Abstract
The EMAGE (Electronic Mouse Atlas of Gene Expression) database (http://www.emouseatlas.org/emage) allows users to perform on-line queries of mouse developmental gene expression. EMAGE data are represented spatially using a framework of 3D mouse embryo models, thus allowing uniquely spatial queries to be carried out alongside more traditional text-based queries. This spatial representation of the data also allows a comparison of spatial similarity between the expression patterns. The data are mapped to the models by a team of curators using bespoke mapping software, and the associated meta-data are curated for accuracy and completeness. The data contained in EMAGE are gathered from three main sources: from the published literature, through large-scale screens and collaborations, and via direct submissions from researchers. There are a variety of ways to query the EMAGE database via the on-line search interfaces, as well as via direct computational script-based queries. EMAGE is a free, on-line, community resource funded by the Medical Research Council, UK.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Kaufman MH (1992) The atlas of mouse development. Academic Press, San Diego
Sharpe J et al (2002) Optical projection tomography as a tool for 3D microscopy and gene expression studies. Science 296:541–545
Gray PA et al (2004) Mouse brain organization revealed through direct genome-scale TF expression analysis. Science 306:2255–2257
Vendrell V et al (2009) Gene expression analysis of canonical Wnt pathway transcriptional regulators during early morphogenesis of the facial region in the mouse embryo. Gene Expr Patterns 9:296–305
Deutsch EW et al (2008) Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol 26:305–312
http://www.emouseatlas.org/emap/analysis_tools_resources/software/eMAP-apps.html
Theiler K (1989) The house mouse atlas of embryonic development. Springer, New York
http://www.emouseatlas.org/emage/about/data_annotation_methods.html#auto_eurexpress
Bard JL et al (1998) An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature. Mech Dev 74:111–120
http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm#ctv
Acknowledgments
The authors would like to gratefully acknowledge Dr. Martin Ringwald and all the curators at the GXD for a long-standing collaboration and the provision of the textual annotations used in EMAGE. We would also like to acknowledge all the staff members who have contributed to EMAP and EMAGE over the years, as well as the innumerous data providers. The work described in this chapter is funded by the Medical Research Council, UK.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media, New York
About this protocol
Cite this protocol
Richardson, L. et al. (2014). EMAGE: Electronic Mouse Atlas of Gene Expression. In: Lewandoski, M. (eds) Mouse Molecular Embryology. Methods in Molecular Biology, vol 1092. Humana Press, Boston, MA. https://doi.org/10.1007/978-1-60327-292-6_5
Download citation
DOI: https://doi.org/10.1007/978-1-60327-292-6_5
Published:
Publisher Name: Humana Press, Boston, MA
Print ISBN: 978-1-60327-290-2
Online ISBN: 978-1-60327-292-6
eBook Packages: Springer Protocols