Interpret GSEA results

2

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7.7 years ago

Ron ★ 1.2k

Hi all,

I have a question on interpreting GSEA results. The output provides us with two files na_pos and na_neg phenotype. As per my understanding the upregulated signatures are in na_pos and down regulated signatures are in na_neg category. (Assuming looking at only significant enriched pathways with p-value < .05 and FDR < .25 only)

But the pathway names make it a bit confusing to understand.If I want to look at upregulated AR pathway. AR_UP_V1_UP is a perfect result in na_pos category.

But for down regulated AR pathway(even AR down is not important I know,but only for understanding purpose).Which ones of the two is an ideal result ?

a) AR_DOWN_V1_DOWN in na_pos

b)AR_DOWN_V1_DOWN in na_neg

Also,if we look at AR_UP_V1_UP to be enriched in na_neg phenotype,is this also an ideal result for down regulated AR pathway ?if it means that the pathway should be up but its down in our case?

Let me know your thoughts.Please correct if I am wrong.I looked at one of the posts but it was not clear: question about GSEA