Transcriptional features of genomic regulatory blocks

Table 1 Over-represented TFBSs in GRB target promoters

		Background: bystander gene promoters		Background: other CpG island promoters
Family	Name	Hit p-value	Sequence occurrence p-value	Hit p-value	Sequence occurrence p-value
FORKHEAD	Foxa2	0.009	0.0001	0.0001	0.0001
FORKHEAD	Foxd3	0.0001	0.0001	0.0001	0.0001
FORKHEAD	FOXI1	0.0001	0.0001	0.0001	0.0001
FORKHEAD	FOXL1	0.0001	0.0001	0.0001	0.0001
FORKHEAD	Foxq1	0.0001	0.0001	0.0002	0.0001
ZN-FINGER, C2H2	Gfi	0.0068	0.0001	0.0001	0.0001
HOMEO	Lhx3	0.0003	0.0001	0.0001	0.0001
MADS	MEF2A	0.0001	0.0001	0.0008	0.0001
HOMEO	Nkx2-5	0.0001	0.0001	0.0001	0.0001
HOMEO	Nobox	0.0002	0.0001	0.0001	0.0001
HOMEO	Pdx1	0.0001	0.0001	0.0001	0.0001
HOMEO	Prrx2	0.0001	0.0001	0.0001	0.0001
ZN-FINGER, C2H2	RREB1	0.0001	0.0001	0.0001	0.0001
HMG	Sox5	0.0001	0.0001	0.0001	0.0001
HMG	SOX9	0.0025	0.0001	0.0005	0.0001
HMG	SRY	0.0001	0.0001	0.0001	0.0001
HOMEO	TCF1	0.0017	0.0001	0.0001	0.0001

TFBS content of target gene promoters was compared to two different background sets. The ones over-represented in both comparisons are output in the table. Two distinct p-values represent the significance of the number of profile hits in the target set (hit p-value) and the significance of the number of sequences having at least one hit in the target set (sequence occurrence p-value).

ISSN: 1474-760X