title: Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution.
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 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.
authors.affiliation: School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada.
authors.forename: Fereydoun
authors.initials: F
authors.lastname: Hormozdiari
authors.forename: Petra
authors.initials: P
authors.lastname: Berenbrink
authors.forename: Natasa
authors.initials: N
authors.lastname: Przulj
authors.forename: S Cenk
authors.initials: SC
authors.lastname: Sahinalp
mesh_terms: D016000:Cluster Analysis; D003198:Computer Simulation; D030562:Databases, Protein; D019143:Evolution, Molecular; D020440:Gene Duplication; D053263:Gene Regulatory Networks / Q000502:physiology*; D016571:Neural Networks, Computer; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D012015:Reference Standards; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D015398:Signal Transduction; D049490:Systems Biology / Q000379:methods; D013598:Systems Theory
chemical_list: D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins