| 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 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-33 | -7.755e+01 | 0.0000 | 143.0 | 53.36% | 9652.6 | 19.67% | motif file (matrix) |
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| 2 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-32 | -7.426e+01 | 0.0000 | 129.0 | 48.13% | 8134.0 | 16.57% | motif file (matrix) |
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| 3 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-29 | -6.689e+01 | 0.0000 | 79.0 | 29.48% | 3288.1 | 6.70% | motif file (matrix) |
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| 4 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-28 | -6.528e+01 | 0.0000 | 91.0 | 33.96% | 4513.3 | 9.20% | motif file (matrix) |
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| 5 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-27 | -6.370e+01 | 0.0000 | 134.0 | 50.00% | 9704.1 | 19.77% | motif file (matrix) |
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| 6 |  | NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer | 1e-26 | -6.011e+01 | 0.0000 | 152.0 | 56.72% | 12640.5 | 25.75% | motif file (matrix) |
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| 7 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-24 | -5.712e+01 | 0.0000 | 137.0 | 51.12% | 10784.3 | 21.97% | motif file (matrix) |
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| 8 |  | Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer | 1e-20 | -4.625e+01 | 0.0000 | 158.0 | 58.96% | 15328.6 | 31.23% | motif file (matrix) |
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| 9 |  | Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer | 1e-15 | -3.511e+01 | 0.0000 | 213.0 | 79.48% | 27472.1 | 55.97% | motif file (matrix) |
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| 10 |  | Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer | 1e-13 | -3.148e+01 | 0.0000 | 166.0 | 61.94% | 19084.4 | 38.88% | motif file (matrix) |
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| 11 |  | Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer | 1e-13 | -3.123e+01 | 0.0000 | 51.0 | 19.03% | 2774.3 | 5.65% | motif file (matrix) |
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| 12 |  | X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-8 | -2.051e+01 | 0.0000 | 30.0 | 11.19% | 1491.9 | 3.04% | motif file (matrix) |
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| 13 |  | Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer | 1e-8 | -1.945e+01 | 0.0000 | 216.0 | 80.60% | 31525.9 | 64.23% | motif file (matrix) |
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| 14 |  | E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-7 | -1.691e+01 | 0.0000 | 141.0 | 52.61% | 17860.7 | 36.39% | motif file (matrix) |
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| 15 |  | Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-6 | -1.530e+01 | 0.0000 | 38.0 | 14.18% | 2785.0 | 5.67% | motif file (matrix) |
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| 16 |  | E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer | 1e-6 | -1.519e+01 | 0.0000 | 136.0 | 50.75% | 17448.8 | 35.55% | motif file (matrix) |
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| 17 |  | Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.511e+01 | 0.0000 | 70.0 | 26.12% | 7011.6 | 14.29% | motif file (matrix) |
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| 18 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-6 | -1.424e+01 | 0.0000 | 22.0 | 8.21% | 1167.6 | 2.38% | motif file (matrix) |
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| 19 |  | Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer | 1e-6 | -1.395e+01 | 0.0000 | 63.0 | 23.51% | 6232.4 | 12.70% | motif file (matrix) |
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| 20 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-5 | -1.313e+01 | 0.0000 | 70.0 | 26.12% | 7395.5 | 15.07% | motif file (matrix) |
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| 21 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-5 | -1.247e+01 | 0.0000 | 19.0 | 7.09% | 1007.5 | 2.05% | motif file (matrix) |
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| 22 |  | NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-4 | -1.139e+01 | 0.0001 | 152.0 | 56.72% | 21414.0 | 43.63% | motif file (matrix) |
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| 23 |  | SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer | 1e-4 | -1.030e+01 | 0.0004 | 253.0 | 94.40% | 42561.4 | 86.72% | motif file (matrix) |
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| 24 |  | RBPJ:Ebox(?,bHLH)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-4 | -9.484e+00 | 0.0008 | 47.0 | 17.54% | 4835.1 | 9.85% | motif file (matrix) |
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| 25 |  | CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer | 1e-3 | -8.899e+00 | 0.0014 | 84.0 | 31.34% | 10610.6 | 21.62% | motif file (matrix) |
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| 26 |  | Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-3 | -7.456e+00 | 0.0059 | 62.0 | 23.13% | 7562.0 | 15.41% | motif file (matrix) |
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| 27 |  | GFY(?)/Promoter/Homer | 1e-3 | -7.279e+00 | 0.0067 | 11.0 | 4.10% | 618.7 | 1.26% | motif file (matrix) |
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| 28 |  | NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer | 1e-3 | -6.995e+00 | 0.0086 | 13.0 | 4.85% | 848.3 | 1.73% | motif file (matrix) |
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| 29 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-3 | -6.965e+00 | 0.0086 | 18.0 | 6.72% | 1421.9 | 2.90% | motif file (matrix) |
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| 30 |  | Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer | 1e-2 | -6.837e+00 | 0.0094 | 150.0 | 55.97% | 22783.2 | 46.42% | motif file (matrix) |
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| 31 |  | AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer | 1e-2 | -6.695e+00 | 0.0105 | 241.0 | 89.93% | 40832.3 | 83.20% | motif file (matrix) |
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| 32 |  | Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer | 1e-2 | -6.666e+00 | 0.0105 | 143.0 | 53.36% | 21587.7 | 43.98% | motif file (matrix) |
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| 33 |  | Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.597e+00 | 0.0109 | 85.0 | 31.72% | 11547.4 | 23.53% | motif file (matrix) |
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| 34 |  | GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.517e+00 | 0.0115 | 24.0 | 8.96% | 2245.2 | 4.57% | motif file (matrix) |
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| 35 |  | MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer | 1e-2 | -5.857e+00 | 0.0216 | 33.0 | 12.31% | 3626.9 | 7.39% | motif file (matrix) |
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| 36 |  | NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-2 | -5.717e+00 | 0.0241 | 24.0 | 8.96% | 2390.8 | 4.87% | motif file (matrix) |
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| 37 |  | TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer | 1e-2 | -5.616e+00 | 0.0260 | 85.0 | 31.72% | 11934.1 | 24.32% | motif file (matrix) |
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| 38 |  | Tbet(T-box)/CD8-Tbet-ChIP-Seq(GSE33802)/Homer | 1e-2 | -5.547e+00 | 0.0271 | 103.0 | 38.43% | 15030.5 | 30.62% | motif file (matrix) |
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| 39 |  | Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer | 1e-2 | -5.428e+00 | 0.0297 | 32.0 | 11.94% | 3584.3 | 7.30% | motif file (matrix) |
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| 40 |  | Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.270e+00 | 0.0339 | 11.0 | 4.10% | 803.5 | 1.64% | motif file (matrix) |
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| 41 |  | Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer | 1e-2 | -5.205e+00 | 0.0353 | 10.0 | 3.73% | 697.6 | 1.42% | motif file (matrix) |
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| 42 |  | Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer | 1e-2 | -4.963e+00 | 0.0440 | 100.0 | 37.31% | 14786.2 | 30.13% | motif file (matrix) |
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| 43 |  | MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer | 1e-2 | -4.862e+00 | 0.0475 | 90.0 | 33.58% | 13115.2 | 26.72% | motif file (matrix) |
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| 44 |  | Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer | 1e-2 | -4.781e+00 | 0.0503 | 210.0 | 78.36% | 35207.0 | 71.73% | motif file (matrix) |
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| 45 |  | GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer | 1e-2 | -4.697e+00 | 0.0535 | 33.0 | 12.31% | 3925.0 | 8.00% | motif file (matrix) |
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| 46 |  | Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer | 1e-2 | -4.629e+00 | 0.0560 | 210.0 | 78.36% | 35284.9 | 71.89% | motif file (matrix) |
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