| 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 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-432 | -9.968e+02 | 0.0000 | 2235.0 | 65.75% | 13337.2 | 28.81% | motif file (matrix) |
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| 2 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-340 | -7.843e+02 | 0.0000 | 2867.0 | 84.35% | 24183.0 | 52.23% | motif file (matrix) |
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| 3 |  | Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer | 1e-326 | -7.526e+02 | 0.0000 | 2032.0 | 59.78% | 12934.1 | 27.93% | motif file (matrix) |
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| 4 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-322 | -7.419e+02 | 0.0000 | 2779.0 | 81.76% | 23185.0 | 50.07% | motif file (matrix) |
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| 5 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-303 | -6.984e+02 | 0.0000 | 2692.0 | 79.20% | 22286.7 | 48.13% | motif file (matrix) |
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| 6 |  | c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-42 | -9.701e+01 | 0.0000 | 560.0 | 16.48% | 4190.1 | 9.05% | motif file (matrix) |
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| 7 |  | Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer | 1e-36 | -8.410e+01 | 0.0000 | 787.0 | 23.15% | 6890.1 | 14.88% | motif file (matrix) |
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| 8 |  | Oct4:Sox17(POU,Homeobox,HMG)/F9-Sox17-ChIP-Seq(GSE44553)/Homer | 1e-35 | -8.120e+01 | 0.0000 | 325.0 | 9.56% | 2078.6 | 4.49% | motif file (matrix) |
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| 9 |  | Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer | 1e-33 | -7.612e+01 | 0.0000 | 593.0 | 17.45% | 4889.6 | 10.56% | motif file (matrix) |
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| 10 |  | MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer | 1e-31 | -7.276e+01 | 0.0000 | 1085.0 | 31.92% | 10680.0 | 23.07% | motif file (matrix) |
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| 11 |  | Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-29 | -6.771e+01 | 0.0000 | 1258.0 | 37.01% | 12971.0 | 28.01% | motif file (matrix) |
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| 12 |  | Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer | 1e-24 | -5.667e+01 | 0.0000 | 997.0 | 29.33% | 10064.4 | 21.74% | motif file (matrix) |
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| 13 |  | Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer | 1e-24 | -5.559e+01 | 0.0000 | 1588.0 | 46.72% | 17633.5 | 38.08% | motif file (matrix) |
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| 14 |  | MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer | 1e-21 | -4.909e+01 | 0.0000 | 1329.0 | 39.10% | 14499.9 | 31.32% | motif file (matrix) |
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| 15 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-20 | -4.722e+01 | 0.0000 | 687.0 | 20.21% | 6611.5 | 14.28% | motif file (matrix) |
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| 16 |  | JunD(bZIP)/K562-JunD-ChIP-Seq/Homer | 1e-20 | -4.695e+01 | 0.0000 | 183.0 | 5.38% | 1155.1 | 2.49% | motif file (matrix) |
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| 17 |  | Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer | 1e-18 | -4.267e+01 | 0.0000 | 919.0 | 27.04% | 9556.3 | 20.64% | motif file (matrix) |
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| 18 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-17 | -4.137e+01 | 0.0000 | 482.0 | 14.18% | 4392.7 | 9.49% | motif file (matrix) |
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| 19 |  | NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-16 | -3.901e+01 | 0.0000 | 551.0 | 16.21% | 5247.1 | 11.33% | motif file (matrix) |
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| 20 |  | Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer | 1e-14 | -3.401e+01 | 0.0000 | 1413.0 | 41.57% | 16220.4 | 35.03% | motif file (matrix) |
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| 21 |  | GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer | 1e-13 | -3.144e+01 | 0.0000 | 431.0 | 12.68% | 4068.4 | 8.79% | motif file (matrix) |
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| 22 |  | Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan et al.)/Homer | 1e-13 | -3.036e+01 | 0.0000 | 2084.0 | 61.31% | 25471.3 | 55.01% | motif file (matrix) |
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| 23 |  | CRE(bZIP)/Promoter/Homer | 1e-11 | -2.710e+01 | 0.0000 | 291.0 | 8.56% | 2595.7 | 5.61% | motif file (matrix) |
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| 24 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-11 | -2.548e+01 | 0.0000 | 593.0 | 17.45% | 6183.4 | 13.35% | motif file (matrix) |
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| 25 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-10 | -2.524e+01 | 0.0000 | 358.0 | 10.53% | 3402.7 | 7.35% | motif file (matrix) |
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| 26 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-10 | -2.498e+01 | 0.0000 | 1157.0 | 34.04% | 13322.3 | 28.77% | motif file (matrix) |
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| 27 |  | Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer | 1e-10 | -2.468e+01 | 0.0000 | 354.0 | 10.41% | 3372.1 | 7.28% | motif file (matrix) |
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| 28 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-10 | -2.468e+01 | 0.0000 | 940.0 | 27.66% | 10546.2 | 22.78% | motif file (matrix) |
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| 29 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-10 | -2.449e+01 | 0.0000 | 471.0 | 13.86% | 4751.0 | 10.26% | motif file (matrix) |
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| 30 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-9 | -2.287e+01 | 0.0000 | 838.0 | 24.65% | 9339.0 | 20.17% | motif file (matrix) |
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| 31 |  | NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-9 | -2.222e+01 | 0.0000 | 1836.0 | 54.02% | 22527.8 | 48.66% | motif file (matrix) |
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| 32 |  | Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer | 1e-9 | -2.176e+01 | 0.0000 | 1085.0 | 31.92% | 12560.5 | 27.13% | motif file (matrix) |
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| 33 |  | E-box(bHLH)/Promoter/Homer | 1e-9 | -2.165e+01 | 0.0000 | 109.0 | 3.21% | 776.7 | 1.68% | motif file (matrix) |
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| 34 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-8 | -2.033e+01 | 0.0000 | 713.0 | 20.98% | 7885.2 | 17.03% | motif file (matrix) |
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| 35 |  | Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer | 1e-8 | -1.962e+01 | 0.0000 | 1402.0 | 41.25% | 16850.6 | 36.39% | motif file (matrix) |
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| 36 |  | CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer | 1e-7 | -1.671e+01 | 0.0000 | 727.0 | 21.39% | 8246.0 | 17.81% | motif file (matrix) |
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| 37 |  | Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer | 1e-7 | -1.620e+01 | 0.0000 | 1657.0 | 48.75% | 20502.6 | 44.28% | motif file (matrix) |
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| 38 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-6 | -1.609e+01 | 0.0000 | 815.0 | 23.98% | 9402.1 | 20.31% | motif file (matrix) |
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| 39 |  | GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer | 1e-5 | -1.379e+01 | 0.0000 | 242.0 | 7.12% | 2411.0 | 5.21% | motif file (matrix) |
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| 40 |  | Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer | 1e-5 | -1.275e+01 | 0.0000 | 1915.0 | 56.34% | 24284.7 | 52.45% | motif file (matrix) |
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| 41 |  | Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer | 1e-5 | -1.188e+01 | 0.0000 | 312.0 | 9.18% | 3319.5 | 7.17% | motif file (matrix) |
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| 42 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-5 | -1.161e+01 | 0.0001 | 1484.0 | 43.66% | 18533.4 | 40.03% | motif file (matrix) |
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| 43 |  | Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer | 1e-4 | -1.048e+01 | 0.0002 | 267.0 | 7.86% | 2834.7 | 6.12% | motif file (matrix) |
pdf |
| 44 |  | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1e-4 | -9.931e+00 | 0.0003 | 1184.0 | 34.83% | 14670.4 | 31.68% | motif file (matrix) |
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| 45 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-3 | -8.969e+00 | 0.0007 | 663.0 | 19.51% | 7913.8 | 17.09% | motif file (matrix) |
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| 46 |  | MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer | 1e-3 | -8.888e+00 | 0.0008 | 1020.0 | 30.01% | 12591.0 | 27.19% | motif file (matrix) |
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| 47 |  | Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer | 1e-3 | -8.432e+00 | 0.0012 | 632.0 | 18.59% | 7553.8 | 16.31% | motif file (matrix) |
pdf |
| 48 |  | Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer | 1e-3 | -8.162e+00 | 0.0016 | 351.0 | 10.33% | 3987.3 | 8.61% | motif file (matrix) |
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| 49 |  | Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-3 | -7.971e+00 | 0.0019 | 561.0 | 16.50% | 6672.2 | 14.41% | motif file (matrix) |
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| 50 |  | NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-3 | -7.513e+00 | 0.0029 | 975.0 | 28.68% | 12124.1 | 26.19% | motif file (matrix) |
pdf |
| 51 |  | CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer | 1e-3 | -7.144e+00 | 0.0041 | 827.0 | 24.33% | 10207.1 | 22.05% | motif file (matrix) |
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| 52 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-3 | -6.998e+00 | 0.0046 | 1240.0 | 36.48% | 15706.3 | 33.92% | motif file (matrix) |
pdf |
| 53 |  | Srebp1a(bHLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.805e+00 | 0.0055 | 257.0 | 7.56% | 2890.1 | 6.24% | motif file (matrix) |
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| 54 |  | SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer | 1e-2 | -6.616e+00 | 0.0065 | 296.0 | 8.71% | 3389.6 | 7.32% | motif file (matrix) |
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| 55 |  | PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer | 1e-2 | -6.602e+00 | 0.0065 | 2336.0 | 68.73% | 30694.2 | 66.29% | motif file (matrix) |
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| 56 |  | CArG(MADS)/PUER-Srf-ChIP-Seq(Sullivan et al.)/Homer | 1e-2 | -6.571e+00 | 0.0066 | 363.0 | 10.68% | 4240.0 | 9.16% | motif file (matrix) |
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| 57 |  | Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-2 | -6.480e+00 | 0.0071 | 241.0 | 7.09% | 2709.6 | 5.85% | motif file (matrix) |
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| 58 |  | Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.431e+00 | 0.0073 | 80.0 | 2.35% | 768.7 | 1.66% | motif file (matrix) |
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| 59 |  | NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-2 | -6.424e+00 | 0.0073 | 219.0 | 6.44% | 2439.8 | 5.27% | motif file (matrix) |
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| 60 |  | NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer | 1e-2 | -6.350e+00 | 0.0077 | 1054.0 | 31.01% | 13294.2 | 28.71% | motif file (matrix) |
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| 61 |  | Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer | 1e-2 | -6.147e+00 | 0.0093 | 270.0 | 7.94% | 3091.3 | 6.68% | motif file (matrix) |
pdf |
| 62 |  | Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer | 1e-2 | -5.856e+00 | 0.0122 | 71.0 | 2.09% | 682.2 | 1.47% | motif file (matrix) |
pdf |
| 63 |  | Sp1(Zf)/Promoter/Homer | 1e-2 | -5.716e+00 | 0.0138 | 136.0 | 4.00% | 1456.0 | 3.14% | motif file (matrix) |
pdf |
| 64 |  | Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer | 1e-2 | -5.683e+00 | 0.0140 | 728.0 | 21.42% | 9049.2 | 19.54% | motif file (matrix) |
pdf |
| 65 |  | MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.519e+00 | 0.0163 | 300.0 | 8.83% | 3511.4 | 7.58% | motif file (matrix) |
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| 66 |  | Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.377e+00 | 0.0185 | 163.0 | 4.80% | 1802.9 | 3.89% | motif file (matrix) |
pdf |
| 67 |  | IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.329e+00 | 0.0191 | 497.0 | 14.62% | 6061.4 | 13.09% | motif file (matrix) |
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| 68 |  | GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer | 1e-2 | -5.171e+00 | 0.0221 | 164.0 | 4.82% | 1825.8 | 3.94% | motif file (matrix) |
pdf |
| 69 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.164e+00 | 0.0221 | 342.0 | 10.06% | 4073.6 | 8.80% | motif file (matrix) |
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| 70 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-2 | -5.152e+00 | 0.0221 | 692.0 | 20.36% | 8631.8 | 18.64% | motif file (matrix) |
pdf |
| 71 |  | NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.951e+00 | 0.0263 | 80.0 | 2.35% | 816.3 | 1.76% | motif file (matrix) |
pdf |
| 72 |  | GATA(Zf),IR3/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer | 1e-2 | -4.667e+00 | 0.0345 | 174.0 | 5.12% | 1977.5 | 4.27% | motif file (matrix) |
pdf |
| 73 |  | PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -4.664e+00 | 0.0345 | 127.0 | 3.74% | 1395.9 | 3.01% | motif file (matrix) |
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| 74 |  | Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer | 1e-2 | -4.622e+00 | 0.0351 | 1061.0 | 31.22% | 13598.9 | 29.37% | motif file (matrix) |
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