Gilchrist MJ et al. (2009), Database of queryable gene expression patterns ...

XB-ART-39455

Dev Dyn 2009 Jun 01;2386:1379-88. doi: 10.1002/dvdy.21940.

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Database of queryable gene expression patterns for Xenopus.

Gilchrist MJ , Christensen MB , Bronchain O , Brunet F , Chesneau A , Fenger U , Geach TJ , Ironfield HV , Kaya F , Kricha S , Lea R , Massé K , Néant I , Paillard E , Parain K , Perron M , Sinzelle L , Souopgui J , Thuret R , Ymlahi-Ouazzani Q , Pollet N .

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The precise localization of gene expression within the developing embryo, and how it changes over time, is one of the most important sources of information for elucidating gene function. As a searchable resource, this information has up until now been largely inaccessible to the Xenopus community. Here, we present a new database of Xenopus gene expression patterns, queryable by specific location or region in the embryo. Pattern matching can be driven either from an existing in situ image, or from a user-defined pattern based on development stage schematic diagrams. The data are derived from the work of a group of 21 Xenopus researchers over a period of 4 days. We used a novel, rapid manual annotation tool, XenMARK, which exploits the ability of the human brain to make the necessary distortions in transferring data from the in situ images to the standard schematic geometry. Developmental Dynamics 238:1379-1388, 2009. (c) 2009 Wiley-Liss, Inc.

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Species referenced: Xenopus laevis
Genes referenced: ak1 apobec2 atp2a1 cav1 chrd ferry3 hacd1 klhl41 lama5 mt-cyb mtfr1l myh8 nexn nxpe2 olig4 rab5b rbm24 sesn2 sparc srl ssr2 thbs4 tnni1.2 ttn

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	Figure 5. Image retrieval with an expression pattern from another in situ image. The annotated images may be searched with the expression pattern from another in situ image, although the user remains unaware of the actual annotation data involved. The database uses the expression pattern recorded for the selected image to search against all the expression patterns for that stage and view, ranking the results by the degree of similarity. Here, annotated expression in the somites from an image of a stage 30 embryo is used to instigate a search.Download figure to PowerPoint