GenMAPP User

Gene Database Project Links
Overview	Deliverables	Reference Format	Guilds	Project Manager	GenMAPP User	Quality Assurance	Coder
			Teams	Heavy Metal HaterZ	The Class Whoopers	GÉNialOMICS	Oregon Trail Survivors

The GenMAPP user runs GenMAPP with the microarray dataset (Expression Dataset Manager, MAPPFinder, GenMAPP MAPP). His or her tasks generally correspond to the work done during the DNA microarray analysis exercise (part 1, part 2), as applicable to the team’s chosen bacterium.

Guild Members

• Species 1 (Shewanella oneidensis): Ron Legaspi & Emily Simso
• Species 2: (Bordetella pertussis): Mahrad Saeedi and Lena Olufson
• Species 3: (Burkholderia cenocepacia): Kevin Wyllie & Veronica Pacheco
• Species 4: (Shigella flexneri): Kristin Zebrowski & Erich Yanoschik

Milestones

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

Milestone 1: Startup from Original Microarray Paper and Data

1. Find and acquire the microarray paper for your team (done Week 10).
   • Provide the proper bibliographic reference for your paper.
   • Link to the HTML version of the paper on the journal website.
   • Upload the PDF version of the paper to the wiki (if no copyright restrictions); otherwise provide a download link to the publisher site.
2. Download microarray data in its “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 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: Data Preparation

1. Read the microarray paper to understand the experiment.
2. Create a flow chart that shows the experimental design and 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 and/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).

Milestone 3: On-going Analysis Cycle

This milestone represents the on-going work of the GenMAPP user, as the project gradually converges toward a final version of its gene database and compares its own results to the results in the original microarray paper.

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 Coder/Quality Assurance team members 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.

Gene Database Project Links
Overview	Deliverables	Reference Format	Guilds	Project Manager	GenMAPP User	Quality Assurance	Coder
			Teams	Heavy Metal HaterZ	The Class Whoopers	GÉNialOMICS	Oregon Trail Survivors