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Yeast Expression Analysis And Visualization
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Data Analysis and Visualizations
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The yeast expression database we used are the results of
De Risi, et.al. Science, 278, 680-686 (1997).
In this study, two yeast cell populations were studied, one growing
anaerobically (reference), the other having undergone a diauxic shift,
from an anaerobic to an aerobic metabolism. The object of the study was
to assay for changes in gene expression over the time course of the
diauxic shift and to correlate the gene subsets whose synthesis was induced
or repressed with the known enzyme metabolic pathways involved in the diauxic
shift. These altered expression genes may be known or unknown.
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Total mRNA was isolated from each yeast cell population at a
series of time points over 21 hrs. The mRNAs were copied into cDNA
copies using reverse transcriptase in the presence of fluorescent
Cy3(Green)- or Cy5(Red)- labelled deoxyuridine triphosphate. For
the initial 'reference' time point, Cy3(G) label was used. For
each subsequent time point Cy5(R) label was used. Each Cy5(R)
labelled time point was then mixed with the 'reference' Cy3(G)
labelled cDNA population and the mixtures were independently
applied to and hybridized to a DNA microarray. Following
hybridization and washing, the relative fluorescence intensity
for Cy3(G) and Cy5(R) was measured at each DNA array element
position, representing 6400 genes or open reading frames (ORFs).
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The following values were then computed:
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G corrected for background fluorescence
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R corrected for fluorescence background;
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fluorescence ratio G/R (ratio). For microarray readings that
were corrupt, a value of 1.0 was assigned.
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log(ratio)
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absolute value of log(ratio)
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n-fold change in expression value at each time point (time1
through time7), transformed to remove the discontinuity
between -1 and 1, computed as:
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ratio-1
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if(ratio >= 1)
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-(1/ratio)
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if(ratio < 1)
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We use these computed values in the visualizations referenced
below.
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LINK 1:
Data available from Stanford University. (Off site link)
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LINK 2:
The defined DeRisi et.al. yeast expression profile clusters.
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LINK 3:
Visualizations from the initial analysis.
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LINK 4:
Multivariate visualizations.
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LINK 5:
Visualizations based on statistical analysis.
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LINK 6:
Kohonen neural network visualizations.
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LINK 7:
Visualization grand tour. (14 Mb mpg file of 1400 frames)
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