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.

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Genevestigator was started in January 2004 by scientists from ETH Zurich. The analysis tool can be accessed at the Genevestigator website.

Keywords: microarray databases, meta-analysis, Affymetrix, bioinformatics, systems biology

Genevestigator - A 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 microarrray experiments. Plant Methods 2 , 1