PlateletWeb - Systems Biology Workbench

6. How to extract subnetworks for proteins of interest and download files to visualize in Cytoscape?

The "Extract subnetwork" option in the main menu is introduced for the analysis of a set of proteins. The aim of this feature is to extract networks of interest from PlateletWeb and to visualize the interactions between a group of pre-selected proteins. The names of the proteins are entered in the search field, separated by a tab or comma. Click on the submit button to go to the next step.

If one of the entered proteins is not found in the database, the following message occurs: "The proteins not matching the database are...".
If there is a mistake in the entered protein's name, the user is given the opportunity to reexamine all proteins and search for available similar names.

After finding the right protein, the user can go back and correct the list on the previous page. Non-platelet proteins can also be added and analyzed. Proteins, which are not interacting with the resulting subnetwork, are not included in the cytoscape file as the singleton proteins are not a part of the network.

If the proper list of proteins is already available, the user can now choose between a graphical presentation of the constructed network or a list of interactions given in a text-format.

By clicking on the "network format" the network appears on the screen, depicting the proteins as nodes and the interactions between them as edges.

• A grey line represents an interaction
• A red arrow stands for a human phosphorylation event from HPRD or PhosphoSite
• A blue arrow indicates a kinase-prediction for a platelet phosphorylation site (NetworKIN)
• A green line depicts dephosphorylation events from HPRD

More information on the source of interaction and phosphorylation data is given under "Question 4".

Additionally, an option for downloading the subnetwork as pdf file is also available.

If the user prefers extracting the data and creating a visualization with Cytoscape, there is a compressed Cytoscape file available for download. It contains a .sif file of the extracted interactome network, as well as edge and node attributes files (.eda, .noa), which can be added into Cytoscape to visualize specific features of the nodes and edges.

The edge attribute file contains the phosphorylation sites for each phosphorylated protein and the node attribute files include information about the node itself: name of the protein, whether the protein is a "kinase or not", whether it is "phosphorylated or not" etc.
An easy option is to save the file on the desktop and then extract the folders. The visualization characteristics and legends are contained in the .props file in the folder "properties". The phosphorylation state of each protein is described as "phoshprd" if the phosphorylation site is derived from HPRD or PhosphoSite and as "phosexp" if the site is detected in platelets.

Steps for importing the files into Cytoscape:

1. File -> Import -> Network (multiple file types) -> .sif file from tmp folder
2. File -> Import -> Node attributes -> .noa files from tmp folder
3. File -> Import -> Edge attributes -> .eda files from tmp folder
4. File -> Import -> Vizmap property file -> cytoscapevisuals.props from properties folder

In order to view the optimal network in Cytoscape, select Layout -> yFiles -> Organic. The final version of the created network should be visible and available for further analysis.