Abstract
Analysis of large-scale gene expression data sets is proving to be a powerful tool for gene function prediction, cis-element discovery and hypothesis generation using Arabidopsis thaliana. Public initiatives led by the AtGenExpress Consortium and experiments conducted by individual researchers to document the transcriptome of Arabidopsis thaliana have led to a large numbers of data sets being made publicly available for data mining by so-called “electronic northerns”, co-expression analysis and other means. Given that approximately 50% genes in Arabidopsis have no function ascribed to them by “traditional” homology searches, and that only around 10% of the genes have had their function confirmed in the laboratory, these analyses can accelerate the identification of potential gene function with a mouse-click. This chapter covers the use of data mining tools available at the Bio-Array Resource (www.bar.utoronto.ca) for hypothesis generation in the context of plant hormone biology.
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References
Lee, H. K., Hsu, A. K., Sajdak, J., Qin, J., and Pavlidis, P. (2004). Coexpression analysis of human genes across many microarray data sets. Genome Res 14, 1085–94.
Wolfe, C., Kohane, I., and Butte, A. (2005). Systematic survey reveals general applicability of “guilt-by-association” within gene coexpression networks. BMC Bioinformatics 6, 227.
Zhang, W., Morris, Q., Chang, R., Shai, O., Bakowski, M., Mitsakakis, N., Mohammad, N., Robinson, M., Zirngibl, R., Somogyi, E., Laurin, N., Eftekharpour, E., Sat, E., Grigull, J., Pan, Q., Peng, W.-T., Krogan, N., Greenblatt, J., Fehlings, M., van der Kooy, D., Aubin, J., Bruneau, B., Rossant, J., Blencowe, B., Frey, B., and Hughes, T. (2004). The functional landscape of mouse gene expression. J Biol 3, 21.
Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M., Scholkopf, B., Weigel, D., and Lohmann, J. U. (2005). A gene expression map of Arabidopsis thaliana development.Nat Genet 37, 501–06.
Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D'Angelo, C., Bornberg-Bauer, E., Kudla, J., and Harter, K. (2007). The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses.Plant J 50, 347–63.
Edgar, R., Domrachev, M., and Lash, A. E. (2002). Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucl Acids Res 30, 207–10.
Rocca-Serra, P., Brazma, A., Parkinson, H., Sarkans, U., Shojatalab, M., Contrino, S., Vilo, J., Abeygunawardena, N., Mukherjee, G., Holloway, E., Kapushesky, M., Kemmeren, P., Lara, G. G., Oezcimen, A., and Sansone, S. A. (2003). ArrayExpress: a public database of gene expression data at EBI. Current Res Biol 326, 1075–78.
Garcia-Hernandez, M., Berardini, T. Z., Chen, G., Crist, D., Doyle, A., Huala, E., Knee, E., Lambrecht, M., Miller, N., Mueller, L. A., Mundodi, S., Reiser, L., Rhee, S. Y., Scholl, R., Tacklind, J., Weems, D. C., Wu, Y., Xu, I., Yoo, D., Yoon, J., and Zhang, P. (2002). TAIR: a resource for integrated Arabidopsis data. Funct Integr Genomics 2, 239–53.
Craigon, D. J., James, N., Okyrere, J., Higgins, J., Jotham, J., and May, S. (2004). NASCArrays: a repository for microarray data generated by NASC s transciptomics service. Nucl Acids Res 32, D575–D77.
Zimmermann, P., Hirsch-Hoffman, M., Hennig, L., and Gruissem, W. (2004). GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136, 2621–32.
Toufighi, K., Brady, M., Austin, R., Ly, E., and Provart, N. (2005). The botany array resource: e-Northerns, expression angling, and promoter analyses. Plant J 43, 153–63.
Obayashi, T., Kinoshita, K., Nakai, K., Shibaoka, M., Hayashi, S., Saeki, M., Shibata, D., Saito, K., and Ohta, H. (2007). ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucl Acids Res 35, D863–69.
Manfield, I. W., Jen, C.-H., Pinney, J. W., Michalopoulos, I., Bradford, J. R., Gilmartin, P. M., and Westhead, D. R. (2006). Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Nucl Acids Res 34, W504–09.
Steinhauser, D., Usadel, B., Luedemann, A., Thimm, O., and Kopka, J. (2004). CSB.DB: a comprehensive systems-biology database. Bioinformatics 20, 3647–51.
Aoki, K., Ogata, Y., and Shibata, D. (2007). Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48, 381–90.
Wille, A., Zimmermann, P., Vranova, E., Furholz, A., Laule, O., Bleuler, S., Hennig, L., Prelic, A., von Rohr, P., Thiele, L., Zitzler, E., Gruissem, W., and Buhlmann, P. (2004). Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana. Genome Biol 5, R92.
Ehlting, J., Provart, N. J., and Werck-Reichhart, D. (2006). Functional annotation of the Arabidopsis P450 superfamily based on large-scale co-expression analysis. Biochem Soc Trans 34, 1192–98.
Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G. V., and Provart, N. J. (2007). An ‘electronic fluorescent pictograph’ browser for exploring and analyzing large-scale biological data sets. PLoS One 2, e718.
Geisler-Lee, J., O'Toole, N., Ammar, R., Provart, N. J., Millar, A. H., and Geisler, M. (2007). A predicted interactome for Arabidopsis. Plant Physiol 145, 317–29.
Trewavas, A. (2006). A brief history of systems biology: “Every object that biology studies is a system of systems.” Plant Cell 18, 2420–30.
Gutierrez, R. A., Shasha, D. E., and Coruzzi, G. M. (2005). Systems biology for the virtual plant. Plant Physiol 138, 550–54.
O'Connor, T. R., Dyreson, C., and Wyrick, J. J. (2005). Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences. Bioinformatics 21, 4411–13.
Crooks, G. E., Hon, G., Chandonia, J.-M., and Brenner, S. E. (2004). WebLogo: a sequence logo generator. Genome Res 14, 1188–90.
Leonhardt, N., Kwak, J. M., Robert, N., Waner, D. L. G., and Schroeder, J. L. (2004). Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive ABA hypersensitive protein phosphatase 2C mutant. Plant Cell 16, 596–615.
Higo, K., Ugawa, Y., Iwamoto, M., and Higo, H. (1998). PLACE: a database of plant cis-acting regulatory DNA elements. Nucl Acids Res 26, 358–59.
McGinnis, K. M., Thomas, S. G., Soule, J. D., Strader, L. C., Zale, J. M., Sun, T.-p., and Steber, C. M. (2003). The Arabidopsis SLEEPY1 gene encodes a putative F-Box subunit of an SCF E3 ubiquitin ligase. Plant Cell 15, 1120–30.
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Bassel, G.W., Provart, N.J. (2009). Gene Expression Analyses for Elucidating Mechanisms of Hormonal Action in Plants. In: Cutler, S., Bonetta, D. (eds) Plant Hormones. Methods in Molecular Biology, vol 495. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59745-477-3_3
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DOI: https://doi.org/10.1007/978-1-59745-477-3_3
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