Improved Duplication Models for Proteome Network Evolution

Protein-protein interaction networks, particularly that of the yeast S. Cerevisiae, have recently been studied extensively. These networks seem to satisfy the small world property and their (1-hop) degree distribution seems to form a power law. More recently, a number of duplication based random graph models have been been proposed with the aim of emulating the evolution of protein-protein interaction networks and satisfying these two graph theoretical properties. In this paper, we show that the proposed model of Pastor-Satorras et al. does not generate the power law degree distribution with exponential cutoff as claimed and the more restrictive model by Chung et al. cannot be interpreted unconditionally. It is possible to slightly modify these models to ensure that they generate a power law degree distribution. However, even after this modification, the more general k-hop degree distribution achieved by these models, for k > 1, are very different from that of the yeast proteome net...

• Type: Conference
• Year: 2005
• Where: RECOMB
• Authors: Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Süleyman Cenk Sahinalp
• Keywords: Computational Biology, Degree Distribution, Power Law, Protein-protein Interaction Networks, RECOMB 2005