{"id":"W4311582782","doi":"10.7554/elife.80207","title":"Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells","year":2022,"lang":"en","type":"article","venue":"eLife","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":60,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Brain Tumour Charity; National Science Foundation; Cancer Research UK; Wellcome Trust; Medical Research Foundation; Medical Research Council; Wellcome; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung","keywords":"Biology; Extrachromosomal DNA; Oncogene; Stem cell; PDGFRA; Genetics; Gene; Cancer research; Cell cycle; Stromal cell; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00007091383,0.0001224172,0.0001237734,0.0000183919,0.0001108353,0.00003122161,0.0001291658,0.00007924858,0.0001431628],"category_scores_gemma":[0.000007169623,0.0001235806,0.00003438166,0.00003743224,0.00002982863,0.000005619601,0.0003084198,0.00008733742,0.000006270039],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004846476,"about_ca_system_score_gemma":0.00004370095,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002340933,"about_ca_topic_score_gemma":0.0002852693,"domain_scores_codex":[0.9990472,0.00004871769,0.0002074565,0.0003801984,0.0001557307,0.0001607647],"domain_scores_gemma":[0.9995472,0.00002485025,0.00009539334,0.0002400233,0.00002298484,0.00006948614],"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":[0.0002017203,0.00005325052,0.005026423,0.000007232689,0.00000911264,0.000004964557,0.0002095949,0.0001721253,0.9883356,0.000001693054,0.002868511,0.003109789],"study_design_scores_gemma":[0.0006403258,0.000125302,0.0005826293,0.00001092247,0.000006747215,0.000003188542,0.0001398712,0.0006234943,0.9663559,0.000006933089,0.03133587,0.0001687856],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9966763,0.000365153,0.001442698,0.000116239,0.0002817821,0.0001539073,0.0009180505,0.000007970249,0.00003793593],"genre_scores_gemma":[0.9982733,0.0003096451,0.0002785983,0.0004858651,0.0002553274,0.00005542414,0.0001219023,0.00002403244,0.0001959569],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02846736,"threshold_uncertainty_score":0.503947,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007719542313814088,"score_gpt":0.2341177437696723,"score_spread":0.2263982014558582,"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."}}