{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002977228,0.000167923,0.0003224052,0.0002201055,0.0001523394,0.0005707815,0.0002564163,0.0002981372,0.001166615],"category_scores_gemma":[0.000534418,0.00028522,0.0002001352,0.0001665595,0.0004533514,0.0004407726,0.000415372,0.0004833371,0.0003790395],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003404954,"about_ca_system_score_gemma":0.000175491,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002692336,"about_ca_topic_score_gemma":0.0005783246,"domain_scores_codex":[0.9996312,0.00007593659,0.00002249889,0.0001322022,0.00009827806,0.00003989993],"domain_scores_gemma":[0.9995304,0.0002377367,0.00008632668,0.00005998574,0.0000391021,0.00004643316],"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":[0.00006028994,0.000009657188,0.000322576,0.00001992711,0.000002446878,0.00001274985,0.00002415023,0.00009178068,0.9982645,0.0001630305,0.000006678374,0.001022098],"study_design_scores_gemma":[0.000009644918,0.00009606341,0.009555991,0.000005505092,0.000006061189,0.0001146082,0.00005295329,0.001551983,0.9871803,0.0001961934,0.001225328,0.000005316736],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9860532,0.001153126,0.010869,0.00009251157,0.00001387214,0.00001328986,0.0001277039,0.0000696877,0.00160757],"genre_scores_gemma":[0.9960343,0.0004098918,0.002360644,0.00002613579,0.000005839336,0.00001775883,0.0001434758,0.00002543999,0.0009764719],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001166615,"threshold_uncertainty_score":0.003902733,"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."}}