TY - JOUR
T1 - Using high-density exon arrays to profile gene expression in closely related species
AU - Lin, Lan
AU - Liu, Song
AU - Brockway, Heather
AU - Seok, Junhee
AU - Jiang, Peng
AU - Wong, Wing Hung
AU - Xing, Yi
N1 - Funding Information:
We wish to thank Jerilyn Pecotte, Mary Jo Aivaliotis, Garry Hauser, Elizabeth Zuo, Seiko Sato and Beverly Davidson for assistance. We thank David Eichmann, Ben Rogers and the University of Iowa Institute for Clinical and Translational Science (NIH grant UL1 RR024979) for computer support. This study used biological materials obtained from the Southwest National Primate Research Center, which is supported by NIH-NCRR grant P51 RR013986.
Funding Information:
National Institutes of Health grant U54-GM062119 (to W.H.W.) and R01-HG004634 (to W.H.W. and Y.X.). University of Iowa research startup fund (to Y.X.). Funding for open access charge: National Institutes of Health grant R01-HG004634.
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/gkp420
DO - 10.1093/nar/gkp420
M3 - Article
C2 - 19474342
AN - SCOPUS:67651171447
VL - 37
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 12
M1 - e90
ER -