BIOL398-01/S11:Week 11

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=== Microarray Data Analysis ===
=== 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)
 +
#* We will use software called STEM for this
 +
#Map onto biological pathways
 +
#Create mathematical model of transcriptional network
 +
<!--
 +
On this spreadsheet, each row contains the data for one gene (one spot on the microarray).  The first column contains the gene identifier from the Saccharomyces Genome Database.  The second column contains the gene symbol and a description of the function (if known).  Each subsequent column contains the log2 ratio of the red/green fluorescence from each microarray hybridized in the experiment derived from the GenePix Pro software.
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t30:  30 minutes of cold shock; 5 replicates of the experiment
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t60:  60 minutes of cold shock; 4 replicates of the experiment
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t90:  60 minutes of cold shock followed by 30 minutes of recovery; 5 replicates of the experiment
 +
t120:  60 minutes of cold shock followed by 60 minutes of recovery; 5 replicates of the experiment
 +
-->
== Shared Journal Assignment ==
== Shared Journal Assignment ==

Revision as of 00:40, 29 March 2011

BIOL398-01: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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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.

  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)
    • We will use software called STEM for this
  9. Map onto biological pathways
  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).

Reflection

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