not all scale-free networks are born equal the role of the seed graph in ppi network evolution并不是所有的无标度网络生来平等的角色在ppi网络进化的种子图.pdfVIP

Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution 1 1 ˇ ˇ 2 1* Fereydoun Hormozdiari , Petra Berenbrink , Natasa Przulj , S. Cenk Sahinalp 1 School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada, 2 Department of Computer Science, University of California Irvine, California, United States of America 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 generally similar. 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 (typically a dense subgraph of the protein–protein interaction network analyzed), the duplication model captures many topological features of publicly available protein–protein interaction networks very well. ˇ Citation: Hormozdiari F, Berenbrink P, Przulj N, Sahinalp SC (2007) Not all scale-free networks are born equal: The role of the seed graph in PPI network evolution. PLoS Comput Biol 3(7): e118. doi:10.1371/journal.pcbi.0030118 Introduction used to compare PPI networks with random network models. The first such measure is based on the k-hop reachability. The 1- In the past few years, protein–protein interaction (PPI) hop reachability of a node is simply its degree (i.e., the networks of several organisms have been derived and made