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.

Chen et al.

Chen et al. BMC Genomics 2012 13:152   doi:10.1186/1471-2164-13-152

Open Data