GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox
Reads0
Chats0
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
More filters
Journal ArticleDOI
Identification of a peroxisomal acyl-activating enzyme involved in the biosynthesis of jasmonic acid in Arabidopsis.
TL;DR: These findings establish a physiological role for OPCL1 in the activation of JA biosynthetic precursors in leaf peroxisomes, and indicate that OPC-8:0 is a physiological substrate for the activation step.
Journal ArticleDOI
The Arabidopsis Multistress Regulator TSPO Is a Heme Binding Membrane Protein and a Potential Scavenger of Porphyrins via an Autophagy-Dependent Degradation Mechanism
TL;DR: A role for TSPO in porphyrin binding and scavenging during stress in plants is supported, and downregulation of T SPO coincided with the return to steady state levels of unbound heme, suggesting that a physiological consequence of active TSPo downregulation may be heme scavenging.
Journal ArticleDOI
The Type B Phosphatidylinositol-4-Phosphate 5-Kinase 3 Is Essential for Root Hair Formation in Arabidopsis thaliana
Irene Stenzel,Till Ischebeck,Sabine König,Anna Holubowska,Marta Sporysz,Bettina Hause,Ingo Heilmann +6 more
TL;DR: Reestablishment of root hair formation in T-DNA mutants as a bioassay for physiological functionality of engineered PIP5K3 variants, catalytic activity was found to be essential for physiological function, indicating that PtdIns(4,5)P2 formation is required for root hair development.
Journal ArticleDOI
50 years of Arabidopsis research: highlights and future directions
Nicholas J. Provart,Jose M. Alonso,Sarah M. Assmann,Dominique C. Bergmann,Siobhan M. Brady,Jelena Brkljacic,John Browse,Clint Chapple,Vincent Colot,Sean R. Cutler,Jeff Dangl,David W. Ehrhardt,Joanna Friesner,Wolf B. Frommer,Erich Grotewold,Elliot M. Meyerowitz,Jennifer L. Nemhauser,Magnus Nordborg,Craig S. Pikaard,John Shanklin,Chris Somerville,Mark Stitt,Keiko U. Torii,Jamie Waese,Doris Wagner,Peter McCourt +25 more
TL;DR: A citational network analysis of papers that mention Arabidopsis thaliana in the title, abstract or keywords is presented, to touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species.
Journal ArticleDOI
Defining the Mitochondrial Stress Response in Arabidopsis thaliana
Olivier Van Aken,Botao Zhang,Chris Carrie,Vindya Uggalla,Ellen Paynter,Estelle Giraud,James Whelan +6 more
TL;DR: These genes provide new model systems to study mitochondrial retrograde regulation, in addition to the widely used alternative oxidase model, as changes in proteins responsive to stress did not correlate well with changes at a transcript level, it suggests that post-transcriptional mechanisms also play an important role in defining the MSR.
References
More filters
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.
Related Papers (5)
Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana
Steven J. Clough,Andrew F. Bent +1 more
Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana
Jose M. Alonso,Anna Stepanova,Thomas J. Leisse,Christopher J. Kim,Huaming Chen,Paul Shinn,Denise K. Stevenson,Justin Zimmerman,Pascual Barajas,Rosa Cheuk,Carmelita Gadrinab,Collen Heller,Albert Jeske,Eric Koesema,Cristina C. Meyers,Holly Parker,Lance Prednis,Yasser Ansari,Nathan Choy,Hashim Deen,Michael Geralt,Nisha Hazari,Emily Hom,Meagan Karnes,Celene Mulholland,Ral Ndubaku,Ian Thomas Schmidt,Plinio Guzmán,Laura Aguilar-Henonin,Markus Schmid,Detlef Weigel,David E. Carter,Trudy Marchand,Eddy Risseeuw,Debra Brogden,Albana Zeko,William L. Crosby,Charles C. Berry,Joseph R. Ecker +38 more
A revised medium for rapid growth and bio assays with tobacco tissue cultures
Toshio Murashige,Folke Skoog +1 more