| 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 |  | PAX5(Paired/Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.508e+01 | 0.0001 | 11.0 | 4.56% | 0.4 | 0.22% | motif file (matrix) |
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| 2 |  | STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer | 1e-5 | -1.341e+01 | 0.0002 | 14.0 | 5.81% | 2.6 | 1.53% | motif file (matrix) |
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| 3 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-4 | -1.072e+01 | 0.0022 | 18.0 | 7.47% | 5.0 | 2.95% | motif file (matrix) |
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| 4 |  | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1e-4 | -1.072e+01 | 0.0022 | 69.0 | 28.63% | 30.9 | 18.25% | motif file (matrix) |
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| 5 |  | STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer | 1e-4 | -9.498e+00 | 0.0045 | 17.0 | 7.05% | 4.7 | 2.79% | motif file (matrix) |
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| 6 |  | AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer | 1e-3 | -9.101e+00 | 0.0045 | 8.0 | 3.32% | 1.9 | 1.12% | motif file (matrix) |
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| 7 |  | Hnf1(Homeobox)/Liver-Foxa2-Chip-Seq(GSE25694)/Homer | 1e-3 | -9.101e+00 | 0.0045 | 8.0 | 3.32% | 1.5 | 0.88% | motif file (matrix) |
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| 8 |  | PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer | 1e-3 | -9.101e+00 | 0.0045 | 8.0 | 3.32% | 0.0 | 0.00% | motif file (matrix) |
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| 9 |  | RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer | 1e-3 | -9.101e+00 | 0.0045 | 8.0 | 3.32% | 1.5 | 0.86% | motif file (matrix) |
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| 10 |  | STAT6/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer | 1e-3 | -8.689e+00 | 0.0051 | 11.0 | 4.56% | 3.0 | 1.75% | motif file (matrix) |
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| 11 |  | Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer | 1e-3 | -8.336e+00 | 0.0066 | 16.0 | 6.64% | 4.1 | 2.45% | motif file (matrix) |
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| 12 |  | GFX(?)/Promoter/Homer | 1e-3 | -7.331e+00 | 0.0153 | 7.0 | 2.90% | 1.4 | 0.85% | motif file (matrix) |
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| 13 |  | p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer | 1e-3 | -7.331e+00 | 0.0153 | 7.0 | 2.90% | 1.9 | 1.12% | motif file (matrix) |
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| 14 |  | ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer | 1e-2 | -5.774e+00 | 0.0673 | 33.0 | 13.69% | 14.6 | 8.60% | motif file (matrix) |
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| 15 |  | STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer | 1e-2 | -5.691e+00 | 0.0673 | 6.0 | 2.49% | 0.4 | 0.22% | motif file (matrix) |
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| 16 |  | Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer | 1e-2 | -5.691e+00 | 0.0673 | 6.0 | 2.49% | 0.8 | 0.50% | motif file (matrix) |
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| 17 |  | SeqBias: CG-repeat | 1e-2 | -5.145e+00 | 0.1039 | 90.0 | 37.34% | 50.7 | 29.93% | motif file (matrix) |
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