Difference between revisions of "Imacarae Week 9"
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(→Data and Files: edited names, added go list) |
(→Methods and Results: pasted procedure from week 9) |
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==Purpose== | ==Purpose== | ||
==Methods and Results== | ==Methods and Results== | ||
| + | # '''Analyzing and Interpreting STEM Results''' | ||
| + | ## Select '''''one''''' of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. '''''Each member of your group should choose a different profile.''''' Answer the following: | ||
| + | ##* '''''Why did you select this profile? In other words, why was it interesting to you?''''' | ||
| + | ##* '''''How many genes belong to this profile?''''' | ||
| + | ##* '''''How many genes were expected to belong to 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. | ||
| + | ##* 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?''''' | ||
| + | ##* Select the top 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05). | ||
| + | <!--##** Each member of the group will be reporting on his or her own cluster in your research presentation. You should take care to choose terms that are the most significant, but that are also not too redundant. For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.--> | ||
| + | ##*** 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 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 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 [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 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. [http://amigo.geneontology.org/amigo/term/GO:0044848 here]. | ||
| + | |||
==Data and Files== | ==Data and Files== | ||
*[[Media:DCIN5_allprofiles_genelist_IM.zip|Stem Profiles: dCIN5 Gene List]] | *[[Media:DCIN5_allprofiles_genelist_IM.zip|Stem Profiles: dCIN5 Gene List]] | ||
Revision as of 14:18, 28 October 2019
Contents
Purpose
Methods and Results
- Analyzing and Interpreting STEM Results
- Select one of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. Each member of your group should choose a different profile. Answer the following:
- Why did you select this profile? In other words, why was it interesting to you?
- How many genes belong to this profile?
- How many genes were expected to belong to 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.
- 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?
- 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.
- Select one of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. Each member of your group should choose a different profile. Answer the following:
