|Title||Constructing an enzyme-centric view of metabolism.|
|Authors||Horne, A.B., Hodgman, T.C., Spence, H.D. and Dalby, A.R.|
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.
|Journal citation||20 (13), pp. 2050-2055|
|Publisher||Oxford University Press|
|Digital Object Identifier (DOI)||https://doi.org/10.1093/bioinformatics/bth199|
|Web address (URL)||http://europepmc.org/abstract/med/15073012|