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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.