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
The COMATOSE ATP-binding cassette transporter is required for full fertility in Arabidopsis.
Steven Footitt,Daniela Dietrich,Aaron Fait,Alisdair R. Fernie,Michael J. Holdsworth,Alison Baker,Frederica L. Theodoulou +6 more
TL;DR: The data support an important role for β-oxidation in fertility in Arabidopsis (Arabidopsis thaliana) and suggest that this pathway could play a role in the mobilization of lipids in both pollen and female tissues.
Journal ArticleDOI
Synergistic use of plant-prokaryote comparative genomics for functional annotations
Svetlana Y. Gerdes,Basma El Yacoubi,Marc Bailly,Ian K. Blaby,Crysten E. Blaby-Haas,Linda Jeanguenin,Aurora Lara-Núñez,Anne Pribat,Jeffrey C. Waller,Andreas Wilke,Ross Overbeek,Andrew D. Hanson,Valérie de Crécy-Lagard +12 more
TL;DR: This approach bridges the gap between automated homology-based annotations and the classical gene discovery efforts of experimentalists, and is more powerful than purely computational approaches to identifying gene-function associations.
Journal ArticleDOI
The Arabidopsis TRM1–TON1 Interaction Reveals a Recruitment Network Common to Plant Cortical Microtubule Arrays and Eukaryotic Centrosomes
Stéphanie Drevensek,Magali Goussot,Yann Duroc,Anna Christodoulidou,Sylvie Steyaert,Estelle Schaefer,Evelyne Duvernois,Olivier Grandjean,Marylin Vantard,David Bouchez,Martine Pastuglia +10 more
TL;DR: A novel superfamily of 34 proteins conserved in land plants, the TON1 Recruiting Motif (TRM) proteins, which share six short conserved motifs, including a Ton1-interacting motif present in all TRMs are identified, suggest conservation of eukaryotic centrosomal components in plant cells.
Journal ArticleDOI
The Arabidopsis tetratricopeptide repeat-containing protein TTL1 is required for osmotic stress responses and abscisic acid sensitivity.
Abel Rosado,Arnaldo L. Schapire,Ray A. Bressan,Antoine Harfouche,Paul M. Hasegawa,Victoriano Valpuesta,Miguel A. Botella +6 more
TL;DR: TTL1 is identified as a positive regulator of ABA signaling during germination and seedling development under stress and is associated with gibberellin responses and ethylene biosynthesis.
Journal ArticleDOI
Arabidopsis 10-Formyl Tetrahydrofolate Deformylases Are Essential for Photorespiration
Eva Collakova,Aymeric Goyer,Valeria Naponelli,Inga Krassovskaya,Jesse F. Gregory,Andrew D. Hanson,Yair Shachar-Hill +6 more
TL;DR: These findings are consistent with the involvement of At4g17360 and At5g47435 proteins in photorespiration, which is to prevent excessive accumulation of 5-formyl THF, a potent inhibitor of the Gly decarboxylase/Ser hydroxymethyltransferase complex.
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