Integrative Proteo-genomic Analysis to Construct CNA-protein Regulatory Map in Breast and Ovarian Tumors.

ABSTRACT: Recent development in high throughput proteomics and genomics profiling enable one to study regulations of genome alterations on protein activities in a systematic manner. In this article, we propose a new statistical method, ProMAP, to systematically characterize the regulatory relationships between proteins and DNA copy number alterations (CNA) in breast and ovarian tumors based on proteogenomic data from the CPTAC-TCGA studies. Because of the dynamic nature of mass spectrometry instruments, proteomics data from labeled mass spectrometry experiments usually have non-ignorable batch effects. Moreover, mass spectrometry based proteomic data often possesses high percentages of missing values and non-ignorable missing-data patterns. Thus, we use a linear mixed effects model to account for th

SUBMITTER: Ma W 

PROVIDER: S-EPMC6692778 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature