AffyTrees: facilitating comparative analysis of Affymetrix plant microarray chips.

Microarrays measure the expression of large numbers of genes simultaneously and can be used to delve into interaction networks involving many genes at a time. However, it is often difficult to decide to what extent knowledge about the expression of genes gleaned in one model organism can be transferred to other species. This can be examined either by measuring the expression of genes of interest under comparable experimental conditions in other species, or by gathering the necessary data from comparable microarray experiments. However, it is essential to know which genes to compare between the organisms. To facilitate comparison of expression data across different species, we have implemented a Web-based software tool that provides information about sequence orthologs across a range of Affymetrix microarray chips. AffyTrees provides a quick and easy way of assigning which probe sets on different Affymetrix chips measure the expression of orthologous genes. Even in cases where gene or genome duplications have complicated the assignment, groups of comparable probe sets can be identified. The phylogenetic trees provide a resource that can be used to improve sequence annotation and detect biases in the sequence complement of Affymetrix chips. Being able to identify sequence orthologs and recognize biases in the sequence complement of chips is necessary for reliable cross-species microarray comparison. As the amount of work required to generate a single phylogeny in a nonautomated manner is considerable, AffyTrees can greatly reduce the workload for scientists interested in large-scale cross-species comparisons.