{"id":"W2418153904","doi":"10.1093/bioinformatics/btw337","title":"CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs","year":2016,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"","keywords":"Opossum; Perl; Transcription factor; DNA binding site; Computational biology; Biology; Gene; Promoter; Binding site; Motif (music); Computer science; Genetics; World Wide Web; Gene expression","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0004313475,0.0006390315,0.0005470593,0.000863479,0.0003597221,0.0005701341,0.0009580873,0.0004342412,0.01512983],"category_scores_gemma":[0.001160923,0.0002751566,0.0008944477,0.0009707886,0.0002615317,0.0004385282,0.0009236465,0.0006979117,0.00477217],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002532626,"about_ca_system_score_gemma":0.0004057544,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002015229,"about_ca_topic_score_gemma":0.005203619,"domain_scores_codex":[0.9997641,0.0000186021,0.00001407211,0.00009460648,0.00007904576,0.00002954378],"domain_scores_gemma":[0.9995875,0.0001449108,0.00007783034,0.00007522425,0.00005863295,0.00005593877],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.003040429,0.0001491493,0.04131024,0.002540405,0.0004707148,0.0008995971,0.0004701994,0.008241547,0.7021686,0.003618945,0.07365245,0.1634377],"study_design_scores_gemma":[0.0004299248,0.0009123428,0.1100255,0.0002595353,0.0005066619,0.00228815,0.0004068201,0.1210778,0.5904683,0.00683515,0.1665284,0.0002613992],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.5293564,0.002703305,0.2130555,0.0005721955,0.0004105255,0.0002259316,0.1707623,0.07218619,0.01072759],"genre_scores_gemma":[0.4700529,0.0008696994,0.246993,0.0004379026,0.00008495549,0.0003916713,0.2637625,0.01097244,0.006434997],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.01512983,"threshold_uncertainty_score":0.05061436,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005895834575798081,"score_gpt":0.2108232657155318,"score_spread":0.2049274311397337,"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."}}