{"id":"W2103990329","doi":"10.1101/gr.156539.113","title":"Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm","year":2013,"lang":"en","type":"article","venue":"Genome Research","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":203,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; BC Cancer Agency","funders":"National Institute of Environmental Health Sciences; National Institute of General Medical Sciences; National Cancer Institute; Program for New Century Excellent Talents in University; National Human Genome Research Institute; National Institute on Drug Abuse; National Natural Science Foundation of China; Dermatology Foundation; March of Dimes Foundation; Foundation for Barnes-Jewish Hospital; Sontag Foundation; National Institutes of Health; Program for Changjiang Scholars and Innovative Research Team in University; Edward Mallinckrodt, Jr. Foundation; National Science Foundation","keywords":"Methylated DNA immunoprecipitation; DNA methylation; Biology; Illumina Methylation Assay; Differentially methylated regions; Epigenomics; Bisulfite sequencing; Epigenetics; Genetics; Methylation; Computational biology; DNA; Gene; 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":[0.0009958377,0.0001095774,0.0001107088,0.00005108064,0.0004051563,0.0001854932,0.0001672457,0.0001379922,0.00008729819],"category_scores_gemma":[0.0000644316,0.00007949856,0.00003259715,0.0001649976,0.0001805898,0.00001060393,0.0002749308,0.0001719992,0.00003970772],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002015954,"about_ca_system_score_gemma":0.00006406135,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002533813,"about_ca_topic_score_gemma":0.0000210659,"domain_scores_codex":[0.9985043,0.0002718144,0.0001736153,0.0003108386,0.0003839795,0.000355471],"domain_scores_gemma":[0.9992909,0.00009616948,0.00005444665,0.0002672848,0.000200639,0.00009052228],"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":[0.000005301035,0.00002444738,0.02622611,0.00001460799,0.00005708609,1.816883e-7,0.0003368332,0.00005084434,0.9437221,0.00001039151,0.0001018955,0.02945022],"study_design_scores_gemma":[0.0005269184,0.0002581344,0.7537393,0.000008878258,0.00002182964,0.000001901549,0.0005785908,0.0003271603,0.2080992,0.003746254,0.03236129,0.0003304881],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9827805,0.006012131,0.0103913,0.0001669914,0.0000469151,0.0003281362,0.00009373242,0.000004007073,0.0001763372],"genre_scores_gemma":[0.9949595,0.0006491824,0.002109904,0.00001034383,0.0004622142,0.00002932528,0.0003842553,0.00001714339,0.00137814],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7356228,"threshold_uncertainty_score":0.3241857,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1107019112592982,"score_gpt":0.3748909152111597,"score_spread":0.2641890039518615,"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."}}