{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001219055,0.0001327713,0.0001094123,0.00005773005,0.00004190612,0.0000124652,0.00008341107,0.0002598727,0.00002007062],"category_scores_gemma":[0.00007882293,0.00009279436,0.00005683853,0.00006144634,0.00005470861,0.000005467573,0.00003412223,0.00007009562,0.000001360504],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007870126,"about_ca_system_score_gemma":0.00003176003,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":6.046917e-7,"about_ca_topic_score_gemma":0.000005147518,"domain_scores_codex":[0.9992243,0.00005757693,0.0001837676,0.000267126,0.0001255106,0.0001417239],"domain_scores_gemma":[0.9994642,0.00002474812,0.00009112681,0.0002251281,0.000106078,0.0000887539],"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":[0.00003915305,0.00001788412,0.02126935,0.00001872674,0.00002528946,2.737088e-7,0.00004736714,0.000007845733,0.9608522,0.00003159348,0.00001503036,0.01767528],"study_design_scores_gemma":[0.0003507973,0.00009234847,0.1493774,0.0000176193,0.00002042367,3.65674e-7,0.0000065234,0.00004280357,0.8469135,0.0006772933,0.002379471,0.0001214629],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9825291,0.007926751,0.008790025,0.0001352319,0.0001615229,0.0001426006,0.0002559524,0.000006354248,0.00005248544],"genre_scores_gemma":[0.9970766,0.001222829,0.001265636,0.00003940502,0.0001657105,0.000003902723,0.00006269215,0.00001941571,0.0001437655],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1281081,"threshold_uncertainty_score":0.3784044,"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."}}