Tools for network active module identification?

Question

[enricoferrero]

Hello,

I'm looking for tools that allow identification of active modules in networks.

A typical scenario is where you have a protein-protein interaction network and some gene expression data overlaid on top of it and you want to identify set of connected nodes in the network that show significant levels of differential expression.

I came across jActiveModules but unfortunately it doesn't seem to cope well with a larger network (15K nodes, 150K interactions).

Are there any good alternatives that I can use?

Thanks!