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Bioinformatics Advance Access originally published online on October 12, 2007
Bioinformatics 2007 23(23):3193-3199; doi:10.1093/bioinformatics/btm498
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Carbon-fate maps for metabolic reactions

Fangping Mu 1, Robert F. Williams 2, Clifford J. Unkefer 2, Pat J. Unkefer 2, James R. Faeder 3 and William S. Hlavacek 1,4,*

1Theoretical Biology and Biophysics Group, Theoretical Division, 2National Stable Isotope Resource, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 and 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Stable isotope labeling of small-molecule metabolites (e.g. 13C-labeling of glucose) is a powerful tool for characterizing pathways and reaction fluxes in a metabolic network. Analysis of isotope labeling patterns requires knowledge of the fates of individual atoms and moieties in reactions, which can be difficult to collect in a useful form when considering a large number of enzymatic reactions.

Results: We report carbon-fate maps for 4605 enzyme-catalyzed reactions documented in the KEGG database. Every fate map has been manually checked for consistency with known reaction mechanisms. A map includes a standardized structure-based identifier for each reactant (namely, an InChITM string); indices for carbon atoms that are uniquely derived from the metabolite identifiers; structural data, including an identification of homotopic and prochiral carbon atoms; and a bijective map relating the corresponding carbon atoms in substrates and products. Fate maps are defined using the BioNetGenTM language (BNGL), a formal model-specification language, which allows a set of maps to be automatically translated into isotopomer mass-balance equations.

Availability: The carbon-fate maps and software for visualizing the maps are freely available (http://cellsignaling.lanl.gov/FateMaps/).

Contact: wish{at}lanl.gov

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alfonso Valencia

Received on June 6, 2007; revised on August 23, 2007; accepted on September 28, 2007

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