{"id":"W4390668729","doi":"10.1186/s13059-023-03070-0","title":"Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet","year":2024,"lang":"en","type":"article","venue":"Genome biology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":28,"is_retracted":false,"has_abstract":true,"ca_institutions":"Vector Institute; St. Michael's Hospital; Princess Margaret Cancer Centre; University of Toronto; University Health Network","funders":"National Institute of General Medical Sciences; Medical Research Council; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Agencia Nacional de Investigación y Desarrollo; China Scholarship Council; Ministry of Training, Colleges and Universities; University of Toronto; Comisión Nacional de Investigación Científica y Tecnológica; Canadian Cancer Society; Government of Ontario; Agenția Națională pentru Cercetare și Dezvoltare; National Institutes of Health; Ontario Ministry of Research, Innovation and Science; Ontario Ministry of Research and Innovation; Western Canada Research Grid; Cancer Research UK; CHIST-ERA; Temerty Faculty of Medicine, University of Toronto; Ontario Institute for Cancer Research; Wellcome Trust; Princess Margaret Cancer Foundation","keywords":"Biology; Transcription factor; Computational biology; DNA binding site; Genetics; Transcription (linguistics); DNA; DNA methylation; General transcription factor; Promoter; Gene; 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":[0.0002767744,0.000526066,0.0003309677,0.0002880929,0.0001876852,0.0003432828,0.0008067829,0.0008614553,0.001806353],"category_scores_gemma":[0.0007800808,0.0002755188,0.0005519565,0.0002444737,0.0002611485,0.0003810361,0.0003000917,0.0005908653,0.0003614275],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005569668,"about_ca_system_score_gemma":0.0004325282,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003011066,"about_ca_topic_score_gemma":0.003420405,"domain_scores_codex":[0.9999051,0.00002047017,0.000004389766,0.00002851838,0.0000251269,0.00001635265],"domain_scores_gemma":[0.9997248,0.0001705045,0.00003524254,0.0000248197,0.00002289802,0.00002174583],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00006420161,0.00003990971,0.001542303,0.00004257598,0.00002001164,0.00007203272,0.00002190967,0.9743863,0.01856531,0.001545803,0.0001495599,0.003550009],"study_design_scores_gemma":[0.000007231286,0.00001506616,0.0001873696,0.000001669796,0.000004249817,0.00001557353,0.000003966596,0.995689,0.003020947,0.0007961743,0.0002553735,0.000003457385],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6587614,0.0002393999,0.3341063,0.0001726015,0.00003560997,0.00005187935,0.0006536089,0.0008264668,0.005152734],"genre_scores_gemma":[0.9155601,0.0002262688,0.08047745,0.00008855126,0.00001510686,0.0001590265,0.0005271601,0.0001431755,0.002803274],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003011066,"threshold_uncertainty_score":0.006042838,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01420481302186787,"score_gpt":0.2491402192983455,"score_spread":0.2349354062764777,"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."}}