Module organization and variance in protein-protein interaction networks

Scientific Reports
Chun-Yu LinJinn-Moon Yang

Abstract

A module is a group of closely related proteins that act in concert to perform specific biological functions through protein-protein interactions (PPIs) that occur in time and space. However, the underlying module organization and variance remain unclear. In this study, we collected module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database. We then derived PPI evolution scores and interface evolution scores to describe the module elements, including core and ring components. Functions of core components were highly correlated with those of essential genes. In comparison with ring components, core proteins/PPIs were conserved across multiple species. Subsequently, protein/module variance of PPI networks confirmed that core components form dynamic network hubs and play key roles in various biological functions. Based on the analyses of gene essentiality, module variance, and gene co-expression, we summarize the observations of module organization and variance as follows: 1) a module consists of core and ring components; 2) core components perform major biological functions and collaborate with ring components to execute ...Continue Reading

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Citations

Apr 29, 2016·Scientific Reports·Junyang YueYongsheng Liu
Jun 21, 2016·Methods : a Companion to Methods in Enzymology·Xianjun ShenJincai Yang
Nov 25, 2017·Scientific Reports·Guangming LiuXuezhong Zhou
Feb 6, 2019·BMC Bioinformatics·Rama Kaalia, Jagath C Rajapakse
Jul 11, 2019·Journal of Bioinformatics and Computational Biology·Chun-Yu LinTatsuya Akutsu
Jul 18, 2019·Nature Communications·Chun-Yu LinJinn-Moon Yang

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Methods Mentioned

BETA
pull
fluorescence microscopy

Software Mentioned

BLASTP

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