Hi all,

I've just used GOseq on my list of differentially expressed genes, and think I've missed something in terms of how to interpret the output.

I've compared two groups using two separate scripts for: 1) A vs B, for A UP subset 2) A vs B, for B UP subset

I thought I would be looking at 1) GO categories that are 'enriched' in A relative to B, and 2) GO categories that are 'enriched' in B relative to A, and thus the lists/outputs shouldn't have overlap.

Out puts for both scripts are:

1a) A vs B, A UP enriched 1b) A vs B, A UP depleted

2a) A vs B, B UP enriched 2b) A vs B, B UP depleted

My 'problem' is that when I look at the outputs: 1a vs 2a (A vs B, A UP enriched and A vs B, B UP enriched), there are overlapping terms. For example, both A and B are both apparently enriched for GO:1902339. The analysis is based on differentially expressed transcripts, so how can the analysis show that both A and B are enriched for the same term relative to each other?

I think I've missed something in the interpretation of the results.... Can it be that both process are enriched, but are enriched due to the contribution of different genes in the pathway for each sample?

If someone can help me clear this p I'd be grateful :-)

Kel