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A consensus reconstruction of yeast metabolism |
Latest version: Yeast consensus reconstructions are now made available at yeast.sf.net, this page is left here only for historical purposes
SBML file with compartments| SBML file without compartments
This page is a portal to the consensus network model, as published in the article Herrgård, Swainston et al. (2008) "A consensus yeast metabolic reconstruction obtained from a community approach to systems biology" Nature Biotechnol. 26, 1155-1160.
Introduction
A number of reconstructions of the metabolic network of yeast based on genomic and literature data have been published. However, due to different approaches utilized in the reconstruction as well as different interpretations of the literature, the earlier reconstructions have significant number of differences. A community effort resulted in a consensus network model of yeast metabolism, combining results from previous models.
Jamboree meeting
The members of the yeast systems biology network recognised that a single consensus reconstruction of the yeast metabolic network was highly desirable. A jamboree meeting took place in April 2007 at the Manchester Centre for Integrative Systems Biology where several groups engaged in creating a consensus network of yeast. While reconciling the different reconstructions was a major focus, the team was also very interested in standardizing the naming of metabolites and following other standard annotation procedures (eg MIRIAM).
Metabolic reconstruction
The starting point for this consensus reconstruction were two freely available metabolic network reconstructions, iMM904 and iLL672 containing information from 904 and 672 yeast genes, respectively. Both were derived from the first genome-scale metabolic network reconstruction for yeast iFF708, but they followed different processes and their results were also significantly different.
This reconstruction is provided in the following formats:
- an SBML file containing the reaction network and annotations, located to specific sub-cellular compartments
- an SBML file containing the reaction network and annotations without subcellular compartmentation (all reactions happening in a single compartment).