Genevestigator

Genevestigator is an innovative online platform enabling researchers to globally explore public and proprietary expression data for research and clinical applications. It's a web-based application developed for biologists and medical researchers to rapidly find out how genes are expressed in different tissues, stimuli, drug treatments, diseases, or genetic modifications. Results are processed from a large database of manually curated and quality-controlled microarrays and RNAseq samples from a large variety of tissues and conditions. Currently, data is available for human, mouse, rat, pig, drosophila, arabidopsis, barley, rice, wheat, tomato, tobacco, moss and soybean.

Genevestigator was started in January 2004 by scientists from ETH Zurich and is currently developed and commercialized by Nebion AG.

Tool for biologists and medical researchers

Genevestigator is currently serving a community of 44,000 registered users (mostly biologists) from the animal and plant research fields. Its tools have been used in molecular biology, toxicogenomics, and biomarker discovery/validation.

As of May 2014, its original articles have been cited more than 2,500 times by researchers using the tools.

Three tool sets, each containing several tools, are available:

• CONDITION SEARCH tools: find conditions that are relevant for your genes of interest
• GENE SEARCH tools: find genes that are specifically expressed in conditions of interest
• SIMILARITY SEARCH tools: find genes that are similar within a data space.

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. This holds true also for stages of development or perturbations, which are also summarized into representative expression responses.

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

See also

• Spatiotemporal gene expression

References

• Prasad A, Suresh Kumar S, Dessimoz C, Bleuler S, Laule O, Hruz T, Gruissem W, and P Zimmermann (2013) Global regulatory architecture of human, mouse and rat tissue transcriptomes. BMC Genomics 2013, 14:716.
• Hruz T, Wyss M, Lucas C, Laule O, von Rohr P, Zimmermann P, and S Bleuler (2013) A Multilevel Gamma-Clustering Layout Algorithm for Visualization of Biological Networks. Advances in Bioinformatics, vol. 2013, Article ID 920325, 10 pages, 2013. doi:10.1155/2013/920325.
• Hruz T, Wyss M, Docquier M, Pfaffl MW, Masanetz S, Borghi L, Verbrugge P, Kalaydjieva L, Bleuler S, Laule O, Descombes P, Gruissem W and P Zimmermann (2011) RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization. BMC Genomics 2011, 12:156.
• Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W and P Zimmermann (2008) Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Advances in Bioinformatics 2008, 420747
• 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