Cytoscape is an open source project designed to help scientists visualize biomolecular networks. It’s written in Java and thus runs on most operating systems. Its main sponsors are UCSD’s Trey Ideker Lab, Memorial Sloan-Kettering, Institute for Systems Biology, and the Pasteur Institute. Cytoscape has a rich set of plugins provided by a large number of contributors. One of the more recent additions is a KEGG Pathway reader.
- Go to the Cytoscape download page. Fill out the short form, and submit it. You will be taken to a page containing a list of download links.
- Select the link that’s appropriate for your operating system. After your browser finishes downloading the installer program, start the installer, and follow the installation instructions.
One of the first things that you’ll want to do is load a pathway for your target of interest. In my example, I want to see the pathways that contain VEGF.
- From the File menu, select Import Network from Web Services. A dialog box will appear as shown below:
- My search for VEGF returned a number of different entries. To refine the list, I click on VEGF/Rho/ROCK/Integrin Complex. This causes a pathway to appear in the network selection box on the right-hand side of the dialog. I double-click the Signaling events mediated by VEGFR1 and VEGFR2 from the NCI Pathways database, and the network is then downloaded. I click the close button to dismiss the dialog and I can now see a network.
- At first glance, the network is a real rats nest of nodes and edges. However, if you select the Layout > yFiles > Organic layout you’ll soon see the nodes laid out in a more intuitive format. The one comment here is that there doesn’t seem to be a way to layout the nodes based on their cellular localization. I found an out-of-date plugin called Cerebral which was designed to do just this, but I couldn’t get it to create a new view based on the GO cellular localization data that I had. I’m hoping to find out more at the Barcamp meeting next month.