| 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 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-5 | -1.300e+01 | 0.0006 | 45.0 | 7.17% | 1414.9 | 3.35% | motif file (matrix) |
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| 2 |  | Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-5 | -1.201e+01 | 0.0008 | 72.0 | 11.46% | 2812.2 | 6.65% | motif file (matrix) |
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| 3 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-4 | -1.148e+01 | 0.0009 | 45.0 | 7.17% | 1503.9 | 3.56% | motif file (matrix) |
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| 4 |  | X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-3 | -8.103e+00 | 0.0200 | 37.0 | 5.89% | 1340.1 | 3.17% | motif file (matrix) |
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| 5 |  | OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -6.441e+00 | 0.0842 | 35.0 | 5.57% | 1368.9 | 3.24% | motif file (matrix) |
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| 6 |  | Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer | 1e-2 | -6.352e+00 | 0.0842 | 59.0 | 9.39% | 2671.4 | 6.32% | motif file (matrix) |
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| 7 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-2 | -6.310e+00 | 0.0842 | 164.0 | 26.11% | 8960.8 | 21.19% | motif file (matrix) |
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| 8 |  | Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.789e+00 | 0.1010 | 69.0 | 10.99% | 3312.8 | 7.83% | motif file (matrix) |
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| 9 |  | Brachyury(T-box)/Mesoendoderm-Brachyury-ChIP-exo(GSE54963)/Homer | 1e-2 | -4.792e+00 | 0.2434 | 52.0 | 8.28% | 2476.0 | 5.85% | motif file (matrix) |
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| 10 |  | Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -4.782e+00 | 0.2434 | 70.0 | 11.15% | 3523.7 | 8.33% | motif file (matrix) |
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| 11 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-2 | -4.749e+00 | 0.2434 | 305.0 | 48.57% | 18509.2 | 43.76% | motif file (matrix) |
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