(Difference between revisions)
 Revision as of 11:38, 23 April 2013 (view source) (→Analyzing and Interpreting STEM Results)← Previous diff Revision as of 11:39, 23 April 2013 (view source) (→Analyzing and Interpreting STEM Results)Next diff → Line 13: Line 13: **I selected this profile because of the significant ones there were two that opposed each other. Profile 45 increases and then drops and my partner picked that one so I picked Profile 9 which decreases initially. **I selected this profile because of the significant ones there were two that opposed each other. Profile 45 increases and then drops and my partner picked that one so I picked Profile 9 which decreases initially. *How many genes belong to this profile? *How many genes belong to this profile? - **246 + **248 *How many genes were expected to belong to this profile? *How many genes were expected to belong to this profile? - **34.8 + **41.9 *What is the p value for the enrichment of genes in this profile?  Bear in mind that in the week 9 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. *What is the p value for the enrichment of genes in this profile?  Bear in mind that in the week 9 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. **6.2E-165 **6.2E-165

## Week 12

### Analyzing and Interpreting STEM Results

• For the purposes of this assignment average log fold change values from Kasey E. O'Connor was used.
• Why did you select this profile? In other words, why was it interesting to you?
• I selected this profile because of the significant ones there were two that opposed each other. Profile 45 increases and then drops and my partner picked that one so I picked Profile 9 which decreases initially.
• How many genes belong to this profile?
• 248
• How many genes were expected to belong to this profile?
• 41.9
• What is the p value for the enrichment of genes in this profile? Bear in mind that in the week 9 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.
• 6.2E-165
• 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? 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 61 GO terms with p < 0.05.
• 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?
1. Nucleolus: A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus.
2. preribosome, large subunit precursor: A preribosomal complex consisting of 27SA, 27SB, and/or 7S pre-rRNA, 5S rRNA, ribosomal proteins including late-associating large subunit proteins, and associated proteins; a precursor of the eukaryotic cytoplasmic large ribosomal subunit.
3. nuclear lumen: The volume enclosed by the nuclear inner membrane.
4. ncRNA processing: Any process that results in the conversion of one or more primary non-coding RNA (ncRNA) transcripts into one or more mature ncRNA molecules.
5. S-adenosylmethionine-dependent methyltransferase activity: Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
6. endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA): Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains 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. Primary ribosomal RNA transcripts with three genes, in this order, are produced in the nuclei of many eukaryotic species, including S. cerevisiae.
7. nucleic acid phosphodiester bond hydrolysis: The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
8. organelle lumen: The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen.
9. maturation of SSU-rRNA: Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule.
10. nucleolar part: Any constituent part of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis.

### YEASTRACT

• Top ten transcription factors in the results
1. Ste12p: 28.6%
2. Rap1p: 18.8%
3. Ino4p: 11.7%
4. Sok2p: 11.7%
5. Aft1p: 10.4%
6. Abf1p: 9.7%
7. Yap6p: 8.4%
8. Rfx1p: 7.8%
9. Yap5p: 7.1%
10. Swi4p: 7.1%
• Cin5, Gln3, HMo1, and Zap1 are not included in this list.
• I chose to add the three with the highest percent of genes they regulate because they are more likely to have a connection to these other genes.

STE12 RAP1 INO4