中国物理B ›› 2010, Vol. 19 ›› Issue (1): 10512-010512.doi: 10.1088/1674-1056/19/1/010512

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Evolution of a protein domain interaction network

官山1, 高丽锋2, 石建军2   

  1. (1)College of Physics Science and Technology, Yangzhou University, Yangzhou 225002, China; (2)Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • 收稿日期:2009-03-29 修回日期:2009-04-28 出版日期:2010-01-15 发布日期:2010-01-15
  • 基金资助:
    Project supported by the National Natural Science Foundation of China (Grant Nos. 70671089 and 30871521), and the State Key Program of National Natural Science of China (Grant No. 10635040).

Evolution of a protein domain interaction network

Gao Li-Feng(高丽锋)a), Shi Jian-Jun(石建军)b), and Guan Shan(官山)b)†   

  1. a Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; b College of Physics Science and Technology, Yangzhou University, Yangzhou 225002, China
  • Received:2009-03-29 Revised:2009-04-28 Online:2010-01-15 Published:2010-01-15
  • Supported by:
    Project supported by the National Natural Science Foundation of China (Grant Nos. 70671089 and 30871521), and the State Key Program of National Natural Science of China (Grant No. 10635040).

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摘要： In this paper, we attempt to understand complex network evolution from the underlying evolutionary relationship between biological organisms. Firstly, we construct a Pfam domain interaction network for each of the 470 completely sequenced organisms, and therefore each organism is correlated with a specific Pfam domain interaction network; secondly, we infer the evolutionary relationship of these organisms with the nearest neighbour joining method; thirdly, we use the evolutionary relationship between organisms constructed in the second step as the evolutionary course of the Pfam domain interaction network constructed in the first step. This analysis of the evolutionary course shows: (i) there is a conserved sub-network structure in network evolution; in this sub-network, nodes with lower degree prefer to maintain their connectivity invariant, and hubs tend to maintain their role as a hub is attached preferentially to new added nodes; (ii) few nodes are conserved as hubs; most of the other nodes are conserved as one with very low degree; (iii) in the course of network evolution, new nodes are added to the network either individually in most cases or as clusters with relative high clustering coefficients in a very few cases.

Abstract: In this paper, we attempt to understand complex network evolution from the underlying evolutionary relationship between biological organisms. Firstly, we construct a Pfam domain interaction network for each of the 470 completely sequenced organisms, and therefore each organism is correlated with a specific Pfam domain interaction network; secondly, we infer the evolutionary relationship of these organisms with the nearest neighbour joining method; thirdly, we use the evolutionary relationship between organisms constructed in the second step as the evolutionary course of the Pfam domain interaction network constructed in the first step. This analysis of the evolutionary course shows: (i) there is a conserved sub-network structure in network evolution; in this sub-network, nodes with lower degree prefer to maintain their connectivity invariant, and hubs tend to maintain their role as a hub is attached preferentially to new added nodes; (ii) few nodes are conserved as hubs; most of the other nodes are conserved as one with very low degree; (iii) in the course of network evolution, new nodes are added to the network either individually in most cases or as clusters with relative high clustering coefficients in a very few cases.

Key words: complex network, protein domain, network evolution

中图分类号:  (General theory and mathematical aspects)

  • 87.10.-e
87.14.E- (Proteins) 89.75.Hc (Networks and genealogical trees)