| 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 |  | TATA-box/SacCer-Promoters/Homer | 1e-6 | -1.428e+01 | 0.0002 | 19.0 | 10.00% | 4.1 | 2.62% | motif file (matrix) |
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| 2 |  | GRE/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer | 1e-5 | -1.221e+01 | 0.0008 | 9.0 | 4.74% | 0.0 | 0.00% | motif file (matrix) |
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| 3 |  | MYB(HTH)/ERMYB-Myb-ChIPSeq(GSE22095)/Homer | 1e-5 | -1.153e+01 | 0.0010 | 65.0 | 34.21% | 32.5 | 20.86% | motif file (matrix) |
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| 4 |  | Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer | 1e-4 | -1.094e+01 | 0.0013 | 21.0 | 11.05% | 6.5 | 4.20% | motif file (matrix) |
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| 5 |  | PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer | 1e-4 | -1.032e+01 | 0.0020 | 30.0 | 15.79% | 11.3 | 7.25% | motif file (matrix) |
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| 6 |  | GAGA-repeat/SacCer-Promoters/Homer | 1e-4 | -9.302e+00 | 0.0046 | 73.0 | 38.42% | 40.8 | 26.23% | motif file (matrix) |
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| 7 |  | HIF2a(HLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-3 | -9.034e+00 | 0.0052 | 37.0 | 19.47% | 16.9 | 10.85% | motif file (matrix) |
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| 8 |  | STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer | 1e-3 | -8.239e+00 | 0.0100 | 7.0 | 3.68% | 0.7 | 0.46% | motif file (matrix) |
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| 9 |  | NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-3 | -7.451e+00 | 0.0196 | 25.0 | 13.16% | 10.3 | 6.64% | motif file (matrix) |
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| 10 |  | Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-2 | -6.891e+00 | 0.0308 | 26.0 | 13.68% | 11.3 | 7.26% | motif file (matrix) |
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| 11 |  | AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer | 1e-2 | -6.446e+00 | 0.0370 | 6.0 | 3.16% | 0.8 | 0.50% | motif file (matrix) |
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| 12 |  | MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.446e+00 | 0.0370 | 6.0 | 3.16% | 0.3 | 0.19% | motif file (matrix) |
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| 13 |  | Unknown6/Drosophila-Promoters/Homer | 1e-2 | -6.446e+00 | 0.0370 | 6.0 | 3.16% | 1.9 | 1.24% | motif file (matrix) |
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| 14 |  | EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer | 1e-2 | -5.868e+00 | 0.0612 | 23.0 | 12.11% | 10.9 | 7.01% | motif file (matrix) |
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| 15 |  | Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.468e+00 | 0.0852 | 10.0 | 5.26% | 3.7 | 2.38% | motif file (matrix) |
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| 16 |  | STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer | 1e-2 | -5.122e+00 | 0.1129 | 17.0 | 8.95% | 7.4 | 4.77% | motif file (matrix) |
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| 17 |  | SeqBias: CG-repeat | 1e-2 | -5.086e+00 | 0.1129 | 65.0 | 34.21% | 40.2 | 25.84% | motif file (matrix) |
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| 18 |  | Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-2 | -4.805e+00 | 0.1241 | 5.0 | 2.63% | 1.9 | 1.21% | motif file (matrix) |
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| 19 |  | HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson et al.)/Homer | 1e-2 | -4.805e+00 | 0.1241 | 5.0 | 2.63% | 0.3 | 0.21% | motif file (matrix) |
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| 20 |  | c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.805e+00 | 0.1241 | 5.0 | 2.63% | 0.8 | 0.51% | motif file (matrix) |
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