Phylogenetic tree facilitates the understanding of gene expression data on drug metabolizing enzymes obtained by microarray analysis.

The gene expression data of drug metabolizing enzymes (DMEs) in male F344 rat livers were examined after treatments with phenobarbital (PB), clofibrate (CPIB), 3-methylcholanthrene (3-MC) or butylated hydroxyanisole (BHA) using an Affymetrix GeneChip system. Nucleotide sequence-based phylogenetic trees combined with a heat map, that presents both quantitative and qualitative data, were created. Most DME gene probes were successfully classified into the corresponding gene families, although a few were not due to the presence of non-coding or promoter region sequences in the target gene. There were also some data discrepancies among probes of the same gene family, indicating the inappropriate design of these probes. With this method, microarray probes with confusing nomenclature and quality differences can be identified. In addition, a good correlation between the gene expression data and protein data was confirmed, indicating the usefulness of this method for the comprehensive monitoring of DME activity in rat livers treated with xenobiotics.