HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Supplemental Material All Versions of this Article: 22/3/346    most recent 00260.2004v1 Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in ISI Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via ISI Web of Science (18) Citing Articles via Google Scholar Google Scholar Articles by Jolly, R. A. Articles by Estrem, S. T. Search for Related Content PubMed PubMed Citation Articles by Jolly, R. A. Articles by Estrem, S. T.

Pooling samples within microarray studies: a comparative analysis of rat liver transcription response to prototypical toxicants

¹ Lilly Research Laboratories, Greenfield, Indiana
² Lilly Research Laboratories, Indianapolis, Indiana
³ Lilly Research Laboratories, Mont-Saint-Guibert, Belgium, A Division of Eli Lilly and Company

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 (80%), a substantial number were greater than twofold (20%). 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

This article has been cited by other articles:

				J. N. McGuire, J. Overgaard, and F. Pociot Mass spectrometry is only one piece of the puzzle in clinical proteomics Brief Funct Genomic Proteomic, February 28, 2008; (2008) eln005v1. [Abstract] [Full Text] [PDF]

				Y. Guo, R. A. Jolly, B. W. Halstead, T. K. Baker, J. P. Stutz, M. Huffman, J. N. Calley, A. West, H. Gao, G. H. Searfoss, et al. Underlying Mechanisms of Pharmacology and Toxicity of a Novel PPAR Agonist Revealed Using Rodent and Canine Hepatocytes Toxicol. Sci., April 1, 2007; 96(2): 294 - 309. [Abstract] [Full Text] [PDF]

				H. Wintz, L. J. Yoo, A. Loguinov, Y.-Y. Wu, J. A. Steevens, R. D. Holland, R. D. Beger, E. J. Perkins, O. Hughes, and C. D. Vulpe Gene Expression Profiles in Fathead Minnow Exposed to 2,4-DNT: Correlation with Toxicity in Mammals Toxicol. Sci., November 1, 2006; 94(1): 71 - 82. [Abstract] [Full Text] [PDF]

				E. van Lunteren, M. Moyer, and P. Leahy Gene expression profiling of diaphragm muscle in {alpha}2-laminin (merosin)-deficient dy/dy dystrophic mice Physiol Genomics, March 13, 2006; 25(1): 85 - 95. [Abstract] [Full Text] [PDF]

				S.-D. Zhang and T. W. Gant Effect of pooling samples on the efficiency of comparative studies using microarrays Bioinformatics, December 15, 2005; 21(24): 4378 - 4383. [Abstract] [Full Text] [PDF]

				M. Liang and B. Ventura Physiological genomics in PG and beyond: July to September 2005 Physiol Genomics, October 17, 2005; 23(2): 119 - 124. [Full Text] [PDF]