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Bioinformatics Advance Access published online on January 10, 2006
Bioinformatics, 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
Received October 23, 2005
Revised December 12, 2005
Accepted December 28, 2005

Article

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

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

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

* To whom correspondence should be addressed.
Yoram Louzoun, E-mail: louzouy{at}math.biu.ac.il


  Abstract

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: 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.

Associate Editor: Satoru Miyano
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