{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003542051,0.001040042,0.001313972,0.002139139,0.0009141258,0.001269624,0.001762359,0.001504969,0.002740278],"category_scores_gemma":[0.008633397,0.0005714978,0.001980701,0.001148508,0.0008508335,0.0007448334,0.001803966,0.001280298,0.0009046484],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007295972,"about_ca_system_score_gemma":0.001902662,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004233694,"about_ca_topic_score_gemma":0.005570078,"domain_scores_codex":[0.9990693,0.0003009341,0.0000590249,0.0003407958,0.0001505176,0.00007938935],"domain_scores_gemma":[0.9982365,0.00120545,0.0001271905,0.0002120736,0.0001548467,0.00006385142],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001202327,0.0002862477,0.05328435,0.000505055,0.001432155,0.0004967405,0.0003889253,0.3572346,0.03443013,0.02447945,0.01138245,0.5148775],"study_design_scores_gemma":[0.00005487646,0.00006855857,0.002943798,0.00001911168,0.00008150456,0.0001199993,0.00003070942,0.978936,0.003841123,0.01110087,0.002785921,0.00001770506],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.05930315,0.0005241559,0.9346929,0.0003864573,0.00005741087,0.0001665326,0.0009344695,0.002614728,0.00132014],"genre_scores_gemma":[0.1966371,0.0002171779,0.7980649,0.0002870017,0.0000532203,0.0005362501,0.002549881,0.0004729543,0.001181583],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.004233694,"threshold_uncertainty_score":0.01873237,"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."}}