Table 1.

Summary of web servers for GO enrichment analysis of TF ChIP-seq data

Web server	ChIP-seq peaks and genes association method	Measurement of genes as targets	Integrating expression	GO enrichment calculation	Ref
Cistrome-GO	RP score depending on the distance to TSS	continuous values	Yes	Minimum hypergeometric test
GREAT	Within a gene’s regulatory domain	0/1 assignments to genomic regions	No	Binomial test over genomic regions	(4)
ChIP-Enrich	Option from: nearest TSS, nearest gene, ≤1 kb from TSS, ≤5 kb from TSS, etc.	0/1 assignments	No	Wald test for logistic regression	(2)
Enrichr	Nearest TSS	0/1 assignments	No	Fisher’s exact test	(3)