Merging MAPPs in PathVisio

Overview

Merging two or more GenMAPP MAPPs can be useful for MAPP editing, but is currently not possible in the GenMAPP program. This document describes how to merge MAPPs in the PathVisio program. PathVisio is developed by the BiGCaT Bioinformatics group at the University of Maastricht, the Netherlands. The program was partly modeled after GenMAPP and therefore retains many of GenMAPP's editing features.

PathVisio

The PathVisio program is available as a webstart application here. These instructions are limited to the use of PathVisio for the specific purpose of merging MAPPs, for further information on how to use the PathVisio program, please refer to the online Help documentation.

Merging MAPPs

Preparing the MAPPs

1. Make copies of the MAPPs you intend to merge, for backup purposes.
2. Open the MAPPs in GenMAPP to assess the orientation of objects on each MAPP and to decide on the final layout of the combined MAPPs. For the scope of these instructions, MAPP 1 will be the MAPP that you merge into MAPP 2, hence MAPP 2 will be the resulting combined MAPP.

Copy and Paste MAPP content

3. Start PathVisio webstart.
4. Open MAPP 1 by selecting File>Import and browse to the .mapp file. Once the MAPP is open, activate the Edit mode by selecting Edit>Edit mode, or by using the shortcut button on the toolbar . This will activate the editing tools in the toolbar.

   

5. Select all objects, except the MAPP Information object, on the MAPP by clicking and dragging a large rectangle around the objects. If the MAPP is large, you may need to zoom the view to less than 100% to see all objects.

NOTE: It is very important to NOT select the MAPP Information object, since the rest of the protocol will NOT work if you do this.

6. Once you have all objects selected, click on any of the selected objects inside the dotted rectangle and drag the objects to the desired position. Remember that this position should be the approximate position of the final layout.
7. With all objects still selected, copy the objects by selecting Edit>Copy or by typing Ctrl+C on the keyboard.
8. Before closing the MAPP, save it as either gpml (File>Save As) or .mapp (File>Export).
9. Open MAPP 2, under File>Import.
10. Since MAPP 2 will be the final result of the combined MAPPs, you will need to increase the drawing area to accommodate the new objects. This is done by selecting the MAPP Information object:

    

11. In the Properties panel in the right, increase the Board Width and Board Height parameters appropriately. For example, if you plan to copy MAPP 1 into the upper portion of MAPP 2, then double the Board Height parameter.
12. Move the objects of MAPP 2 into the appropriate position in the same way as for MAPP 1 (steps 5-6).
13. Paste the copied objects from MAPP 1 into MAPP 2 by selecting Edit>Paste or by typing Ctrl+V on the keyboard. You should now have the combined MAPP visible:

Editing and Saving the MAPP

14. Save the combined MAPP as gpml format (File>Save As).
15. At this point, you may choose to add additional editing to the MAPP:

• Change the MAPP Information by selecting the MAPP Information and editing the information in the Properties panel on the right.
• Add genes, interactions and annotation labels.
• Optimize the Board Width and Height to fit the MAPP.

16. The final MAPP can be exported to GenMAPP MAPP format under File>Export.