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

作　　者：Jian Zu Yuexi Gu Yu Li Chentong Li Wenyu Zhang Yong E.Zhang UnJin Lee Li Zhang Manyuan Long 

机构地区：[1]School of Mathematics and Statistics, Xi'an Jiaotong University [2]Department of Ecology and Evolution, The University of Chicago [3]Center for Systems Biology, Soochow University [4]State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution,Institute of Zoology, Chinese Academy of Sciences

出　　处：《Science China(Life Sciences)》2019年第4期594-608,共15页中国科学（生命科学英文版）

基　　金：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);the China Postdoctoral Science Foundation(2014M560755)

摘　　要：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.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.

关 键 词：NETWORK biology GENE NETWORK EVOLUTION SCALE-FREE NETWORK natural selection GENE expression self-organization gene DUPLICATION 

分 类 号：Q[生物学]