| 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 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-4 | -1.143e+01 | 0.0029 | 2855.0 | 16.82% | 5169.6 | 15.62% | motif file (matrix) |
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| 2 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-4 | -9.975e+00 | 0.0061 | 1498.0 | 8.82% | 2646.6 | 8.00% | motif file (matrix) |
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| 3 |  | Sp1(Zf)/Promoter/Homer | 1e-4 | -9.822e+00 | 0.0061 | 458.0 | 2.70% | 742.4 | 2.24% | motif file (matrix) |
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| 4 |  | CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer | 1e-3 | -8.944e+00 | 0.0086 | 10794.0 | 63.58% | 20591.3 | 62.23% | motif file (matrix) |
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| 5 |  | GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer | 1e-3 | -6.910e+00 | 0.0527 | 7796.0 | 45.92% | 14805.9 | 44.74% | motif file (matrix) |
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| 6 |  | NRF(NRF)/Promoter/Homer | 1e-2 | -6.682e+00 | 0.0552 | 174.0 | 1.02% | 267.8 | 0.81% | motif file (matrix) |
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| 7 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-2 | -6.575e+00 | 0.0552 | 835.0 | 4.92% | 1468.1 | 4.44% | motif file (matrix) |
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| 8 |  | Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.549e+00 | 0.0552 | 894.0 | 5.27% | 1578.8 | 4.77% | motif file (matrix) |
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| 9 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-2 | -5.549e+00 | 0.1141 | 1151.0 | 6.78% | 2078.0 | 6.28% | motif file (matrix) |
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