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An Introduction to DNA MicroarraysAn Introduction to DNA Microarrays
Jack NewtonUniversity of Alberta
DNA Microarrays
OverviewOverview
Introduction to DNA MicroarraysDNA Microarray AnalysisDNA Microarray Data Characteristics
DNA Microarrays
What are DNA Microarrays?What are DNA Microarrays?
A recent technology that can measure the expression level of thousands of genes at once
A large number of DNA fragments are attached in a systematic way to a solid substrate
DNA Microarrays
DNA Microarray ImageDNA Microarray Image
Reference cDNA
Experimental cDNA
UpregulatedDownregulated
Gene GTF4
DNA Microarrays
How DNA Microarrays WorkHow DNA Microarrays Work
A T G C A A T
T G A C T G C
A G T C G T G
G T C T G A T
T A A G T C GGene TEF4: … …A G T C
T
A
A
G
T
C
G
DNA Microarrays
How DNA Microarrays WorkHow DNA Microarrays Work
DNA microarrays measure gene expression levels by measuring mRNA abundance
Cambell, Neil (1996). Biology.Benjamin/Cummings Publishing.
DNA Microarrays
DNA Microarrays and DNA Microarrays and Gene ExpressionGene Expression
Traditional view of gene expression:– A single gene codes for a single protein
Modern view of gene expression:– A single gene may code for several proteins as a result
of alternate splicing of mRNA and post-translational modifications
– Genes act in concert, not in isolation
Thus, we need to observe genes acting together, not in isolation
DNA Microarrays
From Gene Science to From Gene Science to Genome ScienceGenome Science
DNA Microarrays allow us to see the gene expression levels for tens of thousands of genes at once.
A microarray of 50,000 unique cDNAs allows the expression monitoring of the entire human genome in a single hybridization.
DNA Microarrays
DNA Microarray AnalysisDNA Microarray Analysis
What kinds of questions do we want to ask?– What genes have similar function?– What regulatory pathways exist?– Can we subdivide experiments or genes into
meaningful classes?– Can we correctly classify an unknown experiment or
gene into a known class?– Can we make better treatment decisions for a cancer
patient based on his or her gene expression profile?
DNA Microarrays
Characteristics of DNA Characteristics of DNA Microarray DataMicroarray Data
Extremely high dimensionality– Experiment = (gene1, gene2, …, geneN)– Gene = (experiment1, experiment2, …, experimentM)– N is often on the order of 104
– M is often on the order of 101
Noisy data– Normalization and thresholding are important
Missing data– For some experiments a given gene may have failed
hybridizing
DNA Microarrays
Characteristics of DNA Characteristics of DNA Microarray Data Microarray Data
(Continued)(Continued)
> 8.0
> 1.7
> 2.8
> 1.7
1:1
> 4.8
> 2.8
> 4.8
> 8.0
Gene 1
Gene 2
Gene 3
Gene 4
Exper
imen
t 1
Exper
imen
t 2
Exper
imen
t 6
Exper
imen
t 4
Exper
imen
t 5
Exper
imen
t 3
Exper
imen
t 7
Exper
imen
t 8
Exper
imen
t 9
Exper
imen
t 10
Gene 5
Gene 10,000
… …
DNA Microarrays
Application: ClusteringApplication: Clustering
Eisen et al. formulated a method to group genes with similar patterns of expression together.
Provides scientists with an invaluable tool to visualize and interpret DNA microarray data.
A recently published article in Nature applied this technique to breast cancer research.
DNA Microarrays
Application: ClusteringApplication: Clustering
Perou, Charles M., et al. Nature, 406, 747-752 , 2000.
DNA Microarrays
Application: ClusteringApplication: Clustering
Clustering analysis identified four distinct tumor types that had not previously been reported.
Previous studies examining the same genes one at a time did not reveal that certain groups of genes play an important role in tumor development.
“When you look at one gene at a time, you can't see relationships between genes and groups of genes.” – M. Perou, co-author of study.
