{"id":"W4220883700","doi":"10.1101/2022.01.29.478046","title":"Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Medical Research Council; Institute of Genetics; Cancer Research UK; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; National Science Foundation","keywords":"Extrachromosomal DNA; Biology; Oncogene; Gene; Chromatin; DNA; Genetics; Cell cycle; Genome","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001878334,0.0002155767,0.0001728525,0.0002980039,0.0001075866,0.000435253,0.0002480423,0.0002584202,0.002853358],"category_scores_gemma":[0.0003253955,0.0002320645,0.0002462641,0.0002020522,0.0003290385,0.0002464426,0.0003841427,0.0007677737,0.001305692],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003711508,"about_ca_system_score_gemma":0.0002311494,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008481111,"about_ca_topic_score_gemma":0.001180173,"domain_scores_codex":[0.9997873,0.00001696711,0.00001400688,0.00005962491,0.00009320631,0.00002884532],"domain_scores_gemma":[0.9997087,0.00007864228,0.0000646446,0.00006539263,0.00004111491,0.00004148518],"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":[0.00001789681,0.000006106883,0.0003460296,0.00001852325,0.000002931087,0.00002302286,0.000009540831,0.00006111483,0.9982534,0.0002265124,0.00003382486,0.001001152],"study_design_scores_gemma":[0.000005295238,0.00003779689,0.005135518,0.000005079053,0.000005486473,0.000237088,0.00001693299,0.001632209,0.9895061,0.0001549486,0.003260041,0.000003515072],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9702213,0.00106551,0.02096405,0.0001876256,0.0000423474,0.00003650382,0.0007950181,0.0003248047,0.006362814],"genre_scores_gemma":[0.9755793,0.0005079135,0.01102101,0.00006824124,0.0000123805,0.00003261373,0.002356187,0.0002075188,0.01021496],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002853358,"threshold_uncertainty_score":0.009545445,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009595100412776503,"score_gpt":0.2313568153095424,"score_spread":0.2217617148967659,"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."}}