Imperial College London


Faculty of Natural SciencesDepartment of Life Sciences

Director Centre for Bioinformatics



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BibTex format

author = {Cootes, AP and Muggleton, SH and Sternberg, MJE},
doi = {10.1016/j.jmb.2007.03.013},
journal = {Molecular Biology},
pages = {1126--1139},
title = {The identification of similarities between biological networks: Application to the metabolome and interactome prediction},
url = {},
volume = {369},
year = {2007}

RIS format (EndNote, RefMan)

AB - 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 life, such as purine, pyrimidine and amino acid metabolism. The 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, interestly, 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.
AU - Cootes,AP
AU - Muggleton,SH
AU - Sternberg,MJE
DO - 10.1016/j.jmb.2007.03.013
EP - 1139
PY - 2007///
SP - 1126
TI - The identification of similarities between biological networks: Application to the metabolome and interactome prediction
T2 - Molecular Biology
UR -
UR -
VL - 369
ER -