Question: How To Extract Highly Connected Subgraphs From A Gene Network Representation
0
gravatar for Diwan
6.5 years ago by
Diwan560
United States
Diwan560 wrote:

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

bioconductor cytoscape • 2.9k views
ADD COMMENTlink modified 6.5 years ago by Ramon Vidal10 • written 6.5 years ago by Diwan560
4
gravatar for David
6.5 years ago by
David730
David730 wrote:

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.

ADD COMMENTlink written 6.5 years ago by David730

Excellent! Thanks, David - Diw

ADD REPLYlink written 6.5 years ago by Diwan560
1
gravatar for Ramon Vidal
6.5 years ago by
Ramon Vidal10
UdeM
Ramon Vidal10 wrote:

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

ADD COMMENTlink written 6.5 years ago by Ramon Vidal10

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

ADD REPLYlink written 6.5 years ago by Diwan560
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