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There is a need for improved appreciation of the importance of genome-wide mRNA and protein expression measurements and their role in understanding translation and in relation to genome-wide math. frameworks for gene expression regulation. The authors investigated the use of a high-d. microarray technique for mRNA expression anal. and a two-dimensional protein electrophoresis-tandem mass spectrometry method for protein anal. to monitor changes in gene expression. The authors applied these anal. tools in the context of an environmental perturbation of Escherichia coli cells-the addn. of varying amts. of IPTG. The authors also tested the application of these tools to the study of a genetic perturbation of Escherichia coli cells-the ability of certain strains to hypersecrete the hemolysin protein. A lack of correspondence was obsd. between mRNA and protein expression profiles. Although the data do not include measurements on all expressed genes (because the ability to measure protein expression profiles is limiting), the qual. and quant. behavior of the measurements of a subset of expressed genes is similar to the behavior of the entire system. The change in obsd. av. mRNA and protein amplification factors for 77 and 52 genes coincided with the obsd. change in mRNA amplification factor for the entire system. Furthermore, relative changes in expression could be used to elucidate mechanisms of gene expression regulation for the system studied, even when measurements were made on a small subset of the system. [on SciFinder (R)]