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!
3 answers
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.
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