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Protein interaction networks: centrality, modularity, dynamics, and applications

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Abstract

In the post-genomic era, proteomics has achieved significant theoretical and practical advances with the development of high-throughput technologies. Especially the rapid accumulation of protein-protein interactions (PPIs) provides a foundation for constructing protein interaction networks (PINs), which can furnish a new perspective for understanding cellular organizations, processes, and functions at network level. In this paper, we present a comprehensive survey on three main characteristics of PINs: centrality, modularity, and dynamics. 1) Different centrality measures, which are used to calculate the importance of proteins, are summarized based on the structural characteristics of PINs or on the basis of its integrated biological information; 2) Different modularity definitions and various clustering algorithms for predicting protein complexes or identifying functional modules are introduced; 3) The dynamics of proteins, PPIs and sub-networks are discussed, respectively. Finally, the main applications of PINs in the complex diseases are reviewed, and the challenges and future research directions are also discussed.

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Acknowledgements

This work was supported in part by the National Natural Science Foundation of China (Grants Nos. 61832019, 61622213) and the Fundamental Research Funds for the Central Universities, CSU (2282019SYLB004), Hunan Provincial Science and Technology Program (2019CB1007).

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Authors and Affiliations

  1. School of Computer Science and Engineering, Central South University, Changsha, 410083, China

    Xiangmao Meng, Wenkai Li & Min Li

  2. School of Life Science, Central South University, Changsha, 410083, China

    Xiaoqing Peng

  3. Department of Computer Science, Old Dominion University, Norfolk, 23529-016, USA

    Yaohang Li

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  1. Xiangmao Meng
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Correspondence to Min Li.

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Xiangmao Meng received his BSc and MSc degrees in Jiangxi University of Science and Technology, China in 2012 and 2015, respectively. He is currently a PhD candidate in Computer Science from Central South University, China. His currently research interests include bioinformatics and complex network analysis.

Wenkai Li is a master student in Computer Science from Central South University, China. His currently research interests include bioinformatics, network analysis and essential protein discovery.

Xiaoqing Peng received the PhD degree in Computer Science, Central South University, China in 2016. She is currently a lecturer in Bioinformatics at Central South University, China. Her research interests include genomic data analysis, dynamic protein network construction, and systems biology.

Yaohang Li received the MS and PhD degrees in computer science from Florida State University, USA in 2000 and 2003, respectively. He is an associate professor in the Department of Computer Science at Old Dominion University, USA. His research interests are in computational biology, Monte Carlo methods, and scientific computing.

Min Li received the PhD degree in Computer Science from Central South University, China in 2008. She is the awardee of the NSFC Excellent Young Scholars Program of China in 2016. Currently, she is a professor and vice dean of the School of Computer Science and Engineering, Central South University, China. Her main research interests include bioinformatics and systems biology.

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Meng, X., Li, W., Peng, X. et al. Protein interaction networks: centrality, modularity, dynamics, and applications. Front. Comput. Sci. 15, 156902 (2021). https://doi.org/10.1007/s11704-020-8179-0

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