{"id":"W2952707685","doi":"10.1101/040667","title":"CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs","year":2016,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Children's Hospital","funders":"","keywords":"Perl; Opossum; Transcription factor; Gene; Biology; Computational biology; DNA binding site; Promoter; Transcription (linguistics); Binding site; Genetics; Gene expression; Computer science; World Wide Web","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":[0.0004263156,0.0004598993,0.000497446,0.0008779551,0.0003403367,0.0005105919,0.0006470463,0.0002698352,0.008904324],"category_scores_gemma":[0.0008629419,0.0002475574,0.0007174846,0.0006887226,0.0002319552,0.0003211327,0.0008514808,0.0005892972,0.002169882],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002484323,"about_ca_system_score_gemma":0.0003398125,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002516718,"about_ca_topic_score_gemma":0.004874016,"domain_scores_codex":[0.999779,0.0000189902,0.00001257405,0.00008641826,0.00007412097,0.00002874688],"domain_scores_gemma":[0.9996802,0.0001237965,0.00004898121,0.0000555284,0.00005296354,0.00003869415],"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":[0.002382576,0.0001095832,0.03351441,0.001717391,0.0004191742,0.0008782314,0.0004154658,0.01184303,0.7885845,0.003912871,0.04918344,0.1070393],"study_design_scores_gemma":[0.0003050146,0.0004528377,0.09733649,0.0001808114,0.0003504131,0.001434303,0.0003313875,0.1199132,0.6578702,0.006360508,0.1152605,0.0002043579],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"software","genre_scores_codex":[0.6239372,0.001734603,0.1845716,0.0003896142,0.0002144649,0.0001644431,0.1400243,0.04057824,0.008385481],"genre_scores_gemma":[0.5173019,0.000614646,0.2351039,0.0003508335,0.00005130989,0.0002976406,0.2328956,0.008436084,0.004948095],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.008904324,"threshold_uncertainty_score":0.02978796,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006502631358328762,"score_gpt":0.2041981024891985,"score_spread":0.1976954711308697,"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."}}