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USE OF TRANSCRIPTIONAL COUPLING AND KEGG PATHWAY ANALYSIS OF GLOBAL GENE EXPRESSION TO REVEAL TRANSCRIPTIONAL CHANGES BETWEEN STATIONARY- AND LOG-PHASE SALMONELLA TYPHIMURIUM LT2
Citation:
WARD, W. O., C. SWARTZ, S. PORWOLLIK, N. M. HANLEY, S. H. WARREN, M. MCCLELLAND, AND D. M. DEMARINI. USE OF TRANSCRIPTIONAL COUPLING AND KEGG PATHWAY ANALYSIS OF GLOBAL GENE EXPRESSION TO REVEAL TRANSCRIPTIONAL CHANGES BETWEEN STATIONARY- AND LOG-PHASE SALMONELLA TYPHIMURIUM LT2. Presented at The 9th International Conference on Environmental Mutagens, and the 36th Annual Meeting of the Environmental Mutagen Society, San Francisco, CA, September 03 - 08, 2005.
Description:
DNA microarray analysis is plagued by a lack of data reproducibility and by limits to the detectability of transcripts by hybridization. To mitigate these limitations, we employed transcriptional coupling within the S. typhimurium genome. This genome has 2664 transcriptionally coupled genes in 878 operons that contain from 2 to 20 genes each. We applied an operon-coupled analysis to a comparison of S. typhimurium TA1 00 global gene expression between stationary-phase in minimal medium to logarithmic-�phase in nutrient broth. Differentially expressed genes were selected based on the posterior probability of differential expression (PPDE) (p > 0.95) calculated by Cyber-T. Any operon with a differentially expressed gene was considered differentially expressed, and all the genes in that operon were then considered differentially expressed. This increased the number of differentially expressed genes by 23%, from 2824 to 3476. These data were further subjected to pathway analysis. Of the 4567 genes on our Salmonella array, 1831 genes have been associated with a KEGG pathway. In our experiments 1170 PPDE selected genes were associated with KEGG pathways, and with our operon analysis this number was increased by 26% to 1476. The addition of these 306 genes may be important for interpreting global gene expression data. For example, of the 144 Salmonella KEGG pathways, operon analysis increased the number of significantly altered genes in 39 pathways by 25% or more. Transcriptional coupling also exists in eukaryotes, and an analysis incorporating such data could potentially improve the interpretation of global gene expression experiments in other model organisms.