Genevestigator

Genevestigator

Genevestigator is a web-based application developed for biologists to rapidly find out in which tissues, at which stages of development, and to what stimuli, drug treatments, diseases, or genetic modifications genes of given organisms are activated. Results are processed from a large database of manually curated and quality-controlled Affymetrix microarrays hybridized with RNA samples extracted from a large variety of tissues and conditions. Currently, data is available for human,, mouse, rat, arabidopsis, and barley.

Genevestigator was started in January 2004 by scientists from ETH Zurich. The analysis tool can be accessed at the [http://www.genevestigator.ethz.ch Genevestigator] website.

Keywords

*microarray databases
*meta-analysis
*Affymetrix
*bioinformatics
*systems biology

Tool for biologists

Genevestigator is currently serving a community of 10'000 registered users (mostly biologists) from the animal and plant research fields. Its tools have been used in
*molecular biology
*toxicogenomics
*biomarker discovery
*biotechnology
*pathway analysis

As of September 2007, its original articles have been cited more than 400 times (ISI Thomson) by researchers using the tools.

Four tool sets, each containing several tools, are available:
*Meta-Profile Analysis
*Biomarker Search
*Clustering Analysis
*Pathway Projector

Underlying most of the tools is the concept of "meta-profiles". Meta-profiles are representative vectors of expression for a given type of condition. For example, for a gene of interest, its anatomy meta-profile is the vector of expression values across all anatomy categories that are available in the database for this gene and organism. In simple terms, it shows how strongly a gene is expressed in different anatomy parts.

The concept of meta-profiles has been used in Genevestigator to characterize expression across anatomy, development, stimuli (drug treatments, diseases, stimuli) and mutations.

References

*Grennan AK (2006) Genevestigator. Facilitating web-based gene-expression analysis. Plant Physiology 141(4):1164-6
*Laule O, Hirsch-Hoffmann M, Hruz T, Gruissem W, and P Zimmermann (2006) Web-based analysis of the mouse transcriptome using Genevestigator. BMC Bioinformatics 7:311
*Zimmermann P, Hennig L and W Gruissem (2005) Gene expression analysis and network discovery using Genevestigator. Trends in Plant Science 9 10 , 407-409
*Zimmermann P, Hirsch-Hoffmann M, Hennig L and W Gruissem (2004) GENEVESTIGATOR: Arabidopsis Microarray Database and Analysis Toolbox. Plant Physiology 136 1 , 2621-2632
*Zimmermann P, Schildknecht B, Garcia-Hernandez M, Gruissem W, Craigon D, Mukherjee G, May S, Parkinson H, Rhee S, Wagner U and L Hennig (2006) MIAME/Plant - adding value to plant microarray experiments. Plant Methods 2 , 1

External links

* [http://www.genevestigator.ethz.ch Genevestigator website] .


Wikimedia Foundation. 2010.

Игры ⚽ Поможем решить контрольную работу

Look at other dictionaries:

  • Genevestigator — est une base de données de résultats d analyses de transcriptomes couplée à un outil de méta analyse accessible on line[1]. La base de données contenait début 2009 les données de 20872 expériences de transcriptomes pour 6 organismes modèles… …   Wikipédia en Français

  • Transcriptome — The transcriptome is the set of all messenger RNA (mRNA) molecules,ref|IUPAC glossary or transcripts, produced in one or a population of cells. The term can be applied to the total set of transcripts in a given organism, or to the specific subset …   Wikipedia

  • TranscriptomeBrowser — est un logiciel pour la fouille de données (data mining) de biopuces (cf; Genevestigator)[1]. Il s appuie sur une base de données contenant plusieurs dizaines de milliers de signatures transcriptionnelles ( 20000) elles mêmes issues de l analyse… …   Wikipédia en Français

  • Affymetrix — Infobox Company name = Affymetrix company type = Public foundation = 1992 location city = location country = location = Santa Clara, California High Wycombe, UK Tokyo, Japan Shanghai, China locations = 13 key people = Stephen Fodor area served =… …   Wikipedia

  • Toxicogenomics — is a field of science that deals with the collection, interpretation, and storage of information about gene and protein activity within particular cell or tissue of an organism in response to toxic substances. Toxicogenomics meshes toxicology… …   Wikipedia

  • Spatiotemporal gene expression — is the activation of genes within specific tissues of an organism at specific times during development. Gene activation patterns vary widely in complexity. Some are straightforward and static, such as the pattern of tubulin, which is expressed in …   Wikipedia

  • Microarray analysis techniques — Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail. Microarray analysis techniques are used in interpreting the data generated from experiments on DNA, RNA, and protein microarrays, which allow… …   Wikipedia

  • Microarray databases — The term microarray database is usually used to describe a repository containing microarray gene expression data. The key features of a microarray database are to store the measurement data, manage a searchable index, and make the data available… …   Wikipedia

  • Transcriptome — Le transcriptome est l ensemble des ARN messager (molécules servant de matrice pour la synthèse des protéines) issu de l expression d une partie du génome d un tissu cellulaire ou d un type de cellule. La caractérisation et la quantification du… …   Wikipédia en Français

  • Bioinformática — Saltar a navegación, búsqueda La bioinformática, según una de sus definiciones más sencillas, es la aplicación de tecnología de computadores a la gestión y análisis de datos biológicos.[1] Los términos bioinformática, biología computacional y, en …   Wikipedia Español

Share the article and excerpts

Direct link
… Do a right-click on the link above
and select “Copy Link”