note: at present, GSEA plots are not displayed directly in the Basepair report. To access GSEA plots, you’ll need to go into the Info tab at the top of the differential expression report -> click the GSEA.zip file to download the folder containing all the GSEA plots -> unzip and open the folder, which will contain the GSEA plots.
When the pathway is enriched, you'll see two things in your GSEA plot.
Black bars: The genes, which are the black bars that are in the pathway, tend to be clustered all the way to the left or all the way to the right of the figure. So, if it's all the way to the left, it's enriched in group 1. If it's all the way to the right, it's enriched in group 2.
Green line: Take a look at the green line showing the enrichment score. If it's enriched in group 1, you'll see the peak of this green line will be on the left. But if it's enriched in the other group, the peak of this green line will be on the right.
That’s visually what you expect to see with these plots. But of course, the most important thing to look at is the statistics, like FDR q-value and p-value and so forth.