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The increasing interest in systems biology has resulted in extensive experimental data describing networks of interactions (or associations) between molecules in metabolism, protein protein interactions and gene regulation. Comparative analysis of these networks is central to understanding biological systems. We have developed a novel method (PHUNKEE: Pairing subgrapHs Using NetworK Environment Equivalence) by which similar subgraphs in a pair of networks can be identified. Like other methods, PHUNKEE explicitly considers the graphical form of the data and allows for gaps. However, PHUNKEE is novel in that it includes information about the context of the subgraph within the adjacent network. PHUNKEE was used to find similar subgraphs in metabolic pathways and in protein protein interaction networks.
See Cootes, A.P., S.H. Muggleton, and M.J. Sternberg, The Identification of Similarities between Biological Networks: Application to the Metabolome and Interactome. J Mol Biol, 2007. 369(4): p. 1126-39. |
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