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Evolution of a protein domain interaction network |
| Guan Shana, Gao Li-Fengb, Shi Jian-Junb |
| a College of Physics Science and Technology, Yangzhou University,
Yangzhou 225002, China; b Institute of Crop Sciences, Chinese Academy of Agricultural
Sciences, Beijing 100081, China |
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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.
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Received: 29 March 2009
Revised: 28 April 2009
Published: 15 January 2010
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PACS:
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87.10.-e
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(General theory and mathematical aspects)
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87.14.E-
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(Proteins)
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89.75.Hc
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(Networks and genealogical trees)
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| 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). |
Cite this article:
Gao Li-Feng, Shi Jian-Jun, Guan Shan Evolution of a protein domain interaction network 2010 Chin. Phys. B 19 010512
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