| 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 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-6 | -1.398e+01 | 0.0003 | 109.0 | 8.09% | 50.0 | 3.71% | motif file (matrix) |
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| 2 |  | Sox15(HMG)/CPA-Sox15-ChIP-Seq(GSE62909)/Homer | 1e-5 | -1.346e+01 | 0.0003 | 96.0 | 7.12% | 42.6 | 3.16% | motif file (matrix) |
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| 3 |  | Unknown2/Drosophila-Promoters/Homer | 1e-4 | -1.028e+01 | 0.0044 | 95.0 | 7.05% | 48.1 | 3.57% | motif file (matrix) |
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| 4 |  | PU.1:IRF8(ETS:IRF)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer | 1e-4 | -9.733e+00 | 0.0057 | 14.0 | 1.04% | 0.9 | 0.07% | motif file (matrix) |
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| 5 |  | PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer | 1e-4 | -9.723e+00 | 0.0057 | 202.0 | 14.99% | 135.1 | 10.02% | motif file (matrix) |
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| 6 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-4 | -9.444e+00 | 0.0057 | 99.0 | 7.34% | 53.8 | 3.99% | motif file (matrix) |
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| 7 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-4 | -9.325e+00 | 0.0057 | 55.0 | 4.08% | 22.8 | 1.69% | motif file (matrix) |
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| 8 |  | FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer | 1e-4 | -9.286e+00 | 0.0057 | 85.0 | 6.31% | 43.6 | 3.23% | motif file (matrix) |
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| 9 |  | GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer | 1e-3 | -8.626e+00 | 0.0077 | 160.0 | 11.87% | 104.5 | 7.76% | motif file (matrix) |
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| 10 |  | LHY(Myb)/Seedling-LHY-ChIP-Seq(GSE52175)/Homer | 1e-3 | -8.408e+00 | 0.0086 | 98.0 | 7.27% | 55.4 | 4.11% | motif file (matrix) |
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| 11 |  | SeqBias: TA-repeat | 1e-3 | -7.895e+00 | 0.0131 | 362.0 | 26.85% | 286.2 | 21.24% | motif file (matrix) |
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| 12 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-3 | -7.785e+00 | 0.0134 | 84.0 | 6.23% | 46.0 | 3.42% | motif file (matrix) |
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| 13 |  | ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer | 1e-3 | -7.641e+00 | 0.0143 | 11.0 | 0.82% | 0.0 | 0.00% | motif file (matrix) |
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| 14 |  | PRDM1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.522e+00 | 0.0150 | 38.0 | 2.82% | 14.2 | 1.05% | motif file (matrix) |
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| 15 |  | Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer | 1e-3 | -7.397e+00 | 0.0158 | 80.0 | 5.93% | 44.8 | 3.33% | motif file (matrix) |
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| 16 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-3 | -7.085e+00 | 0.0203 | 43.0 | 3.19% | 18.1 | 1.34% | motif file (matrix) |
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| 17 |  | Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer | 1e-2 | -6.771e+00 | 0.0261 | 55.0 | 4.08% | 27.8 | 2.06% | motif file (matrix) |
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| 18 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-2 | -6.706e+00 | 0.0263 | 109.0 | 8.09% | 69.1 | 5.13% | motif file (matrix) |
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| 19 |  | Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-2 | -6.530e+00 | 0.0297 | 82.0 | 6.08% | 48.4 | 3.59% | motif file (matrix) |
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| 20 |  | FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer | 1e-2 | -6.518e+00 | 0.0297 | 69.0 | 5.12% | 38.7 | 2.87% | motif file (matrix) |
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| 21 |  | caudal(Homeobox)/Drosophila-Embryos-ChIP-Chip(modEncode)/Homer | 1e-2 | -6.489e+00 | 0.0297 | 78.0 | 5.79% | 45.3 | 3.36% | motif file (matrix) |
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| 22 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -6.328e+00 | 0.0314 | 22.0 | 1.63% | 6.5 | 0.48% | motif file (matrix) |
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| 23 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-2 | -5.804e+00 | 0.0508 | 105.0 | 7.79% | 69.3 | 5.14% | motif file (matrix) |
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| 24 |  | AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer | 1e-2 | -5.593e+00 | 0.0601 | 183.0 | 13.58% | 137.6 | 10.21% | motif file (matrix) |
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| 25 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-2 | -5.542e+00 | 0.0606 | 88.0 | 6.53% | 56.9 | 4.22% | motif file (matrix) |
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| 26 |  | PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer | 1e-2 | -5.225e+00 | 0.0801 | 233.0 | 17.28% | 184.5 | 13.69% | motif file (matrix) |
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| 27 |  | ZNF711(Zf)/SHSY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer | 1e-2 | -5.104e+00 | 0.0871 | 110.0 | 8.16% | 76.4 | 5.67% | motif file (matrix) |
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| 28 |  | ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -5.079e+00 | 0.0871 | 98.0 | 7.27% | 66.9 | 4.96% | motif file (matrix) |
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| 29 |  | LXRE(NR),DR4/RAW-LXRb.biotin-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.074e+00 | 0.0871 | 14.0 | 1.04% | 3.7 | 0.28% | motif file (matrix) |
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| 30 |  | PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -4.851e+00 | 0.1009 | 22.0 | 1.63% | 8.8 | 0.65% | motif file (matrix) |
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| 31 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-2 | -4.823e+00 | 0.1009 | 25.0 | 1.85% | 10.9 | 0.81% | motif file (matrix) |
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| 32 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-2 | -4.673e+00 | 0.1130 | 57.0 | 4.23% | 34.6 | 2.57% | motif file (matrix) |
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