error: the geneset: kegg 00511 is not found in the GMT file

[patty.s...@gmail.com]

Hi,

I'm completely new to cytoscape

I'm trying to use the enrichment map app to build a visualization from g:profiler data.

I am using the tutorial provided by the Bader lab.

I get the following message when I hit 'build' on the cytoscape app: the geneset: kegg 00511 is not found in the GMT file

Please advise.

Best,
Patty

[Mike Kucera]

Hi,

What version of EnrichmentMap are you using?

I don't get this error with the latest version (3.1) on the Cytoscape app store.

[Patty Sachamitr]

Thank you for your response, MIke. 

I am using 3.1 too!

I am not sure why I am experiencing trouble. I tried not choosing the 'KEGG' option when running gprofiler but then get some other error message :

the geneset: REAC: R-HSA- 6791226 is not found in the GMT file  

Is it right to think that the problem is in my gmt file? if so, what can i do to fix this?

Thank you,

Patty 

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Supatra (Patty) Sachamitr, PhD

Postdoctoral Fellow, 

Laboratory of Dr. Peter Dirks and Structural Genomics Consortium 

Peter Gilgan Centre for Research and Learning

The Hospital for Sick Children

686 Bay Street

Toronto, Ontario M5G 0A4 Canada

[Mike Kucera]

Try entering the path to the gmt file on the "Common Files" section of the Create EnrichmentMap dialog.

Thanks.

[Ruth Isserlin]

Hi Patty, 

The tutorial that you are using from the website for g:Profiler is a little out of date.

When you created your gProfiler results file we now recommend unselecting kegg because the kegg pathways are no longer available in the downloaded gmt file.  You need to re-run your g:Profiler analysis and unselect kegg and try re-building your enrichment with the updated output file.  (alternately, if it took a long time to generate your output file you can delete any line that contains kegg:)

Thanks, 

Ruth   

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[Ruth Isserlin]

Hi Patty, 

What is the name of the gmt file that you are using and did you download it from the g:profiler website at the same time you did the analysis?

Thanks, 

Ruth 

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[Patty Sachamitr]

i tried unselecting kegg and entering  the gmt file on the "Common Files" section  and that seems to have done the trick!

Thank you for your help!

have a lovely evening!

Patty :D

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[Patty Sachamitr]

yes, that did it!

 thank you so much!

You've made my day! I've been trying this for a while!

On Thu, Sep 27, 2018 at 3:31 PM Mike Kucera <mikek...@gmail.com> wrote:

Try entering the path to the gmt file on the "Common Files" section of the Create EnrichmentMap dialog.

Thanks.

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[Patty Sachamitr]

Thank you for your response, Ruth. 

The gmt file i am using is hsapiens.pathway.NAME.gmt

Best,

Patty

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