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Biochemistry Research International
Volume 2015, Article ID 245075, 12 pages
http://dx.doi.org/10.1155/2015/245075
Research Article

Characterization of Protein Complexes and Subcomplexes in Protein-Protein Interaction Databases

1Intelligent Systems, College of Information Technology, UAEU, Al Ain 17551, UAE
2Department of Management Information Systems, Al Ain University of Science and Technology, Al Ain, UAE
3Laboratory of Integrative Systems Medicine (LISM), CNR, Pisa, Italy

Received 30 October 2014; Revised 5 January 2015; Accepted 6 January 2015

Academic Editor: Seiji Shibasaki

Copyright © 2015 Nazar Zaki et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The identification and characterization of protein complexes implicated in protein-protein interaction data are crucial to the understanding of the molecular events under normal and abnormal physiological conditions. This paper provides a novel characterization of subcomplexes in protein interaction databases, stressing definition and representation issues, quantification, biological validation, network metrics, motifs, modularity, and gene ontology (GO) terms. The paper introduces the concept of “nested group” as a way to represent subcomplexes and estimates that around 15% of those nested group with the higher Jaccard index may be a result of data artifacts in protein interaction databases, while a number of them can be found in biologically important modular structures or dynamic structures. We also found that network centralities, enrichment in essential proteins, GO terms related to regulation, imperfect 5-clique motifs, and higher GO homogeneity can be used to identify proteins in nested complexes.