Hi,
I am having some trouble making sense of the results I've gotten from analyzing RNA seq DEG data with over-representation analysis.
For example, I am analyzing a list of genes that were upregulated after exposure to condition X and put this list through the analysis with a reference list.
Let say I got a hit on "extracellular matrix organization" indicating that there is an over representation with a fold enrichment of 2, and another hit on "DNA metabolic process" indicating an under representation with a fold enrichment of 2.
What does the result tell?
Does that mean that hit genes from the list of upregulated genes are enriching for "extracellular matrix organization" positively (more active pathway?) and negatively enriching for "DNA metabolic process" (less active?)?
Thanks in advance!