Question: How to analyze the num of protein-protein interactions (nodes/edges) of specific proteins in a large scale?
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gravatar for hegelwyc
6 months ago by
hegelwyc0
hegelwyc0 wrote:

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!

ADD COMMENTlink modified 6 months ago by plat30 • written 6 months ago by hegelwyc0
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gravatar for Jean-Karim Heriche
6 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche16k wrote:

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.

ADD COMMENTlink written 6 months ago by Jean-Karim Heriche16k
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gravatar for plat
6 months ago by
plat30
Barcelona
plat30 wrote:

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

ADD COMMENTlink written 6 months ago by plat30
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