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First published online March 19, 2008; 10.1104/pp.108.117366 Plant Physiology 147:41-57 (2008) © 2008 American Society of Plant Biologists OPEN ACCESS ARTICLE
Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis1,[W],[OA]Department of Botany and Plant Sciences (K.H., C.J., J.B.-S., J.-K.Z., T.G.), and Department of Computer Science and Engineering (C.S.), University of California, Riverside, California 92521; Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557 (R.M., J.F.H., J.C.C.); Department of Plant Science, Hebrew University of Jerusalem, Givat Ram Jerusalem 91904, Israel (R.M.); and TimeLogic, Division of Active Motif, Incline Village, Nevada 89451 (M.G.)
About 40% of the proteins encoded in eukaryotic genomes are proteins of unknown function (PUFs). Their functional characterization remains one of the main challenges in modern biology. In this study we identified the PUF encoding genes from Arabidopsis (Arabidopsis thaliana) using a combination of sequence similarity, domain-based, and empirical approaches. Large-scale gene expression analyses of 1,310 publicly available Affymetrix chips were performed to associate the identified PUF genes with regulatory networks and biological processes of known function. To generate quality results, the study was restricted to expression sets with replicated samples. First, genome-wide clustering and gene function enrichment analysis of clusters allowed us to associate 1,541 PUF genes with tightly coexpressed genes for proteins of known function (PKFs). Over 70% of them could be assigned to more specific biological process annotations than the ones available in the current Gene Ontology release. The most highly overrepresented functional categories in the obtained clusters were ribosome assembly, photosynthesis, and cell wall pathways. Interestingly, the majority of the PUF genes appeared to be controlled by the same regulatory networks as most PKF genes, because clusters enriched in PUF genes were extremely rare. Second, large-scale analysis of differentially expressed genes was applied to identify a comprehensive set of abiotic stress-response genes. This analysis resulted in the identification of 269 PKF and 104 PUF genes that responded to a wide variety of abiotic stresses, whereas 608 PKF and 206 PUF genes responded predominantly to specific stress treatments. The provided coexpression and differentially expressed gene data represent an important resource for guiding future functional characterization experiments of PUF and PKF genes. Finally, the public Plant Gene Expression Database (http://bioweb.ucr.edu/PED) was developed as part of this project to provide efficient access and mining tools for the vast gene expression data of this study.
1 This work was supported by National Science Foundation grants 2010–0420033, 2010–0420152, and IGERT–0504249, and National Institutes of Health grant P20–RR–016464. 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: Thomas Girke (tgirke{at}citrus.ucr.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.108.117366 * Corresponding author; e-mail tgirke{at}citrus.ucr.edu. Received February 3, 2008; accepted March 10, 2008; published March 19, 2008. Related articles in Plant Physiol.:
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