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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Resilience of protein-protein interaction networks as determined by their large-scale topological features

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Author(s):
Rodrigues, Francisco A. [1] ; Costa, Luciano da Fontoura [2] ; Barbieri, Andre Luiz [2]
Total Authors: 3
Affiliation:
[1] Univ Sao Paulo, Dept Matemat Aplicada & Estat, Inst Ciencias Matemat & Computacao, BR-13560970 Sao Carlos, SP - Brazil
[2] Univ Sao Paulo, Inst Fs Sao Carlos, BR-13560970 Sao Carlos, SP - Brazil
Total Affiliations: 2
Document type: Journal article
Source: MOLECULAR BIOSYSTEMS; v. 7, n. 4, p. 1263-1269, 2011.
Web of Science Citations: 6
Abstract

The relationship between the structure and function of biological networks constitutes a fundamental issue in systems biology. Particularly, the structure of protein-protein interaction networks is related to important biological functions. In this work, we investigated how such a resilience is determined by the large scale features of the respective networks. Four species are taken into account, namely yeast Saccharomyces cerevisiae, worm Caenorhabditis elegans, fly Drosophila melanogaster and Homo sapiens. We adopted two entropy-related measurements (degree entropy and dynamic entropy) in order to quantify the overall degree of robustness of these networks. We verified that while they exhibit similar structural variations under random node removal, they differ significantly when subjected to intentional attacks (hub removal). As a matter of fact, more complex species tended to exhibit more robust networks. More specifically, we quantified how six important measurements of the networks topology (namely clustering coefficient, average degree of neighbors, average shortest path length, diameter, assortativity coefficient, and slope of the power law degree distribution) correlated with the two entropy measurements. Our results revealed that the fraction of hubs and the average neighbor degree contribute significantly for the resilience of networks. In addition, the topological analysis of the removed hubs indicated that the presence of alternative paths between the proteins connected to hubs tend to reinforce resilience. The performed analysis helps to understand how resilience is underlain in networks and can be applied to the development of protein network models. (AU)

FAPESP's process: 05/00587-5 - Mesh (graph) modeling and techniques of pattern recognition: structure, dynamics and applications
Grantee:Roberto Marcondes Cesar Junior
Support Opportunities: Research Projects - Thematic Grants