| 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 |  | MyoD(HLH)/Myotube-MyoD-ChIP-Seq/Homer | 1e-5 | -1.204e+01 | 0.0014 | 1158.0 | 78.56% | 35775.4 | 73.60% | motif file (matrix) |
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| 2 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq/Homer | 1e-4 | -1.115e+01 | 0.0017 | 320.0 | 21.71% | 8471.7 | 17.43% | motif file (matrix) |
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| 3 |  | CTCF-SatelliteElement/CD4+-CTCF-ChIP-Seq/Homer | 1e-4 | -1.101e+01 | 0.0017 | 68.0 | 4.61% | 1299.0 | 2.67% | motif file (matrix) |
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| 4 |  | HNF4a(NR/DR1)/HepG2-HNF4a-ChIP-Seq/Homer | 1e-4 | -1.054e+01 | 0.0017 | 1059.0 | 71.85% | 32528.9 | 66.92% | motif file (matrix) |
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| 5 |  | Ap4(HLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer | 1e-4 | -1.009e+01 | 0.0019 | 1382.0 | 93.76% | 44193.7 | 90.92% | motif file (matrix) |
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| 6 |  | ETS:E-box/HPC7-Scl-ChIP-Seq/Homer | 1e-4 | -9.768e+00 | 0.0022 | 324.0 | 21.98% | 8745.9 | 17.99% | motif file (matrix) |
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| 7 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq/Homer | 1e-4 | -9.579e+00 | 0.0023 | 439.0 | 29.78% | 12326.6 | 25.36% | motif file (matrix) |
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| 8 |  | STAT1(Stat)/HelaS3-STAT1-ChIP-Seq/Homer | 1e-3 | -8.853e+00 | 0.0041 | 898.0 | 60.92% | 27327.5 | 56.22% | motif file (matrix) |
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| 9 |  | ERG(ETS)/VCaP-ERG-ChIP-Seq/Homer | 1e-3 | -8.754e+00 | 0.0041 | 1461.0 | 99.12% | 47571.6 | 97.87% | motif file (matrix) |
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| 10 |  | Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer | 1e-3 | -8.146e+00 | 0.0066 | 609.0 | 41.32% | 17950.0 | 36.93% | motif file (matrix) |
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| 11 |  | STAT5(Stat)/mCD4+-Stat5a|b-ChIP-Seq/Homer | 1e-3 | -7.443e+00 | 0.0122 | 941.0 | 63.84% | 29009.3 | 59.68% | motif file (matrix) |
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| 12 |  | MYB(HTH)/ERMYB-Myb-ChIPSeq(GSE22095)/Homer | 1e-3 | -7.290e+00 | 0.0130 | 1467.0 | 99.53% | 47943.3 | 98.64% | motif file (matrix) |
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| 13 |  | Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq/Homer | 1e-3 | -7.038e+00 | 0.0155 | 1370.0 | 92.94% | 44047.0 | 90.62% | motif file (matrix) |
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| 14 |  | STAT6(Stat)/CD4-Stat6-ChIP-Seq/Homer | 1e-2 | -6.769e+00 | 0.0188 | 1184.0 | 80.33% | 37428.7 | 77.00% | motif file (matrix) |
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| 15 |  | TRa(NR)/C17.2-TRa-ChIP-Seq(GSE38347)/Homer | 1e-2 | -6.238e+00 | 0.0298 | 1221.0 | 82.84% | 38806.8 | 79.84% | motif file (matrix) |
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| 16 |  | GATA:SCL/Ter119-SCL-ChIP-Seq/Homer | 1e-2 | -6.237e+00 | 0.0298 | 409.0 | 27.75% | 11881.0 | 24.44% | motif file (matrix) |
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| 17 |  | Stat3+il23(Stat)/CD4-Stat3-ChIP-Seq/Homer | 1e-2 | -6.213e+00 | 0.0298 | 1250.0 | 84.80% | 39828.0 | 81.94% | motif file (matrix) |
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| 18 |  | STAT6/Macrophage-Stat6-ChIP-Seq/Homer | 1e-2 | -6.159e+00 | 0.0298 | 1169.0 | 79.31% | 37010.9 | 76.14% | motif file (matrix) |
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| 19 |  | Stat3(Stat)/mES-Stat3-ChIP-Seq/Homer | 1e-2 | -5.820e+00 | 0.0358 | 1036.0 | 70.28% | 32520.2 | 66.90% | motif file (matrix) |
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| 20 |  | NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq/Homer | 1e-2 | -5.695e+00 | 0.0385 | 1465.0 | 99.39% | 47927.8 | 98.60% | motif file (matrix) |
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| 21 |  | Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer | 1e-2 | -5.650e+00 | 0.0385 | 585.0 | 39.69% | 17625.9 | 36.26% | motif file (matrix) |
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| 22 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo et al.)/Homer | 1e-2 | -5.410e+00 | 0.0465 | 1078.0 | 73.13% | 34028.9 | 70.01% | motif file (matrix) |
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| 23 |  | BMYB(HTH)/Hela-BMYB-ChIPSeq(GSE27030)/Homer | 1e-2 | -5.363e+00 | 0.0467 | 1455.0 | 98.71% | 47506.1 | 97.74% | motif file (matrix) |
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| 24 |  | Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer | 1e-2 | -5.337e+00 | 0.0467 | 767.0 | 52.04% | 23637.5 | 48.63% | motif file (matrix) |
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| 25 |  | TCFL2(HMG)/K562-TCF7L2-ChIP-Seq(GSE29196)/Homer | 1e-2 | -5.253e+00 | 0.0479 | 285.0 | 19.34% | 8151.5 | 16.77% | motif file (matrix) |
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| 26 |  | PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer | 1e-2 | -5.192e+00 | 0.0490 | 953.0 | 64.65% | 29852.4 | 61.42% | motif file (matrix) |
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| 27 |  | Tcf12(HLH)/GM12878-Tcf12-ChIP-Seq/Homer | 1e-2 | -5.069e+00 | 0.0533 | 1252.0 | 84.94% | 40087.4 | 82.47% | motif file (matrix) |
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| 28 |  | EGR(Zf)/K562-EGR1-ChIP-Seq/Homer | 1e-2 | -4.634e+00 | 0.0795 | 366.0 | 24.83% | 10809.4 | 22.24% | motif file (matrix) |
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