GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox

doi:10.1104/pp.104.046367

GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox¹^,[w]

Philip Zimmermann², Matthias Hirsch-Hoffmann², Lars Hennig and Wilhelm Gruissem^*

Institute of Plant Sciences, Swiss Federal Institute of Technology and Zurich-Basel Plant Science Center, ETH Center, CH–8092 Zurich, Switzerland (P.Z., M.H.-H., L.H., W.G.); and Functional and Genomics Center Zurich, UNI Irchel, Y32 H52, CH–8057 Zurich, Switzerland (W.G.)

High-throughput gene expression analysis has become a frequentand powerful research tool in biology. At present, however,few software applications have been developed for biologiststo query large microarray gene expression databases using aWeb-browser interface. We present GENEVESTIGATOR, a databaseand Web-browser data mining interface for Affymetrix GeneChipdata. Users can query the database to retrieve the expressionpatterns of individual genes throughout chosen environmentalconditions, growth stages, or organs. Reversely, mining toolsallow users to identify genes specifically expressed duringselected stresses, growth stages, or in particular organs. UsingGENEVESTIGATOR, the gene expression profiles of more than 22,000Arabidopsis genes can be obtained, including those of 10,600currently uncharacterized genes. The objective of this softwareapplication is to direct gene functional discovery and designof new experiments by providing plant biologists with contextualinformation on the expression of genes. The database and analysistoolbox is available as a community resource at https://www.genevestigator.ethz.ch.

¹ This work was supported by ETH, Strategic Excellence Project2–74213–02/TH–8/02–2, and by the FunctionalGenomics Center Zurich.

² These authors contributed equally to the paper.

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

www.plantphysiol.org/cgi/doi/10.1104/pp.104.046367.

^{^*} Corresponding author; e-mail wilhelm.gruissem{at}ipw.biol.ethz.ch; fax 41–1–632–10–79.

Received May 14, 2004; returned for revision July 12, 2004; accepted July 16, 2004.

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J. Cell Sci., July 15, 2008; 121(14): 2372 - 2381.
[Abstract] [Full Text] [PDF]

M. Libault, S. Thibivilliers, D. D. Bilgin, O. Radwan, M. Benitez, S. J. Clough, and G. Stacey
Identification of Four Soybean Reference Genes for Gene Expression Normalization
The Plant Genome, July 1, 2008; 1(1): 44 - 54.
[Abstract] [Full Text] [PDF]

M. R. Malik, F. Wang, J. M. Dirpaul, N. Zhou, J. Hammerlindl, W. Keller, S. R. Abrams, A. M. R. Ferrie, and J. E. Krochko
Isolation of an embryogenic line from non-embryogenic Brassica napus cv. Westar through microspore embryogenesis
J. Exp. Bot., July 1, 2008; 59(10): 2857 - 2873.
[Abstract] [Full Text] [PDF]

M. Mutwil, J. Obro, W. G. T. Willats, and S. Persson
GeneCAT--novel webtools that combine BLAST and co-expression analyses
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W320 - W326.
[Abstract] [Full Text] [PDF]

T. Uehara, Y. Okushima, T. Mimura, M. Tasaka, and H. Fukaki
Domain II Mutations in CRANE/IAA18 Suppress Lateral Root Formation and Affect Shoot Development in Arabidopsis thaliana
Plant Cell Physiol., July 1, 2008; 49(7): 1025 - 1038.
[Abstract] [Full Text] [PDF]

M. Chen, J. E. Markham, C. R. Dietrich, J. G. Jaworski, and E. B. Cahoon
Sphingolipid Long-Chain Base Hydroxylation Is Important for Growth and Regulation of Sphingolipid Content and Composition in Arabidopsis
PLANT CELL, July 1, 2008; 20(7): 1862 - 1878.
[Abstract] [Full Text] [PDF]

E. Collakova, A. Goyer, V. Naponelli, I. Krassovskaya, J. F. Gregory III, A. D. Hanson, and Y. Shachar-Hill
Arabidopsis 10-Formyl Tetrahydrofolate Deformylases Are Essential for Photorespiration
PLANT CELL, July 1, 2008; 20(7): 1818 - 1832.
[Abstract] [Full Text] [PDF]

V. Srinivasasainagendra, G. P. Page, T. Mehta, I. Coulibaly, and A. E. Loraine
CressExpress: A Tool For Large-Scale Mining of Expression Data from Arabidopsis
Plant Physiology, July 1, 2008; 147(3): 1004 - 1016.
[Abstract] [Full Text] [PDF]

D. K. Owens, A. B. Alerding, K. C. Crosby, A. B. Bandara, J. H. Westwood, and B. S.J. Winkel
Functional Analysis of a Predicted Flavonol Synthase Gene Family in Arabidopsis
Plant Physiology, July 1, 2008; 147(3): 1046 - 1061.
[Abstract] [Full Text] [PDF]

GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox1,[w]

GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox¹^,[w]