DNA Microarrays
Patrick Schmid
CSE 497
Spring 2004
What is a DNA Microarray?
Also known as DNA Chip
Allows simultaneous measurement of the
level of transcription for every gene in a
genome (gene expression)
Transcription?
Process of copying of DNA into messenger RNA
(mRNA)
Environment dependant!
Microarray detects mRNA, or rather the more
stable cDNA
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What is a DNA Microarray? (cont.)
Cheung et al. 1999
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How do we manufacture a microarray?
Start with individual genes, e.g. the ~6,200
genes of the yeast genome
Amplify all of them using polymerase chain
reaction (PCR)
“Spot” them on a medium, e.g. an ordinary
glass microscope slide
Each spot is about 100 µm in diameter
Spotting is done by a robot
Complex and potentially expensive task
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How do we manufacture a microarray?
Cheung et al. 1999
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Example
Remember the flash animation?
Yeast
Grow in aerobic and anaerobic environment
Different genes will be activated in order to
adapt to each environment
Extract mRNA
Convert mRNA into colored cDNA
(fluorescently labeled)
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Example (cont.)
Mix cDNA together
Hybridize cDNA with array
Each cDNA sequence hybridizes specifically
with the corresponding gene sequence in the
array
Wash unhybridized cDNA off
Read array with laser
Analyze images
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Overview of Example
Brown & Botstein, 1999
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Reading an array
Laser scans array and produces images
One laser for each color, e.g. one for green, one for
red
Image analysis, main tasks:
Noise suppression
Spot localization and detection, including the extraction of
the background intensity, the spot position, and the spot
boundary and size
Data quantification and quality assessment
Image Analysis is a book on its own:
Kamberova, G. & Shah, S. “DNA Array Image Analysis
Nuts & Bolts“. DNA Press LLC, 2002
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Reading an array (cont.)
Block Column Row Gene Name Red Green Red:Green
Ratio
1 1 1 tub1 2,345 2,467 0.95
1 1 2 tub2 3,589 2,158 1.66
1 1 3 sec1 4,109 1,469 2.80
1 1 4 sec2 1,500 3,589 0.42
1 1 5 sec3 1,246 1,258 0.99
1 1 6 act1 1,937 2,104 0.92
1 1 7 act2 2,561 1,562 1.64
1 1 8 fus1 2,962 3,012 0.98
1 1 9 idp2 3,585 1,209 2.97
1 1 10 idp1 2,796 1,005 2.78
1 1 11 idh1 2,170 4,245 0.51
1 1 12 idh2 1,896 2,996 0.63
1 1 13 erd1 1,023 3,354 0.31
1 1 14 erd2 1,698 2,896 0.59
Campbell & Heyer, 2003
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Real DNA Microarray
Campbell & Heyer, 2003
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Y-fold
Biologists rather deal with folds than with ratios
A fold is nothing else than saying “times”
We express it either as a Y-fold repression, or a Y-
fold induction
It is calculated by taking the inverse of the ratio
Ratio of 0.33 = 3-fold repression
Ratio of 10 = 10-fold induction
Fractional ratios can cause problems with
techniques of analyzing and comparing gene
expression patterns
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Color Coding
Tables are difficult to read Campbell & Heyer, 2003
Data is presented with a color scale
Coding scheme:
Green = repressed (less mRNA) gene in experiment
Red = induced (more mRNA) gene in experiment
Black = no change (1:1 ratio)
Or
Green = control condition (e.g. aerobic)
Red = experimental condition (e.g. anaerobic)
We only use ratio
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Logarithmic transformation
log2 is commonly used
Sometimes log10 is used
Example:
log2(0.0625) = log2(1/16) =
log2(1) – log2(16) = -log2(16) = -4
log2 transformations ease identification of doublings
or halvings in ratios
log10 transformations ease identification of order of
magnitude changes
Key attribute: equally sized induction and repression
receive equal treatment visually and mathematically
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Complication: Time Series
Biologists care more about the process of
adaptation than about the end result
For example, measure every 2 hours for 10 hours
(depletion of oxygen)
31,000 gene expression ratios
Or 6,200 different graphs with five data points each
Question: Are there any genes that responded in
similar ways to the depletion of oxygen?
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