%0 Journal Article
%T Phylogenetic analysis of modularity in protein interaction networks
%A Sinan Erten
%A Xin Li
%A Gurkan Bebek
%A Jing Li
%A Mehmet Koyut¨ırk
%J BMC Bioinformatics
%D 2009
%I BioMed Central
%R 10.1186/1471-2105-10-333
%X In this paper, we propose a phylogenetic framework for analyzing network modules, with applications that extend well beyond network-based phylogeny reconstruction. Our approach is based on identification of modular network components from each network separately, followed by projection of these modules onto the networks of other species to compare different networks. Subsequently, we use the conservation of various modules in each network to assess the similarity between different networks. Compared to traditional methods that rely on topological comparisons, our approach has key advantages in (i) avoiding intractable graph comparison problems in comparative network analysis, (ii) accounting for noise and missing data through flexible treatment of network conservation, and (iii) providing insights on the evolution of biological systems through investigation of the evolutionary trajectories of network modules. We test our method, MOPHY, on synthetic data generated by simulation of network evolution, as well as existing protein-protein interaction data for seven diverse species. Comprehensive experimental results show that MOPHY is promising in reconstructing evolutionary histories of extant networks based on conservation of modularity, it is highly robust to noise, and outperforms existing methods that quantify network similarity in terms of conservation of network topology.These results establish modularity and network proximity as useful features in comparative network analysis and motivate detailed studies of the evolutionary histories of network modules.As a fundamental concept, evolution has profound implications in a variety of applications in modern molecular biology; e.g., functional annotation of DNA/protein sequences through comparative sequence analysis has become an important and integral part of biological sciences [1]. Accurate reconstruction of the evolutionary history of species, usually represented by a phylogenetic tree, is critical for the success
%U http://www.biomedcentral.com/1471-2105/10/333