{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002931785,0.00008948215,0.0001463326,0.00009267664,0.0001349524,0.00002717611,0.0001369233,0.0001165713,0.00001976849],"category_scores_gemma":[0.00001029236,0.00009260732,0.00005210556,0.0001833613,0.00008279761,0.000006662287,0.0004202665,0.0001374635,0.00000209328],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004707854,"about_ca_system_score_gemma":0.0001081711,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003995201,"about_ca_topic_score_gemma":0.000275786,"domain_scores_codex":[0.9990177,0.00008656876,0.0001159367,0.0003309076,0.000176962,0.0002719059],"domain_scores_gemma":[0.9995219,0.00001897439,0.00003487754,0.0002516364,0.0001147367,0.00005795134],"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":[0.00005572848,0.00005497473,0.008535664,0.0001262422,0.00001985182,0.000009014797,0.0003370727,0.00002784448,0.9892653,0.000007353965,0.000006842452,0.001554124],"study_design_scores_gemma":[0.0003295708,0.0001443872,0.01746391,0.00002085141,0.000004062333,0.000004329202,0.0002737146,0.000271574,0.9811543,0.00003317844,0.0001948659,0.0001053037],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9978746,0.001660063,0.00007789685,0.00004705656,0.00002885589,0.0001364764,0.00006096559,0.000003348358,0.0001106935],"genre_scores_gemma":[0.9968728,0.001527891,0.0001113543,0.000003777095,0.00002779338,0.000006823814,0.00002026526,0.00001085732,0.001418425],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.008928241,"threshold_uncertainty_score":0.3776417,"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."}}