| 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 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-10 | -2.371e+01 | 0.0000 | 16.0 | 16.16% | 905.8 | 1.85% | motif file (matrix) |
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| 2 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski et al.)/Homer | 1e-8 | -1.846e+01 | 0.0000 | 10.0 | 10.10% | 395.1 | 0.81% | motif file (matrix) |
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| 3 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.926e+00 | 0.0318 | 32.0 | 32.32% | 8720.0 | 17.84% | motif file (matrix) |
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| 4 |  | Nanog(Homeobox)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-2 | -6.124e+00 | 0.1445 | 51.0 | 51.52% | 18062.1 | 36.96% | motif file (matrix) |
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| 5 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.728e+00 | 0.1719 | 15.0 | 15.15% | 3373.1 | 6.90% | motif file (matrix) |
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| 6 |  | Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer | 1e-2 | -5.690e+00 | 0.1719 | 39.0 | 39.39% | 12929.3 | 26.46% | motif file (matrix) |
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| 7 |  | Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer | 1e-2 | -5.584e+00 | 0.1719 | 47.0 | 47.47% | 16608.4 | 33.98% | motif file (matrix) |
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| 8 |  | NFY(CCAAT)/Promoter/Homer | 1e-2 | -4.884e+00 | 0.2496 | 13.0 | 13.13% | 2998.6 | 6.14% | motif file (matrix) |
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