Download Microarrays: An introduction to the bio

DNA – RNA – Protein
transcription – translation
Double stranded DNA
Microarrays:
An introduction to the biotechnology
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B
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Splitting into two single strands
B
mRNA Transcription from strand B
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B
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Transcribed RNA
RNA splicing results in an mRNA molecule
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mRNA is translated into protein
Jan Komorowski
Central dogma of molecular
biology
Gene expression patterns in
physiology and pathophysiology
normal resting normal stimulated
gastric mucosa gastric mucosa
Jan Komorowski
gastric cancer
type A
type B
Jan Komorowski
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Sample Gene Expression
Regulation
• Physiological and pathophysiological responses
are associated with specific changes in cellular
gene expression
• Insight into the specific patterns of gene
expression associated with physiological and
pathophysiological responses and conditions
enable hypotheses about gene function and
medical diagnosis
a
c
c
f
f
e
b
Why is gene expression worth
studying?
b
d
¾ Physiology is the study of the body in a healthy state
¾ Pathophysiology is the study of disease states.
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Jan Komorowski
Jan Komorowski
Overview
Pharmacogenomics
• Genetic variability in drug response
– Sensitivity of some individuals to debrisoquine: certain
Cytochrome P450 gene mutations incapacitate the protein
enzyme and cause poor drug metabolism, eventually leading to
poisoning due to the extensive exposure to the drug.
– Obtain a DNA test of the patient, make a decision
based on his/her genetic make-up
– Large DB’s of genetic and drug response data are
commercially built for the discovery of geneticallybased rules of drug selection (e.g. Genometrix Inc.)
And much more!
Jan Komorowski
Jan Komorowski
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Hybridization
Image after scanning
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Extracting Data
Jan Komorowski
Hierarchical Cluster Analysis
Experiments
Fluorescence ratios
Samples 1 2 3 4 5 6
Gene 1
Red > green: up-regulated
Gene 7
Red = green
200 10000 50.00 5.64
4800 4800 1.00 0.00
9000
300 0.03 -4.91
Cy3
Cy5
Genes
Gene 6
Gene 8
Green > red : down-regulated
Gene 3
Not available
Cy5 log ( Cy5 )
Cy3
Cy3
Jan Komorowski
Jan Komorowski
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In a few words,
microarrays are …
Data analysis goals
… devices
for measuring
relative gene expression levels
of a large number of preselected genes
What to study?
• Classes of experiments; changes in
expression levels in tissue samples with
different e.g. diseases, treatments,
environmental effects etc.
• Classes of genes; expression profiles of
genes with similar biological function
• Both of the above
Jan Komorowski
Data analysis methods
Jan Komorowski
Example
• Unsupervised learning (clustering, class
discovery); used to “discover” natural
groups of genes/experiments e.g.
– discover subclasses of a form of cancer that is
clinically homogenous
• Supervised learning; used to “learn” a
model of a set of predefined classes of
genes/experiments e.g.
– diagnosis of cancer/subclasses of cancer
Jan Komorowski
96 normal and malignant
lymphocyte samples
Almost 20 000 cDNA clones
Two sub-clusters of DLBCL
were shown to include
patients with significantly
different expected survival
time!
Alizadeh et al., Distinct
types of diffuse large Bcell lymphoma
identified by gene
expression profiling,
Nature, 403:503-511,
2000.
Jan Komorowski
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