BIOL398-01/S11:Week 11

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Microarray Data Analysis: steps)
(Microarray Data Analysis: moved reference to STEM)
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 09:29, 29 March 2011

BIOL398-01: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

Home       People        Metabolic Pathways       Gene Regulatory Pathways       LionShare       Help      

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)
  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).

Reflection

Personal tools