{"id":"W2146368849","doi":"10.1093/nar/gkm427","title":"oPOSSUM: integrated tools for analysis of regulatory motif over-representation","year":2007,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":163,"is_retracted":false,"has_abstract":true,"ca_institutions":"Child and Family Research Institute; University of British Columbia","funders":"Canadian Institutes of Health Research","keywords":"Biology; Opossum; Caenorhabditis elegans; Gene; Transcription factor; DNA binding site; Genetics; Computational biology; Binding site; Promoter; Caenorhabditis; Saccharomyces cerevisiae; Sequence analysis; Motif (music); Gene expression; Anatomy","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":[0.001842868,0.00009948525,0.0002024416,0.0003087537,0.0001044226,0.00004952683,0.0002820331,0.0002165705,0.00007253829],"category_scores_gemma":[0.0002552978,0.00009184939,0.0001855448,0.0007876952,0.0001805655,0.00001048126,0.0001305558,0.0001497312,0.000004422102],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003674268,"about_ca_system_score_gemma":0.00007932507,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005321231,"about_ca_topic_score_gemma":0.00007859486,"domain_scores_codex":[0.9986336,0.00005484896,0.0003674343,0.0002444495,0.0003202052,0.0003794882],"domain_scores_gemma":[0.9987603,0.0001230078,0.00009083225,0.0004849759,0.0004442513,0.00009661989],"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":[0.000959811,0.000171996,0.01255584,0.00008146183,0.001684449,0.00000216809,0.0004751121,0.001069683,0.7980551,0.00310847,0.01937347,0.1624625],"study_design_scores_gemma":[0.003073005,0.001586276,0.2687679,0.00005309289,0.0005343072,0.000005082659,0.00377182,0.059399,0.5414587,0.002179804,0.1184091,0.0007618609],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9604457,0.0001634024,0.03587592,0.00005869809,0.00006834522,0.0003575068,0.00006523162,0.000007481308,0.002957718],"genre_scores_gemma":[0.9955517,0.00005064674,0.002750747,0.00004863137,0.0001219772,0.00001397809,0.0004863643,0.00001669216,0.0009592482],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2565963,"threshold_uncertainty_score":0.3745509,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05177588946621689,"score_gpt":0.3724320420734815,"score_spread":0.3206561526072647,"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."}}