| 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-418 | -9.647e+02 | 0.0000 | 10643.0 | 41.73% | 20387.4 | 26.86% | motif file (matrix) |
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| 2 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-387 | -8.922e+02 | 0.0000 | 11921.0 | 46.74% | 24264.7 | 31.97% | motif file (matrix) |
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| 3 |  | Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer | 1e-34 | -7.877e+01 | 0.0000 | 13487.0 | 52.88% | 36767.2 | 48.44% | motif file (matrix) |
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| 4 |  | Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer | 1e-9 | -2.092e+01 | 0.0000 | 14074.0 | 55.18% | 40234.5 | 53.01% | motif file (matrix) |
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| 5 |  | Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer | 1e-8 | -2.034e+01 | 0.0000 | 8858.0 | 34.73% | 24822.2 | 32.70% | motif file (matrix) |
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| 6 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-8 | -1.896e+01 | 0.0000 | 6443.0 | 25.26% | 17831.6 | 23.49% | motif file (matrix) |
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| 7 |  | NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer | 1e-7 | -1.738e+01 | 0.0000 | 5037.0 | 19.75% | 13823.6 | 18.21% | motif file (matrix) |
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| 8 |  | PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer | 1e-6 | -1.475e+01 | 0.0000 | 2382.0 | 9.34% | 6321.2 | 8.33% | motif file (matrix) |
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| 9 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-6 | -1.461e+01 | 0.0000 | 6614.0 | 25.93% | 18514.8 | 24.39% | motif file (matrix) |
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| 10 |  | Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer | 1e-4 | -1.150e+01 | 0.0004 | 3391.0 | 13.30% | 9311.3 | 12.27% | motif file (matrix) |
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| 11 |  | Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer | 1e-4 | -1.137e+01 | 0.0004 | 5740.0 | 22.51% | 16122.2 | 21.24% | motif file (matrix) |
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| 12 |  | ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer | 1e-4 | -1.044e+01 | 0.0009 | 1818.0 | 7.13% | 4857.2 | 6.40% | motif file (matrix) |
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| 13 |  | Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer | 1e-4 | -9.466e+00 | 0.0023 | 7892.0 | 30.94% | 22532.8 | 29.69% | motif file (matrix) |
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| 14 |  | Tgif1(Homeobox)/mES-Tgif1-ChIP-Seq(GSE55404)/Homer | 1e-3 | -8.748e+00 | 0.0044 | 11552.0 | 45.29% | 33396.5 | 44.00% | motif file (matrix) |
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| 15 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-3 | -8.721e+00 | 0.0044 | 5786.0 | 22.69% | 16400.9 | 21.61% | motif file (matrix) |
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| 16 |  | Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer | 1e-3 | -6.976e+00 | 0.0226 | 942.0 | 3.69% | 2490.6 | 3.28% | motif file (matrix) |
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| 17 |  | Unknown3/Drosophila-Promoters/Homer | 1e-2 | -6.764e+00 | 0.0263 | 564.0 | 2.21% | 1441.3 | 1.90% | motif file (matrix) |
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| 18 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-2 | -6.735e+00 | 0.0263 | 5925.0 | 23.23% | 16933.4 | 22.31% | motif file (matrix) |
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| 19 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-2 | -5.740e+00 | 0.0655 | 1945.0 | 7.63% | 5397.2 | 7.11% | motif file (matrix) |
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| 20 |  | THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer | 1e-2 | -5.739e+00 | 0.0655 | 2262.0 | 8.87% | 6313.0 | 8.32% | motif file (matrix) |
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| 21 |  | ZNF165(Zf)/WHIM12-ZNF165-ChIP-Seq(GSE65937)/Homer | 1e-2 | -5.598e+00 | 0.0683 | 955.0 | 3.74% | 2569.3 | 3.38% | motif file (matrix) |
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| 22 |  | SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer | 1e-2 | -5.330e+00 | 0.0852 | 18762.0 | 73.56% | 55207.8 | 72.73% | motif file (matrix) |
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| 23 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-2 | -4.683e+00 | 0.1556 | 3265.0 | 12.80% | 9288.5 | 12.24% | motif file (matrix) |
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| 24 |  | E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.666e+00 | 0.1556 | 3824.0 | 14.99% | 10923.6 | 14.39% | motif file (matrix) |
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