ReactomeFI Load Pathway error

[Behzad Rowshanravan]

Dear Cytoscape community,

I have recently installed the reactomeFI-Plugin 5.0.0 beta in the Cytoscape 3.4.0. However when I load the reactome database in Cytoscape, the hierarchical view of the pathways show up but I can not see any of the diagram associated when I select "Show diagram" (and I get a Load Pathway error like message with just a red sign on it). I also have problems when I upload a number of proteins and do enrichment analysis since I simply get no enrichment analysis results. When I right click on a node in a network I upload and click the "Fetch FIs" I get an error message saying "interactions for ... could not be found".

I tried installing and un-installing the plug-in and the Cytoscape software several times but it didn’t work. I tried to delete the database that it initially installed on my computer but I couldn’t find the database. Would you know on a Mac system, where that would be installed and if that is the answer? I clicked the full database installation when I opened the app for the first time but maybe thats where it has gone wrong. I no longer get prompted for that installation message.

I would appreciate any help and advice.

P.S. I have the latest java installed and I'm using OS X 10.9.5

Kind regards

[Piet]

Hi, I'm afraid this is an app specific problem: I'll cc one of the authors (mentioned on their app page here http://apps.cytoscape.org/apps/reactomefiplugin)

Op woensdag 1 juni 2016 11:25:15 UTC+2 schreef Behzad Rowshanravan:

[Guanming Wu]

Hi,

We just found out that this feature in ReactomeFIViz, showing pathway diagrams, cannot work in the latest version of Cytoscape 3.4.0. We are working on finding a way to fix it.

At the same time, you may have to use an earlier version of Cytoscape. 3.3.0 works fine.

Sorry about the problem.

Guanming

[hc...@biol.sc.edu]

Dear Dr. Wu,

I am using Reactome 3.7.1 APP in the cytoscape software. I have the similar problem. I uploaded the gene list or paste the gene symbol list in the enter box, and then constructed the FI network. A erro messsage says " cannot construct FI network, no interaction is found" if I don't choose the parameter. If I choose any parameter for construction, only one giant dot, not a network, showed up. That means there are no network constructed.
I am wondering whether I did someting wrong or there are still some issues wiht this version of reactome.
Thanks,