CSC8309 -- Gene Expression and Proteomics

You can open the file that you created with TopTable using excel or open office.

If we select genes with a p<0.05 as being significant, which tissue has the least number of differentially expressed genes when compared to the HUVECs?

Using afflmGUI, set up and compute a set of contrasts that compares the eye tissues to each other.

Using a p-value criterion as above, what are the two most similar tissues?

Note that in the comparisons a number of probesets begin with AFFX and appear to be differentially expressed.

What do these AFFX probesets represent on an Affymetrix chip?

From this we can see the tissues from the eye, although developmentally differentiated are clearly very similar to each other. The HUVEC line differs extensively in its expression of genes when compared to the eye tissues. Perhaps the use of HUVEC lines for the study of epithelial pathophysiology for ocular disorders is not as good a model as it might be.