Title: Multi-level integrative analysis of Protein–Protein Interaction networks: connecting completeness, depth and robustness

Authors: Jaine K. Blayney, Huiru Zheng, Haiying Wang, Francisco Azuaje

Addresses: Faculty of Computing and Engineering, School of Computing and Mathematics, University of Ulster, Jordanstown, BT37 0QB, Northern Ireland. ' Faculty of Computing and Engineering, Computer Science Research Institute, University of Ulster, Jordanstown, BT37 0QB, Northern Ireland. ' Faculty of Computing and Engineering, Computer Science Research Institute, University of Ulster, Jordanstown, BT37 0QB, Northern Ireland. ' Laboratory of Cardiovascular Research, Public Research Centre for Health (CRP-Sante), L-1150, Luxembourg, Luxembourg

Abstract: A fully extended Protein–Protein Interaction (PPI) network can consist of upwards of several thousand nodes and edges. To simplify analysis, smaller child samples are often used in substitution of the global network. In this study, the impact of different levels of sampling was evaluated on six PPI networks. Results from the case studies suggest that restricting analysis to the first network level, using metrics such as degree and BC, could lead to misrepresentative results, omitting potentially significant nodes. Fault-tolerance analysis also indicates that key nodes within the second network level, and above, contribute to the stability of the global network.

Keywords: protein–protein interactions; PPI networks; network analysis; depth; sampling; stability; fault tolerance.

DOI: 10.1504/IJCBDD.2010.034465

International Journal of Computational Biology and Drug Design, 2010 Vol.3 No.1, pp.31 - 51

Published online: 05 Aug 2010 *

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