| 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 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-24 | -5.630e+01 | 0.0000 | 28.0 | 36.84% | 1175.6 | 2.55% | motif file (matrix) |
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| 2 |  | RFX2/HOCOMOCO | 1e-14 | -3.348e+01 | 0.0000 | 11.0 | 14.47% | 155.6 | 0.34% | motif file (matrix) |
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| 3 |  | RFX1/HOCOMOCO | 1e-11 | -2.706e+01 | 0.0000 | 11.0 | 14.47% | 282.3 | 0.61% | motif file (matrix) |
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| 4 |  | RFX1..5_RFXANK_RFXAP.p2/SwissRegulon | 1e-8 | -1.863e+01 | 0.0000 | 12.0 | 15.79% | 800.0 | 1.73% | motif file (matrix) |
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| 5 |  | RFX3/HOCOMOCO | 1e-5 | -1.351e+01 | 0.0001 | 7.0 | 9.21% | 330.6 | 0.72% | motif file (matrix) |
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| 6 |  | Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-4 | -1.088e+01 | 0.0010 | 8.0 | 10.53% | 688.1 | 1.49% | motif file (matrix) |
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| 7 |  | X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-4 | -1.004e+01 | 0.0020 | 6.0 | 7.89% | 383.7 | 0.83% | motif file (matrix) |
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| 8 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-4 | -9.789e+00 | 0.0023 | 19.0 | 25.00% | 4315.2 | 9.36% | motif file (matrix) |
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| 9 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-4 | -9.439e+00 | 0.0029 | 5.0 | 6.58% | 263.7 | 0.57% | motif file (matrix) |
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| 10 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-3 | -9.056e+00 | 0.0038 | 21.0 | 27.63% | 5374.4 | 11.65% | motif file (matrix) |
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| 11 |  | Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan et al.)/Homer | 1e-3 | -8.383e+00 | 0.0067 | 27.0 | 35.53% | 8339.3 | 18.08% | motif file (matrix) |
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| 12 |  | Stat3+il21(Stat)/CD4-Stat3-ChIP-Seq(GSE19198)/Homer | 1e-3 | -8.329e+00 | 0.0067 | 13.0 | 17.11% | 2533.5 | 5.49% | motif file (matrix) |
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| 13 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-3 | -7.624e+00 | 0.0121 | 4.0 | 5.26% | 218.0 | 0.47% | motif file (matrix) |
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| 14 |  | SPDEF(ETS)/VCaP-SPDEF-ChIP-Seq(SRA014231)/Homer | 1e-3 | -7.128e+00 | 0.0185 | 16.0 | 21.05% | 4045.1 | 8.77% | motif file (matrix) |
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| 15 |  | MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer | 1e-2 | -6.757e+00 | 0.0250 | 14.0 | 18.42% | 3382.6 | 7.33% | motif file (matrix) |
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| 16 |  | STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer | 1e-2 | -6.068e+00 | 0.0467 | 14.0 | 18.42% | 3639.6 | 7.89% | motif file (matrix) |
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| 17 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.508e+00 | 0.0770 | 8.0 | 10.53% | 1552.1 | 3.37% | motif file (matrix) |
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| 18 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.346e+00 | 0.0856 | 8.0 | 10.53% | 1595.7 | 3.46% | motif file (matrix) |
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| 19 |  | Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer | 1e-2 | -5.061e+00 | 0.1077 | 24.0 | 31.58% | 8797.5 | 19.08% | motif file (matrix) |
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| 20 |  | Fox:Ebox(Forkhead:HLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer | 1e-2 | -4.983e+00 | 0.1106 | 15.0 | 19.74% | 4551.9 | 9.87% | motif file (matrix) |
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