Bioinformatic

Microarray Data Analysis for Budding Yeast

by

Your Name

MACROBUTTON AcceptAllChangesShown "[Click and type class name]

MACROBUTTON AcceptAllChangesShown "[Type class number]

MACROBUTTON AcceptAllChangesShown "[Type instructor 's name]

MACROBUTTON AcceptAllChangesShown "[Type date]

Analyzing Output Data from a DNA Microarray using SNOMAD

DNA Microarray data are obtained by the levels of intensities for each element of the matrix . These intensities can be compared in to determine a correlation between these sets of data . A statistically significant correlation between the two intensity data sets may indicate that two genes are co-expressed

. The program SNOMAD enables the refinement of paired microarray data . In effect , SNOMAD normalizes and standardizes the data so that a precise comparison may be made between the two intensity data

First plot : uncorrected data

The plot shows the raw data plotted with intensity one on the y-axis and intensity two on the x-axis

Second plot : global mean normalization data

The plot represents the data of the two intensity data sets normalized This is an indication of how much each point deviates from the global mean after normalization . The x /y line is the global mean . The strongest correlation is seen up until y 4 and x 4 where the bulk of the points are located around the line . This means that the genes in that region of the matrix may show a high level of co-expression . Ideally each point should be evenly distributed on either side of the line

Third plot : log /log transformation

However , more mathematical manipulations are needed to eliminate artifacts . After the log transformation , the points are better spread on either side of the line as well as along the line . The log of intensity one versus the log of intensity two shows a better correlation by taking the log of both intensities in to compare them better in terms of expression levels . If the points are located above the line it means that the expression levels of intensity one genes are higher

Fourth plot : mean log intensity x (mean expression level ) versus log ratio (y differential expression

This plot tries to relate the mean expression level of both intensity data sets with their ratio . The ratio gives you a measure of the magnitude of expression levels with one intensity data set with the second one . As shown by the plot , the ratio of intensity one over intensity two (y-axis ) shows a clustering of the points at a value ranges from 0 .2 going to zero . So , intensity one is 0 .2 times brighter than intensity two , indicating a higher expression level for data set one . This correlates with the previous plot results . The bulk of the points with respect to the x-axis are located between zero and -0 .5 which signifies that the mean intensity is low . This can be explained by the fact that if that many genes from intensity one have a higher expression level than intensity two , their mean intensity is lower because even though they have a higher expression level , there...