{"id":"W4284896311","doi":"10.1186/s13059-022-02713-y","title":"Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding","year":2022,"lang":"en","type":"article","venue":"Genome biology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; McGill Genome Centre","funders":"Canadian Institutes of Health Research; Natural Sciences and Engineering Research Council of Canada; Mitacs; Compute Canada","keywords":"Biology; DNA methylation; CpG site; Methylation; Genetics; Transcription factor; DNA; Pioneer factor; Epigenetics; Epigenetics of physical exercise; DNA binding site; Computational biology; Promoter; Gene; Gene expression; Histone methyltransferase","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":[0.0008738351,0.0006788028,0.0005080408,0.0006074373,0.0002574135,0.0007214933,0.0007887606,0.0006826707,0.001753474],"category_scores_gemma":[0.001583716,0.0004994508,0.0006327225,0.0004235035,0.0004948333,0.0008676436,0.0006485849,0.001172184,0.0003509319],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005486018,"about_ca_system_score_gemma":0.000366428,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001068966,"about_ca_topic_score_gemma":0.001718554,"domain_scores_codex":[0.9997543,0.00005336294,0.00001048005,0.00009828005,0.00006114843,0.00002244207],"domain_scores_gemma":[0.9991521,0.0003980656,0.0001811236,0.0001541851,0.00004946198,0.00006503794],"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":[0.0004542072,0.0001158574,0.04083765,0.0006211789,0.0002769571,0.0001248808,0.0002103154,0.08031304,0.835696,0.008182462,0.000736776,0.03243069],"study_design_scores_gemma":[0.00002330734,0.0003045057,0.03286034,0.00005031049,0.0001956837,0.0003775558,0.00014636,0.7285661,0.2173299,0.01396329,0.006119736,0.00006293786],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6833113,0.003022552,0.3080196,0.0003869154,0.00005243502,0.00003685604,0.001275698,0.001461948,0.002432704],"genre_scores_gemma":[0.9507686,0.001158149,0.04646818,0.0001141394,0.00003345497,0.00004171169,0.0009312712,0.0001189621,0.0003655497],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001753474,"threshold_uncertainty_score":0.005865991,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01925897478410205,"score_gpt":0.2519897421726791,"score_spread":0.232730767388577,"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."}}