User Guide

Here you will learn how you can use the RegInt Plugin for PathVisio to visualize regulatory interactions in the side panel of PathVisio.

1. Installing the RegInt plugin

• Start PathVisio
• Go to Plugins -> Plugin Manager -> Select the RegInt plugin in the list
• Click Install

Show Video

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2. Loading regulatory interaction files

Regulatory interaction files usually consist of four columns:

• source identifier
• source system code
• target identifier
• target system code

It is also possible to choose the system code in the import dialog if it is the same for all source / target nodes. Optionally, the user can add pubmed identifiers in an additional column that shows the evidence for the regulatory interaction.

• Go to Plugins -> RegInt -> Load interaction files
• You can select one or multiple files (only txt or csv format allowed)
• For each interaction file you need to select the source and target identifier columns and specify the system codes for each.
• After the interaction files are loaded, the dialog will state how many interactions were loaded. Now you can start investigating your pathway of interest.

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3. Show regulatory interactions in side panel

• The plugin added a side panel called RegInt Plugin.
• Select a data node of interest in the pathway and check if there are known regulators or targets for the data node.
• If you load a dataset that contains data for the data nodes in the side panel, the data will also be visualized on the data nodes there.
• If you click on the info button next to a data node in the side panel, more information about the data node is loaded in the bottom half of the side panel.