{"id":"W2164354446","doi":"10.1101/gr.144840.112","title":"Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types","year":2013,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":102,"is_retracted":false,"has_abstract":true,"ca_institutions":"Artificial Intelligence in Medicine (Canada)","funders":"David Geffen School of Medicine, University of California, Los Angeles; National Human Genome Research Institute; National Institutes of Health; National Science Foundation","keywords":"Chromatin; Biology; ChIA-PET; Bivalent chromatin; Regulator; Enhancer; Genetics; Sequence motif; Scaffold/matrix attachment region; Transcription factor; Histone; Regulatory sequence; Computational biology; Chromatin remodeling; Gene","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":[0.0007278504,0.0001586623,0.0001902621,0.0002136844,0.0001468538,0.0001020429,0.0003304891,0.0001674757,0.0001019765],"category_scores_gemma":[0.00003073314,0.0001576092,0.00003970828,0.0001712743,0.0001919336,0.00000778044,0.0004615248,0.0002526977,0.0001086086],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007270371,"about_ca_system_score_gemma":0.00008290305,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001884562,"about_ca_topic_score_gemma":0.0001122038,"domain_scores_codex":[0.9983504,0.0001437247,0.0002945377,0.0004423213,0.0002324392,0.0005365575],"domain_scores_gemma":[0.9991689,0.00002678838,0.00006074037,0.0004640219,0.0001149202,0.0001645943],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.000005462106,0.00003821918,0.02920885,0.00007684826,0.00002220981,0.000002749357,0.0002030945,0.00002493838,0.9689118,0.00003390001,0.0006207461,0.0008511995],"study_design_scores_gemma":[0.001329565,0.0008425326,0.8539878,0.00006122297,0.000009496379,0.00001093973,0.0005404441,0.0004323094,0.1323141,0.002039849,0.007780331,0.0006514134],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9972807,0.0005687214,0.00001768563,0.00006616516,0.00002377777,0.0003956789,0.00003116461,0.000009012372,0.001607093],"genre_scores_gemma":[0.9949781,0.0001039029,0.0004392033,0.00001238678,0.0001129988,0.00004254903,0.0001517781,0.00004113828,0.004117972],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8365977,"threshold_uncertainty_score":0.6427118,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01627265534250068,"score_gpt":0.308305538857599,"score_spread":0.2920328835150984,"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."}}