# Ashley Rhoades Week 12

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==Week 12== | ==Week 12== | ||

- | [[Image:GNL3 Ashley Rhoades.pptx | + | ===Powerpoint=== |

+ | [[Image:GNL3 Ashley Rhoades.pptx]] | ||

+ | |||

+ | ===Analyzing and Interpreting STEM Results=== | ||

+ | *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 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. | ||

+ | ** | ||

+ | *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 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? | ||

+ | ** | ||

{{Ashley_Rhoades}} | {{Ashley_Rhoades}} |

## Revision as of 02:40, 11 April 2013

## Contents |

## Week 12

### Powerpoint

Image:GNL3 Ashley Rhoades.pptx

### Analyzing and Interpreting STEM Results

- 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 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.
- 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 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?

## Survey of Biomathematics

- Ashley Rhoades
- Loyola Marymount University
- Email me through OpenWetWare
- BIOL398-03/S13