# BIOL398-01/S11:Week 11

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#* Steps 5-7 are performed in Microsoft Excel | #* Steps 5-7 are performed in Microsoft Excel | ||

#Pattern finding algorithms (clustering) | #Pattern finding algorithms (clustering) | ||

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#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 | ||

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

**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.

## Contents |

## 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.

- Quantitate the fluorescence signal in each spot
- Calculate the ratio of red/green fluorescence
- Log transform the ratios
- Normalize the ratios on each microarray slide
- Steps 1-4 are performed by the GenePix Pro software.
- You will perform the following steps:

- Normalize the ratios for a set of slides in an experiment
- Perform statistical analysis on the ratios
- Compare individual genes with known data
- Steps 5-7 are performed in Microsoft Excel

- Pattern finding algorithms (clustering)
- Map onto biological pathways
- We will use software called STEM for the clustering and mapping

- 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).