Merging MAPPFinder results with input data using GO-Quant

Overview

GO-Quant is a program for extracting quantitative gene expression values for genes significantly altered by functional gene categories based on MAPPFinder results. GO-Quant was developed at the University of Washington Institute for Risk Analysis and Risk Communication. A full description of the application can be found in Yu et al, published in Toxicological Sciences. The program as well as supporting documentation can be found at http://depts.washington.edu/irarc/Go-Quant/index.html.

Requirements and installation

System requirements and installation

• Download the GO-Quant program here.
• Operating system: Windows 2000/XP w/SP2
• Software requirements: Microsoft Excel, Microsoft Access, GenMAPP

File requirements

The following files must be available and ready before starting this protocol:

• Expression Dataset file in GenMAPP format (.gex) or as an Excel spreadsheet (.xls)
• MAPPFinder results file in text format (.txt)
• MAPPFinder results file in .gmf format. This file is created by MAPPFinder during analysis and is stored in the same directory as the .gex file

Using GO-Quant

1. Start the GO-Quant program. In the main interface of the program, you will be prompted to check that necessary software is installed.
2. Select a database where the GO-Quant calculations and results will be stored. Creating a new database is recommended.

3. In the next window, select the MAPPFinder results, stored either as .txt or .xls. If you select to import results from a .txt file, you will be prompted to save the results as an Excel file.

4. Next, select the .gmf file with the relevant MAPPFinder results. In the drop-down menu, select the table in the gmf file for import. The table should correspond to the results chosen under 3 above. For example, if the MAPPFinder text file is "DoseT24h-all-Criterion0-GO.txt", select the "DoseT24h-all-Criterion0-GO" table.

5. Next you will be prompted to select the file containing the expression data. This can be either the GenMAPP .gex file or the corresponding Excel file.
6. Finally, you will be asked to select either "Express" or "Custom" processing. Before processing can start, you must close all files involved. Click Next to start the processing.

7. When processing is complete, click Next to continue. You will be prompted to export the results as Excel files.

GO-Quant results

The results of the GO-Quant program are available in two different styles, Average and Summary. The results are exported as separate files with the suffix "_Summary_Single_GOID" and "_Average_Single_GOID".

• Average: Contains averaged data per GO term or pathway
• Summary: Data for each gene is added per GO term or pathway

Results per pathway

GO-Quant does not automatically export the original input data for each gene. This information is calculated by the program, but not exported. The information can be retrieved from the database that GO-Quant uses to process the results.

1. Close the GO-Quant program and go to the directory where you selected to create the database under step 2 above.
2. The database file will have the extension .mdb. Double-click this file to open it in Microsoft Access.
3. In Access, click on the Tables tab to display all tables in the database. The table containing the releveant information will be called "MAPPFinder_Results_with_Gene_Expression".
4. Right-click on the "MAPPFinder_Results_with_Gene_Expression" table and select Export. In the file browser that appears, select Microsoft Excel in the Save as type drop-down menu.
5. Select a name and location for your file and click Export.
6. Close Access. The exported file contains the full MAPPFinder results for the selected criterion as well as the original data for each gene.