The co-expression of genes is the first step in the identification of regulatory networks and can elucidate the evolutionary origin of cells, tissues and organs. High throughput determination of co-expression can be assayed through DNA microarrays that allow easily assessing expression of all genes of a given species. However, especially for differentially expressed developmental genes the knowledge of the actual 3 dimensional expression patterns changing over time (the 4th dimension) is crucial.
Expression patterns can be determined in an easy, straightforward approach through in situ hybridization. Thanks to robotics, many laboratories can now afford a high throughput in situ hybridization approach and expression pattern data are accumulating. Large-scale in situ hybridization screens have been carried out for the major model organisms in developmental biology like zebrafish, mouse, Xenopus, drosophila, C. elegans and ascidia and expression data is stored in databases and accessible through web interfaces. Here at EMBL we have set up two such expression pattern databases, one for Medaka (MEPD) and one for Platynereis (PEPD, in house).
To be able to compare gene expression patterns between species, we are setting up a Cross Species Expression Pattern Database. This database will integrate publicly available data on gene expression patterns for the different model organisms with the data produced in house. In addition we plan to complement this data with microarray and Chip-On-Chip data and provide interfaces to be used by both biologists as well as computer scientists.
The aim of the 4D expression project is the comparison of patterns of high temporal and spatial resolution between different species to be able to identify syn-expression groups, regulatory networks and evolutionary relationships.
| Ivica Letunic | Senior technical officer |
| Peer Bork | Associate Programme Coordinator and Senior Scientist |