User guide

User guide

This is a user guide on COMFI. For an installation guide see here and for a walkthrough example see here.

• The Menu structure
  • Find complexes
    • General options
    • Network options
  • Show results
  • (Re)build index/download dependencies

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The Menu structure

The COMFI menu comprises the submenus:
1. Find complexes
2. Show results
3. (Re)build index/download dependencies

Find complexes

The menu entry “Find complexes” allows the user to find known protein complexes within a Cytoscape network. Human, Mouse and Yeast complexes can be found and identified directly via the CORUM or Cyc2008 databases. Complexes in other organisms can be identified via homology mapping to Human or Yeast complexes via HomoloGene.

After clicking on the “Find complexes” submenu a dialogue as displayed in the figure below will pop up. The dialogue is structured into 2 sections.
1. General options
2. Network options

General options

There you have the possibility so select the organism of your choice (Human, Mouse, Yeast & other) via the combo box displayed on top of the dialogue. After selecting a organism you will be provided with several other options that need to be set according to your data and preferences.
If you choose other you can select whether you want to use homology mapping to Human, Yeast or both organisms to detect potential protein complexes. Then you need to select the column containing either UniProt accession numbers (Human, Mouse & other) or CYGD ids (Yeast). If you don't have the corresponding ids try CyThesaurus to map your ids to the corresponding UniProt accession numbers or CYGD ids.
You then can select several other options via three checkboxes. There you can choose to create nested networks, layout the network after the search and remove proteins which are contained in a protein complex from a network.

Network options

Here you can select your source and target network. The source network specifies the network which is searched for protein complexes, while the target network specifies in which network the complexes are added as nodes. If you want to add you complexes to a new empty network, simply select "create new network" in the target network combo box.

Show results

The menu entry “Show results” allows the user to browse the results of the protein complex search.
When clicking on the “Show results” submenu a dialogue as displayed in the figure below will pop up. There you have the possibility to search the result list via the text box on the bottom or click on different table headers to sort the table according to your interest. The column "NodeID" shows the identifier of the node representing the complex in the network. The column "Homology" indicates if this complex was identified via homology mapping or not.
The checkboxes in "Select Node" can be ticked and the ticked nodes selected in the network via the "select" button.
The button "save all" can be used to export the results as a .tab file (tab delinted text file) that can be easily imported into e.g Excel.

If you want to get some hand on experience with COMFI you can download a test network comprised out of the yeast proteome here and have a look at our walkthrough example.

(Re)build index/download dependencies

The menu entry “(Re)build index/download dependencies” allows the user to download and update protein complex data and to build an index required for homology mapping.

To download files simply click on the button on the right, displaying a folder and an arrow.
To build the index click on the "play" icon. In order to build the index, dependencies 1-3 need to show a green tick. When the index is build it will delete unnecessary files to free up disk space. During this process the status for dependency 1-3 will change to the red cross while the status of the index will switch to a green tick. See also the COMFI Installation and setup guide

It is recommended that from time to time you download all files and build a new index to keep your dependencies up to date, as the UniProt, HomoloGene, YeastGenome CORUM and Cyc2008 content will change over time.

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