{"id":"W3047365219","doi":"10.1038/s41467-020-17673-9","title":"An integrative multi-omics analysis to identify candidate DNA methylation biomarkers related to prostate cancer risk","year":2020,"lang":"en","type":"article","venue":"Nature Communications","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":246,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta; Princess Margaret Cancer Centre","funders":"National Cancer Institute; Cancer Council Victoria; Medical Research Council; Canadian Institutes of Health Research; School of Medicine, Vanderbilt University; Cancer Research Institute; Royal Marsden NHS Foundation Trust; Prostate Cancer Foundation of Australia; National Institute for Health and Care Research; European Commission; Breast Cancer Research Foundation; National Institutes of Health; Ovarian Cancer Research Fund; National Health and Medical Research Council; Cancer Research UK; Prostate Cancer Foundation; National Cancer Research Institute; Vanderbilt University","keywords":"DNA methylation; Prostate cancer; Omics; Computational biology; Bioinformatics; Biomarker discovery; Biomarker; Medicine; Cancer; Biology; Proteomics; Internal medicine; Genetics; 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":[0.0003256995,0.0001719374,0.0001867247,0.0001748245,0.0002448899,0.00007538845,0.0006777075,0.0002896434,0.00001065354],"category_scores_gemma":[0.000439138,0.0001641276,0.0001194371,0.001350803,0.00005022388,0.00001195018,0.0002496816,0.0003843147,0.00001142239],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004637238,"about_ca_system_score_gemma":0.00007538718,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003242806,"about_ca_topic_score_gemma":0.005340988,"domain_scores_codex":[0.9986076,0.0003565361,0.0003134301,0.0004204314,0.0001314797,0.0001705177],"domain_scores_gemma":[0.998007,0.00003783132,0.0001707762,0.001184631,0.0003420747,0.00025768],"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":[0.00009666798,0.00007939101,0.04531522,0.000003263104,0.0009818445,2.775922e-7,0.002613668,0.008993738,0.9336597,0.0001056596,0.0003699625,0.007780639],"study_design_scores_gemma":[0.001128765,0.0005617561,0.3605669,0.00002436581,0.001470199,3.459738e-7,0.001240012,0.04392429,0.5256469,0.0001905178,0.06426528,0.0009806942],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9683812,0.005592997,0.01891576,0.005546745,0.0001012056,0.0006800895,0.0006029839,0.0000396167,0.0001393831],"genre_scores_gemma":[0.9727032,0.002477002,0.02196344,0.0006837737,0.00002975168,0.0001022215,0.001956156,0.00002547236,0.00005901404],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4080128,"threshold_uncertainty_score":0.6692928,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01595322796537514,"score_gpt":0.3673290854439765,"score_spread":0.3513758574786013,"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."}}