The assessment of essential genes in the stability of PPI networks using critical node detection problem

Javad Rezaei, Fatemeh Zare Mirakabad,Sayed-Amir Marashi,Seyed Ali MirHassani

AUT Journal of Mathematics and Computing(2022)

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摘要
Essential genes and proteins as their products encode the basic functions of a cell in a variety of conditions and are vital for the survival of a cell. Analyzing the characteristics of these proteins provides important biological information. An interesting analysis is to demonstrate the correlation between the topological importance of a protein in protein-protein interaction networks and its essentiality. Different centrality criteria such as degree, between ness, closeness, and eigenvector centralities are used to investigate such a correlation. Despite the remarkable results obtained by these methods, it is shown that the centrality criteria in scale-free networks show a high level of correlations which indicate that they share similar topo[1]logical information of the networks. In this paper, we use a different approach for analyzing this correlation and use a well-known problem in the field of graph theory, Critical Node Detection Problem and solve it on the protein-protein interaction networks to obtain a subset of proteins called critical nodes which have the most effect on the network stability. Our results show that essential proteins have a more prominent presence in the set of critical nodes than what is expected at random samples. Furthermore, the essential proteins represented in the set of critical nodes have a different distribution of topological properties compared to the essential proteins recovered by the centrality-based methods. All the source codes and data are available at “http://bioinformatics.aut.ac.ir/CNDP PPI networks/”.
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关键词
essential genes,protein-protein interaction network,centrality,critical node,network stability
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