{"id":"W2415713319","doi":"10.1038/ncomms10528","title":"Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states","year":2016,"lang":"en","type":"article","venue":"Nature Communications","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":22,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Human Genome Research Institute; National Institute of General Medical Sciences; Canadian Institute for Advanced Research; National Institutes of Health; National Science Foundation","keywords":"Chromatin; ChIA-PET; Enhancer; Enhancer RNAs; Bivalent chromatin; Scaffold/matrix attachment region; Computational biology; Chromatin remodeling; Biology; Histone code; Genetics; Epigenetics; Histone-modifying enzymes; Epigenomics; Transcription factor; Cell biology; Gene; Gene expression; Nucleosome; DNA methylation","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003270656,0.0003353412,0.0003233998,0.0004415171,0.0002308212,0.0006355486,0.0004996482,0.0004553502,0.0006171071],"category_scores_gemma":[0.001111479,0.0003307059,0.0005803129,0.0003054249,0.0004669173,0.0005318571,0.0003479749,0.0003939404,0.0001048365],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005386742,"about_ca_system_score_gemma":0.0004529143,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004228635,"about_ca_topic_score_gemma":0.005000099,"domain_scores_codex":[0.9999146,0.00002733729,0.000003887923,0.00002462765,0.00001793404,0.00001154209],"domain_scores_gemma":[0.9996314,0.0002461759,0.00003909184,0.00003415304,0.0000249501,0.00002427474],"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":[0.00002172716,0.000006498248,0.001561373,0.00001445102,0.00001116742,0.00003268231,0.00002273131,0.9869213,0.005172402,0.004893035,0.00004930238,0.001293329],"study_design_scores_gemma":[0.000002089981,0.000002885577,0.0003203032,7.410654e-7,0.000001987898,0.000006033183,0.000002125572,0.9972461,0.0003393062,0.002022722,0.00005336101,0.000002286638],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5527765,0.0001806416,0.4436069,0.000167835,0.000008960042,0.0000239933,0.0004340999,0.0002929498,0.002508209],"genre_scores_gemma":[0.9770447,0.0001153288,0.0218518,0.00001473917,0.000004289629,0.00003589051,0.0002596517,0.00005510639,0.0006184676],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004228635,"threshold_uncertainty_score":0.00840801,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01935373124114869,"score_gpt":0.2429121276847959,"score_spread":0.2235583964436472,"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."}}