| 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 |  | Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer | 1e-3 | -9.134e+00 | 0.0266 | 3.0 | 100.00% | 1.4 | 6.54% | motif file (matrix) |
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| 2 |  | Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer | 1e-3 | -7.054e+00 | 0.1063 | 3.0 | 100.00% | 2.9 | 13.18% | motif file (matrix) |
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| 3 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo et al.)/Homer | 1e-2 | -5.023e+00 | 0.1620 | 2.0 | 66.67% | 1.4 | 6.54% | motif file (matrix) |
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| 4 |  | Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.023e+00 | 0.1620 | 2.0 | 66.67% | 0.0 | 0.00% | motif file (matrix) |
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| 5 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.023e+00 | 0.1620 | 2.0 | 66.67% | 1.7 | 7.65% | motif file (matrix) |
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| 6 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-2 | -5.023e+00 | 0.1620 | 2.0 | 66.67% | 1.4 | 6.54% | motif file (matrix) |
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| 7 |  | Nr5a2(NR)/Pancreas-LRH1-ChIP-Seq(GSE34295)/Homer | 1e-2 | -5.023e+00 | 0.1620 | 2.0 | 66.67% | 1.4 | 6.67% | motif file (matrix) |
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| 8 |  | MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.023e+00 | 0.1620 | 2.0 | 66.67% | 1.4 | 6.45% | motif file (matrix) |
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| 9 |  | NFAT:AP1/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-2 | -5.023e+00 | 0.1620 | 2.0 | 66.67% | 0.0 | 0.00% | motif file (matrix) |
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| 10 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.023e+00 | 0.1620 | 2.0 | 66.67% | 1.4 | 6.58% | motif file (matrix) |
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| 11 |  | Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer | 1e-2 | -4.975e+00 | 0.1620 | 3.0 | 100.00% | 4.5 | 20.80% | motif file (matrix) |
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| 12 |  | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1e-2 | -4.975e+00 | 0.1620 | 3.0 | 100.00% | 4.5 | 20.86% | motif file (matrix) |
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| 13 |  | Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer | 1e-2 | -4.975e+00 | 0.1620 | 3.0 | 100.00% | 4.5 | 20.95% | motif file (matrix) |
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| 14 |  | Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer | 1e-2 | -4.975e+00 | 0.1620 | 3.0 | 100.00% | 4.3 | 19.76% | motif file (matrix) |
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| 15 |  | ZNF711(Zf)/SH-SY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer | 1e-2 | -4.975e+00 | 0.1620 | 3.0 | 100.00% | 4.5 | 20.71% | motif file (matrix) |
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