	GenMAPP Tutorials
	Getting started with GenMAPP
	Importing data to GenMAPP
	Visualizing data on pathways
	Drawing a pathway
	Using MAPPFinder
	Submitting a pathway MAPP to WikiPathways
	Creating publication-quality figures in GenMAPP

Using MAPPFinder

Prerequisites

MAPPFinder analysis on your data requires that you have the following files:

Expression Dataset (.gex), containing your data and the criteria you want to use in MAPPFinder.
MAPP archive or set of MAPPs that you want to use to analyze your data. GenMAPP MAPP archives can be downloaded from the GenMAPP.org.
Gene Database file (.gdb). The appropriate Gene Database for your species of interest must be downloaded from GenMAPP.org. If you are working with a species not yet supported by GenMAPP, you can also create your own custom Gene Database.

Running MAPPFinder

For detailed descriptions of all MAPPFinder options and features, see MAPPFinder Help.

Start MAPPFinder either from the Desktop icon or in GenMAPP under Tools>MAPPFinder.
In the MAPPFinder main menu you will get a set of options. If this is the first time you're running MAPPFinder, choose Load Local MAPPs to load the set of MAPPs you want to use.
In the Load Local MAPPs browser, find the MAPP folder of interest and select it. Double-click the folder to select and expand it, clicking only once to highlight it is not sufficient.
Click Load MAPPs to load the MAPPs.
Once the MAPPs are loaded, select Calculate New Results in the main menu.
Select the Expression Dataset that contains your data.
In the Calculate New Results window, select a Color Set for analysis.
For the selected Color Set, select one or more criteria. Multiple criteria can be selected by holding down the Ctrl key during selection.
Select which type of analysis you want to run, either Gene Ontology, Local MAPPs or both.
Select if you want additional statistics calculated.
Click the Browse button to select a location and name for the results.
Click Run MAPPFinder to start the analysis.

Note: On some configurations, MAPPFinder takes some time to run. The MAPPFinder window may appear as if it is not responding, but it is in fact working. For a faster alternative to MAPPFinder, consider GO-Elite.

Running MAPPFinder

Viewing MAPPFinder results

MAPPFinder results will open automatically once the analysis is complete. Results will be displayed in the MAPPFinder browser. For details on viewing results see MAPPFinder Help.

Note: If you choose to analyze more than one criteria from a Color Set, the results from the last criteria will be displayed in the browser. Results for remaining criteria can be opened in the browser under File>Load Existing Results.

Searching and filtering the results

The browser has several interactive features for browsing your data:

Search pathway or GO term by keyword.
Search for gene ID from a specific gene ID system.
Expand the tree based on a numerical filter, using any or all of the following parameters: Percent of genes changed, number of genes changed and Z-score.

Exporting the results

MAPPFinder also provides several export functions:

Export highlighted portion of tree as text, either based on word/gene ID search or a numerical filter.
Export highlighted portion of tree as MAPPs, either based on word/gene ID search or a numerical filter.

Open results in GenMAPP

Clicking on any of the MAPPs or GO terms in the browser opens the corresponding view in GenMAPP, with appropriate coloring.

Viewing results in the MAPPFinder browser