| 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 |  | Srebp1a(HLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer | 1e-4 | -1.009e+01 | 0.0102 | 7.0 | 1.16% | 2.0 | 0.30% | motif file (matrix) |
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| 2 |  | ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer | 1e-3 | -8.011e+00 | 0.0272 | 6.0 | 1.00% | 1.3 | 0.20% | motif file (matrix) |
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| 3 |  | VDR(NR/DR3)/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer | 1e-3 | -8.011e+00 | 0.0272 | 6.0 | 1.00% | 1.9 | 0.28% | motif file (matrix) |
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| 4 |  | E2A-nearPU.1(HLH)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-3 | -7.634e+00 | 0.0297 | 49.0 | 8.14% | 33.3 | 4.95% | motif file (matrix) |
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| 5 |  | HNF4a(NR/DR1)/HepG2-HNF4a-ChIP-Seq(GSE25021)/Homer | 1e-2 | -6.309e+00 | 0.0895 | 9.0 | 1.50% | 3.8 | 0.56% | motif file (matrix) |
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| 6 |  | HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson et al.)/Homer | 1e-2 | -6.080e+00 | 0.0938 | 5.0 | 0.83% | 1.7 | 0.26% | motif file (matrix) |
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| 7 |  | NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer | 1e-2 | -6.001e+00 | 0.0938 | 7.0 | 1.16% | 2.5 | 0.37% | motif file (matrix) |
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| 8 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.853e+00 | 0.0938 | 16.0 | 2.66% | 8.5 | 1.26% | motif file (matrix) |
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| 9 |  | AMYB(HTH)/Testes-AMYB-ChIP-Seq(GSE44588)/Homer | 1e-2 | -5.744e+00 | 0.0938 | 26.0 | 4.32% | 16.7 | 2.49% | motif file (matrix) |
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| 10 |  | Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.568e+00 | 0.0939 | 10.0 | 1.66% | 4.6 | 0.68% | motif file (matrix) |
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| 11 |  | Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer | 1e-2 | -5.495e+00 | 0.0939 | 28.0 | 4.65% | 18.7 | 2.79% | motif file (matrix) |
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| 12 |  | EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer | 1e-2 | -4.888e+00 | 0.1545 | 27.0 | 4.49% | 18.9 | 2.81% | motif file (matrix) |
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