{"id":"W2152406028","doi":"10.1038/ng.2416","title":"Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression","year":2012,"lang":"en","type":"article","venue":"Nature Genetics","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":377,"is_retracted":false,"has_abstract":false,"ca_institutions":"Princess Margaret Cancer Centre; University of Toronto; University Health Network","funders":"U.S. National Library of Medicine; National Institute of Diabetes and Digestive and Kidney Diseases; National Cancer Institute","keywords":"Single-nucleotide polymorphism; Biology; FOXA1; Genome-wide association study; Epigenomics; Genetics; Breast cancer; Locus (genetics); Chromatin; Epigenome; Imputation (statistics); SNP; 1000 Genomes Project; Gene; Genotype; Cancer; DNA methylation; Gene expression","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":[0.0003615272,0.0001432041,0.0001375084,0.00002173571,0.0001181608,0.00001265181,0.0001292461,0.0003941685,0.000007477332],"category_scores_gemma":[0.00008765997,0.0001033022,0.00007171431,0.00006324845,0.00005989329,0.000003330235,0.00009666363,0.0001612469,3.520135e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001076288,"about_ca_system_score_gemma":0.00002985657,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001406443,"about_ca_topic_score_gemma":0.00003150232,"domain_scores_codex":[0.9991367,0.00008673539,0.0001982687,0.0002004808,0.0001366302,0.0002411846],"domain_scores_gemma":[0.9992207,0.00003801032,0.0002162045,0.0002838875,0.0001681665,0.0000730523],"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":[0.00004824449,0.00005763119,0.05645228,0.00002031438,0.00005566762,4.064349e-8,0.00011352,0.0003430776,0.9371566,0.000004871432,0.0003927028,0.005355028],"study_design_scores_gemma":[0.0004008879,0.00007353431,0.1861643,0.00001211341,0.00005739051,0.000001481873,0.00001335789,0.0003914557,0.8112524,0.0001714397,0.001341702,0.0001198845],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9737742,0.0237556,0.001370495,0.00009344153,0.0002807337,0.0002873527,0.0003915815,0.000005414742,0.0000411534],"genre_scores_gemma":[0.9928222,0.003593868,0.002840528,0.00006975581,0.000452149,0.00003043841,0.00010513,0.0000255324,0.00006042899],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.129712,"threshold_uncertainty_score":0.4212542,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008287996979253618,"score_gpt":0.2735177124095517,"score_spread":0.2652297154302981,"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."}}