How To Extract Highly Connected Subgraphs From A Gene Network Representation

Question

[Diwan]

Hello,

I have a set of genes (~50) obtained from clustering gene expression data. I would like to map it on a network like biogrid/hprd and extract a highly connected subnetwork for these genes. Is there any cytoscape or bioconductor package or other program that can do this? (or) what is the best way to do this?

Previous posts mentioned jactivemodules, Bisogenet. But these plugins do not work with current version (cytoscape 2.8.3).

Your suggestions will be helpful. Thank you, Diwan

Answer 1

[David]

I wrote a R method to obtain the PPI between the gene in a list here. You can easily export the result as a edge list and display it in cytoscape.

[Diwan]

Excellent! Thanks, David - Diw

Answer 2

[Ramon Vidal]

Have you tryed genemania plugin for cytoscape? After create the interactome with your genes you can use mcode plugin to identify subnetworks.

[Diwan]

Thanks, Ramon. I will try this too. -Diw