Identifying protein complexes based on the integration of PPI network and gene expression data.

Identification of protein complexes is crucial to understand principles of cellular organisation and predict protein functions. In this paper, a novel protein complex discovery algorithm IPCIPG is proposed based on the integration of Protein-Protein Interaction network (PPI network) and gene expression data. IPCIPG is a local search algorithm which has two versions: IPCIPG-n for identifying non-overlapping clusters and IPCIPG-o for detecting overlapping clusters. The experimental results on the yeast PPI network show that IPCIPG can identify protein complexes with specific biological meaning more effectively, precisely and comprehensively than six other algorithms: HUNTER, HC-PIN, CMC, SPICi, MOCDE and MCL.