Hi all,

I am trying to use STRING database to analyze the DEGs I identified in RNA-Seq from PMNs of WT vs KO mice after infection with S. pneumoniae. My understanding is that I can use this network to see the interactions between the list of proteins I added on the database and also generate possible protein-protein interaction networks with other known proteins/targets based upon the experimental evidence (but otherwise not present as DEGs in your RNA-seq list). I need help with the later part. I am trying to generate the possible networks by adding more nodes and connections to my protein list, which changes the PPI score and cluster score with every addition. What is the cut off of this PPI score/cluster score and when to stop adding more nodes (when does it get irrelevant?)

Thanks for the help. I haven't used this database before.

Manmeet