How to generate PPI Network work from String data base

[Sandhya]

 PPI network from the STRING database (https://cn.string-db.org/ ) and only considered the interaction whose score was greater than 0.9 how to do this for TCGA multiomics data  . how to  calculated the degree and betweenness centrality of each gene from the BioGrid net work     as in this papaer   Identification of Cancer Driver Genes by Integrating Multiomics Data with Graph Neural Networks Hongzhi Song 1,† , Chaoyi Yin 1,†, Zhuopeng Li 2 , Ke Feng 1 , Yangkun Cao 1 , Yujie Gu 1 and Huiyan Sun 1,

[Mary Goldman]

Hello,

Unfortunately Xena does not calculate PPI networks. The paper you mention in your email I believe details a method to calculate a PPI network. It is called GGraphSAGE: https://github.com/JP909/GGraphSAGE. Is this what you are asking for? You could also reach out to the STRING database to see if they can help.

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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