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Table 2 Transcription factor binding sites over-represented in the promoters of the EGF regulated genes

From: Profiling and metaanalysis of epidermal keratinocytes responses to epidermal growth factor

a

Name

Count

%

PValue

Benjamini

FDR

1 h Up

**BACH2

65

53

5.60E-05

9.80E-03

6.86E-02

IK3

65

53

1.48E-04

1.29E-02

1.81E-01

LMO2COM

80

65

1.93E-04

1.12E-02

2.36E-01

PAX3

63

51

3.25E-04

1.42E-02

3.98E-01

TATA

74

60

3.34E-04

1.17E-02

4.10E-01

**BACH1

70

57

3.52E-04

1.03E-02

4.31E-01

CEBPB

75

61

4.51E-04

1.13E-02

5.52E-01

**AP1

80

65

4.54E-04

9.94E-03

5.56E-01

SOX5

67

54

5.35E-04

1.04E-02

6.54E-01

**NFE2

53

43

6.09E-04

1.07E-02

7.45E-01

4 h Up

**BACH2

142

63

2.35E-17

4.13E-15

2.88E-14

**AP1

172

76

3.74E-16

2.93E-14

4.11E-13

**BACH1

152

67

2.67E-15

1.56E-13

3.28E-12

IK3

127

56

1.18E-09

5.21E-08

1.45E-06

STAT

106

47

5.97E-09

2.10E-07

7.33E-06

SRY

119

52

1.19E-08

3.49E-07

1.46E-05

**NFE2

105

46

1.85E-08

4.66E-07

2.28E-05

TATA

142

63

2.52E-08

5.53E-07

3.09E-05

FOXO1

116

51

4.89E-08

9.56E-07

6.00E-05

LMO2COM

148

65

3.69E-07

6.49E-06

4.52E-04

FREAC3

115

51

7.41E-07

1.19E-05

9.09E-04

RORA2

124

55

8.78E-07

1.29E-05

1.08E-03

TAXCREB

137

60

1.30E-06

1.76E-05

1.59E-03

FOXO4

137

60

1.39E-06

1.75E-05

1.70E-03

HLF

109

48

1.70E-06

2.00E-05

2.09E-03

CHOP

124

55

2.61E-06

2.87E-05

3.20E-03

MYOD

139

61

3.76E-06

3.90E-05

4.62E-03

NFAT

110

48

3.80E-06

3.72E-05

4.67E-03

FREAC7

124

55

4.02E-06

3.72E-05

4.93E-03

HFH1

117

52

4.16E-06

3.66E-05

5.10E-03

MEF2

173

76

5.42E-06

4.54E-05

6.65E-03

MEIS1BHOXA9

127

56

6.44E-06

5.15E-05

7.90E-03

POU3F2

144

63

6.77E-06

5.18E-05

8.30E-03

FREAC4

118

52

8.04E-06

5.90E-05

9.87E-03

TST1

114

50

8.68E-06

6.11E-05

1.07E-02

CREBP1

120

53

1.05E-05

7.09E-05

1.29E-02

FOXO3

79

35

1.23E-05

8.04E-05

1.51E-02

SOX5

121

53

1.47E-05

9.26E-05

1.81E-02

HSF2

108

48

1.96E-05

1.19E-04

2.41E-02

LYF1

102

45

2.33E-05

1.37E-04

2.86E-02

RSRFC4

118

52

2.58E-05

1.46E-04

3.16E-02

FREAC2

88

39

2.62E-05

1.44E-04

3.21E-02

CEBPA

80

35

2.66E-05

1.42E-04

3.27E-02

IK2

83

37

2.78E-05

1.44E-04

3.41E-02

CETS1P54

72

32

3.21E-05

1.62E-04

3.94E-02

b

Term

Count

%

PValue

Benjamini

FDR

1 h Down

SOX5

94

48

1.47E-03

2.28E-01

1.79E + 00

CEBPB

104

54

3.43E-03

2.61E-01

4.13E + 00

STAT

71

37

3.75E-03

1.98E-01

4.51E + 00

POU3F2

109

56

5.57E-03

2.18E-01

6.62E + 00

FOXO3

57

29

6.14E-03

1.95E-01

7.28E + 00

**AP1

107

*

2.33E-02

  

4 h Down

HLF

59

47

7.35E-04

1.21E-01

8.98E-01

POU3F2

77

62

3.05E-03

2.36E-01

3.68E + 00

NCX

61

49

4.17E-03

2.18E-01

5.00E + 00

TATA

70

56

6.68E-03

2.55E-01

7.90E + 00

E4BP4

58

46

8.38E-03

2.56E-01

9.82E + 00

CEBPB

71

57

8.52E-03

2.22E-01

9.96E + 00

**AP1

73

*

3.57E-02

  

24 h Down

**BACH2

47

48

5.35E-03

6.11E-01

6.38E + 00

**AP1

58

*

2.85E-02

  

48 h Down

HLF

92

45

2.37E-04

4.10E-02

2.90E-01

LMO2COM

125

62

2.59E-04

2.26E-02

3.17E-01

MEF2

151

74

3.56E-04

2.08E-02

4.36E-01

FOXJ2

136

67

3.86E-04

1.70E-02

4.74E-01

SOX9

98

48

4.04E-04

1.42E-02

4.96E-01

CEBPB

117

58

6.03E-04

1.76E-02

7.38E-01

**AP1

125

62

7.64E-04

1.91E-02

9.34E-01

TATA

114

56

8.00E-04

1.75E-02

9.78E-01

HFH3

89

44

1.44E-03

2.80E-02

1.76E + 00

IRF7

97

48

1.49E-03

2.61E-02

1.82E + 00

IRF2

89

44

1.66E-03

2.64E-02

2.02E + 00

NFAT

89

44

2.78E-03

4.03E-02

3.37E + 00

TAXCREB

111

55

3.84E-03

5.10E-02

4.61E + 00

HAND1E47

97

48

4.11E-03

5.08E-02

4.94E + 00

E4BP4

91

45

4.99E-03

5.73E-02

5.96E + 00

FREAC2

71

35

5.12E-03

5.52E-02

6.11E + 00

POU3F2

119

59

5.18E-03

5.26E-02

6.18E + 00

STAT1

84

41

5.88E-03

5.63E-02

6.99E + 00

  1. a) Induced genes, b) suppressed genes. The top p-value sites are presented for each time point. Count columns give the number of genes with the respective binding sites, % the percentage of submitted genes that have the site, while Benjamini and FDR (false discovery rate), represent statistical values corrected for multiple comparisons. Note the recurrence of BACH1, BACH2, AP1 and NF-E2 sites, marked with double asterisk, which bind to similar DNA sequences. At 4 and 24 h, in suppressed genes, the AP1 sites barely miss the statistical cut off p-value of 0.01; they are included here nevertheless.
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