Opposite of enrichment analysis

Question

[Jack]

So, we do enrichment analysis in order to see if something that we found is more than expected. But, how can we check for the opposite?

Something that we found is less than expected.

Answer 1

[Qroid]

If you want to specifically check for under-enrichment, you can run a left-tailed one-sided Fisher's exact test. Here you're checking if the observed frequency is significantly smaller than the background frequency, i.e. you have less hits than you'd expect from random chance.

In R, you'd run fisher.test() with the parameter alternative="less" to specify the left tail.

[Jack]

@Qroid more specifically I want to check for depletion.

[Jack]

@Qroid I understand what one-sided Fisher's is, but can you explain the concept of left-tailed?