Contradictions in GSEA results

Question

[Tolga]

Hi all,

When performing gsea between stem cells from a treatment condition and a control group, I get contradicting results. For instance Hedgehog signaling is up- and down-regulated in the treated group: Reactome_Hedgehog_on_state and Reactome_Hedgehof_off_state with almost identical NES Values. Could this be explained via the stem cellness? Because the fate of the cells are not clear at this time.

Cheers,
T