Although several competing microarray platforms are available for tran-scriptional profiling of Arabidopsis thaliana, Affymetrix GeneChip® ATH1 microarrays are certainly among the most powerful. This is in part due to the widespread availability of Affymetrix systems in laboratories and service centers. Because ATH1 microarrays are commercially available and the technology is very robust, researchers do not need to spend time on technology development but can focus on their primary goal - research. Moreover, the use of standardized protocols and microarrays has enabled novel tools for meta-analysis of independent experiments from various groups. One such tool from our own lab, Genevestigator (14), has proven to be extremely popular in the field of plant science. Nonetheless, there are disadvantages of the ATH1 microarrays. First, all disadvantages common to any oligonucleotide array apply to ATH1 arrays. Second, the Arabidopsis genome contains more than 29 700 annotated genes, but only 22 000 genes are probed by the ATH1 array. Finally, many non-coding RNAs are generated from the Arabidopsis genomes (15). These RNAs often have important regulatory roles but are usually not probed by the ATH1 array. However, full-genome tiling arrays will likely become available soon (15) eliminating many of the major current limitations.

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