| 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 |  | GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer | 1e-5 | -1.231e+01 | 0.0017 | 105.0 | 13.32% | 45.5 | 6.44% | motif file (matrix) |
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| 2 |  | PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer | 1e-5 | -1.203e+01 | 0.0017 | 138.0 | 17.51% | 68.7 | 9.72% | motif file (matrix) |
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| 3 |  | ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -6.522e+00 | 0.1898 | 71.0 | 9.01% | 35.1 | 4.96% | motif file (matrix) |
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| 4 |  | FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong_et_al.)/Homer | 1e-2 | -6.424e+00 | 0.1898 | 10.0 | 1.27% | 0.9 | 0.12% | motif file (matrix) |
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| 5 |  | Bapx1(Homeobox)/VertebralCol-Bapx1-ChIP-Seq(GSE36672)/Homer | 1e-2 | -6.077e+00 | 0.1898 | 116.0 | 14.72% | 69.1 | 9.77% | motif file (matrix) |
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| 6 |  | Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.867e+00 | 0.1898 | 70.0 | 8.88% | 37.0 | 5.23% | motif file (matrix) |
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| 7 |  | Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-2 | -5.600e+00 | 0.2044 | 56.0 | 7.11% | 27.9 | 3.94% | motif file (matrix) |
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| 8 |  | CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer | 1e-2 | -5.392e+00 | 0.2201 | 127.0 | 16.12% | 80.5 | 11.40% | motif file (matrix) |
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| 9 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.240e+00 | 0.2280 | 11.0 | 1.40% | 1.6 | 0.23% | motif file (matrix) |
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| 10 |  | EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer | 1e-2 | -4.962e+00 | 0.2707 | 17.0 | 2.16% | 4.6 | 0.66% | motif file (matrix) |
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| 11 |  | PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer | 1e-2 | -4.847e+00 | 0.2764 | 24.0 | 3.05% | 8.7 | 1.22% | motif file (matrix) |
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| 12 |  | Tcf3(HMG)/mES-Tcf3-ChIP-Seq(GSE11724)/Homer | 1e-2 | -4.674e+00 | 0.3011 | 10.0 | 1.27% | 1.5 | 0.21% | motif file (matrix) |
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