The assessment of essential genes in the stability of PPI networks using critical node detection problem | ||
| AUT Journal of Mathematics and Computing | ||
| مقاله 8، دوره 3، شماره 1، اردیبهشت 2022، صفحه 59-76 اصل مقاله (4.64 M) | ||
| نوع مقاله: Original Article | ||
| شناسه دیجیتال (DOI): 10.22060/ajmc.2021.20101.1053 | ||
| نویسندگان | ||
| Javad Rezaei1؛ Fatemeh Zare Mirakabad* 1؛ Sayed-Amir Marashi2؛ Seyed Ali MirHassani1 | ||
| 1Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran | ||
| 2Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran | ||
| چکیده | ||
| 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/”. | ||
| کلیدواژهها | ||
| Essential genes؛ Protein-protein interaction network؛ Centrality؛ Critical node؛ Network stability | ||
| مراجع | ||
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