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First published online August 18, 2006; 10.1104/pp.106.080358 Plant Physiology 142:762-774 (2006) © 2006 American Society of Plant Biologists OPEN ACCESS ARTICLE
Transcriptional Coordination of the Metabolic Network in Arabidopsis1,[W],[OA]Department of Biostatistics (H.W., T.M., V.S., L.C., G.P.P., A.L.) and Department of Genetics (A.L.), University of Alabama, Birmingham, Alabama 35294; Department of Plant Biology, Carnegie Institution, Stanford, California 94305 (S.P., C.S.); and Department of Biological Sciences, Stanford University, Stanford, California 94305 (C.S.)
Patterns of coexpression can reveal networks of functionally related genes and provide deeper understanding of processes requiring multiple gene products. We performed an analysis of coexpression networks for 1,330 genes from the AraCyc database of metabolic pathways in Arabidopsis (Arabidopsis thaliana). We found that genes associated with the same metabolic pathway are, on average, more highly coexpressed than genes from different pathways. Positively coexpressed genes within the same pathway tend to cluster close together in the pathway structure, while negatively correlated genes typically occupy more distant positions. The distribution of coexpression links per gene is highly skewed, with a small but significant number of genes having numerous coexpression partners but most having fewer than 10. Genes with multiple connections (hubs) tend to be single-copy genes, while genes with multiple paralogs are coexpressed with fewer genes, on average, than single-copy genes, suggesting that the network expands through gene duplication, followed by weakening of coexpression links involving duplicate nodes. Using a network-analysis algorithm based on coexpression with multiple pathway members (pathway-level coexpression), we identified and prioritized novel candidate pathway members, regulators, and cross pathway transcriptional control points for over 140 metabolic pathways. To facilitate exploration and analysis of the results, we provide a Web site (http://www.transvar.org/at_coexpress/analysis/web) listing analyzed pathways with links to regression and pathway-level coexpression results. These methods and results will aid in the prioritization of candidates for genetic analysis of metabolism in plants and contribute to the improvement of functional annotation of the Arabidopsis genome.
1 This work was supported by the National Science Foundation (grant no. 0217651), the U.S. Department of Energy (grant no. DE–FG02–03ER20133), and a Swedish Research Council Fellowship (grant no. 623–2004–4254 to S.P.). 2 These authors contributed equally to the paper. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Ann Loraine (aloraine{at}uab.edu). [W] The online version of this article contains Web-only data. [OA] Open Access articles can be viewed online without a subscription. www.plantphysiol.org/cgi/doi/10.1104/pp.106.080358 * Corresponding author; e-mail aloraine{at}uab.edu; fax 205–975–2540. Received March 22, 2006; accepted August 2, 2006; published August 18, 2006. This article has been cited by other articles:
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