| 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 |  | ABF1/SacCer-Promoters/Homer | 1e-238 | -5.497e+02 | 0.0000 | 1555.0 | 33.98% | 3035.8 | 14.47% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-190 | -4.396e+02 | 0.0000 | 975.0 | 21.31% | 1574.4 | 7.50% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-68 | -1.570e+02 | 0.0000 | 2150.0 | 46.98% | 7219.8 | 34.41% | motif file (matrix) |
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| 4 |  | SeqBias: CG-repeat | 1e-50 | -1.163e+02 | 0.0000 | 796.0 | 17.40% | 2119.3 | 10.10% | motif file (matrix) |
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| 5 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-48 | -1.125e+02 | 0.0000 | 573.0 | 12.52% | 1364.7 | 6.50% | motif file (matrix) |
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| 6 |  | SFP1/SacCer-Promoters/Homer | 1e-42 | -9.841e+01 | 0.0000 | 684.0 | 14.95% | 1821.8 | 8.68% | motif file (matrix) |
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| 7 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-41 | -9.457e+01 | 0.0000 | 664.0 | 14.51% | 1772.4 | 8.45% | motif file (matrix) |
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| 8 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-40 | -9.396e+01 | 0.0000 | 416.0 | 9.09% | 931.9 | 4.44% | motif file (matrix) |
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| 9 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-40 | -9.259e+01 | 0.0000 | 1101.0 | 24.06% | 3431.9 | 16.36% | motif file (matrix) |
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| 10 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-38 | -8.765e+01 | 0.0000 | 416.0 | 9.09% | 958.4 | 4.57% | motif file (matrix) |
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| 11 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-35 | -8.222e+01 | 0.0000 | 421.0 | 9.20% | 999.6 | 4.76% | motif file (matrix) |
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| 12 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-28 | -6.653e+01 | 0.0000 | 472.0 | 10.31% | 1256.4 | 5.99% | motif file (matrix) |
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| 13 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-28 | -6.637e+01 | 0.0000 | 603.0 | 13.18% | 1730.8 | 8.25% | motif file (matrix) |
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| 14 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-27 | -6.341e+01 | 0.0000 | 544.0 | 11.89% | 1534.0 | 7.31% | motif file (matrix) |
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| 15 |  | TATA-box/SacCer-Promoters/Homer | 1e-27 | -6.329e+01 | 0.0000 | 2111.0 | 46.13% | 8009.4 | 38.17% | motif file (matrix) |
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| 16 |  | TOD6?/SacCer-Promoters/Homer | 1e-24 | -5.533e+01 | 0.0000 | 365.0 | 7.98% | 947.9 | 4.52% | motif file (matrix) |
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| 17 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-23 | -5.405e+01 | 0.0000 | 890.0 | 19.45% | 2941.9 | 14.02% | motif file (matrix) |
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| 18 |  | E-box/Arabidopsis-Promoters/Homer | 1e-23 | -5.396e+01 | 0.0000 | 511.0 | 11.17% | 1479.4 | 7.05% | motif file (matrix) |
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| 19 |  | E-box(bHLH)/Promoter/Homer | 1e-22 | -5.223e+01 | 0.0000 | 131.0 | 2.86% | 220.8 | 1.05% | motif file (matrix) |
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| 20 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-22 | -5.128e+01 | 0.0000 | 1123.0 | 24.54% | 3919.1 | 18.68% | motif file (matrix) |
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| 21 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-21 | -4.980e+01 | 0.0000 | 1350.0 | 29.50% | 4887.2 | 23.29% | motif file (matrix) |
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| 22 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-20 | -4.754e+01 | 0.0000 | 140.0 | 3.06% | 258.1 | 1.23% | motif file (matrix) |
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| 23 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-19 | -4.553e+01 | 0.0000 | 977.0 | 21.35% | 3386.3 | 16.14% | motif file (matrix) |
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| 24 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-19 | -4.459e+01 | 0.0000 | 412.0 | 9.00% | 1183.3 | 5.64% | motif file (matrix) |
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| 25 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-17 | -3.973e+01 | 0.0000 | 796.0 | 17.40% | 2717.9 | 12.95% | motif file (matrix) |
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| 26 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-15 | -3.574e+01 | 0.0000 | 349.0 | 7.63% | 1017.1 | 4.85% | motif file (matrix) |
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| 27 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-15 | -3.533e+01 | 0.0000 | 803.0 | 17.55% | 2798.9 | 13.34% | motif file (matrix) |
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| 28 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-13 | -3.028e+01 | 0.0000 | 324.0 | 7.08% | 967.6 | 4.61% | motif file (matrix) |
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| 29 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-12 | -2.822e+01 | 0.0000 | 563.0 | 12.30% | 1914.1 | 9.12% | motif file (matrix) |
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| 30 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-12 | -2.820e+01 | 0.0000 | 395.0 | 8.63% | 1254.7 | 5.98% | motif file (matrix) |
pdf |
| 31 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-11 | -2.695e+01 | 0.0000 | 240.0 | 5.24% | 684.8 | 3.26% | motif file (matrix) |
pdf |
| 32 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-11 | -2.641e+01 | 0.0000 | 779.0 | 17.02% | 2819.4 | 13.44% | motif file (matrix) |
pdf |
| 33 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-11 | -2.602e+01 | 0.0000 | 136.0 | 2.97% | 328.4 | 1.57% | motif file (matrix) |
pdf |
| 34 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-10 | -2.482e+01 | 0.0000 | 1043.0 | 22.79% | 3957.0 | 18.86% | motif file (matrix) |
pdf |
| 35 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-10 | -2.394e+01 | 0.0000 | 1418.0 | 30.99% | 5594.5 | 26.66% | motif file (matrix) |
pdf |
| 36 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-10 | -2.339e+01 | 0.0000 | 152.0 | 3.32% | 397.0 | 1.89% | motif file (matrix) |
pdf |
| 37 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-9 | -2.107e+01 | 0.0000 | 152.0 | 3.32% | 410.2 | 1.95% | motif file (matrix) |
pdf |
| 38 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-8 | -2.053e+01 | 0.0000 | 105.0 | 2.29% | 253.2 | 1.21% | motif file (matrix) |
pdf |
| 39 |  | SUT1?/SacCer-Promoters/Homer | 1e-8 | -2.039e+01 | 0.0000 | 3046.0 | 66.56% | 13078.2 | 62.33% | motif file (matrix) |
pdf |
| 40 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-8 | -2.022e+01 | 0.0000 | 287.0 | 6.27% | 916.4 | 4.37% | motif file (matrix) |
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| 41 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-8 | -1.883e+01 | 0.0000 | 1673.0 | 36.56% | 6835.3 | 32.58% | motif file (matrix) |
pdf |
| 42 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-7 | -1.801e+01 | 0.0000 | 451.0 | 9.86% | 1592.1 | 7.59% | motif file (matrix) |
pdf |
| 43 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-7 | -1.784e+01 | 0.0000 | 301.0 | 6.58% | 995.3 | 4.74% | motif file (matrix) |
pdf |
| 44 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-7 | -1.702e+01 | 0.0000 | 520.0 | 11.36% | 1889.9 | 9.01% | motif file (matrix) |
pdf |
| 45 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-7 | -1.648e+01 | 0.0000 | 493.0 | 10.77% | 1786.0 | 8.51% | motif file (matrix) |
pdf |
| 46 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-6 | -1.591e+01 | 0.0000 | 798.0 | 17.44% | 3077.1 | 14.67% | motif file (matrix) |
pdf |
| 47 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.502e+01 | 0.0000 | 59.0 | 1.29% | 130.5 | 0.62% | motif file (matrix) |
pdf |
| 48 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-6 | -1.436e+01 | 0.0000 | 607.0 | 13.26% | 2297.3 | 10.95% | motif file (matrix) |
pdf |
| 49 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-5 | -1.179e+01 | 0.0001 | 1460.0 | 31.91% | 6078.5 | 28.97% | motif file (matrix) |
pdf |
| 50 |  | TATA-box/Drosophila-Promoters/Homer | 1e-4 | -1.104e+01 | 0.0001 | 229.0 | 5.00% | 791.8 | 3.77% | motif file (matrix) |
pdf |
| 51 |  | CRE(bZIP)/Promoter/Homer | 1e-4 | -1.087e+01 | 0.0001 | 197.0 | 4.31% | 667.0 | 3.18% | motif file (matrix) |
pdf |
| 52 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-4 | -1.020e+01 | 0.0003 | 73.0 | 1.60% | 202.8 | 0.97% | motif file (matrix) |
pdf |
| 53 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-4 | -1.020e+01 | 0.0003 | 73.0 | 1.60% | 202.8 | 0.97% | motif file (matrix) |
pdf |
| 54 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-4 | -1.002e+01 | 0.0003 | 44.0 | 0.96% | 104.4 | 0.50% | motif file (matrix) |
pdf |
| 55 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-4 | -9.903e+00 | 0.0004 | 191.0 | 4.17% | 654.6 | 3.12% | motif file (matrix) |
pdf |
| 56 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-4 | -9.620e+00 | 0.0005 | 712.0 | 15.56% | 2849.3 | 13.58% | motif file (matrix) |
pdf |
| 57 |  | PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer | 1e-4 | -9.455e+00 | 0.0005 | 37.0 | 0.81% | 85.0 | 0.41% | motif file (matrix) |
pdf |
| 58 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-4 | -9.400e+00 | 0.0006 | 122.0 | 2.67% | 390.9 | 1.86% | motif file (matrix) |
pdf |
| 59 |  | SeqBias: TA-repeat | 1e-3 | -9.150e+00 | 0.0007 | 4024.0 | 87.94% | 18058.0 | 86.06% | motif file (matrix) |
pdf |
| 60 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.126e+00 | 0.0019 | 1025.0 | 22.40% | 4264.6 | 20.32% | motif file (matrix) |
pdf |
| 61 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-3 | -7.982e+00 | 0.0022 | 43.0 | 0.94% | 111.5 | 0.53% | motif file (matrix) |
pdf |
| 62 |  | Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer | 1e-3 | -7.809e+00 | 0.0025 | 1718.0 | 37.54% | 7377.6 | 35.16% | motif file (matrix) |
pdf |
| 63 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-3 | -7.415e+00 | 0.0037 | 125.0 | 2.73% | 423.5 | 2.02% | motif file (matrix) |
pdf |
| 64 |  | NRF(NRF)/Promoter/Homer | 1e-3 | -7.366e+00 | 0.0038 | 87.0 | 1.90% | 276.7 | 1.32% | motif file (matrix) |
pdf |
| 65 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.195e+00 | 0.0045 | 846.0 | 18.49% | 3505.1 | 16.71% | motif file (matrix) |
pdf |
| 66 |  | Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer | 1e-3 | -7.067e+00 | 0.0050 | 215.0 | 4.70% | 792.4 | 3.78% | motif file (matrix) |
pdf |
| 67 |  | SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer | 1e-3 | -7.059e+00 | 0.0050 | 293.0 | 6.40% | 1117.0 | 5.32% | motif file (matrix) |
pdf |
| 68 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-2 | -6.676e+00 | 0.0072 | 185.0 | 4.04% | 675.9 | 3.22% | motif file (matrix) |
pdf |
| 69 |  | GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer | 1e-2 | -6.552e+00 | 0.0080 | 40.0 | 0.87% | 109.5 | 0.52% | motif file (matrix) |
pdf |
| 70 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-2 | -6.268e+00 | 0.0105 | 518.0 | 11.32% | 2099.5 | 10.01% | motif file (matrix) |
pdf |
| 71 |  | ETS(ETS)/Promoter/Homer | 1e-2 | -6.247e+00 | 0.0106 | 350.0 | 7.65% | 1376.5 | 6.56% | motif file (matrix) |
pdf |
| 72 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-2 | -6.218e+00 | 0.0107 | 116.0 | 2.53% | 402.6 | 1.92% | motif file (matrix) |
pdf |
| 73 |  | Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.623e+00 | 0.0192 | 495.0 | 10.82% | 2018.1 | 9.62% | motif file (matrix) |
pdf |
| 74 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-2 | -5.554e+00 | 0.0202 | 191.0 | 4.17% | 719.3 | 3.43% | motif file (matrix) |
pdf |
| 75 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.440e+00 | 0.0224 | 614.0 | 13.42% | 2544.9 | 12.13% | motif file (matrix) |
pdf |
| 76 |  | ELF1(ETS)/Jurkat-ELF1-ChIP-Seq(SRA014231)/Homer | 1e-2 | -5.117e+00 | 0.0305 | 578.0 | 12.63% | 2397.5 | 11.43% | motif file (matrix) |
pdf |
| 77 |  | Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer | 1e-2 | -5.104e+00 | 0.0305 | 351.0 | 7.67% | 1410.0 | 6.72% | motif file (matrix) |
pdf |
| 78 |  | Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.059e+00 | 0.0315 | 35.0 | 0.76% | 101.1 | 0.48% | motif file (matrix) |
pdf |
| 79 |  | Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.050e+00 | 0.0315 | 69.0 | 1.51% | 230.9 | 1.10% | motif file (matrix) |
pdf |
| 80 |  | NFkB-p50,p52(RHD)/Monocyte-p50-ChIP-Chip(Schreiber_et_al.)/Homer | 1e-2 | -5.008e+00 | 0.0323 | 36.0 | 0.79% | 105.0 | 0.50% | motif file (matrix) |
pdf |
| 81 |  | PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -4.933e+00 | 0.0344 | 73.0 | 1.60% | 247.7 | 1.18% | motif file (matrix) |
pdf |
| 82 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-2 | -4.897e+00 | 0.0353 | 42.0 | 0.92% | 128.6 | 0.61% | motif file (matrix) |
pdf |
| 83 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.839e+00 | 0.0369 | 270.0 | 5.90% | 1068.6 | 5.09% | motif file (matrix) |
pdf |