Identification of additional proteins in differential proteomics using protein interaction networks.

ABSTRACT: In this study, we developed a novel computational approach based on protein-protein interaction networks to identify a list of proteins that might have remained undetected in differential proteomic profiling experiments. We tested our computational approach on two sets of human smooth muscle cell protein extracts that were affected differently by DNase I treatment. Differential proteomic analysis by saturation DIGE resulted in the identification of 41 human proteins. The application of our approach to these 41 input proteins consisted of four steps: (i) Compilation of a human protein-protein interaction network from public databases; (ii) calculation of interaction scores based on functional similarity; (iii) determination of a set of candidate proteins that are needed to efficiently and c

SUBMITTER: Gwinner F 

PROVIDER: S-EPMC3964363 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature