example

Walkthrough example

This is an illustrational guide that will show you how to use PEANuT. For a detailed user guide see here.

• Prerequisites
• Getting started
• Using the plugin
  • Finding protein complexes
  • Show results

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Prerequisites

Before we can dive into the example you need to:
1. Install Cytoscape and COMFI (see our installation guide)
2. Download our example network

Getting started

After you have started Cytoscape open the example session file via "File" --> "Open" and the select the yestTestNetwork.cys you have just downloaded.

Using the plugin

Using the plugin consist of two simple steps:
1. Find protein complexes
2. Review the results

If you want a detailed overview on how to use the different submenus see here.

Finding protein complexes

To start searching for protein complexes in a network go to the menu "Plugins"-->"COMFI"-->"Find complexes".
Then set the following parameters:
1. Set the organism to Yeast
2. Set the CYGDId combobox to "CYGDIDs"
3. Select "Create nested networks"
4. Unselect "Layout network"
5. Select "Remove complex members from source network"
6. Select "Binary-GS.txt" as source and target network
7. Click on the "Search" button
For more information see also the user guide

Show results

When the protein complex search has finished the result menu will pop up. You can search the results by typing into the search field or sort them by clicking on colums. See also the user guide

You can click on "Save all", save the result as a tab separated file and import it into Excel. This is done in Excel via "File"--> "open", setting the file filter to "enable all documents" and then simply selecting and opening it. Afterwards Excel will ask you in a series of dialogues which kind of delimiter this file uses. Just select tab and "Finish".

If you compare the before and after situation you will also note that the number of nodes has increased even though the nodes representing single proteins that are contained within a complex have been removed. This is caused by the possibility that proteins from a set can be combined in various manners to form complexes (e.g. A+B , A+C, B+C, A+B+C).You will also notice that the number of edges has increased. This is because every new complex node has all the connections the single proteins had (and maybe even some new connections to other complex nodes).
You will also notice the long list of new networks which are in fact the nested networks, that contain each member of the complex.