GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox
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TLDR
Genevestigator as mentioned in this paper is a web-browser interface for gene expression analysis using Affymetrix GeneChip data, which allows users to retrieve the expression patterns of individual genes throughout chosen environmental conditions, growth stages, or organs.Abstract:
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.read more
Citations
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Journal ArticleDOI
Unique, Shared, and Redundant Roles for the Arabidopsis SWI/SNF Chromatin Remodeling ATPases BRAHMA and SPLAYED
Staver Bezhani,Cara M. Winter,Steve Hershman,John D. Wagner,John F. Kennedy,Chang Seob Kwon,Jennifer Pfluger,Yanhui Su,Doris Wagner +8 more
TL;DR: Using global expression studies, double mutant analysis, and protein interaction assays, overlapping functions are found for the two SWI/SNF ATPases, providing a conceptual framework for understanding the role of SWI-SNF chromatin remodeling in regulation of Arabidopsis development.
Journal ArticleDOI
Novel Plant-specific Cyclin-dependent Kinase Inhibitors Induced by Biotic and Abiotic Stresses
Adrian Peres,Michelle L. Churchman,Srivaidehirani Hariharan,Srivaidehirani Hariharan,Kristiina Himanen,Kristiina Himanen,Aurine Verkest,Aurine Verkest,Klaas Vandepoele,Klaas Vandepoele,Zoltán Magyar,Zoltán Magyar,Yves Hatzfeld,Els Van Der Schueren,Els Van Der Schueren,Gerrit T.S. Beemster,Gerrit T.S. Beemster,Valerie Frankard,John C. Larkin,Dirk Inzé,Dirk Inzé,Lieven De Veylder,Lieven De Veylder +22 more
TL;DR: Orysa;EL2 encodes a new type of plant CDK inhibitor that links cell cycle progression with biotic and abiotic stress responses and was able to rescue the multicellular trichome phenotype of sim mutants of Arabidopsis, unequivocally demonstrating that Orysa ;EL2 operates as a cell cycle inhibitor.
Journal ArticleDOI
Engineering drought and salinity tolerance in plants: lessons from genome-wide expression profiling in Arabidopsis.
Katherine J. Denby,Chris Gehring +1 more
TL;DR: Examples of how this full-genome expression profiling can contribute to the understanding of complex stress responses and the identification and evaluation of novel transgenes that could hold the key to the development of commercially viable and sustainable crop plants are outlined.
Journal ArticleDOI
Sulfite Reductase Defines a Newly Discovered Bottleneck for Assimilatory Sulfate Reduction and Is Essential for Growth and Development in Arabidopsis thaliana
Muhammad Sayyar Khan,Florian H. Haas,Arman Allboje Samami,Amin Moghaddas Gholami,Andrea S. Bauer,Kurt Fellenberg,Michael Reichelt,Robert Hänsch,Ralf R. Mendel,Andreas J. Meyer,Markus Wirtz,Ruediger Hell +11 more
TL;DR: The results support thatSiR is the only gene with this function in the Arabidopsis genome, that optimal activity of SiR is essential for normal growth, and that its downregulation causes severe adaptive reactions of primary and secondary metabolism.
Journal ArticleDOI
Blue-light-mediated shade avoidance requires combined auxin and brassinosteroid action in Arabidopsis seedlings
Diederik H. Keuskamp,Rashmi Sasidharan,Irene A. Vos,Anton J. M. Peeters,Laurentius A. C. J. Voesenek,Ronald Pierik +5 more
TL;DR: In this paper, both auxin and brassinosteroids (BR) play an important role in the regulation of enhanced hypocotyl elongation of Arabidopsis seedlings in response to blue light depletion.
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