Using high-density exon arrays to profile gene expression in closely related species

Lan Lin, Song Liu, Heather Brockway, Junhee Seok, Peng Jiang, Wing Hung Wong, Yi Xing

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article numbere90
JournalNucleic Acids Research
Volume37
Issue number12
DOIs
Publication statusPublished - 2009 Jul 30
Externally publishedYes

Fingerprint

Transcriptome
Gene expression
Exons
Genes
Pan troglodytes
Microarrays
Human Genome
Macaca mulatta
Primates
Real-Time Polymerase Chain Reaction
Animals
Genome
Tissue
Gene Expression

ASJC Scopus subject areas

  • Genetics

Cite this

Using high-density exon arrays to profile gene expression in closely related species. / Lin, Lan; Liu, Song; Brockway, Heather; Seok, Junhee; Jiang, Peng; Wong, Wing Hung; Xing, Yi.

In: Nucleic Acids Research, Vol. 37, No. 12, e90, 30.07.2009.

Research output: Contribution to journalArticle

Lin, Lan ; Liu, Song ; Brockway, Heather ; Seok, Junhee ; Jiang, Peng ; Wong, Wing Hung ; Xing, Yi. / Using high-density exon arrays to profile gene expression in closely related species. In: Nucleic Acids Research. 2009 ; Vol. 37, No. 12.
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