RNA Bioinformatics

Lately, cross-species microarray hybridization has become a popular approach for gene expression profiling in less-annotated genomes, in particular for comparative genomics analyses of gene expression. The idea is to use a microarray platform designed for one species (e.g. humans) on a second (closely related) species (such as chimpanzees), for which a standard microarray platform is not available.

There are a few nice reviews on this topic. Here is one from Gilad et.al; another one from Bar-Or et.al.

A major issue with cross-species microarray hybridization is the effect of sequence divergence on probe affinity. It is common that a probe that perfectly matches its target in one species doesn't match the same region in the second species. Moreover, due to difference in sequence divergence rates, such effects are not uniform across all genes. For the moment, it's hard to correct for such effects during the analysis of microarray data.

Beyond Genome 2007 will have a 2-day symposium on alternative splicing. Click here for details. The list of speakers is excellent. Unfortunately I'll be in China for IBW2007 during the same week and cannot go to listen to these talks...

ISMB will continue to hold a 2day SIG meeting on alternative splicing in 2007.

This is a simple study with interesting implications for evolutionary genomics and microarray analysis. Here is our paper and online supplemental material.

Assessing the Conservation of Mammalian Gene Expression Using High-density Exon Arrays. Xing Y*, Ouyang Z, Kapur K, Scott MP, Wong WH*. Molecular Biology and Evolution, 2007, In press.

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.