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!
Hi,
from the results you cannot directly infer that a pathway is more or less active (Actually, you can't even really infer that the enriched pathways are affected at all).
These kind of analyses test if genes with a certain property (e.g. involved in ECM organization) occur more often in a list of candidate genes (i.e. your upregulated genes) than expected by chance.
That is, a positve enrichment in ECM organization means among your upregulated genes more than expected just by chance are annotated to be involved in ECM organization. You can take this as a hint that upon the condition you've tested that there is something going on with the ECM. But be aware, that most genes have multiple annotations, since their products are likely to be involved in several biological processes. Furthermore, the annotations are far from being complete or flawless.
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