Modern biological research is increasingly dependent on information technology. The Human Genome Project, together with increased computer availability, has catalyzed the development of a range of tools designed to deduce and catalog genetic information. Evolutionary versions of these tools are being incorporated into academic and commercial laboratories around the globe in order to better mine and extend biological genomic data. The purpose of this study was to evaluate the information, workflow, and rules related to the use of a commercial gene expression analysis system in toxicogenomics and proteomics research.