{"id":"W2058944050","doi":"10.1186/1471-2164-13-152","title":"Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features","year":2012,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":78,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Enhancer; Biology; Chromatin; H3K4me3; Homeobox protein NANOG; Histone; Genetics; Epigenetics; Epigenomics; Gene; Computational biology; Transcription factor; Promoter; Regulation of gene expression; Embryonic stem cell; Gene expression; Induced pluripotent stem cell; DNA methylation","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":[0.0004553148,0.0006022112,0.0003336212,0.0003104219,0.00009494204,0.0002944213,0.0004105842,0.0003516456,0.0005193063],"category_scores_gemma":[0.0004404651,0.0002132579,0.0007520753,0.000170251,0.0002281531,0.0001719891,0.0002850903,0.0003369894,0.0001570457],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004214638,"about_ca_system_score_gemma":0.0003033335,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002236928,"about_ca_topic_score_gemma":0.002211133,"domain_scores_codex":[0.9999286,0.00001865572,0.000002767626,0.00002769629,0.00001393737,0.000008383859],"domain_scores_gemma":[0.9998572,0.00008612938,0.00002764824,0.000006106185,0.00001397192,0.000009007745],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00007889915,0.00005562865,0.00370788,0.00003840938,0.00004310386,0.00004751152,0.00002659427,0.9649382,0.02159359,0.0005133036,0.0001239035,0.008832966],"study_design_scores_gemma":[0.000002232796,0.00001453426,0.0004583658,0.000001006003,0.000003936662,0.000007053596,0.000002291894,0.997707,0.001588828,0.0001522032,0.00006115423,0.000001418754],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6314507,0.0002346869,0.365886,0.00008833173,0.000009694955,0.00004619699,0.0004716383,0.0007434614,0.001069235],"genre_scores_gemma":[0.9376169,0.0001171231,0.05990125,0.00003866607,0.000006928109,0.0001166071,0.0009886876,0.00008942732,0.001124424],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002236928,"threshold_uncertainty_score":0.004447758,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01532748268618507,"score_gpt":0.2447921373530248,"score_spread":0.2294646546668397,"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."}}