{"id":"W2011899558","doi":"10.1101/gr.164871.113","title":"Systems consequences of amplicon formation in human breast cancer","year":2014,"lang":"en","type":"article","venue":"Genome Research","topic":"Gene expression and cancer classification","field":"Biochemistry, Genetics and Molecular Biology","cited_by":29,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Sherbrooke","funders":"Office of International Science and Engineering; National Cancer Institute; New York Genome Center; National Institutes of Health; National Science Foundation","keywords":"Biology; Amplicon; Breast cancer; Locus (genetics); Genetics; Gene; Gene duplication; Carcinogenesis; Cancer; Tumor suppressor gene; Transcriptome; Cancer research; Gene expression; 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":[0.0006330501,0.00004845529,0.00007964299,0.0001268473,0.00005780577,0.00001849523,0.000159922,0.00007032739,0.00002804119],"category_scores_gemma":[0.00001969163,0.00004339955,0.0000190902,0.0001651212,0.0001125416,0.000004049955,0.0000491607,0.00007485055,0.000005146711],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003392764,"about_ca_system_score_gemma":0.00005624212,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003532719,"about_ca_topic_score_gemma":0.00006271245,"domain_scores_codex":[0.9990953,0.0001959984,0.0001709495,0.0001655172,0.0001962554,0.0001760474],"domain_scores_gemma":[0.9994963,0.000008531446,0.00005329798,0.0002220432,0.0001776122,0.00004218878],"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":[0.00002058198,0.00001669337,0.001700851,0.00005604893,0.00000332614,1.187555e-7,0.00005260187,0.0001555199,0.9956301,0.0007177372,0.0003096581,0.001336755],"study_design_scores_gemma":[0.0007027578,0.0002108734,0.06912724,0.00009969295,0.000002780011,0.00001584955,0.0007832816,0.0002880384,0.8862755,0.0003714625,0.04194915,0.0001733552],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9953062,0.0008507166,0.0006399191,0.0002826451,0.00004525828,0.0002014642,0.00001899455,0.000003424037,0.002651405],"genre_scores_gemma":[0.9990646,0.0002741435,0.00001328147,0.00001258979,0.0001020461,0.0000974729,0.00004011724,0.00000604763,0.0003896806],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1093546,"threshold_uncertainty_score":0.1769782,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06750138986666714,"score_gpt":0.3823718321880946,"score_spread":0.3148704423214274,"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."}}