Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features

Table 2 Motif enrichment in mouse ES cell putative enhancers

Motif	Raw score	Max Enh prob	RPKM	PSSM
SP1	339	0.8099	33.5	[12]
KLF4^#	154	†	126.07	[12]
SOX2^#	140	1	942.79	[12]
POU5F1^#	128	0.9487	1318.38	[12]
SOX4	89.6	--	37.06	[70]
SOX11	86.5	0.6035	2.86	[70]
ESRRB^#	72.6	0.9999	162.78	[12]
KLF7	61	--	4.94	[70]
ESRRA	37	--	4.02	[70]
NR4A2	33.7	--	0.03	[12]
STAT3^#	31.6	0.5795	29.92	[12]
ZIC2	31.3	0.4291	13.76	[70]
ZIC1	29.6	0.5901	0.06	[70]
RARA	28.3	0.5909	30.28	[70]
ASCL2	25.1	--	0.72	[70]
NR2F2	19.9	0.5537	0.07	[70]
ZIC3	14	0.9550	15.27	[70]
RORA	7	0.5016	0.13	[12]
NFE2L2 (NRF2)	6.28	0.5947	68.09	[12]
RXR::RAR_DR5	4.89	--	5.34 (Rxra) 17.55 (Rxrb) 30.28 (Rara)	[12]
TEAD1	3.91	0.8987	66.24	[12]

The motifs of the listed TFs are significantly enriched with p < 0.01 in putative enhancer regions compared to random sequences drawn from PrL set, chr19 and promoter 5 kb regions using the Clover algorithm [27] with TF binding matrices reported in PSSM column Raw scores from Clover algorithm are reported. “Max Enh prob” column lists the maximum probabilities of enhancers if at least one Enh is closest to the TSS of the corresponding gene. Probabilities greater than 0.8 are underlined. RPKM column reports the absolute gene expression of the TF in mouse ES cells. † Several putative enhancer located 50 kb downstream of Klf4 are categorized to another non protein-coding transcript. ‘#’ sign denotes the TFs with ChIP-Seq datasets in mouse ES cells.

ISSN: 1471-2164