{"id":"W2152791321","doi":"10.1101/gr.185272.114","title":"The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements","year":2015,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":506,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Ontario Ministry of Research and Innovation; Biotechnology and Biological Sciences Research Council; Medical Research Council; Canadian Institutes of Health Research; Cancer Research UK; Canada Foundation for Innovation; Francis Crick Institute","keywords":"Biology; Promoter; Transcription factor; Chromatin; Genetics; Gene; ChIA-PET; Regulatory sequence; Genome; Regulation of gene expression; Chromatin immunoprecipitation; Histone; Computational biology; Gene expression","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":[0.0001231911,0.000222378,0.00016064,0.0004082083,0.0002962727,0.0004402704,0.0002527847,0.0001806481,0.001369477],"category_scores_gemma":[0.0003989795,0.000180902,0.0001750599,0.0004753017,0.0003161652,0.0003200754,0.0004609041,0.0003181557,0.0005849456],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00019337,"about_ca_system_score_gemma":0.0002541508,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004899839,"about_ca_topic_score_gemma":0.001474125,"domain_scores_codex":[0.9998344,0.0000169949,0.0000066989,0.00007411659,0.00004810488,0.00001961406],"domain_scores_gemma":[0.9997024,0.00008421612,0.0001024503,0.00003347778,0.00004045369,0.00003696906],"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":[0.00007574183,0.00001314816,0.006835347,0.00009909253,0.00002055428,0.00008608725,0.00005421538,0.0003951088,0.9745333,0.001761568,0.0001145343,0.01601134],"study_design_scores_gemma":[0.00002437778,0.0002499654,0.2631777,0.00008939348,0.0001444718,0.001344755,0.0002132823,0.004734235,0.706129,0.004110675,0.01974655,0.00003562456],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8905364,0.005326223,0.09552547,0.0001479282,0.00004034601,0.0000554036,0.002584759,0.0006426694,0.005140784],"genre_scores_gemma":[0.9599556,0.001912969,0.03129935,0.00013833,0.00003299268,0.00004220762,0.003647397,0.00005842571,0.002912731],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001369477,"threshold_uncertainty_score":0.004581332,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06085026846415899,"score_gpt":0.3343343832508382,"score_spread":0.2734841147866792,"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."}}