{"id":"W4321791415","doi":"10.1101/gr.276986.122","title":"The aberrant epigenome of <i>DNMT3B</i> -mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory","year":2023,"lang":"en","type":"article","venue":"Genome Research","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; European Regional Development Fund; Edmond de Rothschild Foundation","keywords":"Biology; H3K4me3; DNMT3B; CTCF; Epigenetics; Epigenome; DNA methylation; Genetics; CRISPR; Epigenomics; Genome instability; Differentially methylated regions; Gene; Enhancer; Promoter; DNA; Gene expression; DNA damage","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001252772,0.0001382656,0.0002002059,0.0001643406,0.0002713598,0.00001968366,0.0002463106,0.00008299248,0.00001475466],"category_scores_gemma":[0.0001067591,0.00007630532,0.00004935323,0.001062499,0.0004685223,0.000003561562,0.0001213849,0.0001356149,0.000003808454],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002931721,"about_ca_system_score_gemma":0.0003499332,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003003633,"about_ca_topic_score_gemma":0.0004463771,"domain_scores_codex":[0.9981058,0.0002903632,0.0003337272,0.0003306939,0.0005560659,0.0003833737],"domain_scores_gemma":[0.9981261,0.0001974134,0.0001697685,0.0006329421,0.0007740357,0.00009977073],"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":[0.001357655,0.0000901445,0.001414119,0.0001034418,0.0001268476,0.000002742772,0.001734342,0.009211913,0.9796653,0.00001102266,0.001014177,0.005268334],"study_design_scores_gemma":[0.0008043577,0.005697696,0.01866175,0.00006827078,0.00004061054,0.00000309743,0.002202079,0.0004553965,0.9567085,0.0001202474,0.01504057,0.000197439],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9944732,0.001403481,0.002013008,0.000972106,0.00003722331,0.0008447705,0.00005874,0.000006799956,0.0001906848],"genre_scores_gemma":[0.9970863,0.001442404,0.0001893007,0.00003245403,0.00003686454,0.0001211542,0.00006716724,0.00002904707,0.0009953444],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02295678,"threshold_uncertainty_score":0.3111641,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03741396271489377,"score_gpt":0.3112123898468742,"score_spread":0.2737984271319804,"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."}}