| 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-74 | -1.707e+02 | 0.0000 | 144.0 | 20.34% | 1433.4 | 2.93% | motif file (matrix) |
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| 2 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-68 | -1.567e+02 | 0.0000 | 131.0 | 18.50% | 1279.7 | 2.62% | motif file (matrix) |
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| 3 |  | Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-57 | -1.332e+02 | 0.0000 | 184.0 | 25.99% | 3233.3 | 6.61% | motif file (matrix) |
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| 4 |  | X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-55 | -1.269e+02 | 0.0000 | 131.0 | 18.50% | 1663.7 | 3.40% | motif file (matrix) |
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| 5 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-37 | -8.547e+01 | 0.0000 | 157.0 | 22.18% | 3436.7 | 7.03% | motif file (matrix) |
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| 6 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-36 | -8.306e+01 | 0.0000 | 252.0 | 35.59% | 7842.4 | 16.04% | motif file (matrix) |
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| 7 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-34 | -7.939e+01 | 0.0000 | 184.0 | 25.99% | 4771.8 | 9.76% | motif file (matrix) |
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| 8 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-33 | -7.825e+01 | 0.0000 | 275.0 | 38.84% | 9280.0 | 18.97% | motif file (matrix) |
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| 9 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-33 | -7.789e+01 | 0.0000 | 297.0 | 41.95% | 10493.4 | 21.46% | motif file (matrix) |
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| 10 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-32 | -7.582e+01 | 0.0000 | 274.0 | 38.70% | 9357.0 | 19.13% | motif file (matrix) |
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| 11 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-26 | -6.042e+01 | 0.0000 | 205.0 | 28.95% | 6599.9 | 13.49% | motif file (matrix) |
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| 12 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-23 | -5.482e+01 | 0.0000 | 326.0 | 46.05% | 13696.5 | 28.01% | motif file (matrix) |
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| 13 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-21 | -4.853e+01 | 0.0000 | 482.0 | 68.08% | 24609.6 | 50.32% | motif file (matrix) |
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| 14 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-19 | -4.540e+01 | 0.0000 | 464.0 | 65.54% | 23625.6 | 48.31% | motif file (matrix) |
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| 15 |  | Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer | 1e-19 | -4.486e+01 | 0.0000 | 110.0 | 15.54% | 2879.0 | 5.89% | motif file (matrix) |
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| 16 |  | Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer | 1e-18 | -4.237e+01 | 0.0000 | 304.0 | 42.94% | 13375.9 | 27.35% | motif file (matrix) |
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| 17 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-16 | -3.802e+01 | 0.0000 | 440.0 | 62.15% | 22699.3 | 46.41% | motif file (matrix) |
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| 18 |  | Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer | 1e-10 | -2.326e+01 | 0.0000 | 401.0 | 56.64% | 21798.8 | 44.57% | motif file (matrix) |
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| 19 |  | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1e-9 | -2.297e+01 | 0.0000 | 296.0 | 41.81% | 14889.3 | 30.44% | motif file (matrix) |
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| 20 |  | NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer | 1e-9 | -2.108e+01 | 0.0000 | 38.0 | 5.37% | 817.0 | 1.67% | motif file (matrix) |
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| 21 |  | Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer | 1e-8 | -1.927e+01 | 0.0000 | 510.0 | 72.03% | 30156.7 | 61.66% | motif file (matrix) |
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| 22 |  | Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer | 1e-8 | -1.856e+01 | 0.0000 | 32.0 | 4.52% | 670.3 | 1.37% | motif file (matrix) |
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| 23 |  | OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-7 | -1.740e+01 | 0.0000 | 78.0 | 11.02% | 2776.6 | 5.68% | motif file (matrix) |
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| 24 |  | NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-7 | -1.667e+01 | 0.0000 | 424.0 | 59.89% | 24397.8 | 49.89% | motif file (matrix) |
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| 25 |  | Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer | 1e-6 | -1.556e+01 | 0.0000 | 101.0 | 14.27% | 4120.1 | 8.42% | motif file (matrix) |
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| 26 |  | NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-6 | -1.484e+01 | 0.0000 | 240.0 | 33.90% | 12455.7 | 25.47% | motif file (matrix) |
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| 27 |  | NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-6 | -1.417e+01 | 0.0000 | 130.0 | 18.36% | 5881.7 | 12.03% | motif file (matrix) |
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| 28 |  | Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-5 | -1.374e+01 | 0.0000 | 139.0 | 19.63% | 6451.9 | 13.19% | motif file (matrix) |
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| 29 |  | Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer | 1e-5 | -1.373e+01 | 0.0000 | 252.0 | 35.59% | 13391.3 | 27.38% | motif file (matrix) |
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| 30 |  | GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer | 1e-5 | -1.299e+01 | 0.0000 | 96.0 | 13.56% | 4087.5 | 8.36% | motif file (matrix) |
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| 31 |  | Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer | 1e-5 | -1.296e+01 | 0.0000 | 30.0 | 4.24% | 783.2 | 1.60% | motif file (matrix) |
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| 32 |  | GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer | 1e-5 | -1.173e+01 | 0.0001 | 64.0 | 9.04% | 2479.1 | 5.07% | motif file (matrix) |
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| 33 |  | Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer | 1e-4 | -1.053e+01 | 0.0002 | 128.0 | 18.08% | 6211.0 | 12.70% | motif file (matrix) |
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| 34 |  | Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-4 | -9.704e+00 | 0.0005 | 143.0 | 20.20% | 7232.6 | 14.79% | motif file (matrix) |
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| 35 |  | Pit1+1bp(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer | 1e-4 | -9.507e+00 | 0.0006 | 99.0 | 13.98% | 4644.0 | 9.50% | motif file (matrix) |
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| 36 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-4 | -9.412e+00 | 0.0006 | 188.0 | 26.55% | 10067.0 | 20.58% | motif file (matrix) |
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| 37 |  | Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-3 | -9.068e+00 | 0.0008 | 261.0 | 36.86% | 14831.5 | 30.33% | motif file (matrix) |
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| 38 |  | Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer | 1e-3 | -8.666e+00 | 0.0012 | 422.0 | 59.60% | 25844.2 | 52.84% | motif file (matrix) |
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| 39 |  | MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer | 1e-3 | -7.700e+00 | 0.0031 | 279.0 | 39.41% | 16327.3 | 33.38% | motif file (matrix) |
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| 40 |  | MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer | 1e-3 | -7.250e+00 | 0.0047 | 83.0 | 11.72% | 4007.2 | 8.19% | motif file (matrix) |
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| 41 |  | E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.022e+00 | 0.0057 | 117.0 | 16.53% | 6081.1 | 12.43% | motif file (matrix) |
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| 42 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-3 | -6.955e+00 | 0.0060 | 315.0 | 44.49% | 18926.0 | 38.70% | motif file (matrix) |
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| 43 |  | Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer | 1e-2 | -6.544e+00 | 0.0088 | 69.0 | 9.75% | 3286.3 | 6.72% | motif file (matrix) |
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| 44 |  | Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer | 1e-2 | -6.310e+00 | 0.0109 | 62.0 | 8.76% | 2912.1 | 5.95% | motif file (matrix) |
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| 45 |  | Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan et al.)/Homer | 1e-2 | -6.184e+00 | 0.0121 | 423.0 | 59.75% | 26568.2 | 54.32% | motif file (matrix) |
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| 46 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-2 | -6.025e+00 | 0.0139 | 52.0 | 7.34% | 2376.9 | 4.86% | motif file (matrix) |
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| 47 |  | MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer | 1e-2 | -6.005e+00 | 0.0139 | 215.0 | 30.37% | 12525.9 | 25.61% | motif file (matrix) |
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| 48 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-2 | -5.947e+00 | 0.0144 | 175.0 | 24.72% | 9944.1 | 20.33% | motif file (matrix) |
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| 49 |  | Oct4:Sox17(POU,Homeobox,HMG)/F9-Sox17-ChIP-Seq(GSE44553)/Homer | 1e-2 | -5.848e+00 | 0.0155 | 44.0 | 6.21% | 1947.5 | 3.98% | motif file (matrix) |
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| 50 |  | Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer | 1e-2 | -5.614e+00 | 0.0193 | 193.0 | 27.26% | 11189.7 | 22.88% | motif file (matrix) |
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| 51 |  | Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer | 1e-2 | -5.565e+00 | 0.0198 | 107.0 | 15.11% | 5729.7 | 11.72% | motif file (matrix) |
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| 52 |  | MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.434e+00 | 0.0222 | 72.0 | 10.17% | 3622.1 | 7.41% | motif file (matrix) |
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| 53 |  | GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer | 1e-2 | -5.275e+00 | 0.0255 | 41.0 | 5.79% | 1844.0 | 3.77% | motif file (matrix) |
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| 54 |  | Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-2 | -5.211e+00 | 0.0267 | 55.0 | 7.77% | 2652.2 | 5.42% | motif file (matrix) |
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| 55 |  | Sp1(Zf)/Promoter/Homer | 1e-2 | -5.103e+00 | 0.0292 | 64.0 | 9.04% | 3197.3 | 6.54% | motif file (matrix) |
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