Evolution of a protein domain interaction network

doi:10.1088/1674-1056/19/1/010512

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.

Keywords: complex network protein domain network evolution

Received: 29 March 2009
Revised: 28 April 2009
Accepted manuscript online:

PACS:	87.10.-e	(General theory and mathematical aspects)
	87.14.E-	(Proteins)
	89.75.Hc	(Networks and genealogical trees)

Fund: 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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Gao Li-Feng(高丽锋), Shi Jian-Jun(石建军), and Guan Shan(官山) Evolution of a protein domain interaction network 2010 Chin. Phys. B 19 010512

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