{"id":"W4221084563","doi":"10.7554/elife.70878","title":"Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs","year":2022,"lang":"en","type":"article","venue":"eLife","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":23,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"H2020 European Research Council; National Institute of Diabetes and Digestive and Kidney Diseases; National Heart, Lung, and Blood Institute; Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers; National Institutes of Health; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; American Heart Association","keywords":"Enhancer; Chromatin immunoprecipitation; Indel; Biology; Transcription factor; Genetics; Promoter; DNA binding site; Histone; Cis-regulatory module; Gene; Chromatin; Binding site; Regulatory sequence; Computational biology; Human genome; Genome; Gene expression; Single-nucleotide polymorphism","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":[0.0001275152,0.0001257679,0.0002579789,0.000145052,0.0002115155,0.0000375364,0.00005692847,0.00005434972,0.00001140794],"category_scores_gemma":[0.00001930748,0.0001239484,0.0001343667,0.0001358768,0.00004027812,0.00001050493,0.0000407705,0.00008890453,2.104299e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002482403,"about_ca_system_score_gemma":0.00001777426,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005773704,"about_ca_topic_score_gemma":0.000282207,"domain_scores_codex":[0.9990931,0.0001080953,0.0002701897,0.0002381911,0.0001642177,0.0001261735],"domain_scores_gemma":[0.9995915,0.00001895168,0.0001243551,0.000152209,0.0000644481,0.00004854403],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0000212266,0.00002850161,0.003058758,0.0004882523,0.0005864822,0.000001274797,0.002510954,0.001389612,0.9918286,0.00003304894,0.00000753447,0.00004574885],"study_design_scores_gemma":[0.002263053,0.0007307279,0.4306955,0.0007728112,0.004273172,0.0001279666,0.02605389,0.1400265,0.3932749,0.00006399155,0.0002458698,0.001471563],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9941118,0.0007669055,0.004319833,0.00005257543,0.0001172672,0.0002356038,0.000376397,0.000009943651,0.000009651441],"genre_scores_gemma":[0.9993243,0.0001438673,0.0001608951,0.00009633633,0.00001526844,0.00002540814,0.0001854376,0.00001148575,0.00003699998],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5985537,"threshold_uncertainty_score":0.5054469,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01131563818715384,"score_gpt":0.2227742123795692,"score_spread":0.2114585741924154,"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."}}