Taking for example a protein-protein interaction network created from
multiple databases,

If two nodes are connected by two edges what does this mean?

Does it mean that there are 2 separate experiments to supporting the
interaction?

or does it mean that there are 2 separate data sources (which in
principle could be duplicates) supporting the interaction?

or does it mean something else entirely?

Thanks in advance for any tips,

Cheers
        Christian

I have a list of 15 proteins.  want to see their
1. interaction among themselves
2. what pathways they are involved

kindly guide me.

You prob need to load external attribute data. Actually if you just
want to see pathways, you could go to use DAVID.
For interactions, try Cytoscape MIMI plugin

Gang