Enrichment Score Direction Interpretation

[Maddie Krieger]

I am having some trouble interpreting the direction of the NES produced by GSEA.

I ran a DESeq2 experiment where I compared my control group to my treatment, so that any upregulation in the treatment group would be represented by a positive Log2FC. This is super easy to verify by looking at the normalized count data for each gene - more transcripts in the treatment group equals a positive Log2FC.

I took the normalized count data from this DESeq2 experiment as input for GSEA (obviously, the Log2FC data didn't factor into GSEA since I'm only giving it the normalized counts). 

When run GSEA from the standalone application, I can select either "Control_vs_Treatment" or "Treatment_vs_Control" as my phenotype labels. 

My question is: When I select "Control_vs_Treatment," are pathways with a positive NES value UPREGULATED in the treatment? I can't figure out any easy way to verify this like I can with the Log2FC direction in DESeq2. 

Thank you so much for the help!

[Anthony Castanza]

If you select control vs treatment, then the enrichment in the treatment group will be represented with negative scores and the control group will be positive scores.

I suspect that you want the other direction, which would be treatment vs control.

On the gene set results page, we produce a heat map of the genes in the set, it you should be able to make a qualitative assessment of the directionality from this plot, assuming that there is reasonably strong signal.

Let me know if you have any other questions

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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