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EMAP
(submitted by Seth)
The Edinburgh Mouse Atlas Project(EMAP) is essentially composed of two major sections. An anatomy browser and gene expression database (EMAGE). Essentially the gene expression database can be accessed through an image interface, an ontological hierarchy of anatomy or a text based search. See the EMAP site (http://genex.hgu.mrc.ac.uk).
The anatomical part is straightforward. Mousing over as structure highlights the anatomical component and displays the name. Clicking on the structure shows it's location in the ontology. Right clicking on the anatomy brings up a menu which will query MGI GXD or EMAGE for the selected anatomy.
EMAGE has two parts; a web based query which, other than minor layout differences, has much of the same functionality as the anatomical browser. The real fun is the JAVA application "EMAGE DB" which can be be downloaded from http://genex.hgu.mrc.ac.uk/Emage/database/emageIntro.html. EMAGE DB allows query and browsing of the EMAGE database either by embryonic stage, gene expressed or anatomical component (stage specifically) that genes are expressed in. It also allows you to "paint" a region on a whole mount image and ask what genes are expressed under the painted region (Not unlike SMARTAtlas). All entries in the database are annotated with photographic plates of the expression pattern, assessment of the signal strength, the "author" of the entry and accession to literature and other databases (i.e. MGI).
The power of EMAP/EMAGE are the links to outside sources and databases.
GenePaint?
(submitted by Rob)
They have integrated a very simple ontology based system to search for expression of genes by structure. http://www.genepaint.org
For "forkhead box A1" try this. Open the Expression Pattern Search. http://www.genepaint.org/cgi-bin/mgrqcgi94?APPNAME=genepaint&PRGNAME=search&ARGUMENTS=-Aforkhead%20box%20A1
Neurome
http://www.neurome.com/company/index.htm
This is a company with some similar interests as mouse BIRN, including a commercial atlas viewer specializing in gene expression data http://www.neurome.com/technology/gallery.htm.
A recent publication is recommended by Allan and you can dowload it at http://www.neurome.com/news/press071905.htm.
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