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

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 the identical set of perfect-match probes for measuring 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. Keywords: analysis of gene expression in tissues We conducted Affymetrix Human Exon Junction array (HJAY array) profiling of RNAs from human, chimpanzee and rhesus macaque cerebellums, with three replicates per species.