Table 5

Motif Enrichment in Genes bound by Oct4 or cMyc TF Groups

Oct4 Group

cMyc Group

Motif

Binding TF

No. of genes

ratio

p-value

No. of genes

ratio

p-value

SoxOct

(Oct4, Sox2)

66

3.41

2.0E-21

103

0.45

6.4E-24

Oct4

(Oct4)

37

2.33

9.9E-08

151

0.81

2.5E-03

Sox2

(Sox2)

51

3.06

3.8E-15

178

0.86

1.4E-02

Nanog

(Nanog)

18

2.20

5.0E-04

122

1.35

3.9E-04

Stat1

(Stat3)

34

2.83

7.3E-09

145

1.32

1.0E-04

Ebox

(cMyc)

6

0.59

9.5E-01

373

4.02

2.6E-207

E2f1

(E2f1)

1

1.44

9.4E-02

284

2.25

1.2E-40

Klf4

(Klf4)

38

1.02

4.0E-01

235

0.61

1.4E-19

Lrh1

(Lrh1)

28

2.22

1.4E-05

158

1.12

6.9E-02

Elk1

(Elk1)

10

0.19

3.1E-02

170

1.64

8.6E-11

Sequences co-bound by all TFs of the Oct4 group (Oct4, Sox2, Nanog, Smad1, and Stat3) or all TFs of the cMyc group (cMyc, nMyc, E2f1, and Zfx) in the Chen et al data set were scanned for relevant motifs, plus the Lrh1 (Nr5a2) and Elk1 motifs. There were 122 genes bound by all TFs in the Oct4 group and 1173 genes bound by all TFs in the cMyc group. Enrichments, computed by comparing against motif scans in control sequences, and p-values are shown below.

Mason et al. BMC Genomics 2009 10:327   doi:10.1186/1471-2164-10-327