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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.