{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001372506,0.0001748473,0.000196968,0.000260824,0.0001073461,0.0003944064,0.0002177943,0.0002434672,0.001390694],"category_scores_gemma":[0.0001709445,0.0002242902,0.0002048445,0.0002018939,0.0002866665,0.0001897143,0.0002841915,0.0005659981,0.0005609444],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004866115,"about_ca_system_score_gemma":0.0002805585,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002174445,"about_ca_topic_score_gemma":0.003939128,"domain_scores_codex":[0.9998173,0.0000120249,0.00001478932,0.00004217542,0.00008569376,0.00002804579],"domain_scores_gemma":[0.9998109,0.00002733669,0.00005154507,0.00003736297,0.00002699678,0.00004592662],"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":[0.00002364486,0.000007871145,0.0003086998,0.00001193174,0.000002980032,0.00002269651,0.00001188281,0.00006701598,0.9985468,0.000107286,0.00002341336,0.0008656536],"study_design_scores_gemma":[0.000007393382,0.00007977166,0.009008432,0.000003806135,0.000006881769,0.0001568261,0.00003155405,0.001381201,0.9872089,0.00007513511,0.002036853,0.000003341337],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9895592,0.000755144,0.006596897,0.0001202237,0.00001603599,0.0000281137,0.0007606266,0.0001721822,0.001991512],"genre_scores_gemma":[0.9885074,0.0003995277,0.005476166,0.00006299798,0.000003602251,0.00002950151,0.001446207,0.00006471411,0.0040098],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002174445,"threshold_uncertainty_score":0.004652321,"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."}}