Nanguiano Week 8

Microarray Data Analysis

Overview of Microarray Data Analysis

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

1. Quantitate the fluorescence signal in each spot in the microarray image.
   • Typically performed by the scanner software, although third party software packages do exist.
   • The image of the microarray slide and this quantitation are considered the "raw-est" form of the data.
   • Ideally, this type of raw data would be made publicly available upon publication.
   • In practice, the image data is usually not made available because the raw image file of one slide could be up to 100 MB in size.
   • Also, some journals do not require data deposition as a requirement for publication, so often published data are not actually available anywhere for download.
   • Microarray data is not centrally located on the web. Some major sources are:
     • NCBI GEO
     • EBI ArrayExpress
     • Stanford Microarray Database (now hosted by Princeton)
     • PUMAdb (Princeton Microarray Database)
     • In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
2. Calculate the ratio of red/green fluorescence
3. Log(base 2) transform the ratios
4. Normalize the log ratios on each microarray slide
5. Normalize the log ratios for a set of slides in an experiment
6. Perform statistical analysis on the log ratios
7. Compare individual genes with known data
8. Look for patterns (expression profiles) in the data (many programs are available to do this; we are going to skip this step)
9. Perform Gene Ontology term enrichment analysis (we will use MAPPFinder for this)
10. Map onto biological pathways (we will use GenMAPP for this)

In this week's exercise, we will do steps 5-7 (part 1, using Microsoft Excel) and 9-10 (part 2, using GenMAPP & MAPPFinder).

Statistical Analysis of Vibrio cholerae Microarray Data (Part 1)

• We will begin this analysis in class on Thursday, October 15.
• The detailed instructions for the microarray data analysis we will carry out can be found on the Sample Microarray Analysis for Vibrio cholerae page hosted by OpenWetWare.org.

MAPPFinder Analysis of Vibrio cholerae Microarray Data (Part 2)

• We will begin this analysis in class on Tuesday, October 20.
• The detailed instructions can be found on the GenMAPP and MAPPFinder Protocols page hosted by OpenWetWare.org.

Conclusion

• Write a paragraph that briefly summarizes and gives a scientific conclusion for the work that you did this week.

Optional: downloading and installing the GenMAPP and MAPPFinder Software

• We will be using GenMAPP and MAPPFinder version 2.1 (http://genmapp.org). This software is Windows-only and is already installed on the machines in the Seaver 120 computer lab.
  • This version is now called "GenMAPP Classic" and can be downloaded from this page.
  • Follow the instructions in the installer.
  • During installation, the installer will open a window called the GenMAPP Data Acquisition Tool. It will not function because it cannot connect to the server. This is OK, you will download your Vibrio cholerae Gene Database from the XMLPipeDB project at SourceForge.org.
    • Half of the class will use the Vc-Std_External_20090622.gdb Gene Database that was created by the Fall 2008 Biological Databases class.
      • To download this Gene Database, follow this link to the XMLPipeDB SourceForge Download page.
    • Half of the class will use a more recent Vc-Std_External_20101022.gdb Gene Database that was created by Drs. Dahlquist and Dionisio in 2010.
      • To download this Gene Database, follow this link to the XMLPipeDB SourceForge Download page.
    • The members of a pair should each choose a different gene database.
• Click on the link for the Gene Database to which you have been assigned, download the file, and save it into the folder C:\GenMAPP 2 Data\Gene Databases (if you accepted the default folders during the installation), and extract it.

Links

Nicole Anguiano
BIOL 367, Fall 2015

Assignment Links

• Week 1 Assignment
• Week 2 Assignment
• Week 3 Assignment
• Week 4 Assignment
• Week 5 Assignment
• Week 6 Assignment
• Week 7 Assignment
• Week 8 Assignment
• Week 9 Assignment
• Week 10 Assignment
• Week 11 Assignment
• Week 12 Assignment
• Week 14 Assignment
• Week 15 Assignment

Individual Journals

• Individual Journal Week 2
• Individual Journal Week 3
• Individual Journal Week 4
• Individual Journal Week 5
• Individual Journal Week 6
• Individual Journal Week 7
• Individual Journal Week 8
• Individual Journal Week 9
• Individual Journal Week 10
• Individual Journal Week 11
• Individual Assessment
• Deliverables

Shared Journals

• Class Journal Week 1
• Class Journal Week 2
• Class Journal Week 3
• Class Journal Week 4
• Class Journal Week 5
• Class Journal Week 6
• Class Journal Week 7
• Class Journal Week 8
• Class Journal Week 9
• Class Journal Week 10
• Class Journal Week 11
• Class Journal Week 12
• Class Journal Week 14
• Class Journal Week 15