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
Functional analysis of transcription factors in Arabidopsis.
TL;DR: This mini-review presents an overview of Arabidopsis TFs and introduces strategies for the functional analysis of plant TFs, which include both traditional and recently developed technologies.
Journal ArticleDOI
Methyl jasmonate stimulates the de novo biosynthesis of vitamin C in plant cell suspensions.
TL;DR: It is shown that methyl jasmonate treatment increases the de novo synthesis of ascorbic acid in Arabidopsis and tobacco Bright Yellow-2 (BY-2) suspension cells, the first report of a hormonal regulation of vitamin C biosynthesis in plants.
Journal ArticleDOI
The Ubiquitination Machinery of the Ubiquitin System
TL;DR: The protein ubiquitin is a covalent modifier of proteins, including itself, and within the ubiquitination machinery “half” of the Ubiquitin system are redundant, partially redundant, and unique components affecting diverse developmental and environmental responses in plants.
Journal ArticleDOI
ARABINAN DEFICIENT 1 Is a Putative Arabinosyltransferase Involved in Biosynthesis of Pectic Arabinan in Arabidopsis
Jesper Harholt,Jacob Krüger Jensen,Susanne Sørensen,Caroline Orfila,Markus Pauly,Henrik Vibe Scheller +5 more
TL;DR: Analysis of mutant lines with T-DNA insertion in the ARABINAN DEFICIENT 1 gene suggested that ARAD1 is an arabinan α-1,5-arabinosyltransferase, a putative glycosyl transferase of type 2 membrane protein with a signal anchor in Arabidopsis.
Journal ArticleDOI
The CCAAT binding factor can mediate interactions between CONSTANS‐like proteins and DNA
Orna Ben-Naim,Ravit Eshed,Anna Parnis,Paula Teper-Bamnolker,Akiva Shalit,George Coupland,Alon Samach,Eliezer Lifschitz +7 more
TL;DR: It is shown that the C-terminal plant-specific CCT domain of both COL proteins binds the trimeric CCAAT binding factor (CBF) via its HAP5/NF-YC component, which is likely to recruit COL proteins to their DNA target motifs in planta.
References
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Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
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.
Journal ArticleDOI
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
TL;DR: The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data and provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-power gene expression and genomic hybridization experiments.
Journal ArticleDOI
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
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.
PatentDOI
Expression monitoring by hybridization to high density oligonucleotide arrays
TL;DR: In this article, the authors proposed a method for monitoring the expression levels of a multiplicity of genes by hybridizing a nucleic acid sample to a high density array of oligonucleotide probes and quantifying the hybridized nucleic acids in the array.
Journal ArticleDOI
Hierarchical Organization of Modularity in Metabolic Networks
TL;DR: It is shown that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, with their number and degree of clustering following a power law.
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