EnrichmentMap

[Nikolaos - Taxiarchis Skenteris]

Hello,

I am new user in Cytoscape. I am using a output of gProfiler of a gene list and then I perform a enrichment analysis in EnrichmentMap in Cytoscape according to this article: "Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap". However, with the new version of profiler when I sort according to  ‘EM#_fdr_qvalue’ there is no difference and everywhere is the same value 1.0 whereas with the previous I could sort and see the more significants pathways. Could anyone help?

Thank you in advance!

Best,

Nikolaos Skenteris

[Ruth Isserlin]

Hi Nikolaos, 

Did you change the default "user threshold" in the g:profiler interface?  Did you modify the g:profiler file before loading it into EM?

There are few irregularities.  It looks like the EM doesn't recognize the FDR value at all because your slider bar only lists p-value (it is supposed to show q-value by default). Can you share your g:profiler output file (or a subset of the file). 

Thanks, 

Ruth 

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[Nikolaos - Taxiarchis Skenteris]

Hey Ruth,

I have the by default thresholds and everything.... check my profiler output in the attachments.

Best,

Nikos

Τη Δευτέρα, 24 Ιουνίου 2019 - 4:27:54 μ.μ. UTC+2, ο χρήστης risserlin έγραψε:

Hi Nikolaos, 

Did you change the default "user threshold" in the g:profiler interface?  Did you modify the g:profiler file before loading it into EM?

There are few irregularities.  It looks like the EM doesn't recognize the FDR value at all because your slider bar only lists p-value (it is supposed to show q-value by default). Can you share your g:profiler output file (or a subset of the file). 

Thanks, 

Ruth 

On Fri, Jun 21, 2019 at 4:44 PM Nikolaos - Taxiarchis Skenteris <skente...@gmail.com> wrote:

Hello,

I am new user in Cytoscape. I am using a output of gProfiler of a gene list and then I perform a enrichment analysis in EnrichmentMap in Cytoscape according to this article: "Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap". However, with the new version of profiler when I sort according to  ‘EM#_fdr_qvalue’ there is no difference and everywhere is the same value 1.0 whereas with the previous I could sort and see the more significants pathways. Could anyone help?

Thank you in advance!

Best,

Nikolaos Skenteris

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[Ruth Isserlin]

Hi Nikolaos, 

You attached the gmt (pathway definition file) not the g:profiler results file. 

Thanks 

Ruth 

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<hsapiens.REAC.name.gmt>

[Nikolaos - Taxiarchis Skenteris]

What do you mean. This is the output of g:Profiler... I download the name.gmt and upload in the Enrichment Cytoscape....

[Ruth Isserlin]

Hi Nikolaos, 

That is the issue then.  There are two files you need to download from g:profiler.  The first is the gmt file (pathway definition file) and the second is the g:profiler results file.  

In the results section

click on the detailed results tab

Next to the download icon there are three different file type you can download —> CSV, PNG and GEM

Click on the GEM button (Generic enrichment map file) and the results file should be automatically downloaded. 

Use the GEM as the enrichment results file in the EM interface

and the gmt file as the geneset definition file (make sure you concatenate all the sources you used into one file though.  )

Thanks, 

Ruth 

On Jun 24, 2019, at 11:13 AM, Nikolaos - Taxiarchis Skenteris <skente...@gmail.com> wrote:

What do you mean. This is the output of g:Profiler... I download the name.gmt and upload in the Enrichment Cytoscape....

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<Screenshot 2019-06-24 at 17.10.37.png>