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MBE Advance Access published online on March 25, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm061
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Letter

Assessing the Conservation of Mammalian Gene Expression Using High-density Exon Arrays

Yi Xing1,2,*, Zhengqing Ouyang3, Karen Kapur2, Matthew P. Scott4 and Wing Hung Wong2,*

1 Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
2 Department of Statistics, Stanford University, Stanford, California 94305, USA
3 Department of Biological Sciences, Stanford University, Stanford, California, 94305, USA
4 Departments of Developmental Biology, Genetics, and Bioengineering, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA

* To whom correspondence should be addressed. E-mail: yi-xing{at}uiowa.edu; whwong{at}stanford.edu.

Received for publication January 11, 2007. Revision received March 6, 2007. Accepted for publication March 19, 2007.

Microarray data from multiple species have been used to study evolutionary constraints on gene expression. Expression measurements from conventional microarray platforms such as the 3’ expression arrays are strongly affected by platform-dependent probe effects that may introduce apparent, but misleading discrepancies between species. In this manuscript, we assess the conservation of mammalian gene expression in adult tissues using data from a high-density exon array platform. The exon arrays have more than six million probes on a single array targeting all exons in a genome. We find that, unlike 3’ array data, gene expression measurements from exon arrays reveal patterns of gene expression that are highly conserved between humans and mice in multiple tissues. Our analysis provides strong evidence for widespread stabilizing selection pressure on transcript abundance during mammalian evolution.

Key Words: evolution • gene expression • selection pressure • microarray • exon array


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