| 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 |  | Stat3+il21(Stat)/CD4-Stat3-ChIP-Seq(GSE19198)/Homer | 1e-5 | -1.280e+01 | 0.0007 | 12.0 | 15.79% | 3.2 | 3.20% | motif file (matrix) |
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| 2 |  | Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer | 1e-4 | -1.133e+01 | 0.0015 | 7.0 | 9.21% | 1.8 | 1.84% | motif file (matrix) |
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| 3 |  | STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer | 1e-4 | -9.681e+00 | 0.0051 | 16.0 | 21.05% | 7.9 | 7.90% | motif file (matrix) |
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| 4 |  | HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer | 1e-3 | -9.027e+00 | 0.0059 | 6.0 | 7.89% | 1.4 | 1.39% | motif file (matrix) |
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| 5 |  | Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer | 1e-3 | -9.027e+00 | 0.0059 | 6.0 | 7.89% | 1.9 | 1.86% | motif file (matrix) |
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| 6 |  | MyoD(HLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer | 1e-3 | -8.846e+00 | 0.0059 | 8.0 | 10.53% | 2.6 | 2.57% | motif file (matrix) |
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| 7 |  | E2A(HLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer | 1e-3 | -7.875e+00 | 0.0117 | 12.0 | 15.79% | 5.6 | 5.54% | motif file (matrix) |
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| 8 |  | HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer | 1e-3 | -7.875e+00 | 0.0117 | 12.0 | 15.79% | 5.4 | 5.34% | motif file (matrix) |
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| 9 |  | Tcf12(HLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-3 | -7.020e+00 | 0.0244 | 10.0 | 13.16% | 4.6 | 4.57% | motif file (matrix) |
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| 10 |  | NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer | 1e-2 | -6.883e+00 | 0.0252 | 5.0 | 6.58% | 1.8 | 1.81% | motif file (matrix) |
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| 11 |  | MyoG(HLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer | 1e-2 | -6.207e+00 | 0.0451 | 8.0 | 10.53% | 3.8 | 3.76% | motif file (matrix) |
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| 12 |  | Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer | 1e-2 | -5.463e+00 | 0.0869 | 6.0 | 7.89% | 2.6 | 2.57% | motif file (matrix) |
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| 13 |  | EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.396e+00 | 0.0869 | 10.0 | 13.16% | 5.8 | 5.81% | motif file (matrix) |
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| 14 |  | Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer | 1e-2 | -5.245e+00 | 0.0927 | 26.0 | 34.21% | 21.8 | 21.77% | motif file (matrix) |
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| 15 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-2 | -5.052e+00 | 0.1050 | 12.0 | 15.79% | 7.5 | 7.45% | motif file (matrix) |
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| 16 |  | STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer | 1e-2 | -4.927e+00 | 0.1050 | 4.0 | 5.26% | 1.5 | 1.46% | motif file (matrix) |
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| 17 |  | TRa(NR)/C17.2-TRa-ChIP-Seq(GSE38347)/Homer | 1e-2 | -4.927e+00 | 0.1050 | 4.0 | 5.26% | 1.5 | 1.52% | motif file (matrix) |
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| 18 |  | CHR/Cell-Cycle-Exp/Homer | 1e-2 | -4.846e+00 | 0.1050 | 7.0 | 9.21% | 3.4 | 3.37% | motif file (matrix) |
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| 19 |  | Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer | 1e-2 | -4.846e+00 | 0.1050 | 7.0 | 9.21% | 3.5 | 3.52% | motif file (matrix) |
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