...
The binomial p-value equals the probability of having k? or more of the n test genomic regions in the regulatory domain of a gene with annotation ? given that the probability of that occurring for a single genomic region is p?.
Binomial P-value = 
What is the hypergeometric test formally?
...
The hypergeometric p-value equals the probability of choosing k? or more genes with annotation ? when randomly drawing n genes from the genome.
Hypergeometric P-value = 
Example
Explicit Background Set
...
The hypergeometric statistic equals the probability of choosing k? or more genomic regions with annotation ? when randomly drawing n genomic regions from the background set.
Hypergeometric P-value =
How should I interpret the statistics provided by GREAT? Which test is more important - the binomial or the hypergeometric?
...