| 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 |  | MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.529e+00 | 0.0486 | 15.0 | 5.62% | 6.2 | 1.95% | motif file (matrix) |
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| 2 |  | HRE(HSF)/HepG2-HSF1-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.252e+00 | 0.0486 | 10.0 | 3.75% | 3.2 | 1.00% | motif file (matrix) |
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| 3 |  | Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer | 1e-3 | -7.033e+00 | 0.0723 | 19.0 | 7.12% | 10.9 | 3.41% | motif file (matrix) |
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| 4 |  | CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-2 | -6.393e+00 | 0.0823 | 5.0 | 1.87% | 1.5 | 0.47% | motif file (matrix) |
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| 5 |  | VDR(NR/DR3)/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer | 1e-2 | -6.393e+00 | 0.0823 | 5.0 | 1.87% | 0.0 | 0.00% | motif file (matrix) |
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| 6 |  | NPAS2(HLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-2 | -5.683e+00 | 0.1396 | 21.0 | 7.87% | 13.1 | 4.11% | motif file (matrix) |
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| 7 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.491e+00 | 0.1449 | 46.0 | 17.23% | 37.8 | 11.82% | motif file (matrix) |
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| 8 |  | EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.139e+00 | 0.1603 | 29.0 | 10.86% | 21.6 | 6.76% | motif file (matrix) |
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| 9 |  | ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer | 1e-2 | -5.139e+00 | 0.1603 | 29.0 | 10.86% | 21.3 | 6.68% | motif file (matrix) |
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| 10 |  | c-Myc/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-2 | -4.940e+00 | 0.1759 | 9.0 | 3.37% | 4.5 | 1.40% | motif file (matrix) |
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| 11 |  | MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer | 1e-2 | -4.928e+00 | 0.1759 | 6.0 | 2.25% | 2.5 | 0.77% | motif file (matrix) |
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| 12 |  | Tbox:Smad/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer | 1e-2 | -4.928e+00 | 0.1759 | 6.0 | 2.25% | 2.6 | 0.81% | motif file (matrix) |
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| 13 |  | Usf2(HLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-2 | -4.928e+00 | 0.1759 | 6.0 | 2.25% | 2.4 | 0.74% | motif file (matrix) |
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| 14 |  | Max(HLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.805e+00 | 0.1759 | 14.0 | 5.24% | 8.6 | 2.70% | motif file (matrix) |
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