| 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 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski et al.)/Homer | 1e-9 | -2.258e+01 | 0.0000 | 65.0 | 19.82% | 25.3 | 8.63% | motif file (matrix) |
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| 2 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-7 | -1.634e+01 | 0.0000 | 69.0 | 21.04% | 32.9 | 11.23% | motif file (matrix) |
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| 3 |  | Srebp2(HLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer | 1e-6 | -1.450e+01 | 0.0000 | 29.0 | 8.84% | 9.5 | 3.24% | motif file (matrix) |
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| 4 |  | GATA-IR4(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer | 1e-3 | -8.752e+00 | 0.0078 | 7.0 | 2.13% | 0.9 | 0.30% | motif file (matrix) |
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| 5 |  | NF1:FOXA1/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-3 | -8.752e+00 | 0.0078 | 7.0 | 2.13% | 2.0 | 0.67% | motif file (matrix) |
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| 6 |  | Srebp1a(HLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.645e+00 | 0.0078 | 30.0 | 9.15% | 13.1 | 4.48% | motif file (matrix) |
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| 7 |  | CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-3 | -7.768e+00 | 0.0149 | 19.0 | 5.79% | 7.6 | 2.60% | motif file (matrix) |
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| 8 |  | FXR(NR/IR1)/Liver-FXR-ChIP-Seq(Chong et al.)/Homer | 1e-3 | -7.767e+00 | 0.0149 | 38.0 | 11.59% | 19.2 | 6.54% | motif file (matrix) |
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| 9 |  | Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.373e+00 | 0.1268 | 157.0 | 47.87% | 119.9 | 40.90% | motif file (matrix) |
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| 10 |  | Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer | 1e-2 | -5.300e+00 | 0.1268 | 136.0 | 41.46% | 101.7 | 34.70% | motif file (matrix) |
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| 11 |  | p53(p53)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.161e+00 | 0.1283 | 5.0 | 1.52% | 0.0 | 0.00% | motif file (matrix) |
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| 12 |  | AMYB(HTH)/Testes-AMYB-ChIP-Seq(GSE44588)/Homer | 1e-2 | -5.079e+00 | 0.1283 | 107.0 | 32.62% | 77.7 | 26.51% | motif file (matrix) |
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