2. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 1 The Mouse Gene-Expression Information Resource Richard Baldock MRC Human Genetics Unit, Edinburgh http://genex.hgu.mrc.ac.uk/

3. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 2 11.5-day old mouse embryo How does this embryo develop?

4. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 3 in situ hybridization data

5. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 4 Image capture James Sharpe et al, Science 296(2002)541-545 Optical Projection Tomography

6. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 5 Flourescent Double Labelling Blue - HNF3b Green - neurofilament Red - autoflourescence of heart

7. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 6 mouse E12.5 nasal region Msx1 mRNA, net Words are not enough -

8. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 7 spatial indexing gene expression database Semi-automatic image mapping

9. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 8 Bioinformatics frameworks gene expression mutant phenotype cell behaviour

10. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 9 Gene expression patterns Mutant phenotypes Cell death, proliferation, migration. Published results of manipulation experiments Map to the same framework Explore relationships between different data

11. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 10 Gene expression patterns Mutant phenotypes Cell death, proliferation, migration. Published results of manipulation experiments Map to the same framework Explore relationships between different data What kind of framework ?

12. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 11 Gene expression patterns Mutant phenotypes Cell death, proliferation, migration. Published results of manipulation experiments Map to the same framework Explore relationships between different data

13. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 12 The structure of the Mouse Atlas Image Text Link - controlled anatomical vocabulary - volumetric digital model embryos - named parts are delineated in the models

14. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 13 Image - Model embryos Time (E days) Theiler Stage Birth 1 2 12 13 14 26 27 18 8.5 918

15. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 14 Model embryos images of serial, stained sections stacked and aligned ….to produce a 3D block

16. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 15 Voxels building blocks of the 3D models

17. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 16 Text - Anatomy Time (E days) Theiler Stage Birth 1 2 12 13 14 26 27 18 8.5 918

18. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 17 Resolution of the vocabulary Jonathan Bard, Matt Kaufman

19. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 18 Voxels Pigeon-holes in a spatial database anatomical name

20. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 19 Mapping anatomy to the models comprehensive exclusive not detailed Renske Brune

21. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 20 EMAP: Spatio-Temporal Framework for Developmental Biology Iconic Symbolic Space

22. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 21 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 E0E17.5 Anatomy ontology: structure, development, lineage

23. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 22 anatomical name gene expression mutant phenotype cell behaviour bibliographic references Using the Atlas: gene-expression database

24. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 23 Mouse Gene-Expression Information Resource Staging criteria (html) Spatially mapped data (EMAGE) Anatomy Ontology mapped data (MGI/GXD) Interfaces/software

25. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 24 Staging and Other data

26. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 25 MGI/GXD

27. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 26 Mouse Atlas - EMAP & EMAGE

28. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 27 Tools

29. MRC Human Genetics Unit www.hgu.mrc.ac.uk 7-Feb-02Richard Baldock 28 MRC Human Genetics Unit, Edinburgh R A Baldock, N Burton, W Hill, D Houghton K Opstad, A Ross, M Stark, A WaterHouse, Y Yang, D Davidson, G Feng, J Rao M Ringwald Biomedical Sciences, University of Edinburgh J B L Bard, R M Brune, M Kaufman, C Oram, L Richardson, D Smith Hubrecht Laboratorium, Utrecht K Lawson Computing and Electrical Engineering Heriot Watt University A Burger Informatics, Jackson Laboratory