# BIOL398-01/S11:Week 11

(Difference between revisions)
 Revision as of 00:40, 29 March 2011 (view source) (→Microarray Data Analysis: steps)← Previous diff Revision as of 10:29, 29 March 2011 (view source) (→Microarray Data Analysis: moved reference to STEM)Next diff → Line 31: Line 31: #* Steps 5-7 are performed in Microsoft Excel #* Steps 5-7 are performed in Microsoft Excel #Pattern finding algorithms (clustering) #Pattern finding algorithms (clustering) - #* We will use software called STEM for this #Map onto biological pathways #Map onto biological pathways + #* We will use software called STEM for the clustering and mapping #Create mathematical model of transcriptional network #Create mathematical model of transcriptional network

## Revision as of 10:29, 29 March 2011

BIOL398-01: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

This journal entry is due on Tuesday, April 5 at midnight PDT (Wednesday night/Thursday morning). NOTE new due date and that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

## Individual Journal Assignment

• Store this journal entry as "username Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links. (HINT: you can do all of this easily by adding them to your template and then using the template on your pages.)
• Link to your journal entry from your user page.
• Link back from your journal entry to your user page.
• Link to this assignment from your journal entry.
• Don't forget to add the "BIOL398-01/S11" category to the end of your wiki page.

### Microarray Data Analysis

#### Background

This is a list of steps required to analyze DNA microarray data.

1. Quantitate the fluorescence signal in each spot
2. Calculate the ratio of red/green fluorescence
3. Log transform the ratios
4. Normalize the ratios on each microarray slide
• Steps 1-4 are performed by the GenePix Pro software.
• You will perform the following steps:
5. Normalize the ratios for a set of slides in an experiment
6. Perform statistical analysis on the ratios
7. Compare individual genes with known data
• Steps 5-7 are performed in Microsoft Excel
8. Pattern finding algorithms (clustering)
9. Map onto biological pathways
• We will use software called STEM for the clustering and mapping
10. Create mathematical model of transcriptional network

## Shared Journal Assignment

• Store your journal entry in the shared Class Journal Week 11 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
• Link to your journal entry from your user page.
• Link back from the journal entry to your user page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL398-01/S11" category to the end of the wiki page (if someone has not already done so).