| Rank | Motif | Name | P-value | log P-pvalue | q-value (Benjamini) | # Target Sequences with Motif | % of Targets Sequences with Motif | # Background Sequences with Motif | % of Background Sequences with Motif | Motif File |
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| 1 |  | EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer | 1e-9 | -2.146e+01 | 0.0000 | 115.0 | 34.95% | 67.7 | 20.47% | motif file (matrix) |
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| 2 |  | PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-6 | -1.395e+01 | 0.0001 | 80.0 | 24.32% | 47.1 | 14.25% | motif file (matrix) |
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| 3 |  | Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski et al.)/Homer | 1e-5 | -1.371e+01 | 0.0001 | 55.0 | 16.72% | 28.8 | 8.71% | motif file (matrix) |
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| 4 |  | TATA-Box(TBP)/Promoter/Homer | 1e-5 | -1.326e+01 | 0.0001 | 140.0 | 42.55% | 100.4 | 30.36% | motif file (matrix) |
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| 5 |  | ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer | 1e-5 | -1.247e+01 | 0.0002 | 217.0 | 65.96% | 177.1 | 53.56% | motif file (matrix) |
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| 6 |  | SPDEF(ETS)/VCaP-SPDEF-ChIP-Seq(SRA014231)/Homer | 1e-5 | -1.211e+01 | 0.0002 | 156.0 | 47.42% | 117.5 | 35.54% | motif file (matrix) |
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| 7 |  | GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer | 1e-4 | -1.032e+01 | 0.0012 | 20.0 | 6.08% | 8.0 | 2.41% | motif file (matrix) |
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| 8 |  | GABPA(ETS)/Jurkat-GABPa-ChIP-Seq(GSE17954)/Homer | 1e-3 | -9.115e+00 | 0.0036 | 157.0 | 47.72% | 124.7 | 37.72% | motif file (matrix) |
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| 9 |  | Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-3 | -8.944e+00 | 0.0038 | 172.0 | 52.28% | 139.9 | 42.30% | motif file (matrix) |
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| 10 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-3 | -8.053e+00 | 0.0084 | 69.0 | 20.97% | 46.8 | 14.16% | motif file (matrix) |
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| 11 |  | Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer | 1e-3 | -7.892e+00 | 0.0090 | 215.0 | 65.35% | 185.9 | 56.22% | motif file (matrix) |
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| 12 |  | EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer | 1e-3 | -7.698e+00 | 0.0100 | 196.0 | 59.57% | 167.0 | 50.50% | motif file (matrix) |
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| 13 |  | Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-3 | -7.502e+00 | 0.0112 | 56.0 | 17.02% | 36.6 | 11.06% | motif file (matrix) |
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| 14 |  | bZIP:IRF(bZIP,IRF)/Th17-BatF-ChIP-Seq(GSE39756)/Homer | 1e-3 | -7.465e+00 | 0.0112 | 41.0 | 12.46% | 24.6 | 7.44% | motif file (matrix) |
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| 15 |  | Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer | 1e-3 | -7.399e+00 | 0.0112 | 158.0 | 48.02% | 129.3 | 39.10% | motif file (matrix) |
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| 16 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-3 | -7.325e+00 | 0.0112 | 78.0 | 23.71% | 55.4 | 16.75% | motif file (matrix) |
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| 17 |  | HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer | 1e-3 | -7.310e+00 | 0.0112 | 96.0 | 29.18% | 71.4 | 21.60% | motif file (matrix) |
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| 18 |  | EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer | 1e-3 | -7.231e+00 | 0.0112 | 109.0 | 33.13% | 83.1 | 25.12% | motif file (matrix) |
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| 19 |  | ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer | 1e-3 | -7.092e+00 | 0.0116 | 113.0 | 34.35% | 87.4 | 26.44% | motif file (matrix) |
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| 20 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-3 | -6.952e+00 | 0.0126 | 84.0 | 25.53% | 61.6 | 18.63% | motif file (matrix) |
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| 21 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-2 | -6.879e+00 | 0.0126 | 50.0 | 15.20% | 32.6 | 9.85% | motif file (matrix) |
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| 22 |  | IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.879e+00 | 0.0126 | 50.0 | 15.20% | 32.1 | 9.70% | motif file (matrix) |
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| 23 |  | TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer | 1e-2 | -6.789e+00 | 0.0129 | 109.0 | 33.13% | 84.1 | 25.43% | motif file (matrix) |
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| 24 |  | ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer | 1e-2 | -6.583e+00 | 0.0152 | 198.0 | 60.18% | 171.4 | 51.83% | motif file (matrix) |
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| 25 |  | EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer | 1e-2 | -6.178e+00 | 0.0219 | 177.0 | 53.80% | 151.6 | 45.85% | motif file (matrix) |
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| 26 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.119e+00 | 0.0223 | 35.0 | 10.64% | 21.4 | 6.46% | motif file (matrix) |
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| 27 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-2 | -5.984e+00 | 0.0246 | 75.0 | 22.80% | 55.6 | 16.82% | motif file (matrix) |
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| 28 |  | ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer | 1e-2 | -5.845e+00 | 0.0273 | 32.0 | 9.73% | 19.7 | 5.94% | motif file (matrix) |
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| 29 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.745e+00 | 0.0291 | 264.0 | 80.24% | 243.6 | 73.68% | motif file (matrix) |
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| 30 |  | MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer | 1e-2 | -5.673e+00 | 0.0302 | 105.0 | 31.91% | 83.9 | 25.37% | motif file (matrix) |
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| 31 |  | Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.642e+00 | 0.0302 | 5.0 | 1.52% | 1.9 | 0.58% | motif file (matrix) |
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| 32 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-2 | -5.542e+00 | 0.0323 | 162.0 | 49.24% | 139.0 | 42.03% | motif file (matrix) |
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| 33 |  | NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer | 1e-2 | -5.305e+00 | 0.0397 | 12.0 | 3.65% | 5.2 | 1.58% | motif file (matrix) |
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| 34 |  | NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -5.305e+00 | 0.0397 | 208.0 | 63.22% | 185.9 | 56.21% | motif file (matrix) |
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| 35 |  | NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-2 | -5.097e+00 | 0.0461 | 98.0 | 29.79% | 78.8 | 23.84% | motif file (matrix) |
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| 36 |  | MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer | 1e-2 | -5.022e+00 | 0.0483 | 143.0 | 43.47% | 121.4 | 36.72% | motif file (matrix) |
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| 37 |  | Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer | 1e-2 | -4.988e+00 | 0.0487 | 147.0 | 44.68% | 125.3 | 37.89% | motif file (matrix) |
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| 38 |  | Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer | 1e-2 | -4.936e+00 | 0.0499 | 200.0 | 60.79% | 178.7 | 54.04% | motif file (matrix) |
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| 39 |  | Nr5a2(NR)/mES-Nr5a2-ChIP-Seq(GSE19019)/Homer | 1e-2 | -4.916e+00 | 0.0499 | 69.0 | 20.97% | 52.2 | 15.80% | motif file (matrix) |
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| 40 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-2 | -4.827e+00 | 0.0529 | 71.0 | 21.58% | 54.3 | 16.42% | motif file (matrix) |
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| 41 |  | PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer | 1e-2 | -4.705e+00 | 0.0583 | 74.0 | 22.49% | 57.9 | 17.50% | motif file (matrix) |
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