Genevestigator is an application consisting of a gene expression database and tools to analyse the data. It exists in two versions, biomedical and plant, depending on the species of the underlying

microarray A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silicon t ...

and RNAseq data. It was started in January 2004 by scientists from

ETH Zurich (colloquially) , former_name = eidgenössische polytechnische Schule , image = ETHZ.JPG , image_size = , established = , type = Public , budget = CHF 1.896 billion (2021) , rector = Günther Dissertori , president = Joël Mesot , ac ...

and is currently developed and commercialized by Nebion AG. Researchers and scientists from academia and industry use it to identify, characterize and validate novel drug targets and biomarkers, identify appropriate research models and in general to understand how gene expression changes with different treatments.

Gene expression database

The Genevestigator database comprises transciptomic data from numerous public repositories including

GEO Geo- is a prefix derived from the Greek word ''γη'' or ''γαια'', meaning "earth", usually in the sense of "ground or land”. GEO or Geo may also refer to: Arts, entertainment, and media * ''GEO'' (magazine), a popular scientific magazine ...

, Array Express and renowned cancer research projects as TCGA. Depending on the license agreement, it may also contain data from private gene expression studies. All data are manually curated, quality-controlled and enriched for sample and experiment descriptions derived from corresponding scientific publications. The number of species from where the samples are derived is constantly increasing. Currently, the biomedical version contains data from

human Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ...

mouse A mouse ( : mice) is a small rodent. Characteristically, mice are known to have a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate. The best known mouse species is the common house mouse (''Mus musculus' ...

rat Rats are various medium-sized, long-tailed rodents. Species of rats are found throughout the order Rodentia, but stereotypical rats are found in the genus ''Rattus''. Other rat genera include ''Neotoma'' ( pack rats), ''Bandicota'' (bandicoot ...

monkey Monkey is a common name that may refer to most mammals of the infraorder Simiiformes, also known as the simians. Traditionally, all animals in the group now known as simians are counted as monkeys except the apes, which constitutes an incomple ...

, fruitfly and other species and used in biomedical research. Gene expression studies are from various research areas including oncology, immunology, neurology, dermatology and cardiovascular diseases. Samples comprise tissue biopsies and cell lines. The plant version contains both, widely used model species such as

arabidopsis ''Arabidopsis'' (rockcress) is a genus in the family Brassicaceae. They are small flowering plants related to cabbage and mustard. This genus is of great interest since it contains thale cress (''Arabidopsis thaliana''), one of the model organi ...

and

medicago ''Medicago'' is a genus of flowering plants, commonly known as medick or burclover, in the legume family (Fabaceae). It contains at least 87 species and is distributed mainly around the Mediterranean basin. The best-known member of the genus is ...

as well as major corp species such as

maize Maize ( ; ''Zea mays'' subsp. ''mays'', from es, maíz after tnq, mahiz), also known as corn (North American and Australian English), is a cereal grain first domesticated by indigenous peoples in southern Mexico about 10,000 years ago. Th ...

rice Rice is the seed of the grass species ''Oryza sativa'' (Asian rice) or less commonly ''Oryza glaberrima ''Oryza glaberrima'', commonly known as African rice, is one of the two domesticated rice species. It was first domesticated and grown i ...

wheat Wheat is a grass widely cultivated for its seed, a cereal grain that is a worldwide staple food. The many species of wheat together make up the genus ''Triticum'' ; the most widely grown is common wheat (''T. aestivum''). The archaeologi ...

and

soybean The soybean, soy bean, or soya bean (''Glycine max'') is a species of legume native to East Asia, widely grown for its edible bean, which has numerous uses. Traditional unfermented food uses of soybeans include soy milk, from which tofu an ...

Gene expression tools

More than 60,000 scientists from academia and industry use Genevestigator for their work in

molecular biology Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physi ...

toxicogenomics Toxicogenomics is a subdiscipline of pharmacology that deals with the collection, interpretation, and storage of information about gene and protein activity within a particular cell or tissue of an organism in response to exposure to toxic substan ...

biomarker In biomedical contexts, a biomarker, or biological marker, is a measurable indicator of some biological state or condition. Biomarkers are often measured and evaluated using blood, urine, or soft tissues to examine normal biological processes, ...

discovery and target validation. The original scientific publication has been cited over 3,500 times. The analysis tools are divided into three major sets: * CONDITION SEARCH tools: find conditions such as a tissue, disease, treatment or genetic background that regulate the gene(s) of interest * GENE SEARCH tools: find genes that are specifically expressed in the condition(s) of interest * SIMILARITY SEARCH tools: find genes or conditions that show a similar gene expression pattern

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 A meta-analysis is a statistical analysis that combines the results of multiple scientific studies. Meta-analyses can be performed when there are multiple scientific studies addressing the same question, with each individual study reporting me ...

of transcriptomes. Advances in Bioinformatics 2008, 420747 * Grennan AK (2006) Genevestigator. Facilitating

web-based A web application (or web app) is application software that is accessed using a web browser. Web applications are delivered on the World Wide Web to users with an active network connection. History In earlier computing models like client-serve ...

gene-expression analysis.

Plant Physiology Plant physiology is a subdiscipline of botany concerned with the functioning, or physiology, of plants. Closely related fields include plant morphology (structure of plants), plant ecology (interactions with the environment), phytochemistry (bi ...

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 Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek wo ...

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 Genetics Bioinformatics software

Gene expression database

Gene expression tools

See also

References