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GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Local Coexpression Domains of Two to Four Genes in the Genome of Arabidopsis^1,[w]

Applied Bioinformatics, Plant Research International, NL–6700 AA Wageningen, The Netherlands (X.-Y.R., M.W.E.J.F., J.-P.N.); Laboratory of Molecular Biology, Plant Sciences Group, Wageningen University and Research Centre, NL–6703 HA Wageningen, The Netherlands (X.-Y.R., W.J.S.); and Centre for BioSystems Genomics, NL–6708 PB, Wageningen, The Netherlands (W.J.S., J.-P.N.)

Expression of genes in eukaryotic genomes is known to cluster, but cluster size is generally loosely defined and highly variable. We have here taken a very strict definition of cluster as sets of physically adjacent genes that are highly coexpressed and form so-called local coexpression domains. The Arabidopsis (Arabidopsis thaliana) genome was analyzed for the presence of such local coexpression domains to elucidate its functional characteristics. We used expression data sets that cover different experimental conditions, organs, tissues, and cells from the Massively Parallel Signature Sequencing repository and microarray data (Affymetrix) from a detailed root analysis. With these expression data, we identified 689 and 1,481 local coexpression domains, respectively, consisting of two to four genes with a pairwise Pearson's correlation coefficient larger than 0.7. This number is approximately 1- to 5-fold higher than the numbers expected by chance. A small (5%–10%) yet significant fraction of genes in the Arabidopsis genome is therefore organized into local coexpression domains. These local coexpression domains were distributed over the genome. Genes in such local domains were for the major part not categorized in the same functional category (GOslim). Neither tandemly duplicated genes nor shared promoter sequence nor gene distance explained the occurrence of coexpression of genes in such chromosomal domains. This indicates that other parameters in genes or gene positions are important to establish coexpression in local domains of Arabidopsis chromosomes.

^[w] The online version of this article contains Web-only data.

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.104.055673.

^* Corresponding author; e-mail janpeter.nap{at}wur.nl; fax 31–317–418094.

Received October 26, 2004; returned for revision February 27, 2005; accepted February 28, 2005.

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