Name
Abstract | ||
|---|---|---|
Stable isotope labeling of small-molecule metabolites (e.g. (13)C-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.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 InChI 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 BioNetGen language (BNGL), a formal model-specification language, which allows a set of maps to be automatically translated into isotopomer mass-balance equations.The carbon-fate maps and software for visualizing the maps are freely available (http://cellsignaling.lanl.gov/FateMaps/). |
Year | DOI | Venue |
|---|---|---|
2007 | 10.1093/bioinformatics/btm498 | Bioinformatics |
Keywords | Field | DocType |
fate map,carbon-fate map,known reaction mechanism,formal model-specification language,enzymatic reaction,bijective map,prochiral carbon atom,metabolic reaction,enzyme-catalyzed reaction,carbon atom,corresponding carbon atom,structured data,metabolic network,reaction mechanism,specification language,mass balance,stable isotope,enzyme | Data mining,Bijection,Identifier,Computer science,Stable Isotope Labeling,Metabolic network,KEGG,Isotopomers,Bioinformatics,Carbon | Journal |
Volume | Issue | ISSN |
23 | 23 | 1367-4811 |
Citations | PageRank | References |
9 | 0.69 | 12 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Fangping Mu | 1 | 46 | 4.62 |
| Robert F. Williams | 2 | 18 | 1.46 |
| Clifford J Unkefer | 3 | 23 | 2.20 |
| Pat J Unkefer | 4 | 29 | 2.38 |
| James R Faeder | 5 | 409 | 31.02 |
| William S. Hlavacek | 6 | 277 | 24.15 |