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Table 2 over-represented motifs detected at <10% false discovery rate

From: Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals

Cluster number

FDR

PFM Number

PFM Annotation

1: Protein synthesis

<2.5%

190

M00025:Elk-1, M00007:Elk-1

 

<2.5%

110

M00050:E2F, MA0024:E2F

 

<2.5%

57

M00108:NRF-2, MA0028:Elk-1, MA0062:NRF-2

 

<2.5%

181

MA0076:SAP-1

 

<10%

18

M00074:c-Ets-1(p54)

 

<10%

78

M00262:Staf

2: Oocyte / fertilized egg

<2.5%

71

M00024:E2F

 

<2.5%

190

M00025:Elk-1, M00007:Elk-1

 

<2.5%

9

M00032:c-Ets-1(p54)

 

<2.5%

110

M00050:E2F, MA0024:E2F

 

<2.5%

57

M00108:NRF-2, MA0028:Elk-1, MA0062:NRF-2

 

<2.5%

181

MA0076:SAP-1

 

<10%

238

MA0088:Staf, M00264:Staf

3: Neural tissues

<2.5%

99

M00189:AP-2

 

<2.5%

115

M00196:Sp1

 

<2.5%

141

M00256:NRSF

 

<10%

75

M00243:Egr-1

4: Lymphocytes

<2.5%

143

MA0050:Irf-1, M00062:IRF-1, M00063:IRF-2

 

<10%

74

M00054:NF-kappaB, MA0061:NF-kappaB

 

<10%

28

M00258:ISRE

5: Testis / spermatogenesis

<2.5%

109

M00281:RFX1

 

<2.5%

142

MA0078:SOX17

 

<10%

108

M00036:v-Jun

 

<10%

248

M00041:CRE-BP1/c-Jun

 

<10%

65

M00100:CdxA

6: Liver

<2.5%

16

M00134:HNF-4

 

<2.5%

212

M00158:COUP-TF / HNF-4, MA0017:COUP-TF

 

<2.5%

33

M00206:HNF-1

 

<2.5%

203

MA0046:HNF-1, M00132:HNF-1

 

<2.5%

234

MA0047:HNF-3beta, M00131:HNF-3beta

 

<2.5%

113

MA0065:PPARgamma-RXRal

 

<10%

46

M00155:ARP-1

 

<10%

212

M00158:COUP-TF / HNF-4, MA0017:COUP-TF

 

<10%

146

MA0071:RORalfa-1, M00156:RORalpha1

8: ECM

<10%

215

M00378:Pax-4

9: Cardiac muscle

<2.5%

223

M00026:RSRFC4

 

<2.5%

144

M00152:SRF

 

<2.5%

59

M00231:MEF-2

 

<2.5%

222

M00232:MEF-2

 

<2.5%

161

M00252:TATA

 

<2.5%

259

M00418:TGIF, M00419:MEIS1

 

<2.5%

160

MA0052:MEF2

 

<10%

60

M00006:MEF-2

12: Skeletal muscle

<2.5%

201

M00184:MyoD, M00001:MyoD

 

<10%

17

M00002:E47

 

<10%

59

M00231:MEF-2

13: Endoplasmatic reticulum

<10%

190

M00025:Elk-1, M00007:Elk-1

 

<10%

57

M00108:NRF-2, MA0028:Elk-1, MA0062:NRF-2

 

<10%

181

MA0076:SAP-1

15: Erythrocyte

<10%

209

M00128:GATA-1, M00127:GATA-1

 

<10%

122

M00203:GATA-X

 

<10%

198

M00413:AREB6

16: B lymphocyte

<2.5%

133

MA0081:SPI-B

17: Kidney

<2.5%

33

M00206:HNF-1

 

<2.5%

188

M00411:HNF-4alpha1

22: Cell cycle genes

<10%

110

M00050:E2F, MA0024:E2F

24: Pancreas

<10%

121

M00071:E47

 

<10%

193

M00080:Evi-1, M00082:Evi-1

30: Small intestine

<10%

31

M00346:GATA-1, M00347:GATA-1, M00348:GATA-2

40: Smooth muscle

<2.5%

144

M00152:SRF

 

<2.5%

245

M00186:SRF, M00215:SRF

 

<2.5%

88

MA0083:SRF

44: Retina

<2.5%

196

M00087:Ik-2

45: Testis (mouse signal only)

<2.5%

164

M00253:cap

49: Lung/endothelium (mouse signal only)

<10%

66

M00199:AP-1, M00037:NF-E2

65: NfkappaB signalling

<2.5%

235

M00051:NF-kappaB (p50), MA0105:p50

  1. Over-represented motifs arranged by cluster number. FDR column: False Discovery Rate (estimated probability for the over-representation to be a spurious detection). Motifs are are shown both by their numerical identifiers (PFM number) and by their annotation (PFM annotation). In cases where a PFM is a composite based on more than one source, the components are given separated by commas. The data where generated from the PCC = 0.75 clustering, 2 kb sequence database, at 90% phylogenetic conservation.