Imacarae Week 9

Imacarae's User Page

Assignment	Shared Entries	Individual Entries
Week 1	Class Journal Week 1	----
Week 2	Class Journal Week 2	Imacarae Week 2
Week 3	Class Journal Week 3	HSF1/YGL073W Week 3
Week 4	Class Journal Week 4	Imacarae Week 4
Week 5	Class Journal Week 5	CancerSEA Week 5
Week 6	Class Journal Week 6	Imacarae Week 6
Week 7	Class Journal Week 7	Imacarae Week 7
Week 8	Class Journal Week 8	Imacarae Week 8
Week 9	Class Journal Week 9	Imacarae Week 9
Week 10	Class Journal Week 10	Imacarae Week 10
Week 11	Sulfiknights	Imacarae Week 11
Week 12/13	Sulfiknights	Sulfiknights DA Week 12/13
----	Sulfiknights	Sulfiknights DA Week 14

Methods and Results

1. Analyzing and Interpreting STEM Results
   1. I selected Profile 45 for further intepretation of the data.
      • Why did you select this profile? In other words, why was it interesting to you?

        - I selected this Profile 45 because it was the first profile on the STEM page. It has the most genes assigned to it out of all of the dCIN5 STEM profiles.

      • How many genes belong to this profile?

        - There are 455 genes assigned to this profile.

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

        - There are 36.5 genes expected in this profile.

      • What is the p value for the enrichment of genes in this profile? Bear in mind that we just finished computing 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 p=0.00.

      • 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 65 GO terms that are associated with Profile 45 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 8 GO terms associated with Profile 45 with a corrected p value < 0.05.

      • Select the top 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
        • Note whether the same GO terms are showing up in multiple clusters.
        • Look up the definitions for each of the terms at http://geneontology.org. In your research presentation, you will discuss 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? Also, what does this have to do with the transcription factor being deleted (for the groups working with deletion strain data)?
        • To easily look up the definitions, go to http://geneontology.org.
        • Copy and paste the GO ID (e.g. GO:0044848) into the search field on the left of the page.
        • In the results page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
        • The definition will be on the next results page, e.g. here.

        - GO:0032040: "small-subunit processome"

        • - Definition: "A large ribonucleoprotein complex that is an early preribosomal complex."

        - GO:0000466: "maturation of 5.8S rRNA from tricistronic rRNA transcript"

        • - Definition: "Any process involved in the maturation of an rRNA molecule originally produced as part of a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript."

Data and Files

• Stem Profiles: dCIN5 Gene List
• Stem Profiles: dCIN5 GO List