ABSTRACT:
This is an SBML version of the reaction network used in the article:
Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks
Tunahan Çakir, Betül Kirdar, Kutlu Ö. Ülgen. Biotechnol Bioeng 2004 86:251-60;
PubmedID: 15083505
; DOI: 10.1002/bit.20020
Abstract:
Central carbon metabolism of the yeast Saccharomyces cerevisiae was analyzed using metabolic pathway analysis tools. Elementary flux modes for three substrates (glucose, galactose, and ethanol) were determined using the catabolic reactions occurring in yeast. Resultant elementary modes were used for gene deletion phenotype analysis and for the analysis of robustness of the central metabolism and network functionality. Control-effective fluxes, determined by calculating the efficiency of each mode, were used for the prediction of transcript ratios of metabolic genes in different growth media (glucose-ethanol and galactose-ethanol). A high correlation was obtained between the theoretical and experimental expression levels of 38 genes when ethanol and glucose media were considered. Such analysis was shown to be a bridge between transcriptomics and fluxomics. Control-effective flux distribution was found to be promising in in silico predictions by incorporating functionality and regulation into the metabolic network structure.
Some typographical errors in the paper have been corrected:
Reaction (49) has substrate NADcyt (rather than NADmit)
Reaction (53) is missing products 90 NADPcyt
CO2 and O2 are also set as external metabolites
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
Kieran Smallbone 
