Hi,

I downloaded a file from the IntAct database (first column -> a uniprotID, second column -> the interacting protein with a uniprotID).

I have to add to it a file containing my own double-hybrid results (first column -> one uniprotID, second column -> the interacting protein with gene_name (uniprotID is not existing)).  I did it by two different ways : 1. I concatenated myself the 2 files ("cat" command) 2. I merged the 2 networks in cytoscape The formed "hairball" seems to be identical with the two concatenation methods. But when I "Glay"-ed them, results are different : my proteins are not clustered the same way.  I don't understand why Glay is giving two differents clustering results since the starting files are supposedly to be the same (?). What happened durng the "network merge" ? why is it so diifferent as a "simple" concatenation ? 

Could you please explain me what is the best way to merge two different networks ? (manually or in Cytoscape) and why it gave diffrenet clustering results?

Thanks