CNAI
Integrative Proteo-genomic Analysis to Construct CNA-protein Regulatory Map in Breast and Ovarian TumorsWe propose a new method, ProMAP, to characterize regulatory relationships between somatic CNAs and proteins based on proteogenomic data. ProMAP employs a panelized multivariate regression framework to handle high-dimensionality of proteogenomic data and uses proper statistical models to handle multiplex structure and abundance-dependent-missing-data mechanism in proteomics data. Applying ProMAP to breast and ovarian cancer TCGA-CPTAC data sets, we identified novel CNAs associated with many protein/phosphoprotein abundances. The findings help to characterize important CNAs and their functional impact in these tumors.