{"id":"W2113833510","doi":"10.1093/nar/gki624","title":"oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes","year":2005,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":378,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research","keywords":"Biology; Gene; DNA binding site; Genetics; Computational biology; Opossum; Transcription factor; False positive paradox; Promoter; Functional genomics; Gene expression profiling; Genomics; Genome; Gene expression; 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":[0.0006823875,0.0001037859,0.0001352604,0.0001954431,0.0000849229,0.00004826597,0.0002989877,0.0001946946,0.0001077199],"category_scores_gemma":[0.00005705391,0.000103017,0.00006636685,0.0002296558,0.0001326579,0.00001765681,0.00007753789,0.00019541,0.00003587313],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003866993,"about_ca_system_score_gemma":0.000048655,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003189095,"about_ca_topic_score_gemma":0.00005287434,"domain_scores_codex":[0.9985711,0.0001075256,0.0004129044,0.0002523442,0.0003270651,0.0003290779],"domain_scores_gemma":[0.999317,0.00002473125,0.00008154369,0.0003779474,0.0001322602,0.00006653812],"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":[0.0000885289,0.00007500519,0.00685255,0.00003738419,0.00001992259,4.532557e-7,0.0002928047,0.0001537644,0.9775211,0.00005340457,0.001346605,0.01355844],"study_design_scores_gemma":[0.0007498148,0.0001158417,0.01699288,0.0000227754,0.000003753983,0.00000162592,0.0002833015,0.008071976,0.9561682,0.00008954719,0.01735336,0.000146918],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9974096,0.0004787072,0.0007735845,0.0001737607,0.00004120074,0.0002765288,0.00006900192,0.000007816976,0.0007698295],"genre_scores_gemma":[0.9980835,0.0004825384,0.0003430145,0.00001852867,0.0001576698,0.00001851516,0.0002116658,0.00001775708,0.0006668168],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02135293,"threshold_uncertainty_score":0.4200912,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04135626195073181,"score_gpt":0.3443882632611404,"score_spread":0.3030320013104086,"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."}}