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Bioinformatics Advance Access originally published online on January 10, 2006
Bioinformatics 2006 22(5):581-588; doi:10.1093/bioinformatics/btk030
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Copying nodes versus editing links: the source of the difference between genetic regulatory networks and the WWW

Yoram Louzoun 1,*, Lev Muchnik 2 and Sorin Solomon 3

1Department of mathematics, Bar Ilan University Ramat Gan 52900, Israel
2Department of Physics, Bar Ilan University Ramat Gan 52900, Israel
3Department of Physics, Hebrew University Jerusalem, Israel

*To whom correspondence should be addressed.

We study two kinds of networks: genetic regulatory networks and the World Wide Web. We systematically test microscopic mechanisms to find the set of such mechanisms that optimally explain each networks' specific properties. In the first case we formulate a model including mainly random unbiased gene duplications and mutations. In the second case, the basic moves are website generation and rapid surf-induced link creation (/destruction). The different types of mechanisms reproduce the appropriate observed network properties. We use those to show that different kinds of networks have strongly system-dependent macroscopic experimental features. The diverging properties result from dissimilar node and link basic dynamics. The main non-uniform properties include the clustering coefficient, small-scale motifs frequency, time correlations, centrality and the connectivity of outgoing links. Some other features are generic such as the large-scale connectivity distribution of incoming links (scale-free) and the network diameter (small-worlds). The common properties are just the general hallmark of autocatalysis (self-enhancing processes), while the specific properties hinge on the specific elementary mechanisms.

Contact: louzouy{at}math.biu.ac.il

Supplementary information: Supplementary data are available at Bioinformatics Online.

Received on October 23, 2005; revised on December 12, 2005; accepted on December 28, 2005

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