Hello,

I have been trying to use a Java-based tool called BubbleGUM for gene set enrichment that allows multiple comparisons within groups, generally not possible with GSEA. I tried to run for reactome as well as 'all' pathways and I see the same output- some 10 pathways, whereas technically there should be hundreds. Running hallmark on the same gives an error: no gene sets passed the seize threshold.

I have 4 groups in my data:

• Genotype 1: control, treated
• Genotype 2: control, treated

If anyone knows about this tool or any other method to visualised pathway enrichment in all 4 groups simultaneously, please let me know!

Thanks,
Sonal