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EMAGE


NAR Molecular Biology Database Collection entry number 812
Richardson L, Venkataraman S, Stevenson P, Yang Y, Moss J, Graham L, Burton N, Hill B, Rao J, Baldock RA, Armit C.
MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK

Database Description

EMAGE is a free community resource housing in situ gene expression patterns in the developing mouse embryo. The data have been generated using methods such as in situ hybridisation, immunohistochemistry and in situ genetic reporter techniques (e.g. gene-trap, knock-in reporter). Gene expression domains from raw images are converted into digital domains and these are integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development. This 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.
Graphical User Interface: A HTML search interface is provided at http://www.emouseatlas.org/emage.Several search approaches are supported: using Embryo Space (the user can paint an arbitrary region on a virtual embryo to retrieve gene expression patterns that include a domain similar to the query domain); using a Gene/Protein Symbol/Name/ID, or using the Name of an Anatomical Structure. Additionally, an interface is available to analyse/mine the data in EMAGE to find gene expression patterns with globally similar expression patterns (this analysis is based on hierarchical clustering of spatial similarity values of all expression patterns in a set).
Direct Access Methods: Several direct computational access methods are provided to EMAGE data and functions. These include a standard-format URL, WebServices, SQL query, Java API and DAS. See http://www.emouseatlas.org/emage/search/all_direct_access.html.
Submitting Data: Data submissions are very welcome from the community. Either use the EMAGE Java Client (http://www.emouseatlas.org/emage/data_submission/via_submission_tool.html) to prepare a local database, of which any number of local entries can be uploaded to EMAGE for curation, or contact EMAGE curatorial staff directly using ma-edit@hgu.mrc.ac.uk. />EMAGE User Group and User Support Users can register to join the EMAGE User Group: http://www.emouseatlas.org/emage/help/user_group.html. Regular updates and news about the project are sent to subscribers. Help is also available regarding any aspect of the database by emailing the EMAGE Editorial Office on ma-edit@hgu.mrc.ac.uk.

Acknowledgements

All funding of EMAGE is provided by the Medical Research Council.


Go to the abstract in the NAR 2014 Database Issue.
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