Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology

We describe an algorithm, IsoRank, for global alignment of two protein-protein interaction (PPI) networks. IsoRank aims to maximize the overall match between the two networks; in contrast, much of previous work has focused on the local alignment problem-- identifying many possible alignments, each corresponding to a local region of similarity. IsoRank is guided by the intuition that a protein should be matched with a protein in the other network if and only if the neighbors of the two proteins can also be well matched. We encode this intuition as an eigenvalue problem, in a manner analogous to Google's PageRank method. We use IsoRank to compute the first known global alignment between the S. cerevisiae and D. melanogaster PPI networks. The common subgraph has 1420 edges and describes conserved functional components between the two species. Comparisons of our results with those of a well-known algorithm for local network alignment indicate that the globally optimized alignment reso...

• Type: Conference
• Year: 2007
• Where: RECOMB
• Authors: Rohit Singh, Jinbo Xu, Bonnie Berger
• Keywords: Computational Biology, Global Alignment, Melanogaster Ppi Networks, Ortholog Prediction Method, RECOMB 2007