Constructing an enzyme-centric view of metabolism.

Horne, A.B., Hodgman, T.C., Spence, H.D. and Dalby, A.R. 2004. Constructing an enzyme-centric view of metabolism. Bioinformatics. 20 (13), pp. 2050-2055. https://doi.org/10.1093/bioinformatics/bth199

TitleConstructing an enzyme-centric view of metabolism.
TypeJournal article
AuthorsHorne, A.B., Hodgman, T.C., Spence, H.D. and Dalby, A.R.
Abstract

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.

JournalBioinformatics
Journal citation20 (13), pp. 2050-2055
ISSN1367-4803
1460-2059
Year2004
PublisherOxford University Press
Digital Object Identifier (DOI)https://doi.org/10.1093/bioinformatics/bth199
PubMed ID15073012
Web address (URL)http://europepmc.org/abstract/med/15073012
Publication dates
PublishedSep 2004

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