May someone please tell me what is the difference between Signaling Networks (that can be found in the databases like KEGG) and Protein-Protein Interaction Networks (that can be found in the databases like STRING)?
a signalling network is a network indicating how signals are being passed throughout the cell. Protein interaction is for proteins that bind other proteins (or DNA in some cases) .
A protein-protein interaction is not necessarily signal related, it could be that they need to form a dimer to function for instance. Signalling on the other hand does not necessarily means that proteins have to bind (can also be phosphorylation and such)
EDIT: phosphorylation might not be the best example here, as Jean-Karim Heriche indicated, signalling via small molecules is a better example)
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To nitpick, phosphorylation involves at least transient interactions (sometimes they can also be long lived). I think a better example would be signalling involving a diffusing small molecule.
true indeed. though it's still not really like 'binding' each other, no? (as in : forming multi-protein complexes)
No it is binding. Kinases have a substrate binding site in their catalytic domain and many also have specific substrate-binding domains in other regions. If you want to get more details on kinases interactions with their substrates, here is a review.