Drawing a pathway

Adding identifiers to a pathway

GenMAPP provides a set of drawing tools for creating custom MAPPs and for editing existing MAPPs. Creating a MAPP from scratch can be done for any process or event for which you have adequate information about the genes and/or proteins involved. Once you have a list of identifiers, you can create a pathway by entering the identifiers in GenMAPP either using the MAPPBuilder feature or with the Gene Finder.

Using MAPPBuilder

The MAPPBuilder feature allows you to rapidly import lists of identifiers to GenMAPP, creating a simple MAPP file that can be used as a starting point for MAPP curation. The MAPPBuilder input file can contain lists for several MAPPs.

Formatting data for MAPPBuilder

MAPPBuilder requires a specific input file format. Below is an example of the input file for the "Glycogen metabolism" MAPP. In the example, Entrez Gene IDs where used as identifiers, and the corresponding Entrez Gene symbol was used as the Label.

Note that the file is displayed in MS Excel, but should be saved as a .txt file for MAPPBuilder.

Using MAPPBuilder

1. Launch MAPPBuilder in GenMAPP under Tools>MAPPBuilder.
2. Make sure you have the correct Gene Database loaded in GenMAPP, otherwise select a database in MAPPBuilder under File>Choose Gene Database.
3. Click the Select File button to select your input file.
4. Click the Select Destination Folder to choose where to save your MAPP.
5. In the MAPP Information area, fill out information about author, contact and any other relevant information about the pathway. Note that you can also add/edit this information later on in GenMAPP.
6. Click Make MAPPs to start MAPPBuilder.

Adding genes using MAPPBuilder

Using Gene Finder

You can also add genes one-by-one to a new or existing pathway using the Gene Finder interface. This interface provides a look-up function for the Gene Database.

1. Load the appropriate Database in GenMAPP under Data>Choose Gene Database.
2. Open a blank pathway in GenMAPP by selecting File>New.
3. Click the Gene object in the Drafting Board Toolbar and click anywhere in the Drafting Board to place the gene.
4. Right-click on the gene to bring up the Gene Finder interface.
5. In the Gene ID field, type the gene or protein identifier for the gene.
6. Select the system the identifier is from in the Gene ID System drop-down. Click on the Search button to search the database.
7. If the identifier is found, click the OK button to assign the identifier to the gene object.
8. Repeat steps 3-7 with remaining identifiers.
9. Save the pathway with an appropriate name.

Adding genes using the Gene Finder

Adding graphical layout and annotation

Once the identifiers for a new MAPP have been added, graphical layout and annotation can also be added. This type of information includes interactions between genes and/or proteins, and spatial and temporal information.

1. Starting with the list of genes in GenMAPP, re-arrange the genes by clicking and dragging.
2. Add arrows, lines and other interaction types to illustrate how the various genes/proteins interact.
3. Add graphical objects, such as brackets, rectangles and ovals, to illustrate for example sub-cellular localization.
4. When the MAPP is complete, change the Drafting Board Size so that there is not excessive empty space in the pathway. For example, select View>Drafting Board Size>Size to fit objects to optimize the Drafting Board Size.
5. Save the pathway.
6. Submit your pathway to WikiPathways!

Adding graphical layout and annotation to a pathway

Do you have comments or questions about this tutorial? Contact GenMAPP Support.