DIGITAL ATLAS OF GENE EXPRESSION ON THE EXAMPLE OF THE MOUSE GENOME (GenePaint)
Under the umbrella of GenePaint scientists have access to the world's first comprehensive overview of the spatial and temporal activity of all known genes (gene expression) of an entire mammalian organism at any given moment in its development on the example of the mouse genome. By means of this data, it is possible, for example, to determine candidate genes for genetic and complex diseases. One of the project’s long-term goals is to build a European online service, "European Database of Gene Expression“.
The results of the completed European project EURExpress have been incorporated in the GenePaint platform. The project had the objective of creating a high-resolution anatomic atlas of the transcriptome of the mouse embryo (transcriptome = The sum of all genes of a cell transcribed from DNA in RNA. The RNA processes the genetic information into proteins). For this purpose, the first step was to create a large number of tissue sections from mouse embryos in various locations in Europe, and to make thousands of genes visible using molecular biological methods. The activity of 18,000 genes and 400 microRNAs, 1,420 anatomic structures and 1,002 marker genes
The internet-based expression atlas METscout for the mouse genome (mapping of the genomes’ activity) was created as part of the project EURExpress. METscout allows the exploration of the metabolism based on the gene expression atlas. Using the web application, metabolic processes can be examined throughout their course of development. Solute carriers (SLC; transport proteins which carry solutes inside and outside of cells or to other locations in the organism), for example, can be observed as they transport an enzyme or carbohydrate from one organ to another.
The GenePaint platform provides a virtual microscope (high definition zoom). This Zoom Viewer offers scientists the opportunity to view the image data at a high resolution, approximately the same as the original.
- The data pool of the GenePaint project consists of almost 42 terrabytes.
- Approximately 2,000 scientists worldwide use the GenePaint applications.
- On average, there are 250,000 hits per month.
GWDG’s Role in the Project
The GWDG operates the servers and handels the conversion, provision and saving of the image data in the archive, as well as user administration.
- As part of the EURExpress project, the image data in TIFF format was submitted to the GWDG and archived. The data was automatically converted into various image formats for web display and the virtual microscope.
- Additionally the GWDG was responsible for system administration, application support, database and web development, as well as database administration. The web development for MetScout was also handeled by the GWDG.
- The project has been completed and is now in standard operation.
- The applications are permanently adjusted to technical progress. Raw image data in TIFF format was converted into the png format with lossless compression, saving memory and offering researchers access to image data in jpeg format.
- Since 2015 the project has been revised according to the collected research data. A reprogramming with modern web technologies has been under way since January. This applies to the present data, database interfaces and the presentation. The implementation is realized using mySQL, Node.js and AngularJS.
EURExpress: European Union, Sixth Framework Programme for Research and Technological Development.
GenePaint: A Collaboration of the Max Planck Institute for Biophysical Chemistry and the GWDG.
GenePaint is a project and website offered by the Max Planck Institute for Biophysical Chemistry. The GWDG is responsible for technical support.
The EURExpress consortium was an international group of scientists from twelve European research facilities. The project had been initiated by Professor Dr. Gregor Eichele, Max Planck Institute for Biophysical Chemistry, Göttingen.
Responsible for the project coordination was TIGEM, Instituto di Genetica e Medicina, Naples, Italy.
- Max Planck Society (ed.), Erster anatomischer Atlas für die Genaktivität eines Säugetiers (First Anatomical Atlas of the gene activity of a mammal, German only) 02/2011, online
- Geffers, Lars, Benjamin Tetzlaff (GWDG), Cui Xiao, Jun Yan and Gregor Eichele, METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters, in: Oxford Journals, Nucleic Acids Research, 2013, Vol 41, download online version 09/2012