EMAGE--Edinburgh Mouse Atlas of Gene Expression: 2008 update

Abstract

EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a database of in situ gene expression patterns in the developing mouse embryo. Domains of expression from raw data images are spatially integrated into a set of standard 3D virtual mouse embryos at different stages of development, allowing data interrogation by spatial methods. Sites of expression are also described using an anatomy ontology and data can be queried using text-based methods. Here we describe recent enhancements to EMAGE which include advances in spatial search methods including: a refined local spatial similarity search algorithm, a method to allow global spatial comparison of patterns in EMAGE and subsequent hierarchical-clustering, and spatial searches across multiple stages of development. In addition, we have extended data access by the introduction of web services and new HTML-based search interfaces, which allow access to data that has not yet been spatially annotated. We have also started incorporating full 3D images of gene expression that have been generated using optical projection tomography (OPT).

Figure 1.

Example results table from the EMAGE Data Repository. The results from a Gene/Protein search of the EMAGE repository for the unofficial gene symbol ‘krox20’ is shown. Results are retrieved and listed under the currently approved symbol for Krox20: Egr2. The list has been ordered by ascending Theiler Stage value. Examples of data from a number of original sources, for ISH and IHC as well as wild-type and heterozygous mutant specimens are shown. Thumbnail images are linked to the full-size originals.

Figure 2.

Display of spatial pattern comparison hierarchical clustering results in the JavaTreeView Applet. An example dataset of 49 images of WM TS11 embryos showing a wide variety of different expression patterns was selected for spatial comparison and subsequent hierarchical clustering analysis. The results are displayed in a version of JavaTreeView modified to run as an applet and with the ability to load images. The dendrogram and associated matrix (which offer the user information about pattern relatedness) appear on the left. On the right, visual feedback of the common spatial pattern found in all annotations on the selected branch is shown in the form of a ‘heat-map’ (yellow on black). In this case, the ‘raw data images’ tab is selected to show the 3 images that have contributed to the pattern in the heat map (expression in the images is in blue/purple).