EMAGE mouse embryo spatial gene expression database: 2010 update

Lorna Richardson, Shanmugasundaram Venkataraman, Peter Stevenson, Yiya Yang, Nicholas Burton, Jianguo Rao, Malcolm Fisher, Richard Baldock, Duncan R. Davidson, Jeffrey H. Christiansen

Research output: Contribution to journalArticlepeer-review

Abstract

EMAGE (http://www.emouseatlas.org/emage) is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Here, we describe recent enhancements to EMAGE including: the release of a completely re-designed website, which offers integration of many different search functions in HTML web pages, improved user feedback and the ability to find similar expression patterns at the click of a button; back-end refactoring from an object oriented to relational architecture, allowing associated SQL access; and the provision of further access by standard formatted URLs and a Java API. We have also increased data coverage by sourcing from a greater selection of journals and developed automated methods for spatial data annotation that are being applied to spatially incorporate the genome-wide (similar to 19 000 gene) 'EURExpress' dataset into EMAGE.

Original languageEnglish
Pages (from-to)D703-D709
Number of pages7
JournalNucleic Acids Research
Volume38
Issue numbersuppl 1
DOIs
Publication statusPublished - Jan 2010

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