Leishmania Major Group Project Report

Methods

Data Source Files

The Uniprot XML proteome set was downloaded from the Uniprot complete proteomes page for Leishmania major. We used the version that was last updated on October 16th 2013. The GOA (GO association) file was downloaded from the Uniprot-GOA downloads page. Our version was downloaded on November 14th 2013. The GO file was downloaded from the Ontology Downloads page (we used the beta version of the page). The version was from November 4th 2013, ‏‎2:03:38 AM in the obo-xml.gz format.

Generating Gene Database

In PostgresSQL, a new database was created called Leishmania_05112013_Lena_Gabe. GenMAPP Builder tables were then created in PostgresSQL. GenMAPP builder was downloaded from Source Forge (version: GenMAPP Builder 2.0b71.) The Leishmania database that was created in PostgresSQL was then configured to GenMAPP Builder and we imported our Uniprot XML and GOA files and our GOA file. Once all the files were imported, we exported a GenMAPP Gene Database for Leishmania major was saved as Leishmania_05112013_Lena_Gabe.gdb.

Inspecting Database

To make sure our Gene Database export had worked, we ran Tally Engine to make sure our XML count matched our Database count. We also used XMLpipedb Match and SQL query to make sure we could match our Gene IDs.

1. Prepare microarray data (organize, normalize, perform statistical analysis)
2. Run GenMAPP using the Gene Database.
3. Microarray data (import using Expression Dataset Manager)
4. Run MAPPFinder analysis
5. Place genes on MAPP and draw pathway