How to fuse information from multiple apps?

k.scu...@gmail.com

unread,

Apr 9, 2018, 11:18:27 AM4/9/18

to cytoscape-helpdesk

Dear help desk,

I have a rather short gene list and what I am trying to do is to create a network of these genes to see their interaction and then to further expand the information on this network by seeing to which pathways and biological processes these genes belongs. Furthermore, information such as known disease implications from the literature is welcomed.

I have used geneMANIA for creating the initial network. However I am having difficulties subjecting the created network by GeneMANIA to any pathway annotation/analysis. etc.

Can you please point me in the good direction?

thank you very much!

cheers,
Klara

adam.t...@gladstone.ucsf.edu

unread,

Apr 26, 2018, 12:02:09 PM4/26/18

to cytoscape-helpdesk

adam.t...@gladstone.ucsf.edu

unread,

Apr 26, 2018, 12:03:16 PM4/26/18

to cytoscape-helpdesk

Klara,

Can you send me an example file offline and I'll try to give you a set of apps to handle your workflow.

Adam

On Monday, April 9, 2018 at 8:18:27 AM UTC-7, Klara Scupakova wrote:

Lars Juhl Jensen

unread,

Apr 27, 2018, 11:54:08 AM4/27/18

to cytoscape-helpdesk

You may want try the Cytoscape stringApp to see if it does what you want. It fetches the network from the STRING database instead of GeneMania, but also has enrichment functionality within the same app and the ability to query for genes/proteins related to a disease of interest. We have an online tutorial, which illustrates how to do these types of analyses.