High participation ratio genes in the interaction network structure

TL;DR

This study uses random matrix theory and node participation ratio to identify key genes in yeast, revealing that essential genes have higher structural influence and specific roles within the gene interaction network.

Contribution

It introduces a novel framework combining random matrix theory and node participation ratio to detect structurally influential genes in biological networks.

Findings

Essential genes exhibit higher node participation ratios than nonessential ones.

A small subset of genes significantly influences network structure.

Significant genes are associated with specific bioprocesses.

Abstract

Genes have specific functional roles, however, since they are dependent on each other, they can play a structural role within a network structure of their interactions. In this study, we analyze the structure of the gene interaction network and detect the most contributing genes through the random matrix theory. Specifically, we compare the interaction network of essential and nonessential genes of the yeast Saccharomyces cerevisiae. Most remarkably, this well-established combined framework by measuring the node participation ratio $(NPR)$ index helps detect important genes, which control the insightful structural patterns in the underlying networks. Results indicate that the essential genes have higher values of $NPR$ rather than the nonessential ones which means that they have the most contribution to the network structure. It is worth mentioning that among all essential genes, the $NPR$ value of 5 significant ones is considerably higher than the other essential genes, and also the same is for 15 significant nonessential genes compared to the others. Thus, the significant essential genes strongly manage their network structure, while the significant nonessential genes, besides their global contributions, have weak effects on their network structure. Most strikingly, these genes existing in a limited number of structural patterns are responsible for the specific bioprocesses which are the signature of their networks.