{"id":"W1985265438","doi":"10.1093/nar/gku1390","title":"DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors","year":2015,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":42,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; University of Toronto","funders":"","keywords":"Biology; Cooperativity; Enhancer; DNA; Genetics; Transcription factor; Transcription (linguistics); PAX6; Computational biology; Cooperative binding; Gene; Binding site","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0007558338,0.0001053512,0.0001181639,0.00003770453,0.0001524955,0.00004538463,0.0001679147,0.0001327458,0.00003643447],"category_scores_gemma":[0.0002019758,0.000074347,0.00003210298,0.0001415367,0.0004123717,0.000008713058,0.00004651096,0.0001682004,0.000007601601],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003462126,"about_ca_system_score_gemma":0.0001319697,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001302364,"about_ca_topic_score_gemma":0.00007901816,"domain_scores_codex":[0.9988288,0.0002441133,0.0001625488,0.000237878,0.0002846626,0.0002420275],"domain_scores_gemma":[0.999394,0.00004915734,0.00003786143,0.0001585798,0.0002691655,0.00009120793],"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":[0.00004795181,0.00003780087,0.00686004,0.00001924479,0.00002669288,1.691654e-7,0.0007376647,0.00001564901,0.9899334,0.00003460516,0.001718589,0.0005682072],"study_design_scores_gemma":[0.0006106081,0.001078507,0.00742811,0.00001147939,0.000009938946,0.000004087881,0.00287413,0.002841221,0.9742644,0.0002239868,0.01047021,0.000183341],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9983961,0.0004995873,0.0002216936,0.0001788823,0.00003591412,0.0002103589,0.00008416828,0.000006825715,0.0003664983],"genre_scores_gemma":[0.9989174,0.00038991,0.00007110549,0.00001535286,0.0000295137,0.00001733308,0.0001516558,0.00001209706,0.0003956407],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.015669,"threshold_uncertainty_score":0.3031783,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03913740705901358,"score_gpt":0.3176595141329068,"score_spread":0.2785221070738932,"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."}}