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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E. Sousa, B. Kost, and R. Malho
Arabidopsis Phosphatidylinositol-4-Monophosphate 5-Kinase 4 Regulates Pollen Tube Growth and Polarity by Modulating Membrane Recycling
PLANT CELL, November 1, 2008; 20(11): 3050 - 3064.
[Abstract] [Full Text] [PDF]

C. Polge, M. Jossier, P. Crozet, L. Gissot, and M. Thomas
{beta}-Subunits of the SnRK1 Complexes Share a Common Ancestral Function Together with Expression and Function Specificities; Physical Interaction with Nitrate Reductase Specifically Occurs via AKIN{beta}1-Subunit
Plant Physiology, November 1, 2008; 148(3): 1570 - 1582.
[Abstract] [Full Text] [PDF]

R. Galletti, C. Denoux, S. Gambetta, J. Dewdney, F. M. Ausubel, G. De Lorenzo, and S. Ferrari
The AtrbohD-Mediated Oxidative Burst Elicited by Oligogalacturonides in Arabidopsis Is Dispensable for the Activation of Defense Responses Effective against Botrytis cinerea
Plant Physiology, November 1, 2008; 148(3): 1695 - 1706.
[Abstract] [Full Text] [PDF]

J. Li, B. G. Hansen, J. A. Ober, D. J. Kliebenstein, and B. A. Halkier
Subclade of Flavin-Monooxygenases Involved in Aliphatic Glucosinolate Biosynthesis
Plant Physiology, November 1, 2008; 148(3): 1721 - 1733.
[Abstract] [Full Text] [PDF]

T. Ogawa, K. Yoshimura, H. Miyake, K. Ishikawa, D. Ito, N. Tanabe, and S. Shigeoka
Molecular Characterization of Organelle-Type Nudix Hydrolases in Arabidopsis
Plant Physiology, November 1, 2008; 148(3): 1412 - 1424.
[Abstract] [Full Text] [PDF]

M. Tanaka, I. S. Wallace, J. Takano, D. M. Roberts, and T. Fujiwara
NIP6;1 Is a Boric Acid Channel for Preferential Transport of Boron to Growing Shoot Tissues in Arabidopsis
PLANT CELL, October 1, 2008; 20(10): 2860 - 2875.
[Abstract] [Full Text] [PDF]

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

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