{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001303221,0.0002058791,0.0002279558,0.00008357989,0.00009421891,0.00005103827,0.0003047078,0.0001632298,0.0001039498],"category_scores_gemma":[0.00004285374,0.0001480717,0.0001999412,0.0001587054,0.00006709277,0.000008304289,0.0001819432,0.00004773606,0.0001108897],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004397401,"about_ca_system_score_gemma":0.00006108962,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006041104,"about_ca_topic_score_gemma":0.0001257275,"domain_scores_codex":[0.9988741,0.00002451826,0.0004217586,0.0002117985,0.0001744708,0.0002933098],"domain_scores_gemma":[0.9989442,0.00002047052,0.000193823,0.0006387297,0.00007503746,0.0001276928],"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":[0.0000843344,0.0002108161,0.03047863,0.00007086113,0.003348226,0.000009145567,0.001338689,0.001037598,0.9207808,0.0002724571,0.007935936,0.03443246],"study_design_scores_gemma":[0.008853354,0.001295105,0.1492997,0.0001462722,0.003421522,0.00003473637,0.003316377,0.09095915,0.5969599,0.00156285,0.1397448,0.004406184],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9270307,0.0001392354,0.0704527,0.000140317,0.0001618947,0.0001387357,0.0002903804,0.00002526718,0.001620777],"genre_scores_gemma":[0.9835593,0.0003356531,0.01441931,0.0002430619,0.0001206981,0.00001153096,0.000459094,0.00001980582,0.0008315763],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3238209,"threshold_uncertainty_score":0.603819,"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."}}