Protein protein network analysis

Question

[Liftedkris]

During protein protein network interaction analysis, we have in-degree and out-degree and we also have EdgeCount. Please in calculating the hub nodes, which of the values is used? In degree or out degree? Or EdgeCount which is sum of in-degree and out-degree

Thanks

[Kevin Blighe]

It will depend on the hub score metric that is being used (there are different ones). Please confirm the program that you are using for your network analysis.

[Kevin Blighe]

Also, please follow up on your previous threads: R analysis for read counts using edgeR

If you do not follow up consistently, then people will eventually stop responding to you.

[Liftedkris]

Sorry for the late response, I’m using cytoscape

[Kevin Blighe]

Cool. Which exact plugin / function are you using? You can simply do a search in a search engine to see how it calculates the hub scores.

[Liftedkris]

Ok thanks. I was able to fix it

Thanks 🙏