Bioinformatics Advance Access published online on July 29, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth436
Bioinformatics © Oxford University Press 2004; all rights reserved
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1 Department of Computer Science, University of Toronto, Toronto, M5S 3G4, Canada
* To whom correspondence should be addressed. E-mail: juris{at}cs.utoronto.ca.
Motivation: Networks have been used to model many real-world phenomena to better understand the phenomena and to guide experiments in order to predict their behavior. Since incorrect models lead to incorrect predictions, it is vital to have as accurate a model as possible. As a result, new techniques and models for analyzing and modeling real-world networks have recently been introduced. Results: One example of large and complex networks involves protein-protein interaction (PPI) networks. We analyze PPI networks of yeast S. cerevisiae and fruitfly D. melanogaster using a newly introduced measure of local network structure as well as the standardly used measures of global network structure. We examine the fit of four different network models, including Erdös-Rényi, scale-free, and geometric random network models, to these PPI networks with respect to the measures of local and global network structure. We demonstrate that the currently accepted scale-free model of PPI networks fails to fit the data in several respects and show that a random geometric model provides a much more accurate model of the PPI data. We hypothesize that only the noise in these networks is scale-free. Conclusions: We systematically evaluate how well different network models fit the PPI networks. We show that the structure of PPI networks is better modeled by a geometric random graph than by a scale-free model. Contact: Jurisica, I., Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Division of Cancer Informatics, 610 University Avenue, Toronto, ON, M5G 2M9, Canada. Supplementary Information: Supplementary information is available and submitted together with this manuscript.
Revised July 19, 2004
Accepted July 24, 2004
Article
Modeling interactome: scale-free or geometric?
ulj 1,
2 Ontario Cancer Institute, Division of Cancer Informatics, Toronto, M5G 2M9, Canada
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