pvalue calculation of newly created protein-protein network with permutation test

Question

[ahmedakhokhar]

Dear All,

I have performed a network recreation analysis based on the interactions of proteins from String db.

I wanted to know if the interactions have significance by reshuffling the proteins with permutation against the background network. Since, its first time for me to perform permutation test on PPI, Can someone guide me to a tool or a tutorial to perform permutation test on newly created PPI network.

I try looking at a tutorial and read some articles like following but not very useful for my purpose:

https://github.com/DavisLaboratory/prosperiti/blob/master/prosperiti.py

[Jean-Karim Heriche]

What you're trying to achieve is unclear. The script you linked to seems to generate graphs by randomly selecting proteins and adding edges between them if the corresponding interaction exists in a reference PPI data set. It's unclear how this is suitable for your situation.

[Devon Ryan]

Hello ahmedakhokhar!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/2551/pvalue-calculation-of-protein-protein-network-with-permutation-test

This is typically not recommended as it runs the risk of annoying people in both communities.