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Published on December 7, 2007; 10.1104/pp.107.109603

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Received September 23, 2007
Accepted December 3, 2007

AffyTrees: facilitating comparative analysis of Affymetrix plant microarray chips

Tancred Frickey , Vagner Augusto Benedito , Michael Udvardi , and Georg Weiller *

ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601 Australia; The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401

* Corresponding author; email: georg.weiller{at}anu.edu.au.

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 non-automated manner is considerable, AffyTrees can greatly reduce the workload for scientists interested in large-scale cross-species comparisons.






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