To further clarify, I did two GO analysis: (i) up, (ii)down, and (ii) all DEGs. The output from up regulation category showed 120 gene sets, down regulation showed 5 gene sets and for all DEGs show 40 gene sets. I can see that GO from down-regulation category with high number of genes ( >10 per set) has been absorbed into "all DEGs", however, not all GO from up-regulated DEG has been included into the "all DEGs" category, despite having >60 genes (high cluster frequency) in some of the sets.
From previous posts I see others comment about the stringency of all DEGs category will be higher than separating into up- and down- category, however, it doesn't explain why gene sets with high cluster frequency(20%) and small q-value (1.32E-02 ) from up-regulation category does not showed up when I did GO with all DEGs?
Thank you very much for your time.