| 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 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-3 | -8.115e+00 | 0.0245 | 7.0 | 3.33% | 1.7 | 1.04% | motif file (matrix) |
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| 2 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-3 | -8.115e+00 | 0.0245 | 7.0 | 3.33% | 1.7 | 1.04% | motif file (matrix) |
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| 3 |  | TCFL2(HMG)/K562-TCF7L2-ChIP-Seq(GSE29196)/Homer | 1e-3 | -8.115e+00 | 0.0245 | 7.0 | 3.33% | 0.0 | 0.00% | motif file (matrix) |
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| 4 |  | PAX3:FKHR-fusion(Paired/Homeobox)/Rh4-PAX3:FKHR-ChIP-Seq(GSE19063)/Homer | 1e-3 | -7.620e+00 | 0.0302 | 22.0 | 10.48% | 8.7 | 5.16% | motif file (matrix) |
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| 5 |  | GATA-IR3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer | 1e-3 | -7.408e+00 | 0.0302 | 18.0 | 8.57% | 6.8 | 4.02% | motif file (matrix) |
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| 6 |  | OCT4-SOX2-TCF-NANOG((POU/Homeobox/HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -6.743e+00 | 0.0483 | 21.0 | 10.00% | 8.3 | 4.93% | motif file (matrix) |
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| 7 |  | Pax7(Paired/Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer | 1e-2 | -6.469e+00 | 0.0545 | 11.0 | 5.24% | 3.2 | 1.92% | motif file (matrix) |
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| 8 |  | PAX5-shortForm(Paired/Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.344e+00 | 0.0545 | 6.0 | 2.86% | 1.6 | 0.96% | motif file (matrix) |
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| 9 |  | RBPJ:Ebox/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-2 | -5.723e+00 | 0.0894 | 18.0 | 8.57% | 7.6 | 4.51% | motif file (matrix) |
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| 10 |  | Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.526e+00 | 0.0980 | 8.0 | 3.81% | 2.2 | 1.28% | motif file (matrix) |
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| 11 |  | ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer | 1e-2 | -5.273e+00 | 0.1147 | 109.0 | 51.90% | 72.9 | 43.35% | motif file (matrix) |
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| 12 |  | MyoD(HLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer | 1e-2 | -4.979e+00 | 0.1411 | 45.0 | 21.43% | 25.3 | 15.03% | motif file (matrix) |
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| 13 |  | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1e-2 | -4.730e+00 | 0.1670 | 79.0 | 37.62% | 50.5 | 30.05% | motif file (matrix) |
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| 14 |  | Egr2/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-2 | -4.723e+00 | 0.1670 | 5.0 | 2.38% | 1.3 | 0.75% | motif file (matrix) |
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| 15 |  | c-Myc/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-2 | -4.676e+00 | 0.1670 | 28.0 | 13.33% | 14.9 | 8.87% | motif file (matrix) |
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