Name
Abstract | ||
|---|---|---|
Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species. |
Year | DOI | Venue |
|---|---|---|
2009 | 10.1007/978-3-642-04241-6_29 | WABI |
Keywords | Field | DocType |
graph kernel,modular graph kernel,species tree,alignment toolkit,biomolecular network,pair-wise alignment,large biomolecular network,large protein-protein interaction network,protein-protein interaction data,homo sapiens protein-protein interaction,open source biomolecular network,structure function,comparative analysis,score function,biological systems,protein protein interaction | Graph kernel,Graph,Phylogenetic tree,Computer science,Network alignment,Modular design,Bioinformatics | Conference |
Volume | ISSN | ISBN |
5724 | 0302-9743 | 3-642-04240-6 |
Citations | PageRank | References |
5 | 0.46 | 22 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Fadi Towfic | 1 | 39 | 4.92 |
| M. Heather West Greenlee | 2 | 16 | 2.56 |
| Vasant Honavar | 3 | 3353 | 468.10 |