| 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 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-4 | -9.569e+00 | 0.0172 | 3503.0 | 42.78% | 7180.7 | 40.70% | motif file (matrix) |
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| 2 |  | RARg(NR)/ES-RARg-ChIP-Seq(GSE30538)/Homer | 1e-3 | -8.182e+00 | 0.0344 | 79.0 | 0.96% | 112.2 | 0.64% | motif file (matrix) |
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| 3 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.115e+00 | 0.0667 | 1403.0 | 17.13% | 2795.9 | 15.85% | motif file (matrix) |
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| 4 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-2 | -6.896e+00 | 0.0667 | 3580.0 | 43.72% | 7414.9 | 42.03% | motif file (matrix) |
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| 5 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -6.866e+00 | 0.0667 | 3671.0 | 44.83% | 7610.7 | 43.14% | motif file (matrix) |
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| 6 |  | OCT4-SOX2-TCF-NANOG((POU/Homeobox/HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -6.700e+00 | 0.0667 | 444.0 | 5.42% | 828.3 | 4.69% | motif file (matrix) |
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| 7 |  | ETS(ETS)/Promoter/Homer | 1e-2 | -6.507e+00 | 0.0667 | 899.0 | 10.98% | 1760.7 | 9.98% | motif file (matrix) |
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| 8 |  | ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer | 1e-2 | -6.435e+00 | 0.0667 | 3584.0 | 43.77% | 7436.3 | 42.15% | motif file (matrix) |
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| 9 |  | ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer | 1e-2 | -5.557e+00 | 0.1055 | 2689.0 | 32.84% | 5550.2 | 31.46% | motif file (matrix) |
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| 10 |  | PAX5(Paired/Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.412e+00 | 0.1098 | 919.0 | 11.22% | 1822.1 | 10.33% | motif file (matrix) |
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| 11 |  | Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer | 1e-2 | -5.195e+00 | 0.1239 | 1215.0 | 14.84% | 2444.0 | 13.85% | motif file (matrix) |
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| 12 |  | Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer | 1e-2 | -5.164e+00 | 0.1239 | 2271.0 | 27.73% | 4673.7 | 26.49% | motif file (matrix) |
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| 13 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -5.030e+00 | 0.1239 | 232.0 | 2.83% | 423.7 | 2.40% | motif file (matrix) |
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| 14 |  | EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer | 1e-2 | -4.804e+00 | 0.1440 | 1626.0 | 19.86% | 3318.8 | 18.81% | motif file (matrix) |
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| 15 |  | Pax8(Paired/Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-2 | -4.740e+00 | 0.1440 | 858.0 | 10.48% | 1709.6 | 9.69% | motif file (matrix) |
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