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
An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets
TL;DR: The eFP Browser software is easily adaptable to microarray or other large-scale data sets from any organism and thus should prove useful to a wide community for visualizing and interpreting these data sets for hypothesis generation.
Journal ArticleDOI
Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes.
Tomas Hruz,Oliver Laule,Gabor Szabo,Frans Wessendorp,Stefan Bleuler,Lukas Oertle,Peter Widmayer,Wilhelm Gruissem,Philip Zimmermann +8 more
TL;DR: Genevestigator V3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis.
Journal ArticleDOI
Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation.
Cyril Zipfel,Gernot Kunze,Delphine Chinchilla,Anne Caniard,Jonathan D. G. Jones,Thomas Boller,Georg Felix +6 more
TL;DR: It is shown that flagellin and EF-Tu activate a common set of signaling events and defense responses but without clear synergistic effects, and that plant defense responses induced by PAMPs such as EF- Tu reduce transformation by Agrobacterium.
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Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks
Miki Fujita,Yasunari Fujita,Yoshiteru Noutoshi,Fuminori Takahashi,Yoshihiro Narusaka,Kazuko Yamaguchi-Shinozaki,Kazuo Shinozaki +6 more
TL;DR: Emerging evidence suggests that hormone signaling pathways regulated by abscisic acid, salicylic acid, jasmonic acid and ethylene, as well as ROS signaling pathways, play key roles in the crosstalk between biotic and abiotic stress signaling.
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Toxic metal accumulation, responses to exposure and mechanisms of tolerance in plants
TL;DR: This review discusses the molecular mechanisms of toxic metal accumulation in plants and algae, the responses to metal exposure, as well as the understanding of metal tolerance and its evolution.
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