Not all scale free networks are Born equal: the role of the seed graph in PPI network emulation

Authors:
Fereydoun Hormozdiari;Petra Berenbrink;Nataša Pržulj;Cenk Sahinalp
Affiliations:
School of Computing Science, Simon Fraser University, Canada;School of Computing Science, Simon Fraser University, Canada;Department of Computer Science, University of California, Irvine;School of Computing Science, Simon Fraser University, Canada
Venue:
RECOMB'06 Proceedings of the joint 2006 satellite conference on Systems biology and computational proteomics
Year:
2006

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Abstract

The (asymptotic) degree distributions of the best known "scale free" network models are all similar and are independent of the seed graph used. Hence it has been tempting to assume that networks generated by these models are similar in general. In this paper we observe that several key topological features of such networks depend heavily on the specific model and the seed graph used. Furthermore, we show that starting with the "right" seed graph, the duplication model captures many topological features of publicly available PPI networks very well.