Constructing an enzyme-centric view of metabolism

  • Authors:

  • A. B. Horne;T. C. Hodgman;H. D. Spence;A. R. Dalby

  • Affiliations:

  • School of Biological and Chemical Sciences, University of Exeter, Washington Singer Laboratories, Exeter, Devon, EX4 4PS, UK,;Medicines Research Centre, GlaxoSmithKline, Stevenage, SG1 2NY, UK,;Medicines Research Centre, GlaxoSmithKline, Stevenage, SG1 2NY, UK,;Schools of Biological and Chemical Sciences and Engineering Computer Science and Mathematics, University of Exeter, Washington Singer Laboratories, Exeter, Devon, EX4 4PS, UK

  • Venue:
  • Bioinformatics
  • Year:
  • 2004

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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.