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Data visualization in the post-genomics era

Data visualization in the post-genomics era. Carol Morita Genentech, Inc. Pre-Genomics : assembling the pieces. GenBank. Genome project initiated. Where we are today. American view of the genome. Entrez Genome Browser. National Center for Biotechnology Information

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Data visualization in the post-genomics era

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  1. Data visualization in the post-genomics era Carol Morita Genentech, Inc.

  2. Pre-Genomics:assembling the pieces GenBank Genome project initiated

  3. Where we are today

  4. American view of the genome Entrez Genome Browser National Center for Biotechnology Information National Institutes of Health http://www.ncbi.nlm.nih.gov:80/PMGifs/Genomes/euk_g.html

  5. European view of the genome Ensembl Genome Browser European Molecular Biology Laboratory http://www.ensembl.org/

  6. What the genomes of model organisms tell us Almost every human gene has a counterpart in the mouse and some blocks of DNA are proving impossible to tell apart

  7. Human genes mapped onto mouse chromosomes If we are so similar genetically,why are we so different?

  8. Proteomics:the real work begins Definition: Description and functional characterization of the full complement of an organism’s proteins what’s at play… • Multiple proteins can be derived from one gene • Protein interactions can be complex and are poorly understood • ‘Plasticity’ of the genome • Spatial and temporal regulation

  9. Increased diversity due to alternative splicing gene A

  10. Alternative splicing • Plays an important role in: • expanding protein diversity • generating proteins with subtle or opposing functional roles • enabling an organism to respond to environmental pressures • >35% of human genes undergo alternate splicing; probably higher

  11. Complexity due to protein interactions Death Receptor Signaling pathway

  12. DNA Microarrays Microarray chips may contain 50,000 known DNA fragments on a single slide

  13. Visualizing microarray data Source: Silicon Genetics: GeneSpring

  14. Limitations of DNA microarrays • ‘snapshots’ of the DNA activity in a cell -- prefer movies! • Many important biological events cannot be detected because transcription of DNA is not involved • Protein array technology is still in its infancy

  15. The curse of dimensionality Source: Klausner, 2002 Cancer Cell1, p. 3-10

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