{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00188031,0.003199745,0.001807471,0.004245421,0.0008202251,0.001968912,0.002820645,0.0009359288,0.02710954],"category_scores_gemma":[0.003187763,0.00160303,0.002272887,0.002923432,0.0006383348,0.00252375,0.003982024,0.002220818,0.007500688],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007758064,"about_ca_system_score_gemma":0.001143935,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002142688,"about_ca_topic_score_gemma":0.00315281,"domain_scores_codex":[0.9990383,0.0001360934,0.00009121546,0.0002604692,0.0003630344,0.0001109229],"domain_scores_gemma":[0.9990712,0.0004166907,0.0001526046,0.0001950903,0.0000749794,0.00008940647],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.006107099,0.0005289764,0.0137624,0.005152168,0.001588031,0.002383344,0.001962679,0.01234773,0.1988827,0.02003087,0.3102847,0.4269693],"study_design_scores_gemma":[0.001795279,0.0006226561,0.03547138,0.0006725678,0.0008300217,0.004259923,0.0005337906,0.2295207,0.1558853,0.05401042,0.5155589,0.0008390805],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"software","genre_gemma":"methods","genre_scores_codex":[0.01795492,0.001005076,0.457533,0.0002397604,0.0002321077,0.0003722727,0.05976204,0.4594921,0.003408714],"genre_scores_gemma":[0.0893259,0.001402226,0.6869755,0.0003804217,0.0001121739,0.002420006,0.1448237,0.06833138,0.006228639],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.02710954,"threshold_uncertainty_score":0.09069043,"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."}}