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EMAGE: Electronic Mouse Atlas of Gene Expression

  • Lorna Richardson
  • Peter Stevenson
  • Shanmugasundaram Venkataraman
  • Yiya Yang
  • Nick Burton
  • Jianguo Rao
  • Jeffrey H. Christiansen
  • Richard A. Baldock
  • Duncan R. Davidson
Part of the Methods in Molecular Biology book series (MIMB, volume 1092)

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.

Key words

Mouse Gene expression Database Development Anatomy Embryo Atlas Curated In situ hybridization Immunohistochemistry Knock-in Wild-type Resource Transcription 

Notes

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.

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Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  • Lorna Richardson
    • 1
  • Peter Stevenson
    • 2
  • Shanmugasundaram Venkataraman
    • 3
  • Yiya Yang
    • 3
  • Nick Burton
    • 2
  • Jianguo Rao
    • 2
  • Jeffrey H. Christiansen
    • 4
  • Richard A. Baldock
    • 3
  • Duncan R. Davidson
    • 3
  1. 1.MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
  2. 2.MRC Human Genetics UnitInstitute of Genetics and Molecular MedicineEdinburghUK
  3. 3.Human Genetics UnitInstitute of Genetics and Molecular MedicineEdinburghUK
  4. 4.Australian National Data ServiceMonash UniversityMelbourneAustralia

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