{"id":"W3133944950","doi":"10.1101/gr.272468.120","title":"A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells","year":2021,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":63,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Ontario Ministry of Research and Innovation; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Canada Foundation for Innovation","keywords":"Biology; Enhancer; DNA binding site; SOX2; Transcription factor; Genetics; Homeobox protein NANOG; Binding site; Computational biology; Conserved sequence; Regulatory sequence; Induced pluripotent stem cell; Gene; Promoter; Embryonic stem cell; Gene expression; Peptide sequence","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":[0.0002335922,0.0001919476,0.0003865595,0.0003908123,0.0001287858,0.0003724418,0.0001934526,0.0002351863,0.0006912141],"category_scores_gemma":[0.0003770294,0.0003146182,0.0001948938,0.0001926798,0.0003500424,0.0002582515,0.0003249767,0.0003873633,0.0003967847],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002358554,"about_ca_system_score_gemma":0.0001638192,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001916017,"about_ca_topic_score_gemma":0.0004281396,"domain_scores_codex":[0.9997377,0.00002902994,0.00002059199,0.00009093464,0.00008324514,0.00003851796],"domain_scores_gemma":[0.9996989,0.00008333564,0.00007568565,0.00003357528,0.0000274746,0.00008098671],"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":[0.00002807795,0.000004050876,0.0008861835,0.00001164123,0.000003069665,0.00001697269,0.0000071164,0.0001383278,0.9976063,0.00006820694,0.000005952204,0.001224097],"study_design_scores_gemma":[0.00002218095,0.0002217028,0.07252831,0.00001998763,0.00003700439,0.001020331,0.00005410285,0.005913383,0.9175075,0.0008219371,0.001827591,0.00002596334],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9880652,0.0008168852,0.01021264,0.00002690355,0.000004111221,0.000008293497,0.0001603795,0.0001195088,0.0005860493],"genre_scores_gemma":[0.9955766,0.0002199471,0.003465779,0.00002747557,0.000006268225,0.00001053632,0.000287611,0.00003306005,0.0003726658],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0006912141,"threshold_uncertainty_score":0.002312303,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05696045962582858,"score_gpt":0.3045833414883116,"score_spread":0.247622881862483,"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."}}