{"id":"W3207470655","doi":"10.1016/j.ab.2021.114429","title":"Identification of in vitro JMJD lysine demethylase candidate substrates via systematic determination of substrate preference","year":2021,"lang":"en","type":"article","venue":"Analytical Biochemistry","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":false,"ca_institutions":"Carleton University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"H3K4me3; Demethylase; Histone; Histone methylation; Histone H3; Histone methyltransferase; Biology; Biochemistry; Lysine; Proteome; Histone H2A; Methylation; Gene expression; Gene; DNA methylation; Amino acid; Promoter","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":[0.0003699289,0.0001350399,0.0002975783,0.0000525688,0.00001813708,0.00001469852,0.0001393256,0.0001821588,0.00001140369],"category_scores_gemma":[0.0004491973,0.0001369623,0.0001002025,0.0002791835,0.00009119583,0.000005767497,0.00004521568,0.0000720682,0.000001643686],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001902106,"about_ca_system_score_gemma":0.0001192576,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001927141,"about_ca_topic_score_gemma":0.00002093616,"domain_scores_codex":[0.9984843,0.00008443777,0.0007560752,0.0003257283,0.0001930583,0.0001563933],"domain_scores_gemma":[0.9988182,0.00004294135,0.0003194342,0.0004124265,0.0003446798,0.00006227143],"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":[0.00004080171,0.0001130703,0.001988131,0.00197552,0.0000300638,0.000003908644,0.00001342056,0.00002718176,0.9954978,0.00001536304,0.000001416855,0.0002933712],"study_design_scores_gemma":[0.0002589199,0.00003202591,0.002133152,0.000164052,0.00007739497,0.00000312276,0.00005134066,0.003917811,0.9930105,0.0002252039,0.000001400668,0.0001250348],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9931338,0.001470031,0.005053622,0.0000272882,0.00002924958,0.0001106329,0.00003480119,0.000003279704,0.0001372541],"genre_scores_gemma":[0.9988217,0.0001808905,0.0004105858,0.000006237713,0.00002527793,0.00001236359,0.0003532215,0.0000100685,0.0001796156],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005687898,"threshold_uncertainty_score":0.5585161,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01412097400049366,"score_gpt":0.2678053191841553,"score_spread":0.2536843451836617,"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."}}