{"id":"W2155484811","doi":"10.1093/nar/gkl879","title":"PReMod: a database of genome-wide mammalian cis-regulatory module predictions","year":2006,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":89,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Montreal Clinical Research Institute; McGill University and Génome Québec Innovation Centre","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Physicians Committee for Responsible Medicine; Génome Québec; Genome Canada","keywords":"Biology; Genome; Genome browser; Context (archaeology); Gene; Genetics; Computational biology; DNA binding site; Cis-regulatory module; Genomics; Transcription factor; Database; Promoter; Computer science; Enhancer; Gene expression","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"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":[0.001194399,0.002881639,0.00220093,0.004231343,0.0007560268,0.001918703,0.004199736,0.001578648,0.02482934],"category_scores_gemma":[0.003160127,0.001799227,0.001340053,0.003964636,0.0002594134,0.0016362,0.002563624,0.001578354,0.02259803],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008121839,"about_ca_system_score_gemma":0.001738091,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004505438,"about_ca_topic_score_gemma":0.009685979,"domain_scores_codex":[0.9992466,0.00009388375,0.00008184713,0.0003165952,0.0002021995,0.00005895503],"domain_scores_gemma":[0.9992263,0.0002498424,0.0001163891,0.000181694,0.0001194688,0.0001062957],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001921464,0.0002599851,0.01023929,0.007369962,0.0008330137,0.001239166,0.000310952,0.01286588,0.0506645,0.008620242,0.7682655,0.1374101],"study_design_scores_gemma":[0.0008302839,0.0002554964,0.01641208,0.0005573062,0.0004628084,0.001491697,0.0001330886,0.02794497,0.0305987,0.01279587,0.9082127,0.0003050499],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"dataset","genre_gemma":"dataset","genre_scores_codex":[0.007286321,0.002333379,0.03706857,0.0001427469,0.0001034203,0.0001324764,0.8974758,0.04989725,0.005559996],"genre_scores_gemma":[0.008640453,0.0008851722,0.04055715,0.0001655856,0.00002199312,0.0003703846,0.9450401,0.002831572,0.001487496],"genre_candidate":"dataset","genre_consensus":"dataset","teacher_disagreement_score":0.02482934,"threshold_uncertainty_score":0.08306247,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01668678522604314,"score_gpt":0.2759709852762874,"score_spread":0.2592842000502443,"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."}}