| 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 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-19 | -4.490e+01 | 0.0000 | 239.0 | 9.30% | 1854.7 | 4.93% | motif file (matrix) |
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| 2 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-18 | -4.276e+01 | 0.0000 | 230.0 | 8.95% | 1791.3 | 4.76% | motif file (matrix) |
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| 3 |  | X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-12 | -2.873e+01 | 0.0000 | 189.0 | 7.35% | 1582.6 | 4.21% | motif file (matrix) |
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| 4 |  | Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer | 1e-12 | -2.828e+01 | 0.0000 | 308.0 | 11.98% | 2976.0 | 7.91% | motif file (matrix) |
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| 5 |  | Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-11 | -2.594e+01 | 0.0000 | 332.0 | 12.91% | 3332.9 | 8.86% | motif file (matrix) |
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| 6 |  | Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer | 1e-10 | -2.346e+01 | 0.0000 | 307.0 | 11.94% | 3096.5 | 8.23% | motif file (matrix) |
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| 7 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-8 | -2.038e+01 | 0.0000 | 634.0 | 24.66% | 7463.1 | 19.84% | motif file (matrix) |
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| 8 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.594e+01 | 0.0000 | 626.0 | 24.35% | 7579.9 | 20.15% | motif file (matrix) |
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| 9 |  | NRF(NRF)/Promoter/Homer | 1e-6 | -1.527e+01 | 0.0000 | 605.0 | 23.53% | 7329.1 | 19.48% | motif file (matrix) |
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| 10 |  | REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer | 1e-5 | -1.291e+01 | 0.0001 | 38.0 | 1.48% | 238.0 | 0.63% | motif file (matrix) |
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| 11 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-5 | -1.211e+01 | 0.0001 | 634.0 | 24.66% | 7915.2 | 21.04% | motif file (matrix) |
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| 12 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski et al.)/Homer | 1e-4 | -1.076e+01 | 0.0005 | 279.0 | 10.85% | 3197.4 | 8.50% | motif file (matrix) |
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| 13 |  | Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-4 | -1.005e+01 | 0.0009 | 276.0 | 10.74% | 3191.5 | 8.48% | motif file (matrix) |
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| 14 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-3 | -8.944e+00 | 0.0025 | 1491.0 | 57.99% | 20462.9 | 54.40% | motif file (matrix) |
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| 15 |  | Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer | 1e-3 | -8.117e+00 | 0.0053 | 1188.0 | 46.21% | 16111.5 | 42.83% | motif file (matrix) |
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| 16 |  | CRE(bZIP)/Promoter/Homer | 1e-3 | -7.910e+00 | 0.0061 | 392.0 | 15.25% | 4869.9 | 12.95% | motif file (matrix) |
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| 17 |  | Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer | 1e-3 | -7.761e+00 | 0.0066 | 267.0 | 10.39% | 3190.2 | 8.48% | motif file (matrix) |
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| 18 |  | Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer | 1e-3 | -7.059e+00 | 0.0126 | 1199.0 | 46.64% | 16380.9 | 43.55% | motif file (matrix) |
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| 19 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo et al.)/Homer | 1e-2 | -6.588e+00 | 0.0191 | 1021.0 | 39.71% | 13855.5 | 36.83% | motif file (matrix) |
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| 20 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-2 | -6.334e+00 | 0.0234 | 585.0 | 22.75% | 7670.2 | 20.39% | motif file (matrix) |
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| 21 |  | Sp1(Zf)/Promoter/Homer | 1e-2 | -6.306e+00 | 0.0234 | 1142.0 | 44.42% | 15636.7 | 41.57% | motif file (matrix) |
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| 22 |  | STAT6(Stat)/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer | 1e-2 | -6.188e+00 | 0.0247 | 393.0 | 15.29% | 5007.4 | 13.31% | motif file (matrix) |
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| 23 |  | STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer | 1e-2 | -6.029e+00 | 0.0276 | 371.0 | 14.43% | 4716.7 | 12.54% | motif file (matrix) |
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| 24 |  | Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer | 1e-2 | -5.936e+00 | 0.0291 | 832.0 | 32.36% | 11213.9 | 29.81% | motif file (matrix) |
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| 25 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.892e+00 | 0.0292 | 402.0 | 15.64% | 5155.3 | 13.70% | motif file (matrix) |
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| 26 |  | Pit1+1bp(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer | 1e-2 | -5.834e+00 | 0.0297 | 167.0 | 6.50% | 1967.2 | 5.23% | motif file (matrix) |
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| 27 |  | Brachyury(T-box)/Mesoendoderm-Brachyury-ChIP-exo(GSE54963)/Homer | 1e-2 | -5.542e+00 | 0.0383 | 216.0 | 8.40% | 2637.2 | 7.01% | motif file (matrix) |
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| 28 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-2 | -5.136e+00 | 0.0555 | 1423.0 | 55.35% | 19881.4 | 52.85% | motif file (matrix) |
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| 29 |  | Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer | 1e-2 | -5.034e+00 | 0.0593 | 506.0 | 19.68% | 6684.9 | 17.77% | motif file (matrix) |
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| 30 |  | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1e-2 | -4.853e+00 | 0.0687 | 553.0 | 21.51% | 7365.8 | 19.58% | motif file (matrix) |
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| 31 |  | E-box(bHLH)/Promoter/Homer | 1e-2 | -4.812e+00 | 0.0693 | 170.0 | 6.61% | 2064.1 | 5.49% | motif file (matrix) |
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| 32 |  | OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -4.611e+00 | 0.0820 | 93.0 | 3.62% | 1059.0 | 2.82% | motif file (matrix) |
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