{"id":"W4398250349","doi":"10.1371/journal.pgen.1011277","title":"Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity","year":2024,"lang":"en","type":"article","venue":"PLoS Genetics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":28,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Medical Research Council; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; National Science Foundation","keywords":"Enhancer; Enhancer RNAs; Chromatin; Biology; Promoter; Chromosome conformation capture; Estrogen receptor alpha; Transcription factor; Regulation of gene expression; Transcription (linguistics); ChIA-PET; RNA polymerase II; Estrogen receptor; Molecular biology; Gene; Gene expression; Genetics; Chromatin remodeling","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009225718,0.0001624934,0.0001310407,0.00004997864,0.00003546188,0.00007300428,0.0001065257,0.0001493752,0.00001977619],"category_scores_gemma":[0.00001044365,0.0001594562,0.00003848173,0.00004272909,0.0000438538,0.000003542974,0.00005470617,0.00009673506,0.000004287955],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002948477,"about_ca_system_score_gemma":0.00006339661,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003913938,"about_ca_topic_score_gemma":0.003137618,"domain_scores_codex":[0.9991203,0.00002737872,0.0001713177,0.0003504306,0.000111945,0.0002186557],"domain_scores_gemma":[0.999692,0.000006978131,0.00002917375,0.0001833668,0.00003132435,0.00005719399],"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":[0.0000153883,0.00004492024,0.002440296,0.0001185667,0.00004306925,0.000008369197,0.0002271617,0.00003431297,0.9919497,0.00006837908,0.00001119542,0.005038666],"study_design_scores_gemma":[0.0002837249,0.0003471497,0.001891638,0.00005348457,0.00004015804,0.00001931142,0.00008278839,0.02043697,0.9752315,0.0004162349,0.0009638406,0.0002332114],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9911823,0.007038862,0.0009851776,0.0001822005,0.0001609224,0.0002647053,0.00006707159,0.00001750982,0.0001012041],"genre_scores_gemma":[0.9962568,0.002611955,0.0006774302,0.00005140999,0.0001774279,0.00004141252,0.00008355499,0.00002967187,0.00007035105],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02040265,"threshold_uncertainty_score":0.6502436,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01226964259449715,"score_gpt":0.2246146926333634,"score_spread":0.2123450500388663,"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."}}