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

Authors: Weijie Chen; Min Li; Xuehong Wu; Jianxin Wang

Addresses: School of Information Science and Engineering, Central South University, Changsha 410083, China ' School of Information Science and Engineering, Central South University, Changsha 410083, China ' School of Information Science and Engineering, Central South University, Changsha 410083, China ' School of Information Science and Engineering, Central South University, Changsha 410083, China

Abstract: 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.

Keywords: protein complexes; protein-protein interaction; PPI networks; gene expression data; clusters; bioinformatics.

DOI: 10.1504/IJBRA.2015.067337

International Journal of Bioinformatics Research and Applications, 2015 Vol.11 No.1, pp.30 - 44

Received: 07 May 2013
Accepted: 20 May 2013
Published online: 06 Feb 2015 *

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