Venkataraman Shanmugasundaram, Stevenson Peter, Yang Yiya, Richardson Lorna, Burton Nicholas, Perry Thomas P, Smith Paul, Baldock Richard A, Davidson Duncan R, Christiansen Jeffrey H
MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
Nucleic Acids Res. 2008 Jan;36(Database issue):D860-5. doi: 10.1093/nar/gkm938. Epub 2007 Dec 12.
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).
