The Mouse Gene-Expression Information Resource

1
The Mouse Gene-Expression Information Resource

• Richard Baldock
• MRC Human Genetics Unit, Edinburgh
• http//genex.hgu.mrc.ac.uk/

2
How does this embryo develop?
11.5-day old mouse embryo
3
in situ hybridization data
4
Image capture
Optical Projection Tomography
James Sharpe et al, Science 296(2002)541-545
5
Flourescent Double Labelling
Blue - HNF3b Green - neurofilament Red -
autoflourescence of heart
6
Words are not enough -
mouse E12.5 nasal region Msx1 mRNA, net
7
spatial indexing
8
Bioinformatics frameworks
9
Map to the same framework
Gene expression patterns
Mutant phenotypes
Cell death, proliferation, migration.
Published results of manipulation experiments
10
Map to the same framework
What kind of framework ?
Gene expression patterns
Mutant phenotypes
Cell death, proliferation, migration.
Published results of manipulation experiments
11
Map to the same framework
Gene expression patterns
Mutant phenotypes
Cell death, proliferation, migration.
Published results of manipulation experiments
12
The structure of the Mouse Atlas

• Image
• Text
• Link

- volumetric digital model embryos
- controlled anatomical vocabulary
- named parts are delineated in the models
13
Image - Model embryos
Time (E days)
1 2 12 13 14
26 27
Theiler Stage
Birth
14
Model embryos
15
Voxels
building blocks of the 3D models
16
Text - Anatomy
Time (E days)
1 2 12 13 14
26 27
Theiler Stage
Birth
17
Resolution of the vocabulary
Jonathan Bard, Matt Kaufman
18
Voxels
Pigeon-holes in a spatial database
19
Mapping anatomy to the models

• comprehensive
• exclusive
• not detailed

Renske Brune
20
EMAP
Spatio-Temporal Framework for Developmental
Biology
Space
21
EMAP Time
22
Using the Atlas gene-expression database
anatomical name
23
Mouse Gene-Expression Information Resource

• Staging criteria (html)
• Spatially mapped data (EMAGE)
• Anatomy Ontology mapped data (MGI/GXD)
• Interfaces/software

24
Staging and Other data
25
MGI/GXD
26
Mouse Atlas - EMAP EMAGE
27
Tools
28
J B L Bard, R M Brune, M Kaufman, C Oram, L
Richardson, D Smith
M Ringwald