Nucleic Acids Research Advance Access originally published online on May 27, 2009
Nucleic Acids Research 2009 37(12):e90; doi:10.1093/nar/gkp420
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Nucleic Acids Research, 2009, Vol. 37, No. 12 e90
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Methods Online |
Using high-density exon arrays to profile gene expression in closely related species
1Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, 2Department of Biostatistics, Roswell Park Cancer Institute, The State University of New York at Buffalo, Buffalo, NY 14203, 3Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA, 4Department of Electrical Engineering, 5Department of Statistics and Department of Health Research and Policy, Stanford University, Stanford, CA 94305 and 6Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242
*To whom correspondence should be addressed. Tel: +1 319 384 3099; Fax: +1 319 384 3150; Email: yi-xing{at}uiowa.edu
Received January 11, 2009. Revised May 5, 2009. Accepted May 7, 2009.
Global comparisons of gene expression profiles between species provide significant insight into gene regulation, evolutionary processes and disease mechanisms. In this work, we describe a flexible and intuitive approach for global expression profiling of closely related species, using high-density exon arrays designed for a single reference genome. The high-density probe coverage of exon arrays allows us to select identical sets of perfect-match probes to measure expression levels of orthologous genes. This eliminates a serious confounding factor in probe affinity effects of species-specific microarray probes, and enables direct comparisons of estimated expression indexes across species. Using a newly designed Affymetrix exon array, with eight probes per exon for approximately 315 000 exons in the human genome, we conducted expression profiling in corresponding tissues from humans, chimpanzees and rhesus macaques. Quantitative real-time PCR analysis of differentially expressed candidate genes is highly concordant with microarray data, yielding a validation rate of 21/22 for human versus chimpanzee differences, and 11/11 for human versus rhesus differences. This method has the potential to greatly facilitate biomedical and evolutionary studies of gene expression in nonhuman primates and can be easily extended to expression array design and comparative analysis of other animals and plants.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.