Toxicogenomic analysis incorporating operon-transcriptional coupling and toxicant concentration-expression response: analysis of

Background: Deficiencies in microarray technology cause unwanted variation in the hybridization signal, obscuring the true measurements of intracellular transcript levels. Here we describe a general method that can improve microarray analysis of toxicant-exposed cells that uses the intrinsic power of transcriptional coupling and toxicant concentrationexpression response data. To illustrate this approach, we characterized changes in global gene expression induced in Salmonella typhimurium TA100 by 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX), the primary mutagen in chlorinated drinking water. We used the co-expression of genes within an operon and the monotonic increases or decreases in gene expression relative to increasing toxicant concentration to augment our identification of differentially expressed genes beyond Bayesian-t analysis. Results: Operon analysis increased the number of altered genes by 95% from the list identified by a Bayesian t-test of control to the hig...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: William O. Ward, Carol D. Swartz, Steffen Porwollik, Sarah H. Warren, Nancy M. Hanley, Geremy W. Knapp, Michael McClelland, David M. DeMarini
• Keywords: Analysis, BMCBI 2007, Expressed Genes, Gene Expression