CNA-protein/phosphosite regulatory map

  • Integrative Proteo-genomic Analysis to Construct CNA-protein Regulatory Map in Breast and Ovarian Tumors
    Integrative Proteo-genomic Analysis to Construct CNA-protein Regulatory Map in Breast and Ovarian Tumors
    Weiping Ma, Lin S. Chen, Umut Özbek, Sung Won Han, Chenwei Lin, Amanda G. Paulovich, Hua Zhong and Pei Wang
    Molecular & Cellular Proteomics August 9, 2019, First published on July 7, 2019, 18 (8 suppl 1) S66-S81; https://doi.org/10.1074/mcp.RA118.001229

    We 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.