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- Let G be the size of the genome in base pairs.
- Let g? be the portion of the genome in the regulatory domain of a gene with annotation ?.
- p? = g? / G
- Let n be the number of test genomic regions.
- Let k? be the number of test genomic regions in the regulatory domain of a gene with annotation ?.
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?
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- Let N be the number of genes in the genome.
- Let n be the number of genes in the test gene set.
- Let K? be the number of genes in the genome with annotation ?.
- Let k? be the number of genes in the test gene set with annotation ?.
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- Let N be the number of genomic regions in the background set.
- Let n be the number of genomic regions in the foreground set.
- Let K? be the number of genomic regions in the background set in the regulatory domain of a gene with annotation ?.
- Let k? be the number of genomic regions in the foreground set in the regulatory domain of a gene with annotation ?.
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