| 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 |  | TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer | 1e-6 | -1.562e+01 | 0.0000 | 14.0 | 6.60% | 2.2 | 1.22% | motif file (matrix) |
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| 2 |  | Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer | 1e-4 | -1.101e+01 | 0.0025 | 123.0 | 58.02% | 78.0 | 43.40% | motif file (matrix) |
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| 3 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-3 | -9.027e+00 | 0.0121 | 28.0 | 13.21% | 12.0 | 6.67% | motif file (matrix) |
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| 4 |  | CRE(bZIP)/Promoter/Homer | 1e-3 | -8.437e+00 | 0.0121 | 7.0 | 3.30% | 1.0 | 0.57% | motif file (matrix) |
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| 5 |  | NRF1/Promoter/Homer | 1e-3 | -8.437e+00 | 0.0121 | 7.0 | 3.30% | 0.0 | 0.00% | motif file (matrix) |
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| 6 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-3 | -8.437e+00 | 0.0121 | 7.0 | 3.30% | 1.2 | 0.69% | motif file (matrix) |
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| 7 |  | Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer | 1e-3 | -8.081e+00 | 0.0134 | 50.0 | 23.58% | 26.0 | 14.47% | motif file (matrix) |
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| 8 |  | MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.241e+00 | 0.0271 | 9.0 | 4.25% | 2.9 | 1.59% | motif file (matrix) |
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| 9 |  | HIF-1a(HLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-3 | -7.203e+00 | 0.0271 | 19.0 | 8.96% | 7.7 | 4.30% | motif file (matrix) |
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| 10 |  | SeqBias: CG bias | 1e-2 | -6.694e+00 | 0.0375 | 136.0 | 64.15% | 97.0 | 53.93% | motif file (matrix) |
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| 11 |  | HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer | 1e-2 | -6.613e+00 | 0.0375 | 6.0 | 2.83% | 0.8 | 0.47% | motif file (matrix) |
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| 12 |  | E-box/Arabidopsis-Promoters/Homer | 1e-2 | -6.532e+00 | 0.0375 | 20.0 | 9.43% | 8.8 | 4.90% | motif file (matrix) |
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| 13 |  | ABF1/SacCer-Promoters/Homer | 1e-2 | -6.532e+00 | 0.0375 | 20.0 | 9.43% | 8.8 | 4.87% | motif file (matrix) |
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| 14 |  | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1e-2 | -5.871e+00 | 0.0610 | 49.0 | 23.11% | 28.2 | 15.69% | motif file (matrix) |
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| 15 |  | CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-2 | -5.847e+00 | 0.0610 | 8.0 | 3.77% | 2.2 | 1.23% | motif file (matrix) |
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| 16 |  | Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer | 1e-2 | -5.847e+00 | 0.0610 | 8.0 | 3.77% | 2.6 | 1.44% | motif file (matrix) |
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| 17 |  | Oct2(POU/Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.744e+00 | 0.0610 | 12.0 | 5.66% | 4.9 | 2.73% | motif file (matrix) |
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| 18 |  | Esrrb(NR)/mES-Esrrb-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.696e+00 | 0.0610 | 10.0 | 4.72% | 3.5 | 1.93% | motif file (matrix) |
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| 19 |  | Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer | 1e-2 | -5.507e+00 | 0.0647 | 22.0 | 10.38% | 10.3 | 5.71% | motif file (matrix) |
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| 20 |  | SUT1?/SacCer-Promoters/Homer | 1e-2 | -5.491e+00 | 0.0647 | 106.0 | 50.00% | 73.6 | 40.95% | motif file (matrix) |
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| 21 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-2 | -4.941e+00 | 0.0985 | 5.0 | 2.36% | 2.0 | 1.10% | motif file (matrix) |
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| 22 |  | Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer | 1e-2 | -4.941e+00 | 0.0985 | 5.0 | 2.36% | 1.0 | 0.58% | motif file (matrix) |
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| 23 |  | ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer | 1e-2 | -4.798e+00 | 0.1086 | 21.0 | 9.91% | 10.7 | 5.97% | motif file (matrix) |
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| 24 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.754e+00 | 0.1087 | 24.0 | 11.32% | 12.8 | 7.12% | motif file (matrix) |
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| 25 |  | ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer | 1e-2 | -4.633e+00 | 0.1179 | 16.0 | 7.55% | 7.3 | 4.07% | motif file (matrix) |
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| 26 |  | Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer | 1e-2 | -4.624e+00 | 0.1179 | 65.0 | 30.66% | 42.6 | 23.70% | motif file (matrix) |
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