Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes

By T. Hrúz, Oliver Laule, Gábor Szabó, Frans Wessendorp, Stefan Bleuler, Lukas Oertle, P. Widmayer, Wilhelm Gruissem, Philip Zimmermann. Adv. Bioinformatics, 2008

1,968 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/269b9e182815a5d805cfa1f5c1137763b0b2b7cf

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Citations in the corpus

Genotype-by-Environment Interaction and Plasticity: Exploring Genomic Responses of Plants to the Abiotic Environment (2013, background): “Genome-wide assays of gene expression were rapidly adopted by molecular biologists focused on model or crop species, and public databases now host results from hundreds of studies and plant species identifying stress responsive genes [e.g., see Plexdb (Dash et al. 2012) or GeneInvestigator (Hruz et ”
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses (2012, neutral): “jsp Hruz et al. (2008)”
Magical mystery tour: Salicylic acid signalling (2015, methodology): “We examined the expression level of each “signalling module” gene by mining microarray data from the Genevestigator public database (Hruz et al., 2008).”
The role of gibberellin signalling in plant responses to abiotic stress (2014, methodology): “Data were extracted from Genevestigator v3 (Hruz et al., 2008), applying a foldchange cut-off of 1.”
RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization (2011, background): “The Genevestigator database contains a large set of systematically annotated and quality controlled microarray data from several organisms [29].”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “4D, E).”
The plant heat stress transcription factor (Hsf) family: structure, function and evolution. (2012, background): “9, [4, 166–168] or comprehensive analyses of metabolic changes [163, 169–171].”
The Apoplastic Oxidative Burst Peroxidase in Arabidopsis Is a Major Component of Pattern-Triggered Immunity[W][OA] (2012, background): “Moreover, Genevestigator analysis (Hruz et al., 2008) revealed that At5g01075 did not show any significant differential expression in response to treatment by several common biotic stresses or MAMPs (see Supplemental Figure 2 online).”
A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production (2009, methodology): “Cell Wall Development Genes To provide further support for selection of candidate NAC genes for cell wall modification study, we performed gene coexpression and induction pattern analysis with all the Arabidopsis NAC and secondary cell wall development marker genes using the GENEVESTIGATOR program [”
Glutathione (2011, positive): “(B) Expression of GSH1 and GSH2 in response to a range of environmental stresses (www.genevestigator.com; Hruz et al., 2008).”
Catalase function in plants: a focus on Arabidopsis mutants as stress-mimic models. (2010, methodology): “Data were obtained using Genevestigator V3 (https://www.genevestigator.ethz.ch; Hruz et al., 2008) and transcript abundance is represented on a scale from white (low) to deep blue (high).”
The Roles of Reactive Oxygen Metabolism in Drought: Not So Cut and Dried[1][C][W] (2014, methodology): “Of these genes, 302 were represented by probes on the most commonly used microarray chip (ATH1) and therefore Genevestigator data were available on their expression in response to drought and associated stresses (Supplemental Table S1B).”