Genemania network support only without gene set expansion

[Anton Kratz]

Dear Genemania team,

I am using the Genemania 3.5.2 plugin with Cytoscape 3.7.2.

I would like to use Genemania to display the network support for a list of genes only, *without* doing the network expansion. I.e. I do not want additional genes, I only want to see the network weighting for the query list.

I.e. by entering 11 genes, I would like to see the network support by type for these 11 genes only in the way Genemania does, with the different support classes adding up to 100% (and not have additional suggested genes in the network).

This is with custom support networks.

Is this possible (either with the Cytoscape plugin or the web server)?

Best,

Anton

--
Anton Kratz, Ph.D.
Assistant Research Scientist
Ideker Lab
University of California, San Diego - School of Medicine

[Gary Bader]

Hi Anton. You should be able to do that by setting the number of related genes parameter to zero.

Let us know how it goes.

Best,

Gary

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[Anton Kratz]

Thank you Gary, that works! I have a follow-up question. I am struggling to get my own evidence networks in.

I have the networks loaded in Cytoscape. They have three columns: from, to and score. I go to:

Local search > Install Data > Convert Cytoscape Network

I fill out all the fields - it's a weighted network and click "Import", I get: "An error has occurred: value cannot be null". I get that all the time.

I *think* the problem is related to the fact that I am trying to "<Create New Group>". It does import if I add to an existing group - but I think this is not what I need to do (?) and anyway my network does not show up in the extracted network anyway.

I think my question is: given a series of networks which I already loaded in cytoscape, how can I create evidence networks from those for Genemania? "Convert Cytoscape Network" doesn't seem to work for me or I am using it wrong.

Thanks!
Anton

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[Gary Bader]

Hi Anton - Sorry, I'm not sure of the answer, but Christian will be back in the office on Monday and should be able to look into this.

Best,
Gary

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[Christian Lopes]

Hi Anton,

Could you please send me the session file (.cys) with the network you are trying to convert, so I can try it myself and maybe debug it, if necessary?

Thanks,

Christian 

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