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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.

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Journal ArticleDOI

Large-scale analysis of the GRAS gene family in Arabidopsis thaliana.

TL;DR: A large-scale analysis provides a comprehensive evaluation on the Arabidopsis GRAS members, and the phenome-ready unimutant collection will be a useful resource to better understand individual GRAS proteins that play diverse roles in plant growth and development.
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Abiotic stress and ABA-inducible Group 4 LEA from Brassica napus plays a key role in salt and drought tolerance

TL;DR: expression analysis revealed that abscisic acid, salt, cold and osmotic stresses induce expression of LEA4-1 gene in leaf tissues in Brassica species, and results demonstrate that LEA 4-1 plays a crucial role in abiotic stress tolerance during vegetative stage of plant development.
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PHOSPHATIDIC ACID PHOSPHOHYDROLASE1 and 2 Regulate Phospholipid Synthesis at the Endoplasmic Reticulum in Arabidopsis

TL;DR: The data suggest that PAH1/2 play a regulatory role in phospholipid synthesis that is analogous to that described in Saccharomyces cerevisiae, however, the target enzymes differ, and key components of the signal transduction pathway do not appear to be conserved.
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Type B Phosphatidylinositol-4-Phosphate 5-Kinases Mediate Arabidopsis and Nicotiana tabacum Pollen Tube Growth by Regulating Apical Pectin Secretion

TL;DR: The data indicate that excessive PtdIns(4,5)P2 production by type B PI4P 5-kinases disturbs the balance of membrane trafficking and apical pectin deposition.
References
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Journal ArticleDOI

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TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
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TL;DR: This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.
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Journal ArticleDOI

Hierarchical Organization of Modularity in Metabolic Networks

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