Difference between revisions of "GenMAPP User"

Revision as of 18:26, 5 November 2013

• Gene Database Project
• Gene Database Project Report Guidelines

Guild Members

• Dillon
• Kevin Meilek
• Kevin McGee and Viktoria
• Lauren and Miles

Milestones

The milestones do not necessarily correspond to particular weeks, instead they are sets of tasks grouped together.

Milestone 1

1. Find and acquire the microarray paper for your team (done Week 10).
   • Provide the proper bibliographic reference for your paper
   • Link to the online version of the paper on the journal web site
   • Upload the pdf version of the paper to the wiki (if no copyright restrictions)
2. Download microarray data in it's "rawest" form that you can find. (Consult with Dr. Dahlquist about this.)
3. Verify that the gene IDs in the microarray data match the chosen species and strain that is being used to create the .gdb.
   • This last task needs to be done in conjunction with the Quality Assurance person and Coder.
4. File management: on your team's home page
   • Link to the source of the microarray data
   • Upload the microarray data files to the wiki

Milestone 2

1. Read the microarray paper to understand the experiment.
2. Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
3. Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
4. Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
5. Consult with Dr. Dahlquist on how to process the data (normalization, statistics).

Future Milestones

1. Perform the statistical analysis in Excel
2. Format the gene expression data for import into GenMAPP.
3. Import data into GenMAPP, create ColorSets, and run MAPPFinder.
4. Document and take notes on test runs with GenMAPP.
   • Use the EX.txt file to help the Coders/ID Minders to validate the .gdb
5. Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
6. Create a .mapp file showing one pathway that is changed in your data.