{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001380527,0.0002317304,0.0002006775,0.00007763407,0.00007383651,0.00003935458,0.0001519803,0.0002403871,0.00002145807],"category_scores_gemma":[0.000007399508,0.0001937847,0.00008564031,0.00008250678,0.00007416215,0.000006663128,0.00004238155,0.0001130697,0.00001730837],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003399076,"about_ca_system_score_gemma":0.00008392663,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000342763,"about_ca_topic_score_gemma":0.00007187827,"domain_scores_codex":[0.9987206,0.00009794255,0.0002135348,0.0005169275,0.00005884633,0.0003921618],"domain_scores_gemma":[0.9994722,0.000007619793,0.00002899597,0.0003052063,0.00006051936,0.0001254824],"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":[0.00006032675,0.00003438133,0.0001538438,0.00002320324,0.0001291446,0.000004131948,0.0003878167,0.003386474,0.9931762,0.0002160877,0.00000336471,0.002424982],"study_design_scores_gemma":[0.003226167,0.0112413,0.009070627,0.0001055165,0.0004567114,0.0005550443,0.002590386,0.4541108,0.4864378,0.003434649,0.02505468,0.003716265],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9006637,0.002552009,0.09595326,0.00004820575,0.0002518926,0.0001868752,0.0001565239,0.0000399722,0.0001475414],"genre_scores_gemma":[0.9946727,0.0004040883,0.003367504,0.0001171101,0.0003386036,0.00002402893,0.0008987243,0.00004915856,0.0001281533],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5067384,"threshold_uncertainty_score":0.7902312,"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."}}