AbstractCentral 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. © 2004 Wiley Periodicals, Inc.