| 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 |  | Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer | 1e-5 | -1.292e+01 | 0.0006 | 14.0 | 8.70% | 4.8 | 2.24% | motif file (matrix) |
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| 2 |  | GRHL2(CP2)/HBE-GRHL2-ChIP-Seq(GSE46194)/Homer | 1e-3 | -8.999e+00 | 0.0152 | 6.0 | 3.73% | 1.9 | 0.87% | motif file (matrix) |
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| 3 |  | HRE(HSF)/HepG2-HSF1-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.778e+00 | 0.0152 | 8.0 | 4.97% | 2.0 | 0.94% | motif file (matrix) |
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| 4 |  | MyoD(HLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer | 1e-3 | -8.150e+00 | 0.0178 | 15.0 | 9.32% | 7.5 | 3.48% | motif file (matrix) |
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| 5 |  | NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer | 1e-3 | -7.048e+00 | 0.0428 | 7.0 | 4.35% | 2.3 | 1.09% | motif file (matrix) |
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| 6 |  | HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer | 1e-2 | -6.876e+00 | 0.0428 | 5.0 | 3.11% | 1.6 | 0.74% | motif file (matrix) |
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| 7 |  | Tbox:Smad/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer | 1e-2 | -6.876e+00 | 0.0428 | 5.0 | 3.11% | 1.6 | 0.76% | motif file (matrix) |
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| 8 |  | ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer | 1e-2 | -6.488e+00 | 0.0468 | 17.0 | 10.56% | 10.8 | 5.05% | motif file (matrix) |
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| 9 |  | NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer | 1e-2 | -6.387e+00 | 0.0468 | 18.0 | 11.18% | 11.9 | 5.56% | motif file (matrix) |
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| 10 |  | ZNF711(Zf)/SH-SY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer | 1e-2 | -5.598e+00 | 0.0911 | 30.0 | 18.63% | 24.4 | 11.35% | motif file (matrix) |
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| 11 |  | MyoG(HLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer | 1e-2 | -5.578e+00 | 0.0911 | 16.0 | 9.94% | 10.3 | 4.82% | motif file (matrix) |
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| 12 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.451e+00 | 0.0911 | 6.0 | 3.73% | 2.8 | 1.30% | motif file (matrix) |
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| 13 |  | Tcf3(HMG)/mES-Tcf3-ChIP-Seq(GSE11724)/Homer | 1e-2 | -5.451e+00 | 0.0911 | 6.0 | 3.73% | 2.1 | 0.97% | motif file (matrix) |
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| 14 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo et al.)/Homer | 1e-2 | -4.962e+00 | 0.1230 | 12.0 | 7.45% | 7.9 | 3.70% | motif file (matrix) |
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| 15 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski et al.)/Homer | 1e-2 | -4.934e+00 | 0.1230 | 4.0 | 2.48% | 1.2 | 0.54% | motif file (matrix) |
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| 16 |  | Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer | 1e-2 | -4.828e+00 | 0.1231 | 7.0 | 4.35% | 3.1 | 1.45% | motif file (matrix) |
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| 17 |  | Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer | 1e-2 | -4.781e+00 | 0.1231 | 14.0 | 8.70% | 9.6 | 4.49% | motif file (matrix) |
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| 18 |  | E2A(HLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer | 1e-2 | -4.718e+00 | 0.1231 | 22.0 | 13.66% | 17.7 | 8.26% | motif file (matrix) |
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