NEMo: An Evolutionary Model with Modularity for PPI Networks
Modelling the evolution of biological networks is a major challenge. Biological networks are usually represented as graphs; evolutionary events include addition and removal of vertices and edges, but also duplication of vertices and their associated edges. Since duplication is viewed as a primary driver of genomic evolution, recent work has focused on duplication-based models. Missing from these models is any embodiment of modularity, a widely accepted attribute of biological networks. Some models spontaneously generate modular structures, but none is known to maintain and evolve them.
We describe NEMo (Network Evolution with Modularity), a new model that embodies modularity. NEMo allows modules to emerge and vanish, to fission and merge, all driven by the underlying edge-level events using a duplication-based process. We introduce measures to compare biological networks in terms of their modular structure and use them to compare NEMo and existing duplication-based models and to compare both generated and published networks.
KeywordsGenerative model Evolutionary model PPI network Evolutionary event Modularity Network topology
- 6.Dittrich, M., et al.: Identifying functional modules in protein-protein interaction networks: an integrated exact approach. In: Proceedings of 16th International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), in Bioinformatics, vol. 24, pp. i223–i231 (2008)Google Scholar
- 27.Saraph, V., Milenkovi, T.: Magna: maximizing accuracy in global network alignment. Bioinformatics 30(20), 2931–2940 (2014). http://bioinformatics.oxfordjournals.org/content/30/20/2931.abstract CrossRefGoogle Scholar
- 28.Schlosser, G., Wagner, G.: Modularity in Development and Evolution. University of Chicago Press, Chicago (2004)Google Scholar