What to choose as background in statistic test genetics

Question

[adigershon8897]

Hi i have to list of genes changing in expression each list is tested for same condition but one is from tissue A and the other for tissue B.

I want to check if there is a significant overlap between the 2 lists I wanted to use Fisher's exact test but im not sure what i should put in the bacground

all genes that were expressed in both tissues?

[Dunois]

The background should be the set of all genes that are common to both tissues. The foreground is the set of "significant" genes (e.g., based on some statistical cutoff) that is common to both tissues.