Genevestigator
Encyclopedia
Genevestigator is a web-based application
developed for biologists and medical researchers 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
, barley, rice, wheat and soybean.
Genevestigator was started in January 2004 by scientists from ETH Zurich
.
, toxicogenomics, and biomarker discovery/validation.
As of April 2009, its original articles have been cited more than 900 times (ISI Thomson) by researchers using the tools.
Four tool sets, each containing several tools, are available:
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.
Web application
A web application is an application that is accessed over a network such as the Internet or an intranet. The term may also mean a computer software application that is coded in a browser-supported language and reliant on a common web browser to render the application executable.Web applications are...
developed for biologists and medical researchers to rapidly find out in which tissues, at which stages of development
Developmental stage
One of the major controversies in developmental psychology centres around whether development is continuous or discontinuous. Stage theories of development rest on the assumption that development is a discontinuous process involving distinct stages which are characterised by qualitative differences...
, 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
Affymetrix
Affymetrix is a company that manufactures DNA microarrays; it is based in Santa Clara, California, United States. The company was founded by Dr. Stephen Fodor in 1992. It began as a unit in Affymax N.V...
microarrays
DNA microarray
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
hybridized with RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
samples extracted from a large variety of tissues and conditions. Currently, data is available for human, mouse, rat, Arabidopsis
Arabidopsis thaliana
Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics...
, barley, rice, wheat and soybean.
Genevestigator was started in January 2004 by scientists from ETH Zurich
ETH Zurich
The Swiss Federal Institute of Technology Zurich or ETH Zürich is an engineering, science, technology, mathematics and management university in the City of Zurich, Switzerland....
.
Tool for biologists and medical researchers
Genevestigator is currently serving a community of 22,000 registered users (mostly biologists) from the animal and plant research fields. Its tools have been used in molecular biologyMolecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
, toxicogenomics, and biomarker discovery/validation.
As of April 2009, its original articles have been cited more than 900 times (ISI Thomson) by researchers using the tools.
Four tool sets, each containing several tools, are available:
- Meta-Profile Analysis
- Biomarker Search
- Clustering Analysis
- Network 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. 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.