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. 2014 Jan;42(Database issue):D835-44.
doi: 10.1093/nar/gkt1155. Epub 2013 Nov 21.

EMAGE Mouse Embryo Spatial Gene Expression Database: 2014 Update

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Free PMC article

EMAGE Mouse Embryo Spatial Gene Expression Database: 2014 Update

Lorna Richardson et al. Nucleic Acids Res. .
Free PMC article

Abstract

EMAGE (http://www.emouseatlas.org/emage/) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descriptions of gene expression plus spatial maps of gene expression patterns. This mapping allows spatial queries to be accomplished alongside more traditional text-based queries. Here, we describe our recent progress in spatial mapping and data integration. EMAGE has developed a method of spatially mapping 3D embryo images captured using optical projection tomography, and through the use of an IIP3D viewer allows users to view arbitrary sections of raw and mapped 3D image data in the context of a web browser. EMAGE now includes enhancer data, and we have spatially mapped images from a comprehensive screen of transgenic reporter mice that detail the expression of mouse non-coding genomic DNA fragments with enhancer activity. We have integrated the eMouseAtlas anatomical atlas and the EMAGE database so that a user of the atlas can query the EMAGE database easily. In addition, we have extended the atlas framework to enable EMAGE to spatially cross-index EMBRYS whole mount in situ hybridization data. We additionally report on recent developments to the EMAGE web interface, including new query and analysis capabilities.

Figures

Figure 1.
Figure 1.
Use of IIP3D web browser-based section viewer in EMAGE (a) The IIP3D viewer allows arbitrary sections through OPT 3D data images to be viewed. The IIP3D viewer displays sections through large 3D objects (>100GB) by only downloading the pixels that you see. The advantage of this system is that large 3D images can be accessed using a modern web browser, such as recent versions of Firefox, Chrome or Safari, and software downloads are not required. A context menu offers additional options, including measurement mode that allows a user to measure the distance between two points. (b) Mapped OPT data can also be viewed using the IIP3D viewer. This image shows the data in panel (a) spatially mapped onto the appropriate EMAP model. The ‘expression detected’ domain is coloured red and ‘possible expression’ is coloured green. (c) Eurexpress section data. The tiling method of the IIP image server allows users to access the original serial section images within the context of a web browser. This obviates the need to download large image files. In the large central panel, an automated segmentation method has been used to generate coloured domains representing different levels of expression (red: strongest; yellow: moderate; green: possible; cyan: not detected). Section navigation is accomplished using the left panel. The original section images can be seen in the smaller panel to the right.
Figure 2.
Figure 2.
New and novel features of EMAGE. This figure shows a screen capture of an EMAGE results table with some new and novel features highlighted. (a) The ‘find similar function’ option retrieves a list of spatially similar EMAGE expression patterns, ranked by similarity, and can be accessed by clicking on the x-X-x icon. (b) EMAGE has implemented direct links to screens and resources whose data we represent. The enhancer data were obtained from the VISTA enhancer screen, and this is acknowledged in the data source column. (c) Quick search, which can be found on every page, allows users to select a category and perform a single criteria query. (d) The ‘Analysis’ option allows a user to export a gene list generated by EMAGE to ToppGene for extended analysis.
Figure 3.
Figure 3.
Using eMouseatlas to cross-index EMAGE and EMBRYS. The central panel shows the eMouseAtlas TS19 reference model (left) and additionally this model with multiple anatomical components delineated (right). Anatomical domains were prioritized for segmentation if they were included in the text annotation of the EMBRYS whole mount ISH screen. Segmenting these domains allows the eMouseAtlas framework to bridge between EMAGE (spatial- and text-annotation) and EMBRYS (text-annotation) database resources and allows EMAGE to develop inferred spatial annotation for EMBRYS gene expression patterns.
Figure 4.
Figure 4.
Querying EMAGE using eMouseAtlas. (a) eMouseAtlas (EMAP) provides 3D models of mouse embryos across development. These models are used as a framework to store spatial information such as delineated anatomical domains. (b) An IIP3D section viewer allows arbitrary sections through 3D EMAP models to be viewed. A context menu offers additional options, including query mode that allows a user to query EMAGE and GXD. (c) Multiple anatomical domains can be selected for an EMAGE query, and these appear as coloured domains in the section viewer. Section navigation is accomplished using the left panel. On the panel to the right, checkboxes allow users to toggle on/off the anatomical domains that are displayed in the section viewer.

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