Data visualization in the post-genomics era Carol Morita Genentech, Inc.
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Transcript of Data visualization in the post-genomics era Carol Morita Genentech, Inc.
Data visualization in the post-genomics era
Carol MoritaGenentech, Inc.
Pre-Genomics: assembling the pieces
Genome project initiated
GenBank
Where we are today
Organism Size (bp) # genes
E.coli (bacteria) 4.67 million 3,237
Arabidopsis (plant) 100 million 25,000
C. elegans (worm) 97 million 19,099
Drosophila (fly) 136 million 13,061
Mouse 3 billion ~40,000
Human 3 billion ~40,000
American view of the genome
Entrez Genome Browser
National Center for Biotechnology InformationNational Institutes of Health
http://www.ncbi.nlm.nih.gov:80/PMGifs/Genomes/euk_g.html
European view of the genome
Ensembl Genome Browser
European Molecular Biology Laboratoryhttp://www.ensembl.org/
What the genomes of model organisms tell us
Maturation 10 days 9 weeks 20-25 years
Genome 165 million bp 3 billion bp 3 billion bp
Genes 13,600 ~40,000 ~40,000
Almost every human gene has a counterpart in the mouse and some blocks of DNA are proving impossible to tell apart
If we are so similar genetically,why are we so different?
Human genes mapped onto mouse chromosomes
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
Increased diversity due to alternative splicing
gene A
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
Complexity due to protein interactions
Death Receptor Signaling pathway
DNA Microarrays
Microarray chips may contain 50,000
known DNA fragments on a single slide
Visualizing microarray data
Source: Silicon Genetics: GeneSpring
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
Source: Klausner, 2002 Cancer Cell1, p. 3-10
The curse of dimensionality