{"id":"W2912314577","doi":"10.1016/j.clinbiochem.2019.01.005","title":"Proteome-wide onco-proteogenomic somatic variant identification in ER-positive breast cancer","year":2019,"lang":"en","type":"article","venue":"Clinical Biochemistry","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":false,"ca_institutions":"Sinai Health System; Canada Research Chairs; Mount Sinai Hospital; Lunenfeld-Tanenbaum Research Institute; University Health Network; University of Toronto","funders":"","keywords":"Proteogenomics; Biology; Proteome; Proteomics; Computational biology; Genetics; Exome sequencing; DNA sequencing; Single-nucleotide polymorphism; Exome; Gene; Massive parallel sequencing; Transcriptome; Genome; Genomics; Gene expression; Genotype; Phenotype","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":[0.0004713264,0.0002200932,0.0003007924,0.00003070807,0.00004116348,0.00004937432,0.0003419722,0.0003734111,0.0001338031],"category_scores_gemma":[0.0003342666,0.0002284231,0.0001753824,0.0001175594,0.000116653,0.000005343782,0.0001852901,0.0002469921,0.0001343893],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001094093,"about_ca_system_score_gemma":0.0004263743,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008103951,"about_ca_topic_score_gemma":0.00003337533,"domain_scores_codex":[0.9979889,0.00005980741,0.0007341344,0.0007584222,0.0001365775,0.0003221989],"domain_scores_gemma":[0.9986519,0.0001054778,0.0002695176,0.0007084591,0.0001119646,0.0001526642],"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":[0.0002286092,0.0002769492,0.09591624,0.0001025213,0.00007241292,0.00001095525,0.00001883353,0.00008697114,0.8989588,0.00001398176,0.001085129,0.003228616],"study_design_scores_gemma":[0.002068802,0.000173701,0.2196851,0.0001901211,0.00004855007,0.0000353626,0.00007313426,0.0002396223,0.7748061,0.0002339248,0.001874679,0.0005708392],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9964883,0.0005232691,0.0001770949,0.0007672543,0.0004258741,0.0006458519,0.0002987084,0.0000126621,0.0006609256],"genre_scores_gemma":[0.9967027,0.0005247935,0.0002512813,0.000585647,0.0005430686,0.000151457,0.0002773549,0.00003539811,0.0009282752],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1241526,"threshold_uncertainty_score":0.9314824,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01061539553273895,"score_gpt":0.2998904546000883,"score_spread":0.2892750590673494,"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."}}