Constructing an enzyme-centric view of metabolism

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...

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Bibliographic Details
Published in:Bioinformatics 2004-09, Vol.20 (13), p.2050-2055
Main Authors: Horne, A. B., Hodgman, T. C., Spence, H. D., Dalby, A. R.
Format: Article
Language:English
Subjects:
Biological and medical sciences
Computer Simulation
Databases, Protein
Enzymes - chemistry
Enzymes - metabolism
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Metabolism - physiology
Models, Biological
Multienzyme Complexes - chemistry
Multienzyme Complexes - metabolism
Protein Interaction Mapping - methods
Signal Transduction - physiology
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Summary: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.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bth199