GENE_ASSOCIATION:(YLR044C OR YDR081C OR YLR134W) PROTEIN_ASSOCIATION:(PDC1 OR PDC2 OR PDC5)
GENE_ASSOCIATION:YCR012W PROTEIN_ASSOCIATION:PGK1
GENE_ASSOCIATION:YLR354C PROTEIN_ASSOCIATION:TAL1
GENE_ASSOCIATION:YMR303C PROTEIN_ASSOCIATION:ADH2
GENE_ASSOCIATION:(YPR074C OR YBR117C) PROTEIN_ASSOCIATION:(TKL1 OR TKL2)
GENE_ASSOCIATION:(YNL037C OR YOR136W) PROTEIN_ASSOCIATION:(IDH1 OR IDH2)
isocitrate dehydrogenase (NADmit- dependent)
GENE_ASSOCIATION:YML042W PROTEIN_ASSOCIATION:CAT2
GENE_ASSOCIATION:(YIL053W OR YER062C) PROTEIN_ASSOCIATION:(GPP1 OR GPP2)
GENE_ASSOCIATION:(YKL152C OR YDL021W OR YOL056W) PROTEIN_ASSOCIATION:(GPM1 OR GPM2 OR GPM3)
GENE_ASSOCIATION:YOL126C PROTEIN_ASSOCIATION:MDH2
GENE_ASSOCIATION:YLR304C PROTEIN_ASSOCIATION:ACO1
GENE_ASSOCIATION:YKL029C PROTEIN_ASSOCIATION:MAE1
GENE_ASSOCIATION:(YOR142W OR YGR244C) PROTEIN_ASSOCIATION:(LSC1 OR LSC2)
GENE_ASSOCIATION:(YNR034W OR YCR073W-A OR YHR163W OR YGR248W) PROTEIN_ASSOCIATION:(SOL1 OR SOL2 OR SOL3 OR SOL4)
GENE_ASSOCIATION:YDR050C PROTEIN_ASSOCIATION:TPI1
GENE_ASSOCIATION:YPL061W PROTEIN_ASSOCIATION:ALD6
aldehyde dehydrogenase (NADPcyt- dependent)
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. For more information see the terms of use . 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.
Çakir2004 - Central Carbon Metabolism of S.cerevisiae
GENE_ASSOCIATION:(YGR240C OR YMR205C) PROTEIN_ASSOCIATION:(PFK1 OR PFK2)
GENE_ASSOCIATION:(YKL148C OR YLL041C OR YKL141W) PROTEIN_ASSOCIATION:(SDH1 OR SDH2 OR SDH3)
GENE_ASSOCIATION:YNL241C PROTEIN_ASSOCIATION:ZWF1
GENE_ASSOCIATION:YCR005C PROTEIN_ASSOCIATION:CIT2
GENE_ASSOCIATION:(YJL052W OR YJR009C OR YGR192C) PROTEIN_ASSOCIATION:(TDH1 OR TDH2 OR TDH3)
glyceraldehyde-3-phosphate dehydrogenase
GENE_ASSOCIATION:YOR374W PROTEIN_ASSOCIATION:ALD4
aldehyde dehydrogenase (NADPmit- dependent)
GENE_ASSOCIATION:(YDL022W OR YOL059W) PROTEIN_ASSOCIATION:(GPD1 OR GPD2)
GENE_ASSOCIATION:YBR196C PROTEIN_ASSOCIATION:PGI1
GENE_ASSOCIATION:YJL121C PROTEIN_ASSOCIATION:RPE1
GENE_ASSOCIATION:(YOL086C OR YGL256W) PROTEIN_ASSOCIATION:(ADH1 OR ADH4)
GENE_ASSOCIATION:(YAL038W OR YOR347C) PROTEIN_ASSOCIATION:(PYK1 OR PYK2)
GENE_ASSOCIATION:YJR051W PROTEIN_ASSOCIATION:OSM1
reoxidation of cytosolic NADH to mitochondrial NADH
GENE_ASSOCIATION:YKR097W PROTEIN_ASSOCIATION:PCK1
GENE_ASSOCIATION:YKL060C PROTEIN_ASSOCIATION:FBA1
GENE_ASSOCIATION:YDL066W PROTEIN_ASSOCIATION:IDP1
isocitrate dehydrogenase (NADPmit- dependent)
GENE_ASSOCIATION:(YAL054C OR YLR153C) PROTEIN_ASSOCIATION:(ACS1 OR ACS2)
GENE_ASSOCIATION:YKL085W PROTEIN_ASSOCIATION:MDH1
GENE_ASSOCIATION:YOR095C PROTEIN_ASSOCIATION:RKI1
GENE_ASSOCIATION:(YCL040W OR YFR053C OR YGL253W) PROTEIN_ASSOCIATION:(GLK1 OR HXK1 OR HXK2)
GENE_ASSOCIATION:YLR377C PROTEIN_ASSOCIATION:FBP1
GENE_ASSOCIATION:YER065C PROTEIN_ASSOCIATION:ICL1
GENE_ASSOCIATION:YLR174W PROTEIN_ASSOCIATION:IDP2
isocitrate dehydrogenase (NADPcyt- dependent)
GENE_ASSOCIATION:(YER178W OR YNL071W OR YBR221C) PROTEIN_ASSOCIATION:(PDA1 OR PDA2 OR PDB1)
GENE_ASSOCIATION:(YHR183W OR YGR256W) PROTEIN_ASSOCIATION:(GND1 OR GND2)
GENE_ASSOCIATION:YPL262W PROTEIN_ASSOCIATION:FUM1
GENE_ASSOCIATION:(YBR020W OR YMR105C OR YBR018C) PROTEIN_ASSOCIATION:(GAL1 OR GAL5 OR GAL7)
GENE_ASSOCIATION:YNL117W PROTEIN_ASSOCIATION:MLS1
GENE_ASSOCIATION:(YGR254W OR YHR174W) PROTEIN_ASSOCIATION:(ENO1 OR ENO2)
GENE_ASSOCIATION:(YNR001C OR YPR001W) PROTEIN_ASSOCIATION:(CIT1 OR CIT3)
GENE_ASSOCIATION:(YGL062W OR YBR218C) PROTEIN_ASSOCIATION:(PYC1 OR PYC2)
GENE_ASSOCIATION:(YIL125W OR YDR148C) PROTEIN_ASSOCIATION:(KGD1 OR KGD2)