Protein Subnetwork Biomarkers for Yeast Using Brute Force Method

Abstract

A simple brute force method to identify protein subnetwork biomarkers is developed for yeast using protein-protein interaction network and differentially expressed genes. Subnetworks related to different cellular roles for yeast are considered in this study. Four different PPI networks, namely-coexpressed PPI, genetic PPI, physical PPI and scored PPI are explored in identifying subnetworks for different cellular roles. Our results showed that all four PPI networks are capable of identifying subnetworks with different level of accuracy. Scored PPI network provides better coverage in terms of both single protein biomarker and PPI biomarker. Scored PPI network is also capable of producing large subnetwork biomarker for a specific cellular role. Our investigation showed that PPIs with high score have inherent capability of identifying subnetwork biomarkers.