Carmen E. Castaneda: Week 12

Clustering and Gene Ontology Analysis with STEM

Analyzing and Interpreting STEM Results Select one of the profiles you saved in the previous step for further intepretation of the data. We suggest that you choose one that has a pattern of up- or down-regulated genes at the early (first three) timepoints. Answer the following:

• Why did you select this profile? In other words, why was it intersting to you?

I picked this profile because it showed an interesting pattern of fluctuation in its early time periods. I would want to see how the cold shock affected these genes and what kind of genes where involved.

• How many genes belong to this profile?

There are 128.5 genes in this profile.

• How many genes were expected to belong to this profile?

There were 82 genes expected to belong to this profile.

• What is the p value for the enrichment of genes in this profile? Bear in mind that in last week's assignment, you computed p values to determine whether each individual gene had a significant change in gene expression at each time point. This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.

The p value for the enrichment of genes in this profile is 7.07 x 10^(-7)

• Open the GO list file you saved for this profile in Excel. This list shows all of the Gene Ontology terms that are associated with genes that fit this profile. Select the third row and then choose from the menu Data > Filter > Autofilter. Filter on the "p-value" column to show only GO terms that have a p value of < 0.05. How many GO terms are associated with this profile at p < 0.05?

There are 24 GO terms associated with this profile at p < 0.05.

• The GO list also has a column called "Corrected p-value". This correction is needed because the software has performed thousands of significance tests. Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05. How many GO terms are associated with this profile with a corrected p value < 0.05?

There are zero GO terms associated with this profile.

• Select 10 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05). Look up the definitions for each of the terms at http://geneontology.org. Write a paragraph that describes the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms?
  • sulfur compound biosynthetic process
  • transition metal ion transport
  • sulfur compound metabolic process
  • ion transport
  • amine metabolic process
  • protein folding
  • carboxylic acid metabolic process
  • organic acid metabolic process
  • cellular nitrogen compound biosynthetic process

plasma membrane