{"id":"W2560510482","doi":"10.1038/ng.3721","title":"Disease variants alter transcription factor levels and methylation of their binding sites","year":2016,"lang":"en","type":"article","venue":"Nature Genetics","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":564,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Toronto; Ontario Institute for Cancer Research","funders":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek; ZonMw","keywords":"Biology; DNA methylation; Genetics; Methylation; Single-nucleotide polymorphism; DNA binding site; CpG site; Expression quantitative trait loci; Quantitative trait locus; Differentially methylated regions; Transcription factor; CTCF; Genome-wide association study; Computational biology; Gene; Promoter; Gene expression; Genotype; Enhancer","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002768966,0.0005874145,0.0004270029,0.0007211761,0.0002639128,0.0004988175,0.0003587075,0.0008831343,0.007170626],"category_scores_gemma":[0.0008248142,0.0003157417,0.0003900065,0.0005422428,0.0003859797,0.0002405328,0.0002881805,0.0006650156,0.0005623032],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002464828,"about_ca_system_score_gemma":0.0001069411,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001487013,"about_ca_topic_score_gemma":0.001714531,"domain_scores_codex":[0.9996091,0.00006898857,0.00005587631,0.000152261,0.00005981861,0.00005405517],"domain_scores_gemma":[0.9994843,0.0001821617,0.0001477848,0.00006202742,0.00003636951,0.00008743841],"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":[0.001591927,0.00006994374,0.02675352,0.00008700739,0.0003863315,0.000951856,0.0001179536,0.0004983865,0.9614544,0.001206233,0.0004453897,0.006437053],"study_design_scores_gemma":[0.0002934195,0.0009050475,0.3988895,0.00005780608,0.0009073905,0.01257289,0.0003008636,0.004901482,0.5666737,0.004063593,0.01033042,0.0001039396],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9914514,0.001336476,0.00371954,0.0003130584,0.0001201355,0.000008910612,0.001442757,0.0001474837,0.001460241],"genre_scores_gemma":[0.9975235,0.0002289027,0.0007083341,0.00007813076,0.00002408931,0.000005739999,0.0003586947,0.00004796084,0.001024512],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007170626,"threshold_uncertainty_score":0.02398813,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02096819672398866,"score_gpt":0.2761229753333763,"score_spread":0.2551547786093877,"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."}}