Plant Physiology 136:2621-2632 (2004)
© 2004 American Society of Plant Biologists
BIOINFORMATICS
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, CH8092 Zurich, Switzerland (P.Z., M.H.-H., L.H., W.G.); and Functional and Genomics Center Zurich, UNI Irchel, Y32 H52, CH8057 Zurich, Switzerland (W.G.)
High-throughput gene expression analysis has become a frequent and powerful research tool in biology. At present, however, few software applications have been developed for biologists to query large microarray gene expression databases using a Web-browser interface. We present GENEVESTIGATOR, a database and Web-browser data mining interface for Affymetrix GeneChip data. Users can query the database to retrieve the expression patterns of individual genes throughout chosen environmental conditions, growth stages, or organs. Reversely, mining tools allow users to identify genes specifically expressed during selected stresses, growth stages, or in particular organs. Using GENEVESTIGATOR, the gene expression profiles of more than 22,000 Arabidopsis genes can be obtained, including those of 10,600 currently uncharacterized genes. The objective of this software application is to direct gene functional discovery and design of new experiments by providing plant biologists with contextual information on the expression of genes. The database and analysis toolbox is available as a community resource at https://www.genevestigator.ethz.ch.
1 This work was supported by ETH, Strategic Excellence Project 27421302/TH8/022, and by the Functional Genomics 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 4116321079.
Received May 14, 2004;
returned for revision July 12, 2004;
accepted July 16, 2004.
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2860 - 2875.
[Abstract]
[Full Text]
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N. Y. Komarova, K. Thor, A. Gubler, S. Meier, D. Dietrich, A. Weichert, M. Suter Grotemeyer, M. Tegeder, and D. Rentsch
AtPTR1 and AtPTR5 Transport Dipeptides in Planta
Plant Physiology,
October 1, 2008;
148(2):
856 - 869.
[Abstract]
[Full Text]
[PDF]
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F. Borges, G. Gomes, R. Gardner, N. Moreno, S. McCormick, J. A. Feijo, and J. D. Becker
Comparative Transcriptomics of Arabidopsis Sperm Cells
Plant Physiology,
October 1, 2008;
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[Abstract]
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[PDF]
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L.-R. Zeng, C. H. Park, R.C. Venu, J. Gough, and G.-L. Wang
Classification, Expression Pattern, and E3 Ligase Activity Assay of Rice U-Box-Containing Proteins
Mol Plant,
September 1, 2008;
1(5):
800 - 815.
[Abstract]
[Full Text]
[PDF]
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P. Zimmermann, O. Laule, J. Schmitz, T. Hruz, S. Bleuler, and W. Gruissem
Genevestigator Transcriptome Meta-Analysis and Biomarker Search Using Rice and Barley Gene Expression Databases
Mol Plant,
September 1, 2008;
1(5):
851 - 857.
[Abstract]
[Full Text]
[PDF]
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M. Battaglia, Y. Olvera-Carrillo, A. Garciarrubio, F. Campos, and A. A. Covarrubias
The Enigmatic LEA Proteins and Other Hydrophilins
Plant Physiology,
September 1, 2008;
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B. S. Zheng, E. Ronnberg, L. Viitanen, T. A. Salminen, K. Lundgren, T. Moritz, and J. Edqvist
Arabidopsis sterol carrier protein-2 is required for normal development of seeds and seedlings
J. Exp. Bot.,
September 1, 2008;
59(12):
3485 - 3499.
[Abstract]
[Full Text]
[PDF]
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B. K. Zolman, N. Martinez, A. Millius, A. R. Adham, and B. Bartel
Identification and Characterization of Arabidopsis Indole-3-Butyric Acid Response Mutants Defective in Novel Peroxisomal Enzymes
Genetics,
September 1, 2008;
180(1):
237 - 251.
[Abstract]
[Full Text]
[PDF]
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S. Luhua, S. Ciftci-Yilmaz, J. Harper, J. Cushman, and R. Mittler
Enhanced Tolerance to Oxidative Stress in Transgenic Arabidopsis Plants Expressing Proteins of Unknown Function
Plant Physiology,
September 1, 2008;
148(1):
280 - 292.
[Abstract]
[Full Text]
[PDF]
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R. Patel, S.-C. Hsu, J. Bedard, K. Inoue, and P. Jarvis
The Omp85-Related Chloroplast Outer Envelope Protein OEP80 Is Essential for Viability in Arabidopsis
Plant Physiology,
September 1, 2008;
148(1):
235 - 245.
[Abstract]
[Full Text]
[PDF]
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K. Bracha-Drori, K. Shichrur, T. C. Lubetzky, and S. Yalovsky
Functional Analysis of Arabidopsis Postprenylation CaaX Processing Enzymes and Their Function in Subcellular Protein Targeting
Plant Physiology,
September 1, 2008;
148(1):
119 - 131.
[Abstract]
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[PDF]
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S. Park, D. M. Rancour, and S. Y. Bednarek
In Planta Analysis of the Cell Cycle-Dependent Localization of AtCDC48A and Its Critical Roles in Cell Division, Expansion, and Differentiation
Plant Physiology,
September 1, 2008;
148(1):
246 - 258.
[Abstract]
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[PDF]
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J. Azimzadeh, P. Nacry, A. Christodoulidou, S. Drevensek, C. Camilleri, N. Amiour, F. Parcy, M. Pastuglia, and D. Bouchez
Arabidopsis TONNEAU1 Proteins Are Essential for Preprophase Band Formation and Interact with Centrin
PLANT CELL,
August 1, 2008;
20(8):
2146 - 2159.
[Abstract]
[Full Text]
[PDF]
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Z. Xie, X. Li, B. J. Glover, S. Bai, G.-Y. Rao, J. Luo, and J. Yang
Duplication and Functional Diversification of HAP3 Genes Leading to the Origin of the Seed-Developmental Regulatory Gene, LEAFY COTYLEDON1 (LEC1), in Nonseed Plant Genomes
Mol. Biol. Evol.,
August 1, 2008;
25(8):
1581 - 1592.
[Abstract]
[Full Text]
[PDF]
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C. A. Konopka and S. Y. Bednarek
Comparison of the Dynamics and Functional Redundancy of the Arabidopsis Dynamin-Related Isoforms DRP1A and DRP1C during Plant Development
Plant Physiology,
August 1, 2008;
147(4):
1590 - 1602.
[Abstract]
[Full Text]
[PDF]
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Y. Lee, E.-S. Kim, Y. Choi, I. Hwang, C. J. Staiger, Y.-Y. Chung, and Y. Lee
The Arabidopsis Phosphatidylinositol 3-Kinase Is Important for Pollen Development
Plant Physiology,
August 1, 2008;
147(4):
1886 - 1897.
[Abstract]
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[PDF]
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C.-M. Yoo, J. Wen, C. M. Motes, J. A. Sparks, and E. B. Blancaflor
A Class I ADP-Ribosylation Factor GTPase-Activating Protein Is Critical for Maintaining Directional Root Hair Growth in Arabidopsis
Plant Physiology,
August 1, 2008;
147(4):
1659 - 1674.
[Abstract]
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C. Bottcher, E. von Roepenack-Lahaye, J. Schmidt, C. Schmotz, S. Neumann, D. Scheel, and S. Clemens
Metabolome Analysis of Biosynthetic Mutants Reveals a Diversity of Metabolic Changes and Allows Identification of a Large Number of New Compounds in Arabidopsis
Plant Physiology,
August 1, 2008;
147(4):
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[Abstract]
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J. Jeong, C. Cohu, L. Kerkeb, M. Pilon, E. L. Connolly, and M. L. Guerinot
Chloroplast Fe(III) chelate reductase activity is essential for seedling viability under iron limiting conditions
PNAS,
July 29, 2008;
105(30):
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[Abstract]
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[PDF]
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A. Krishnan and A. Pereira
Integrative approaches for mining transcriptional regulatory programs in Arabidopsis
Brief Funct Genomic Proteomic,
July 16, 2008;
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[Abstract]
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[PDF]
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M. Yao, Y. Wakamatsu, T. J. Itoh, T. Shoji, and T. Hashimoto
Arabidopsis SPIRAL2 promotes uninterrupted microtubule growth by suppressing the pause state of microtubule dynamics
J. Cell Sci.,
July 15, 2008;
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[Abstract]
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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]
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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;
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[Abstract]
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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):
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[Abstract]
[Full Text]
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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]
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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]
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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]
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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]
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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]
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[PDF]
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