{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002723591,0.0003016137,0.0003174719,0.0003803128,0.0003445568,0.0009716387,0.0004814831,0.0006363231,0.004781277],"category_scores_gemma":[0.0005770136,0.000499752,0.0003150024,0.0001969593,0.0005710797,0.0009619513,0.0008201631,0.001380367,0.002210347],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004203806,"about_ca_system_score_gemma":0.0001484736,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003029029,"about_ca_topic_score_gemma":0.0005756735,"domain_scores_codex":[0.999756,0.00001983495,0.000009844977,0.00007507158,0.00008468197,0.00005442819],"domain_scores_gemma":[0.9995246,0.0001861799,0.00004703303,0.0001126597,0.00006272862,0.00006678185],"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":[0.00005079753,0.00001291813,0.0002909029,0.00001569204,0.00000253693,0.00006804231,0.00003759345,0.0001615311,0.9948711,0.002705259,0.00006292442,0.00172079],"study_design_scores_gemma":[0.00001896415,0.00005057141,0.004437756,0.000003982312,0.000009923187,0.0003083358,0.00007593196,0.002138974,0.9864956,0.001385082,0.005066763,0.000008217467],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9666594,0.001169596,0.01961599,0.0002997912,0.00008956486,0.00002122891,0.0002390333,0.0006072443,0.01129814],"genre_scores_gemma":[0.9906076,0.0002279224,0.003033934,0.0000982666,0.00002830747,0.00001199627,0.0002402192,0.0002316395,0.005520079],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004781277,"threshold_uncertainty_score":0.01599497,"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."}}