{"id":"W2989609914","doi":"10.1016/j.cell.2019.10.039","title":"Functional Enhancers Shape Extrachromosomal Oncogene Amplifications","year":2019,"lang":"en","type":"article","venue":"Cell","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":366,"is_retracted":false,"has_abstract":false,"ca_institutions":"Ontario Institute for Cancer Research; SickKids Foundation; University Health Network; University of Toronto; Hospital for Sick Children; Princess Margaret Cancer Centre","funders":"National Center for Advancing Translational Sciences; National Institute of General Medical Sciences; National Institute of Neurological Disorders and Stroke; National Institutes of Health; National Cancer Institute; National Institute on Drug Abuse","keywords":"Extrachromosomal DNA; Biology; Enhancer; Chromatin; Genetics; Amplicon; DNA; Oncogene; CRISPR interference; Locus (genetics); Genome; Computational biology; Gene; Cas9; Transcription factor; Cell cycle; Polymerase chain reaction","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":[0.00004224156,0.00008739839,0.00006406061,0.00001529562,0.0000473011,0.00001596604,0.0001175002,0.0000840576,0.0006514158],"category_scores_gemma":[0.000003825276,0.00009218225,0.00006212152,0.00003770324,0.00002378749,0.000001621281,0.00004770475,0.00004800763,0.0005144784],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001637824,"about_ca_system_score_gemma":0.00007030275,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002405473,"about_ca_topic_score_gemma":0.000003902343,"domain_scores_codex":[0.9994327,0.00001008442,0.0001111888,0.0002381809,0.00006668142,0.0001411475],"domain_scores_gemma":[0.9995728,0.000005065752,0.00004854443,0.000282957,0.00004096683,0.00004972632],"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":[0.000009009755,0.00004359934,0.0005605875,0.000009817749,0.00001052956,2.863272e-7,0.00001076824,0.0003906601,0.9967649,0.00008713391,0.001653338,0.0004593807],"study_design_scores_gemma":[0.0006568437,0.0001839344,0.009709002,0.00000475468,0.00001744844,0.00001270064,0.0001010625,0.002952888,0.9043261,0.0001189849,0.0816019,0.0003144187],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9825498,0.0002609974,0.001540366,0.00004241614,0.0002663741,0.0001065382,0.00002195559,0.000009095404,0.01520243],"genre_scores_gemma":[0.9895671,0.00006208718,0.001021623,0.0001387088,0.0001698566,0.00001263983,0.0003706133,0.00001731963,0.008640058],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.09243882,"threshold_uncertainty_score":0.7132546,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007702843151120935,"score_gpt":0.2072748780095255,"score_spread":0.1995720348584046,"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."}}