Constructing an enzyme-centric view of metabolism

Bioinformatics. 2004 Sep 1;20(13):2050-5. doi: 10.1093/bioinformatics/bth199. Epub 2004 Apr 8.

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.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • Databases, Protein*
  • Enzymes / chemistry*
  • Enzymes / metabolism*
  • Metabolism / physiology*
  • Models, Biological*
  • Multienzyme Complexes / chemistry
  • Multienzyme Complexes / metabolism
  • Protein Interaction Mapping / methods*
  • Signal Transduction / physiology*

Substances

  • Enzymes
  • Multienzyme Complexes