Bioinformatics Advance Access originally published online on April 8, 2004
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Bioinformatics 20(13) © Oxford University Press 2004; all rights reserved.
Constructing an enzyme-centric view of metabolism
1 School of Biological and Chemical Sciences, University of Exeter, Washington Singer Laboratories, Exeter, Devon, EX4 4PS, UK, 2 Medicines Research Centre, GlaxoSmithKline, Stevenage, SG1 2NY, UK, and 3 Schools of Biological and Chemical Sciences and Engineering Computer Science and Mathematics, University of Exeter, Washington Singer Laboratories, Exeter, Devon, EX4 4PS, UK
Received on September 29, 2003; revised on February 16, 2004; accepted on February 21, 2004
Advance Access Publication April 8, 2004
Motivation: The current paradigm for viewing metabolism, such as the Boehringer Chart or KEGG, takes a metabolite-centric view that is not ideal for genomics analysis because the same enzyme can appear in multiple places. Therefore an enzyme-centric view is also required.
Results: We have eliminated synonymous compound names taken from the ENZYME database ensuring that it is computationally parseable at all levels. Based on these results, we have written a software to create enzyme-centric graphs from reaction data, and we have created a second dataset with hub molecules removed, allowing a greater depth of information to be extracted from these graphs. We also present a detailed analysis of the various stages of the reconditioning process and the characteristics of the subgraphs resulting from the application of our software to the revised datasets.
Availability: Complete datasets and supplementary material may be downloaded from http://helix.ex.ac.uk/metabolism. The software for the creation of enzyme-centric graphs from reaction data is available on request from the authors.
Contact: a.r.dalby{at}ex.ac.uk
* To whom correspondence should be addressed.
Present address: School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK.
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