Understanding ORA analysis of differentially expressed CCIs

[alvarezprado]

Dear authors,

Thank you for developing scDiffComm, it's a tremendously useful tool. I have carefully read your Nat Aging paper, but I don't fully understand some of the parameters reported in the ORA analyses. I thought that posting the question here would also help future users to find the information, but please feel free to remove the issue and move the discussion to e-mail or other means if you consider it more appropriate.

If I understood correctly, a ORA score is calculated for each pathway for all differentially expressed CCIs (UP, DOWN, FLAT) and then an adjusted p-value is reported (BH_P_VALUE_UP, BH_P_VALUE_DOWN, BH_P_VALUE_FLAT) for the enrichment. But there is also an equivalent for "DIFF" (BH_P_VALUE_DIFF, ORA_SCORE_DIFF). My questions are:

1. How should we interpret pathways for which both UP and DOWN adjusted p-values are very low? This could make sense for generic pathways where we could think about positive and negative regulators, but interpretation gets harder for pathways like "Positive regulation of (X process)". Could we assume that the lower adj. p-value prevails here to consider a pathway up or downregulated based on differential CCIs?

2. What are ORA_SCORE_DIFF and BH_P_VALUE_DIFF measuring? How should we interpret these values? I assume they tell us something about the direction of the change, but I'm unsure about their meaning.

Thanks a lot for your help and my apologies if I missed key information when reading your paper!