Show GSEA graph for the sets below the 50 firsts ?

[Pierre-Alex Laval]

Hello,

I tried to run GSEA on PANCAN TCGA dataset by creating 2 groups (EIF2AK4 high and low).

In the current version you can see the 50 first GSEA with your interactive dashboard,

would it be possible to show the GSEA for the ones after ? 

For example, looking at the csv produced, the pathway i'm after "REGULATION OF RESPONSE TO DNA DAMAGE STIMULUS" is ranking 435 (out of 9000ish sets), with a nes of -3.1 and a pval of 0.001. Would it be possible to get the related GSEA ?

Thank you !

Pierre 

[Mary Goldman]

Hi Pierre,

Unfortunately we limit the detailed dashboard display to the top 50 genesets due to computational constraints. If you need this information you will need to run (blitz)GSEA yourself. Please let me know if you need help extracting any data for this from Xena.

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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[Pierre-Alex Laval]

Heya,

Alright thank you :)

I ll try to do it on my own with the tutorials on the Xenia website 

If I get stuck I’ll come back to you

Thank you ! 

Have a great day

Pierre

[Mary Goldman]

Hi Pierre,

Yes, please do come back if you have any difficulties. Have a great day too!