| 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-4834 | -1.113e+04 | 0.0000 | 26648.0 | 54.29% | 11738.0 | 14.90% | motif file (matrix) |
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| 2 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-4626 | -1.065e+04 | 0.0000 | 28482.0 | 58.02% | 14481.0 | 18.38% | motif file (matrix) |
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| 3 |  | NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer | 1e-28 | -6.536e+01 | 0.0000 | 10169.0 | 20.72% | 14328.4 | 18.19% | motif file (matrix) |
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| 4 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-16 | -3.752e+01 | 0.0000 | 8301.0 | 16.91% | 11945.4 | 15.16% | motif file (matrix) |
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| 5 |  | Unknown3/Drosophila-Promoters/Homer | 1e-11 | -2.600e+01 | 0.0000 | 1065.0 | 2.17% | 1290.6 | 1.64% | motif file (matrix) |
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| 6 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-10 | -2.488e+01 | 0.0000 | 8107.0 | 16.52% | 11915.1 | 15.12% | motif file (matrix) |
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| 7 |  | PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer | 1e-4 | -1.045e+01 | 0.0016 | 4360.0 | 8.88% | 6488.3 | 8.24% | motif file (matrix) |
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| 8 |  | Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer | 1e-4 | -9.799e+00 | 0.0027 | 21629.0 | 44.06% | 33847.8 | 42.96% | motif file (matrix) |
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| 9 |  | Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer | 1e-3 | -7.947e+00 | 0.0152 | 16782.0 | 34.19% | 26210.5 | 33.27% | motif file (matrix) |
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