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
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TLDR
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.Abstract:
The Web-based software tool Genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. Its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. 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. In addition to improved querying features, Genevestigator V3 provides new tools to analyze the expression of genes in many different contexts, to identify biomarker genes, to cluster genes into expression modules, and to model expression responses in the context of metabolic and regulatory networks. Being a reference expression database with user-friendly tools, Genevestigator V3 facilitates discovery research and hypothesis validation.read more
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Sugar transporters for intercellular exchange and nutrition of pathogens
Li Qing Chen,Bi Huei Hou,Sylvie Lalonde,Hitomi Takanaga,Mara L. Hartung,Xiao Qing Qu,Woei Jiun Guo,Jung Gun Kim,William Underwood,Bhavna Chaudhuri,Diane Chermak,Ginny Antony,Frank F. White,Shauna Somerville,Mary Beth Mudgett,Wolf B. Frommer +15 more
TL;DR: Using optical glucose sensors, a new class of sugar transporters are identified, named SWEETs, and it is shown that at least six out of seventeen Arabidopsis, two out of over twenty rice and two of seven homologues in Caenorhabditis elegans, and the single copy human protein, mediate glucose transport.
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The plant heat stress transcription factor (Hsf) family: structure, function and evolution.
TL;DR: Data is compiled for 252 Hsfs from nine plant species (five eudicots and four monocots) with complete or almost complete genome sequences that provide interesting insights into phylogenetic relationships within the Hsf family in plants and allows the refinement of their classification into distinct groups.
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The role of gibberellin signalling in plant responses to abiotic stress
TL;DR: The evidence for the role of GA in these processes, and the regulation of the GA signalling pathway on exposure to abiotic stress are reviewed, are reviewed.
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Catalase function in plants: a focus on Arabidopsis mutants as stress-mimic models
Amna Mhamdi,Guillaume Queval,Sejir Chaouch,Sandy Vanderauwera,Frank Van Breusegem,Graham Noctor +5 more
TL;DR: This review provides an update on plant catalase genes, function, and subcellular localization, with a focus on recent information generated from studies on Arabidopsis.
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A Peptide Hormone and Its Receptor Protein Kinase Regulate Plant Cell Expansion
TL;DR: A signaling system important in the regulation of plant cell size during development is identified and a signaling chain that links a secreted peptide, RALF (rapid alkalinization factor), with its receptor kinase, FERONIA, at the cell surface is identified.
References
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Cluster analysis and display of genome-wide expression patterns
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Journal ArticleDOI
GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox
TL;DR: 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.
Journal ArticleDOI
ArrayExpress—a public repository for microarray gene expression data at the EBI
Helen Parkinson,Ugis Sarkans,Mohammadreza Shojatalab,Niran Abeygunawardena,Sergio Contrino,Richard M.R. Coulson,Anna Farne,Gonzalo Garcia Lara,Ele Holloway,Misha Kapushesky,P. Lilja,Gaurab Mukherjee,Ahmet Oezcimen,Tim F. Rayner,Philippe Rocca-Serra,Anjan Sharma,Susanna-Assunta Sansone,Alvis Brazma +17 more
TL;DR: ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Informa-tion About a Microarray Experiment) requirements and stores well-annotated raw and normalized data.
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NCBI GEO: mining millions of expression profiles—database and tools
Tanya Barrett,Tugba O. Suzek,Dennis B. Troup,Stephen E. Wilhite,Wing-Chi Ngau,Pierre Ledoux,Dmitry Rudnev,Alex E. Lash,Wataru Fujibuchi,Ron Edgar +9 more
TL;DR: Recent database developments that facilitate effective mining and visualization of gene expression data are described, providing features to examine data from both experiment- and gene-centric perspectives using user-friendly Web-based interfaces accessible to those without computational or microarray-related analytical expertise.
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