How do I compare two similar PPI networks using Cytoscape?

Question

[gemmalouisebaldock]

Hi everyone,

For context, I am a university student who is very much new to using Cytoscape, so I am learning how to use the software. The data I have lists the potential binding partners of a protein in two different conditions. I have developed some basic networks but I am wondering the best possible way to compare the different PPI networks together if that is even possible using Cytoscape? I am out of my depth slightly with regards to this, so any help would be much appreciated.

Thanks in advance

Answer 1

[scooter]

Greetings, and welcome to Cytoscape. The short answer is "it depends". There are several ways to "compare" networks, depending on your biological use case. The most sophisticated approach is to do something called "network alignment", and there are several Cytoscape apps that do some sort of network alignment. I would go to the App Store and try to do some searches for network alignment or network comparison and take a look at the apps that come up.

-- scooter