{"id":"W4403533811","doi":"10.1101/gr.278418.123","title":"Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer","year":2024,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; McGill University Health Centre","funders":"Fonds de Recherche du Québec - Santé","keywords":"Biology; Gene duplication; Enhancer; Tandem exon duplication; Genetics; Gene; Chromatin; Enhancer RNAs; Genome; Carcinogenesis; Computational biology; Transcription factor","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":[0.0005468663,0.0000848624,0.0001067032,0.0002045542,0.0000500577,0.0000425027,0.0002290246,0.0001017098,0.0001741378],"category_scores_gemma":[0.00003802809,0.00008626886,0.0000654609,0.0003435365,0.00007177656,0.000005546292,0.0001726367,0.0002079116,0.00006922765],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001307926,"about_ca_system_score_gemma":0.0002479696,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002487061,"about_ca_topic_score_gemma":0.0004349946,"domain_scores_codex":[0.9988877,0.00007610113,0.0002537045,0.0003176738,0.0001912555,0.0002736113],"domain_scores_gemma":[0.9994555,0.00002608824,0.00003363383,0.0003032527,0.000131908,0.00004963228],"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":[0.00001335036,0.00004834674,0.0002774922,0.0001353049,0.00004146649,0.000002803031,0.0001934361,0.0003164701,0.9952312,0.0001634322,0.0006218698,0.00295484],"study_design_scores_gemma":[0.0006314055,0.0004460707,0.03896285,0.000286688,0.00002646972,0.00002853513,0.000864386,0.006456647,0.802913,0.002706041,0.146161,0.0005169015],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9883367,0.009181728,0.0003717363,0.0003146798,0.0001533795,0.0002404623,0.00008366093,0.00000757187,0.001310074],"genre_scores_gemma":[0.9947031,0.003064961,0.0002940366,0.000009071201,0.0001622383,0.0001509893,0.0001788882,0.00002375342,0.001412977],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1923182,"threshold_uncertainty_score":0.3517942,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0405215649606188,"score_gpt":0.4122234931415885,"score_spread":0.3717019281809696,"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."}}