Speaker: Chris Armit
Title: Using the eMouseAtlas Web Resource
Abstract
eMouseAtlas (www.emouseatlas.org) is a comprehensive online resource to visualise mouse
development and investigate gene expression in the mouse embryo. This workshop will serve as an
introduction to using the eMouseAtlas resource, with particular attention focused on novel 3D
visualisation tools such as the IIP3D web tool that allows a user to view arbitrary sections of 3D
embryo reconstructions using a web browser. eMouseAtlas additionally includes EMAGE
(www.emouseatlas.org/emage), a freely available, curated online database of in situ gene expression
patterns where gene expression domains extracted from raw data images are spatially mapped into
atlas embryo models. A novel feature of EMAGE is that it allows users to explore spatial similarity
between gene expression patterns. In this workshop, we will explore embryonic anatomy, find gene
expression patterns associated with specific anatomical components, explore spatial similarity of
gene expression, and determine whether key signaling pathways (Wnt, Notch, Hedgehog) are likely to
be active in anatomical components during embryonic development.
EMBO Worksheets
1.
Exploring the anatomy of the mouse embryo
1.1. IIP3D viewer
1.2. Ontology tree
2.
Finding gene expression patterns
2.1. by gene (gene query)
2.2. by anatomical structure (anatomy query)
2.3. by pattern (paint tool)
2.4. complex queries
2.5. using the spatial similarity tool
2.6. spatial analysis of signaling pathways
1. Exploring the anatomy of the mouse embryo

eMouseAtlas is a comprehensive online resource to visualise postimplantation mouse
development and investigate gene expression in the postimplantation mouse embryo.

The eMouseAtlas portal page (www.emouseatlas.org) allows access to the anatomy atlas
and the EMAGE database of gene expression.

eMouseAtlas uses Theiler staging (see supplementary notes).
The eMouseAtlas Portal Page.
For workshop attendee:
 Click on the button ‘EMA – Mouse Anatomy Atlas’.

The eMouseAtlas Anatomy Atlas website (www.emouseatlas.org/emap/ema) uses a filmstrip
to navigate between Theiler stages.
The eMouseAtlas Anatomy Atlas Website. The film-strip embryo selector (a) is used to select a Theiler
stage. (b) Each Theiler Stage may contain multiple embryo models and these can be individually
chosen using the model selector. (c) Visualisation options include original high resolution sections, 3D
reconstructions, and movies of the embryo and its littermates. In addition, details of litter variation
are also provided.
The eMouseAtlas Anatomy Atlas website is available at the following link:
www.emouseatlas.org/emap/ema
For workshop attendee:
 Use the filmstrip to select Theiler stage 12.
 Select a model.
 Click on ‘3D reconstruction’.
1.1. IIP3D Viewer

An IIP3D web tool allows a user to explore 3D models using a web browser. This viewer is
accessible by clicking on the ‘3D reconstruction’ link for the appropriate Theiler stage.
IIP3D Web Tool. This 3D reconstruction of an eMouseAtlas Theiler stage 12 embryo is visualised using
an IIP3D web tool and can be accessed at the following link:
http://www.emouseatlas.org/eAtlasViewer_ema/application/ema/anatomy/EMA21.php

Manipulations that can be performed on the displayed image include pan-and-zoom;
translating the viewing plane (i.e. distance); and rotating the viewing plane in 3 dimensions
(pitch, yaw).

There is the additional option to select layers and this is particularly useful for visualising the
‘painted’ anatomical domains that are used to delineate anatomy.

Other features of the IIP3D viewer include the ability to measure the distance between two
points on an atlas model, and the ability to query gene expression databases.
For workshop attendee:
 Explore the pan-and-zoom functions of the IIP3D viewer.
 Use the distance tool to choose a different section.
 Rotate the viewing plane using the pitch and yaw functions.
 On the anatomy tree, click ‘select all’ to view painted anatomical domains.
 Mouse over painted domains to see what happens.
1.2. Ontology Tree

The atlas website additionally hosts an interactive anatomy browser that allows a user to
access staged anatomy in an ontology tree.

The eMAP ontology uses a controlled vocabulary and part-of relationships to describe
anatomical components, with stage-specific partonomic (part-of) hierarchies provided from
TS01-TS26.

The interactive ontology tree illustrates the partonomic relationships between the
anatomical terms as a hierarchy where each term may have a number of sub-components.
Interactive Ontology Tree.
For workshop attendee:
 Select a Theiler stage using the film-strip selector.
 Click on ‘Anatomy’.
 Open leaves of the tree to find child terms for anatomical structures.
 Explore what happens when you right click on a leaf of the tree.
2. Finding Gene Expression Patterns

EMAGE is an extension of the atlas resource that has been used to archive and spatially map
~21K gene expression patterns from a variety of sources including, large in situ hybridisation
screens (EurExpress, FaceBase), the GXD and the published literature as well as unpublished
direct submissions from developmental biology labs.
The eMouseAtlas Portal Page.
For workshop attendee:
 From the eMouseAtlas Portal Page, click on the button ‘EMAGE – Mouse Gene Expression
Spatial Database’.
The EMAGE Web Interface.

Gene, Anatomy, and Embryo Space queries allow the user to find gene expression patterns.

To enable users to browse the EMAGE data more effectively, we have developed a
Combination Query that allows complex queries to be built.

The Combination Query includes gene, anatomy, ID, stage, GO term, assay type etc. and
allows a user to construct a complex query step-by-step with additional options to include or
exclude specific query terms.
2.1. Gene Query
For workshop attendee:
 From the EMAGE Web Interface, click on ‘Gene’.
 Type in a Gene Symbol (e.g. Shh) and click on ‘Begin Search’.
 View the retuned list of entries, click on an EMAGE ID for more details.
1. Type in a
Gene Symbol
2. View list of
entries, click on
an EMAGE ID for
more details
3. View a
complete
EMAGE entry
2.2. Anatomy Query
For workshop attendee:
 From the EMAGE Web Interface, click on ‘Anatomy Name’.
 Begin typing the name of an anatomical component (e.g. telencephalon), components with
this string will appear in a list.
 Select items from this list and click on ‘Begin Search’.
 View the retuned list of entries, click on an EMAGE ID for more details.
1. Begin typing the
name of an
anatomical
component, doubleclick to select the
component you wish
to query from the list
2. You are given the
opportunity to
include additional
anatomical
components in your
query
3. View list of entries,
click on an EMAGE ID
for more details
2.3. Paint Tool (Embryo Space)
For workshop attendee:
 From the EMAGE Web Interface, click on ‘Embryo Space’.
 Select a Theiler Stage from the drop-down menu and click on ‘Next Step’.
 Paint a region using the cursor and click on ‘Begin Search’.
 View the retuned list of entries, click on an EMAGE ID for more details.
1. Select a
Theiler Stage
2. Paint a
region
3. View list of
entries, click
on an EMAGE
ID for more
details
2.4. Complex Queries (Combination Query)
For workshop attendee:
 From the EMAGE Web Interface, click on ‘Combination’.
 Select ‘associated with GO term’ from the drop-down menu.
 Type ‘transcription factor’ and select ‘transcription factor binding’ from the list of GO terms.
 Click on the plus symbol.
 Select ‘associated with Anatomy Term’ and begin typing ‘telencephalon’.
 Select ‘telencephalon’ from the list of anatomy terms.
 Click ‘Go’ to perform your query.
 View the returned list of entries, click on an EMAGE ID for more details.
1. Select a Gene
Ontology (GO) term
using predictive text
2. Click on the plus
symbol to add
further nodes to
your combinatorial
query
3. View list of
entries, click on an
EMAGE ID for more
details
2.5. Using the spatial similarity tool

A novel analytical tool that has been developed by EMAGE is the Embryo Space paint tool
(see worksheet 2.3).

This tool allows a user to paint a region on an image of a wholemount embryo and use this
painted domain to query the EMAGE database.

This query tool returns a ranked list of spatially mapped gene expression patterns ordered by
spatial similarity to the query region.

For any mapped EMAGE entry, a modified version of this algorithm is used in the ‘Find
Similar Expression Patterns’ feature.
The ‘Find
Similar’ icon
appears
alongside all
EMAGE entries
with spatially
mapped data
Clicking on the
‘Find Similar’
icon will return a
list of entries
that are ranked
by similarity to
the mapped
expression
pattern
2.6. Spatial analysis of signaling pathways

EMAGE Pathway allows users to view and compare multiple gene expression patterns.

EMAGE Pathway lists all the source images and spatial annotations for a given gene, at each
Theiler stage, in a single ‘gene strip’ that describes multiple EMAGE entries.

The Pathway feature organizes these gene strips using an outside resource – the Kyoto
Encyclopedia of Genes and Genomes (KEGG) – and uses KEGG Pathway Maps to order gene
strips according to their involvement in key signaling pathways.
EMAGE Pathways uses KEGG to find gene expression patterns associated with specific pathways
and/or specific tissues. In this example, EMAGE Pathways is used to find components of the Notch
signaling pathway that are important in somitogenesis. Two tabs are returned from a pathway query.
The first tab (a) is entitled ‘pathway gene’ and shows gene expression summaries associated with all
gene components of the KEGG Notch signaling pathway. Spatially mapped EMAGE data is shown in
the Gene column; if spatially mapped data is unavailable, a thumbnail will display ‘text annotation
only’ (b). The Heatmap column shows the union of all spatially mapped expression patterns for a
single KEGG pathway at a single stage (c).
Clicking on the second tab (d) allows access to the KEGG pathway diagram (e). The KEGG pathway
diagram is marked up to show data available in EMAGE for a given gene by highlighting these genes in
red. A subset of Notch signaling pathway genes can be implicated in somitogenesis by virtue of their
gene expression patterns (f).
For workshop attendee:
 From the EMAGE Web Interface, click on ‘Pathway’.
 Select ‘KEGG Pathway Definition’ from the drop-down menu.
 Begin typing ‘Wnt signaling pathway’ and select this from the list.
 Click ‘Go’ to perform your query.
 A list of ‘gene strips’ are returned, with a Heatmap displaying the union of mapped
expression domains for a single Theiler stage.
 Zoom in on the Heatmap to get an overview of spatial regions that are enriched in Wnt
signaling pathway gene expression.
 Click on a Heatmap to return a list of genes.
 Click on a thumbnail image to view an EMAGE entry.
1. Select a
KEGG
Pathway
2. Browse
expression
patterns of
gene found
in this
pathway
3. Zoom in
on the
Heatmap to
get an
overview of
spatial
regions that
are
enriched in
pathway
gene
expression
For workshop attendee:
 Return to the EMAGE Web Interface, click on ‘Pathway’.
 Select ‘KEGG Pathway Definition’ from the drop-down menu.
 Begin typing ‘Hedgehog signaling pathway’ and select this from the list.
 Click ‘Go’ to perform your query.
 Zoom in on the Heatmap to get an overview of spatial regions that are enriched in Hedgehog
signaling pathway gene expression.