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

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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.
LanguageEnglish
Pages282-289
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume14
Issue number2
Early online date22 Jul 2015
DOIs
Publication statusE-pub ahead of print - 22 Jul 2015

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Cell Communication
Cell Cycle
Proteins
Yeasts
Genes
Protein Interaction Maps
Fungal Proteins
Essential Genes
Viruses
Neoplasms

Keywords

  • Protein interaction networks
  • cell cycle
  • minimum dominating set

Cite this

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title = "Analysis of Organization of the Interactome Using Dominating Sets: a Case Study on Cell Cycle Interaction Networks",
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.",
keywords = "Protein interaction networks, cell cycle, minimum dominating set",
author = "Huiru Zheng and Chaoyang Wang and Wang, {Haiying / HY}",
year = "2015",
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AU - Zheng, Huiru

AU - Wang, Chaoyang

AU - Wang, Haiying / HY

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N2 - 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.

AB - 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.

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