Coexpression of Neighboring Genes in the Genome of Arabidopsis thaliana
Abstract
Large-scale analyses of expression data of eukaryotic organisms are now becoming increasingly routine. The data sets are revealing interesting and novel patterns of genomic organization, which provide insight both into molecular evolution and how structure and function of a genome interrelate. Our study investigates, for the first time, how genome organization affects expression of a gene in the Arabidopsis genome. The analyses show that neighboring genes are coexpressed. This pattern has been found for all eukaryotic genomes studied so far, but as yet, it remains unclear whether it is due to selective or nonselective influences. We have investigated reasons for coexpression of neighboring genes in Arabidopsis, and our evidence suggests that orientation of gene pairs plays a significant role, with potential sharing of regulatory elements in divergently transcribed genes. Using the data available in the KEGG database, we find evidence that genes in the same pathway are coexpressed, although this is not a major cause for the coexpression of neighboring genes.
Footnotes
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[Supplemental material is available online at www.genome.org. All of the raw microarray data and metabolic pathway data will be made available as additional information. Also, all programs used to analyze data will be made available on request as well as any other data used in the analyses.]
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2131104.
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↵1 Corresponding author. E-MAIL wjs3{at}york.ac.uk; FAX 01904-328772.
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- Accepted February 18, 2004.
- Received October 31, 2003.
- Cold Spring Harbor Laboratory Press
