Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors

Science China Life Sciences, Mar 2019

We analyze the global structure and evolution of human gene coexpression networks driven by new gene integration. When the Pearson correlation coefficient is greater than or equal to 0.5, we find that the coexpression network consists of 334 small components and one “giant” connected subnet comprising of 6317 interacting genes. This network shows the properties of power-law degree distribution and small-world. The average clustering coefficient of younger genes is larger than that of the elderly genes (0.6685 vs. 0.5762). Particularly, we find that the younger genes with a larger degree also show a property of hierarchical architecture. The younger genes play an important role in the overall pivotability of the network and this network contains few redundant duplicate genes. Moreover, we find that gene duplication and orphan genes are two dominant evolutionary forces in shaping this network. Both the duplicate genes and orphan genes develop new links through a “rich-gets-richer” mechanism. With the gradual integration of new genes into the ancestral network, most of the topological structure features of the network would gradually increase. However, the exponent of degree distribution and modularity coefficient of the whole network do not change significantly, which implies that the evolution of coexpression networks maintains the hierarchical and modular structures in human ancestors.

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Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors

Science China Life Sciences pp 1–15 | Cite as Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors AuthorsAuthors and affiliations Jian ZuYuexi GuYu LiChentong LiWenyu ZhangYong E. ZhangUnJin LeeLi ZhangManyuan Long Research Paper Thematic Issue: Evolution of genes and genomes First Online: 21 March 2019 13 Downloads Abstract We analyze the global structure and evolution of human gene coexpression networks driven by new gene integration. When the Pearson correlation coefficient is greater than or equal to 0.5, we find that the coexpression network consists of 334 small components and one “giant” connected subnet comprising of 6317 interacting genes. This network shows the properties of power-law degree distribution and small-world. The average clustering coefficient of younger genes is larger than that of the elderly genes (0.6685 vs. 0.5762). Particularly, we find that the younger genes with a larger degree also show a property of hierarchical architecture. The younger genes play an important role in the overall pivotability of the network and this network contains few redundant duplicate genes. Moreover, we find that gene duplication and orphan genes are two dominant evolutionary forces in shaping this network. Both the duplicate genes and orphan genes develop new links through a “rich-gets-richer” mechanism. With the gradual integration of new genes into the ancestral network, most of the topological structure features of the network would gradually increase. However, the exponent of degree distribution and modularity coefficient of the whole network do not change significantly, which implies that the evolution of coexpression networks maintains the hierarchical and modular structures in human ancestors. KeywordsNetwork biology gene network evolution scale-free network natural selection gene expression self-organization gene duplication  Electronic Supplementary Material Supplementary material is available for this article at  https://doi.org/10.1007/s11427-019-9483-6 and is accessible for authorized users. Download to read the full article text Notes Acknowledgements We thank Profs. Yicang Zhou and Yanni Xiao for their valuable discussion. This work was supported by grants from the National Natural Science Foundation of China (11571272, 11201368 and 11631012), the National Science and Technology Major Project of China (2012ZX10002001), the Natural Science Foundation of Shaanxi Province (2015JQ1011) and the China Postdoctoral Science Foundation (2014M560755). 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Jian Zu, Yuexi Gu, Yu Li, Chentong Li, Wenyu Zhang, Yong E. Zhang, UnJin Lee, Li Zhang, Manyuan Long. Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors, Science China Life Sciences, 2019, 1-15, DOI: 10.1007/s11427-019-9483-6