002434868,0.0002491873,0.000194027],"domain_scores_gemma":[0.999229,0.00001355683,0.00006249466,0.0003818376,0.0002409534,0.00007212113],"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":[0.0001457036,0.00004219877,0.01146253,0.00005276306,0.00003096487,3.131484e-7,0.0002103509,0.000001800571,0.9847376,0.00008399379,0.001802522,0.001429226],"study_design_scores_gemma":[0.0007960036,0.0002689692,0.02265045,0.00005641843,0.00001062346,0.000002459537,0.0005322692,0.00003487149,0.9647763,0.000173123,0.01060317,0.00009537389],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9972669,0.00127316,0.00003145492,0.0002176574,0.00007096858,0.0003992624,0.0002938411,7.555693e-7,0.0004459936],"genre_scores_gemma":[0.998349,0.0008928436,0.0004193745,0.00001710563,0.00004054,0.0000217131,0.00002703455,0.00001343361,0.0002190287],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01996136,"threshold_uncertainty_score":0.239605,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1239188975038907,"score_gpt":0.3851422703527098,"score_spread":0.2612233728488191,"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."}}