Building an extended PPI network in Cytoscape without BisoGenet

Question

[amir.rakhimov.b]

Hi, I want to build a protein-protein interaction network in Cytoscape that will include all proteins in a query list right from the beginning. It doesn't need to be a network of direct interactions, so I want it to have the intermediate proteins from a database (e.g. Biogrid). Bisogenet is not working anymore, and StringApp doesn't include all proteins when building the network and even after I expand it. How can this be solved?

Answer 1

[Scooter]

Greetings,

StringApp should certainly include all of the proteins you're interested in, as long as they are in the string database. Can you describe how you are entering the query into stringapp?

-- scooter

[amir.rakhimov.b]

Thank you for your response! I insert a list of gene symbols line-by-line. I've just checked my gene list and realised that some of them are microRNA genes or pseudogenes (not found in the database when queried on string-db.org). Maybe that's why not all query strings were present in the network. Still, if there're nodes that are disconnected from the network, should I just keep expanding the network?