The Identification of Similarities between Biological Networks: Application to the Metabolome and Interactome

Adrian P. Cootes, Stephen H. Muggleton, M. J E Sternberg*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    30 Citations (Scopus)

    Abstract

    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 report 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, it is novel in that it includes information about the context of the subgraph within the adjacent network. We also explore a new approach to quantifying the statistical significance of matching subgraphs. We report similar subgraphs in metabolic pathways and in protein-protein interaction networks. The most similar metabolic subgraphs were generally found to occur in processes central to all life, such as purine, pyrimidine and amino acid metabolism. The most similar pairs of subgraphs found in the protein-protein interaction networks of Drosophila melanogaster and Saccharomyces cerevisiae also include central processes such as cell division but, interestingly, also include protein sub-networks involved in pre-mRNA processing. The inclusion of network context information in the comparison of protein interaction networks increased the number of similar subgraphs found consisting of proteins involved in the same functional process. This could have implications for the prediction of protein function.

    Original languageEnglish
    Pages (from-to)1126-1139
    Number of pages14
    JournalJournal of molecular biology
    Volume369
    Issue number4
    DOIs
    Publication statusPublished - 15 Jun 2007

    Keywords

    • metabolic networks
    • network comparison
    • protein interactions
    • systems biology

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