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
Insights into hypoxic systemic responses based on analyses of transcriptional regulation in Arabidopsis.
TL;DR: Analyzing global transcriptional changes in both shoots and roots found that systemic signals may be transduced from roots to trigger responses in tissues not directly subjected to hypoxia, suggesting regulation of ABA biosynthesis could be required for systemic responses.
Journal ArticleDOI
Impact of AtNHX1, a vacuolar Na + /H + antiporter, upon gene expression during short- and long-term salt stress in Arabidopsis thaliana
TL;DR: Other transcripts with known or putative roles showed the importance of AtNHX1 to key cellular processes that were not necessarily limited to the salt stress response; namely calcium signaling, sulfur metabolism, cell structure and cell growth, as well as vesicular trafficking and protein processing.
Journal ArticleDOI
Whole Genome Analysis of Gene Expression Reveals Coordinated Activation of Signaling and Metabolic Pathways during Pollen-Pistil Interactions in Arabidopsis
TL;DR: This study provides a unique and detailed temporal and spatial gene expression profile of in vivo pollen-pistil interactions, providing a framework to better understand the basis of the molecular mechanisms operating during the reproductive process in higher plants.
Journal ArticleDOI
AtPTR3, a wound-induced peptide transporter needed for defence against virulent bacterial pathogens in Arabidopsis
Saddad Karim,Saddad Karim,Kjell-Ove Holmström,Abul Mandal,Peter Dahl,Stefan Hohmann,Gunther Brader,E. Tapio Palva,Minna Pirhonen +8 more
TL;DR: The results suggest that AtPTR3 protects the plant against biotic and abiotic stresses by being reduced by virulent bacterium by type III dependent fashion.
Journal ArticleDOI
Two GRAS proteins, SCARECROW-LIKE21 and PHYTOCHROME A SIGNAL TRANSDUCTION1, function cooperatively in phytochrome A signal transduction.
TL;DR: In this paper, the biological functions of two GRAS proteins from Arabidopsis (Arabidopsis thaliana), SCARECROW-LIKE21 (SCL21) and PHYtoCHROME A SIGNAL TRANSDUCTION1 (PAT1), which are specifically involved in phytochrome A signal transduction, were described.
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