title: Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison.
abstract: The increase of protein-protein interaction (PPI) data of different species makes it possible to identify common subnetworks (conserved protein complexes) across species via local alignment of their PPI networks, which benefits us to study biological evolution. Local alignment algorithms compare PPI network of different species at both protein sequence and network structure levels. For computational and biological reasons, it is hard to find common subnetworks with strict similar topology from two input PPI networks. Consequently some methods introduce less strict criteria for topological similarity. However those methods fail to consider the differences of the two input networks and adopt equally lenient criteria on them. In this work, a new dividing-and-matching-based method, namely UEDAMAlign is proposed to detect conserved protein complexes. This method firstly uses known protein complexes or computational methods to divide one of the two input PPI networks into subnetworks and then maps the proteins in these subnetworks to the other PPI network to get their homologous proteins. After that, UEDAMAlign conducts unequally lenient criteria on the two input networks to find common connected components from the proteins in the subnetworks and their homologous proteins in the other network. We carry out network alignments between S. cerevisiae and D. melanogaster, H. sapiens and D. melanogaster, respectively. Comparisons are made between other six existing methods and UEDAMAlign. The experimental results show that UEDAMAlign outperforms other existing methods in recovering conserved protein complexes that both match well with known protein complexes and have similar functions.
authors.affiliation: The School of Information Science and Engineering, Central South University, Changsha, Hunan People's Republic of China ; The Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650093 Yunnan People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Peng
authors.affiliation: The School of Information Science and Engineering, Central South University, Changsha, Hunan People's Republic of China.
authors.forename: Jianxin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Division of Biomedical Engineering, Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9 Canada.
authors.forename: Fangxiang
authors.initials: F
authors.lastname: Wu
authors.affiliation: Department of Computer Science, Georgia State University, Atlanta, GA 30302-4110 USA.
authors.forename: Pan
authors.initials: P
authors.lastname: Yi
keywords: Conserved protein complexes; Local network alignment; Network alignment; PPI networks