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Pairwise global alignment of protein interaction networks by matching neighborhood topology (2007)
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| Venue: | Proceedings of the 11th Annual International Conference on Computational Molecular Biology (RECOMB’07 |
| Citations: | 90 - 3 self |
BibTeX
@INPROCEEDINGS{Singh07pairwiseglobal,
author = {Rohit Singh and Jinbo Xu and Bonnie Berger},
title = {Pairwise global alignment of protein interaction networks by matching neighborhood topology},
booktitle = {Proceedings of the 11th Annual International Conference on Computational Molecular Biology (RECOMB’07},
year = {2007},
pages = {16--31}
}
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Abstract
Abstract. We describe an algorithm, IsoRank, for global alignment of two protein-protein interaction (PPI) networks. IsoRank aims to max-imize the overall match between the two networks; in contrast, much of previous work has focused on the local alignment problem | identify-ing 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 rst known global alignment between the S. cerevisiae and D. melanogaster PPI networks. The com-mon subgraph has 1420 edges and describes conserved functional compo-nents between the two species. Comparisons of our results with those of a well-known algorithm for local network alignment indicate that the glob-ally optimized alignment resolves ambiguity introduced by multiple local alignments. Finally, we interpret the results of global alignment to iden-tify functional orthologs between yeast and y; our functional ortholog prediction method is much simpler than a recently proposed approach and yet provides results that are more comprehensive. 1
Keyphrases
protein interaction network neighborhood topology pairwise global alignment global alignment multiple local alignment local network alignment indicate functional compo-nents glob-ally optimized alignment well-known algorithm protein-protein interaction overall match previous work eigenvalue problem iden-tify functional orthologs pagerank method com-mon subgraph melanogaster ppi network functional ortholog prediction method local region
