# Ashley Rhoades Week 12

### From OpenWetWare

(Difference between revisions)

(→Week 12: adding profile 9 image) |
(→Analyzing and Interpreting STEM Results: answering some questions) |
||

Line 10: | Line 10: | ||

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

*Why did you select this profile? In other words, why was it interesting to you? | *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? | *How many genes belong to this profile? | ||

- | ** | + | **286 |

*How many genes were expected to belong to this profile? | *How many genes were expected to belong to this profile? | ||

- | ** | + | **34.8 |

*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 |

*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? | *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? | ||

** | ** |

## Revision as of 10:24, 11 April 2013

## Contents |

## Week 12

### Powerpoint

Image:GNL3 Ashley Rhoades.pptx

### Profile 9

### Analyzing and Interpreting STEM Results

- 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?
- 286

- How many genes were expected to belong to this profile?
- 34.8

- 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?
- 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