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Analysis of Organization of the Interactome Using Dominating Sets: a Case Study on Cell Cycle Interaction Networks

Zheng, Huiru, Wang, Chaoyang and Wang, Haiying / HY (2015) Analysis of Organization of the Interactome Using Dominating Sets: a Case Study on Cell Cycle Interaction Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14 (2). pp. 282-289. [Journal article]

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URL: http://dx.doi.org/10.1109/TCBB.2015.2459712

DOI: 10.1109/TCBB.2015.2459712

Abstract

Abstract—In this study, a minimum dominating set based approach was developed and implemented as a Cytoscape plugin to identify critical and redundant proteins in a protein interaction network. We focused on the investigation of the properties associated with criticalproteins in the context of the analysis of interaction networks specific to cell cycle in both yeast and human. A total of 132 yeast genes and 129 human proteins have been identified as critical nodes while 950 in yeast and 980 in human have been categorized as redundant nodes. A clear distinction between critical and redundant proteins was observed when examining their topological parameters including betweenness centrality, suggesting a central role of critical proteins in the control of a network. The significant differences in terms of gene coexpression and functional similarity were observed between the two sets of proteins in yeast. Criticalproteins were found to be enriched with essential genes in both networks and have a more deleterious effect on the network integrity than their redundant counterparts. Furthermore, we obtained statistically significant enrichments of proteins that govern human diseases including cancer-related and virus-targeted genes in the corresponding set of critical proteins.

Item Type:Journal article
Keywords:Protein interaction networks, cell cycle, minimum dominating set
Faculties and Schools:Faculty of Computing & Engineering
Faculty of Computing & Engineering > School of Computing and Mathematics
Research Institutes and Groups:Computer Science Research Institute > Smart Environments
Computer Science Research Institute
Computer Science Research Institute > Artificial Intelligence and Applications
ID Code:33807
Deposited By: Dr Huiru Zheng
Deposited On:24 Mar 2016 14:46
Last Modified:17 Oct 2017 16:22

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