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Bioinformatics Vol. 19 no. 8 2003
Pages 1027-1034
© 2003 Oxford University Press

Hierarchical analysis of dependency in metabolic networks

Julien Gagneur 1,2,*,{dagger}, David B. Jackson 1,{dagger} and Georg Casari 1,{dagger}

1 Lion Bioscience AG, Waldhoferstr. 98, 69123 Heidelberg, Germany
2 Laboratoire de Mathématiques Appliquées aux Systèmes, Ecole Centrale Paris, Grande Voie des Vignes, 92295 Chatenay-Malabry cedex, France

Received on September 17, 2002 ; revised on November 13, 2002 ; accepted on December 18, 2002

Motivation: Elucidation of metabolic networks for an increasing number of organisms reveals that even small networks can contain thousands of reactions and chemical species. The intimate connectivity between components complicates their decomposition into biologically meaningful sub-networks. Moreover, traditional higher-order representations of metabolic networks as metabolic pathways, suffers from the lack of rigorous definition, yielding pathways of disparate content and size.

Results: We introduce a hierarchical representation that emphasizes the gross organization of metabolic networks in largely independent pathways and sub-systems at several levels of independence. The approach highlights the coupling of different pathways and the shared compounds responsible for those couplings. By assessing our results on Escherichia coli (E.coli metabolic reactions, Genetic Circuits Research Group, University of California, San Diego, http://gcrg.ucsd.edu/organisms/ecoli.html, ‘model v 1.01. reactions’) against accepted biochemical annotations, we provide the first systematic synopsis of an organism’s metabolism. Comparison with operons of E.coli shows that low-level clusters are reflected in genome organization and gene regulation.

Availability: Source code, data sets and supplementary information are available at http://www.mas.ecp.fr/labo/equipe/gagneur/hierarchy/hierarchy.html

Contact: julien.gagneur{at}cellzome.com

* To whom correspondence should be addressed.

{dagger} Present address: Cellzome AG, Meyerhofstr. 1, 69117 Heidelberg, Germany..


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