%0 Journal Article
%T The assessment of essential genes in the stability of PPI networks using critical node detection problem
%J AUT Journal of Mathematics and Computing
%I Amirkabir University of Technology
%Z 2783-2449
%A Rezaei, Javad
%A Zare Mirakabad, Fatemeh
%A Marashi, Sayed-Amir
%A MirHassani, Seyed Ali
%D 2022
%\ 02/01/2022
%V 3
%N 1
%P 59-76
%! The assessment of essential genes in the stability of PPI networks using critical node detection problem
%K Essential genes
%K Protein-protein interaction network
%K Centrality
%K Critical node
%K Network stability
%R 10.22060/ajmc.2021.20101.1053
%X 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 topological importance of a protein in protein-protein interaction networks and its essentiality. Different centrality criteria such as degree, betweenness, 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 topological 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 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/”
%U https://ajmc.aut.ac.ir/article_4505_91e2a84e3ead5466af5dd0b6aaa745ee.pdf