How to analyze the num of protein-protein interactions (nodes/edges) of specific proteins in a large scale?

Question

[wuyc]

BioGrid allow me to search protein-protein interaction (PPI) one by one, however, I have a list of thousands of proteins. However to get the number of nodes/edges protein-protein interactions (PPIs) of those proteins in a large scale way?

Thanks so much!

Answer 1

[Jean-Karim Heriche]

Do you mean you want to know the degree of certain nodes/proteins in the graph ? If so, download the protein-protein interaction file then use a script to find and count all interactions containing your proteins of interest or use a software (e.g. cytoscape) or library (e.g. igraph) to get a table with the degree of all nodes then filter this table to retain only proteins you're interested in.

Answer 2

[plat]

If I understand correctly your question, you can use the multiple proteins input tool from stringDB.