mrc human genetics unit 7-feb-02richard baldock 1 the mouse gene-expression information resource...

7-Feb-02Richard Baldock

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MRC Human Genetics Unit www.hgu.mrc.ac.uk

The Mouse Gene-Expression Information Resource

Richard BaldockMRC Human Genetics Unit, Edinburgh

http://genex.hgu.mrc.ac.uk/


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11.5-day old mouse embryo

How does

this embryo develop?


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in situ hybridization data


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Image capture

James Sharpe et al, Science 296(2002)541-545

Optical Projection Tomography


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Flourescent Double Labelling

Blue - HNF3b

Green - neurofilament

Red - autoflourescence of heart


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mouse E12.5 nasal region Msx1 mRNA, net

Words are not enough -


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spatial indexing

gene expression database

Semi-automatic image mapping


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Bioinformatics frameworks

gene expressionmutant phenotype

cell behaviour


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Gene expression patterns

Mutant phenotypes

Cell death, proliferation,migration.

Published results of manipulation experiments

Map to the same framework

Explore relationships between different data


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Mutant phenotypes





What kind of

framework

?


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Mutant phenotypes






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The structure of the Mouse Atlas

• Image

• Text

• Link

- controlled anatomical vocabulary

- volumetric digital model embryos

- named parts are delineated in the models


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Image - Model embryos

Time (E days)

Theiler Stage

Birth

1 2 12 13 14 26 27

1 8 8.5 9 18


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Model embryos

images of serial, stained sections

stacked and aligned

….to produce a 3D block


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Voxels building blocks of the 3D models


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Text - Anatomy

Time (E days)

Theiler Stage

Birth

1 2 12 13 14 26 27

1 8 8.5 9 18


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Resolution of the vocabulary

Jonathan Bard, Matt Kaufman


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Voxels Pigeon-holes in a spatial database

anatomical name


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Mapping anatomy to the models

• comprehensive

• exclusive

• not detailed

Renske Brune


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EMAP: Spatio-Temporal Framework for Developmental Biology

Iconic SymbolicSpace


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EMAP: Time

Time (E days)

Theiler Stage

Birth

… 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27

… 4.5 5 6 6.5 7 7.5 8 8.5 9 9.5 10 10.5 11 11.5 12 12.5 13 14 15 16 17 18

E0 E17.5Anatomy ontology: structure, development, lineage


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anatomical name

gene expression

mutant phenotype

cell behaviour

bibliographic references

Using the Atlas: gene-expression database


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Mouse Gene-Expression Information Resource

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


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Staging and Other data


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MGI/GXD


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Mouse Atlas - EMAP & EMAGE


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Tools


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MRC Human Genetics Unit, EdinburghR A Baldock, N Burton, W Hill, D HoughtonK Opstad, A Ross, M Stark, A WaterHouse,Y Yang, D Davidson, G Feng, J Rao

M Ringwald

Biomedical Sciences, University of EdinburghJ B L Bard, R M Brune, M Kaufman, C Oram, L Richardson, D Smith

Hubrecht Laboratorium, UtrechtK Lawson

Computing and Electrical Engineering Heriot Watt UniversityA Burger

Informatics, Jackson Laboratory

mrc human genetics unit 7-feb-02richard baldock 1 the mouse gene-expression information resource...

Documents

mgigxd slide

heart slide

lineage slide

tools slide

different data slide

geneexpression database

d block slide

matt kaufman slide