jActiveModules question

[donc...@gmail.com]

Dear colleagues,

My question is addressed particularly to:
Andrew Siegel, Rayan KelleyOwen Ozier, Trey Ideker, Benno Shwikowsky.

I am trying to use jActiveModules app with my merged network (created from imported gmpl files as networks).

Unfortunately when I start the jActiveModule app the merged network is not recognized by the jActiveModules app. Hence I am not able to run it.

Martina Kutmon told me somethin about addition of a group/anchor node, but was not specific enouth what does it means and how to do it.

So please, if somebody can give me a hand and share some experience using this app.

Your help is highly appreciated.

Kind ragards,


Petar

[donc...@gmail.com]

Hi,

I know it is holiday season, but if anyone can give me a hint about my questions above, please feel free to leave a comment.


Regards

[Alex Pico]

Hi Petar,

I think it’s less about the holiday season and more that the question was specifically addressed to folks no longer developing the app :)

Here’s my answer (for what it’s worth).  jActiveModules only works on simple networks, i.e., node-link graphs of biomolecules with basic connections. Pathways, like the ones from WikiPathways, are not simple networks. In addition to biomolecular nodes, they also contain nodes that represent groups and complexes and other processes. And in addition to basic connections, they also contain hypergraph connections (i.e., edges connecting to other edges via anchors). So, jActiveModules will not work with complex networks.

 - Alex

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[Kei]

Hi.

I'm not sure I understand the problem, but if jActiveModules does not find the merged network, it may be caused by bug to find the newly created network.  What happens if you save the session and load it again?  Does the app still miss the merged network?

Thanks,

Kei

2018年8月3日金曜日 1時23分59秒 UTC-7 Petar Donchev:

[Petar Donchev]

Dear Kei,

Your answer comes right after I have done exactly what you are suggesting to me. I have saved the session and than importeted back into Cytoscape. 

Than jActiveModules successfuly recognized the network and the analysis was performed. There after I was able to use clueGO app agin without problem.

I wish you a wonderful rest of the summer.

Kind regards,

Petar

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