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The Mouse Gene-Expression Information Resource

The Mouse Gene-Expression Information Resource. Richard Baldock MRC Human Genetics Unit, Edinburgh http://genex.hgu.mrc.ac.uk/. How does this embryo develop?. 11.5-day old mouse embryo. in situ hybridization data. Image capture. Optical Projection Tomography.

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The Mouse Gene-Expression Information Resource

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

  2. How does this embryo develop? 11.5-day old mouse embryo Richard Baldock

  3. in situ hybridization data Richard Baldock

  4. Image capture Optical Projection Tomography James Sharpe et al, Science 296(2002)541-545 Richard Baldock

  5. Flourescent Double Labelling Blue - HNF3b Green - neurofilament Red - autoflourescence of heart Richard Baldock

  6. Words are not enough - mouse E12.5 nasal region Msx1 mRNA, net Richard Baldock

  7. Semi-automatic image mapping gene expression database spatial indexing Richard Baldock

  8. gene expression mutant phenotype cell behaviour Bioinformatics frameworks Richard Baldock

  9. Explore relationships between different data Map to the same framework Gene expression patterns Mutant phenotypes Cell death, proliferation, migration. Published results of manipulation experiments Richard Baldock

  10. Explore relationships between different data Map to the same framework What kind of framework ? Gene expression patterns Mutant phenotypes Cell death, proliferation, migration. Published results of manipulation experiments Richard Baldock

  11. Explore relationships between different data Map to the same framework Gene expression patterns Mutant phenotypes Cell death, proliferation, migration. Published results of manipulation experiments Richard Baldock

  12. The structure of the Mouse Atlas • Image • Text • Link - volumetric digital model embryos - controlled anatomical vocabulary - named parts are delineated in the models Richard Baldock

  13. 1 8 8.5 9 18 Image - Model embryos Time (E days) 1 2 12 13 14 26 27 Theiler Stage Birth Richard Baldock

  14. images of serial, stained sections stacked and aligned ….to produce a 3D block Model embryos Richard Baldock

  15. Voxels building blocks of the 3D models Richard Baldock

  16. 1 8 8.5 9 18 Text - Anatomy Time (E days) 1 2 12 13 14 26 27 Theiler Stage Birth Richard Baldock

  17. Resolution of the vocabulary Jonathan Bard, Matt Kaufman Richard Baldock

  18. anatomical name Voxels Pigeon-holes in a spatial database Richard Baldock

  19. Mapping anatomy to the models • comprehensive • exclusive • not detailed Renske Brune Richard Baldock

  20. Iconic Symbolic EMAP: Spatio-Temporal Framework for Developmental Biology Space Richard Baldock

  21. Birth Time (E days) … 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 Theiler Stage … 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 E0 E17.5 Anatomy ontology: structure, development, lineage EMAP: Time Richard Baldock

  22. gene expression mutant phenotype cell behaviour bibliographic references Using the Atlas: gene-expression database anatomical name Richard Baldock

  23. Mouse Gene-Expression Information Resource • Staging criteria (html) • Spatially mapped data (EMAGE) • Anatomy Ontology mapped data (MGI/GXD) • Interfaces/software Richard Baldock

  24. Staging and Other data Richard Baldock

  25. MGI/GXD Richard Baldock

  26. Mouse Atlas - EMAP & EMAGE Richard Baldock

  27. Tools Richard Baldock

  28. Biomedical Sciences, University of Edinburgh 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 Informatics, Jackson Laboratory Computing and Electrical Engineering Heriot Watt University Hubrecht Laboratorium, Utrecht A Burger K Lawson J B L Bard, R M Brune, M Kaufman, C Oram, L Richardson, D Smith M Ringwald Richard Baldock

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