. Pooling samples within microarray studies: a comparative analysis of rat liver transcription response to prototypical toxicants. Physiol Genomics 22: 346 -355, 2005. First published May 24, 2005 10.1152/physiolgenomics.00260.2004.-Combining or pooling individual samples when carrying out transcript profiling using microarrays is a fairly common means to reduce both the cost and complexity of data analysis. However, pooling does not allow for statistical comparison of changes between samples and can result in a loss of information. Because a rigorous comparison of the identified expression changes from the two approaches has not been reported, we compared the results for hepatic transcript profiles from pooled vs. individual samples. Hepatic transcript profiles from a single-dose time-course rat study in response to the prototypical toxicants clofibrate, diethylhexylphthalate, and valproic acid were evaluated. Approximately 50% more transcript expression changes were observed in the individual (statistical) analysis compared with the pooled analysis. While the majority of these changes were less than twofold in magnitude (ϳ80%), a substantial number were greater than twofold (ϳ20%). Transcript changes unique to the individual analysis were confirmed by quantitative RT-PCR, while all the changes unique to the pooled analysis did not confirm. The individual analysis identified more hits per biological pathway than the pooled approach. Many of the transcripts identified by the individual analysis were novel findings and may contribute to a better understanding of molecular mechanisms of these compounds. Furthermore, having individual animal data provided the opportunity to correlate changes in transcript expression to phenotypes (i.e., histology) observed in toxicology studies. The two approaches were similar when clustering methods were used despite the large difference in the absolute number of transcripts changed. In summary, pooling reduced resource requirements substantially, but the individual approach enabled statistical analysis that identified more gene expression changes to evaluate mechanisms of toxicity. An individual animal approach becomes more valuable when the overall expression response is subtle and/or when associating expression data to variable phenotypic responses. Affymetrix microarray; statistical; hepatotoxicants MICROARRAY TECHNOLOGY has enabled the measurement of mRNA abundance on a genomic scale, providing deeper insight into cellular physiology. Microarrays have been applied to many types of biological inquiry such as studying responses to environmental changes (15), classification of tumors (37), classification of compound therapeutic mechanism (6), and prediction of cancer prognosis to name only a few. In toxicology, there has been substantial effort in applying microarray technology as a tool to identify biomarkers (35), develop surrogate toxicity assays (22), determine mechanism (42), and predict toxicity (18). There have been a number of reviews covering the application of microarr...