| 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-236 | -5.456e+02 | 0.0000 | 1487.0 | 34.69% | 3131.8 | 14.52% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-195 | -4.512e+02 | 0.0000 | 941.0 | 21.95% | 1605.6 | 7.45% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-78 | -1.813e+02 | 0.0000 | 2019.0 | 47.10% | 7154.9 | 33.18% | motif file (matrix) |
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| 4 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-54 | -1.263e+02 | 0.0000 | 550.0 | 12.83% | 1351.9 | 6.27% | motif file (matrix) |
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| 5 |  | SFP1/SacCer-Promoters/Homer | 1e-51 | -1.183e+02 | 0.0000 | 669.0 | 15.61% | 1828.6 | 8.48% | motif file (matrix) |
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| 6 |  | SeqBias: CG-repeat | 1e-44 | -1.026e+02 | 0.0000 | 738.0 | 17.21% | 2189.8 | 10.15% | motif file (matrix) |
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| 7 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-44 | -1.023e+02 | 0.0000 | 411.0 | 9.59% | 969.1 | 4.49% | motif file (matrix) |
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| 8 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-43 | -1.004e+02 | 0.0000 | 624.0 | 14.56% | 1758.4 | 8.15% | motif file (matrix) |
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| 9 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-41 | -9.456e+01 | 0.0000 | 533.0 | 12.43% | 1446.9 | 6.71% | motif file (matrix) |
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| 10 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-40 | -9.318e+01 | 0.0000 | 1034.0 | 24.12% | 3483.2 | 16.15% | motif file (matrix) |
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| 11 |  | TOD6?/SacCer-Promoters/Homer | 1e-39 | -9.187e+01 | 0.0000 | 385.0 | 8.98% | 924.1 | 4.28% | motif file (matrix) |
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| 12 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-38 | -8.939e+01 | 0.0000 | 381.0 | 8.89% | 921.7 | 4.27% | motif file (matrix) |
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| 13 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-38 | -8.929e+01 | 0.0000 | 378.0 | 8.82% | 911.6 | 4.23% | motif file (matrix) |
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| 14 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-35 | -8.209e+01 | 0.0000 | 453.0 | 10.57% | 1216.1 | 5.64% | motif file (matrix) |
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| 15 |  | E-box/Arabidopsis-Promoters/Homer | 1e-32 | -7.487e+01 | 0.0000 | 496.0 | 11.57% | 1420.3 | 6.59% | motif file (matrix) |
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| 16 |  | E-box(bHLH)/Promoter/Homer | 1e-30 | -7.046e+01 | 0.0000 | 133.0 | 3.10% | 202.3 | 0.94% | motif file (matrix) |
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| 17 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-29 | -6.795e+01 | 0.0000 | 551.0 | 12.85% | 1681.2 | 7.80% | motif file (matrix) |
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| 18 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-29 | -6.751e+01 | 0.0000 | 407.0 | 9.49% | 1126.6 | 5.22% | motif file (matrix) |
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| 19 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-27 | -6.224e+01 | 0.0000 | 830.0 | 19.36% | 2888.9 | 13.40% | motif file (matrix) |
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| 20 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-23 | -5.491e+01 | 0.0000 | 909.0 | 21.20% | 3308.9 | 15.34% | motif file (matrix) |
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| 21 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-23 | -5.488e+01 | 0.0000 | 1270.0 | 29.62% | 4937.2 | 22.89% | motif file (matrix) |
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| 22 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-22 | -5.111e+01 | 0.0000 | 766.0 | 17.87% | 2724.6 | 12.63% | motif file (matrix) |
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| 23 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-22 | -5.104e+01 | 0.0000 | 140.0 | 3.27% | 272.2 | 1.26% | motif file (matrix) |
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| 24 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-21 | -4.840e+01 | 0.0000 | 1027.0 | 23.96% | 3912.9 | 18.14% | motif file (matrix) |
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| 25 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-20 | -4.670e+01 | 0.0000 | 767.0 | 17.89% | 2776.6 | 12.87% | motif file (matrix) |
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| 26 |  | TATA-box/SacCer-Promoters/Homer | 1e-19 | -4.569e+01 | 0.0000 | 1845.0 | 43.04% | 7802.5 | 36.18% | motif file (matrix) |
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| 27 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-18 | -4.156e+01 | 0.0000 | 392.0 | 9.14% | 1243.3 | 5.76% | motif file (matrix) |
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| 28 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-14 | -3.297e+01 | 0.0000 | 1328.0 | 30.98% | 5541.9 | 25.70% | motif file (matrix) |
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| 29 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-14 | -3.257e+01 | 0.0000 | 232.0 | 5.41% | 679.5 | 3.15% | motif file (matrix) |
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| 30 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-14 | -3.254e+01 | 0.0000 | 1006.0 | 23.47% | 4041.0 | 18.74% | motif file (matrix) |
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| 31 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-12 | -2.935e+01 | 0.0000 | 723.0 | 16.86% | 2799.7 | 12.98% | motif file (matrix) |
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| 32 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-12 | -2.885e+01 | 0.0000 | 151.0 | 3.52% | 399.7 | 1.85% | motif file (matrix) |
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| 33 |  | SUT1?/SacCer-Promoters/Homer | 1e-11 | -2.661e+01 | 0.0000 | 2853.0 | 66.55% | 13255.3 | 61.46% | motif file (matrix) |
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| 34 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-11 | -2.637e+01 | 0.0000 | 514.0 | 11.99% | 1911.1 | 8.86% | motif file (matrix) |
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| 35 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-11 | -2.548e+01 | 0.0000 | 292.0 | 6.81% | 974.7 | 4.52% | motif file (matrix) |
pdf |
| 36 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-10 | -2.496e+01 | 0.0000 | 307.0 | 7.16% | 1041.6 | 4.83% | motif file (matrix) |
pdf |
| 37 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-10 | -2.328e+01 | 0.0000 | 145.0 | 3.38% | 409.4 | 1.90% | motif file (matrix) |
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| 38 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-9 | -2.203e+01 | 0.0000 | 440.0 | 10.26% | 1643.8 | 7.62% | motif file (matrix) |
pdf |
| 39 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-9 | -2.185e+01 | 0.0000 | 284.0 | 6.62% | 976.6 | 4.53% | motif file (matrix) |
pdf |
| 40 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-9 | -2.141e+01 | 0.0000 | 488.0 | 11.38% | 1863.5 | 8.64% | motif file (matrix) |
pdf |
| 41 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-8 | -1.989e+01 | 0.0000 | 267.0 | 6.23% | 925.3 | 4.29% | motif file (matrix) |
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| 42 |  | SeqBias: TA-repeat | 1e-8 | -1.889e+01 | 0.0000 | 3765.0 | 87.82% | 18283.9 | 84.78% | motif file (matrix) |
pdf |
| 43 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-8 | -1.872e+01 | 0.0000 | 119.0 | 2.78% | 340.2 | 1.58% | motif file (matrix) |
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| 44 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-7 | -1.647e+01 | 0.0000 | 99.0 | 2.31% | 279.8 | 1.30% | motif file (matrix) |
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| 45 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-7 | -1.616e+01 | 0.0000 | 1532.0 | 35.74% | 6897.3 | 31.98% | motif file (matrix) |
pdf |
| 46 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.519e+01 | 0.0000 | 51.0 | 1.19% | 115.5 | 0.54% | motif file (matrix) |
pdf |
| 47 |  | CRE(bZIP)/Promoter/Homer | 1e-6 | -1.406e+01 | 0.0000 | 182.0 | 4.25% | 630.6 | 2.92% | motif file (matrix) |
pdf |
| 48 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-6 | -1.404e+01 | 0.0000 | 672.0 | 15.68% | 2831.5 | 13.13% | motif file (matrix) |
pdf |
| 49 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-5 | -1.371e+01 | 0.0000 | 733.0 | 17.10% | 3124.9 | 14.49% | motif file (matrix) |
pdf |
| 50 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-5 | -1.355e+01 | 0.0000 | 121.0 | 2.82% | 385.4 | 1.79% | motif file (matrix) |
pdf |
| 51 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-5 | -1.307e+01 | 0.0000 | 118.0 | 2.75% | 378.0 | 1.75% | motif file (matrix) |
pdf |
| 52 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-5 | -1.217e+01 | 0.0000 | 452.0 | 10.54% | 1852.8 | 8.59% | motif file (matrix) |
pdf |
| 53 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-5 | -1.160e+01 | 0.0001 | 181.0 | 4.22% | 653.4 | 3.03% | motif file (matrix) |
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| 54 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-4 | -1.063e+01 | 0.0002 | 1352.0 | 31.54% | 6188.1 | 28.69% | motif file (matrix) |
pdf |
| 55 |  | NRF(NRF)/Promoter/Homer | 1e-4 | -1.018e+01 | 0.0003 | 86.0 | 2.01% | 273.1 | 1.27% | motif file (matrix) |
pdf |
| 56 |  | REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer | 1e-4 | -9.731e+00 | 0.0004 | 5.0 | 0.12% | 2.3 | 0.01% | motif file (matrix) |
pdf |
| 57 |  | TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer | 1e-4 | -9.657e+00 | 0.0004 | 53.0 | 1.24% | 149.4 | 0.69% | motif file (matrix) |
pdf |
| 58 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-4 | -9.542e+00 | 0.0005 | 43.0 | 1.00% | 113.3 | 0.53% | motif file (matrix) |
pdf |
| 59 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-3 | -9.002e+00 | 0.0008 | 527.0 | 12.29% | 2270.1 | 10.53% | motif file (matrix) |
pdf |
| 60 |  | TATA-box/Drosophila-Promoters/Homer | 1e-3 | -8.701e+00 | 0.0011 | 203.0 | 4.74% | 788.7 | 3.66% | motif file (matrix) |
pdf |
| 61 |  | PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-3 | -8.395e+00 | 0.0014 | 79.0 | 1.84% | 260.8 | 1.21% | motif file (matrix) |
pdf |
| 62 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-3 | -8.018e+00 | 0.0021 | 73.0 | 1.70% | 239.8 | 1.11% | motif file (matrix) |
pdf |
| 63 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-3 | -7.470e+00 | 0.0035 | 117.0 | 2.73% | 429.9 | 1.99% | motif file (matrix) |
pdf |
| 64 |  | Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer | 1e-3 | -7.152e+00 | 0.0047 | 194.0 | 4.53% | 773.7 | 3.59% | motif file (matrix) |
pdf |
| 65 |  | PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer | 1e-3 | -6.920e+00 | 0.0059 | 455.0 | 10.61% | 1986.8 | 9.21% | motif file (matrix) |
pdf |
| 66 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-2 | -6.829e+00 | 0.0063 | 79.0 | 1.84% | 275.4 | 1.28% | motif file (matrix) |
pdf |
| 67 |  | ETS(ETS)/Promoter/Homer | 1e-2 | -6.556e+00 | 0.0082 | 310.0 | 7.23% | 1316.3 | 6.10% | motif file (matrix) |
pdf |
| 68 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.382e+00 | 0.0096 | 185.0 | 4.32% | 746.5 | 3.46% | motif file (matrix) |
pdf |
| 69 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.075e+00 | 0.0129 | 758.0 | 17.68% | 3464.1 | 16.06% | motif file (matrix) |
pdf |
| 70 |  | Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer | 1e-2 | -5.995e+00 | 0.0138 | 366.0 | 8.54% | 1592.7 | 7.39% | motif file (matrix) |
pdf |
| 71 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.989e+00 | 0.0138 | 36.0 | 0.84% | 108.6 | 0.50% | motif file (matrix) |
pdf |
| 72 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.843e+00 | 0.0156 | 924.0 | 21.55% | 4280.4 | 19.85% | motif file (matrix) |
pdf |
| 73 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.807e+00 | 0.0159 | 245.0 | 5.71% | 1032.5 | 4.79% | motif file (matrix) |
pdf |
| 74 |  | ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -5.799e+00 | 0.0159 | 48.0 | 1.12% | 158.0 | 0.73% | motif file (matrix) |
pdf |
| 75 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-2 | -5.793e+00 | 0.0159 | 41.0 | 0.96% | 129.3 | 0.60% | motif file (matrix) |
pdf |
| 76 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-2 | -5.775e+00 | 0.0159 | 160.0 | 3.73% | 644.0 | 2.99% | motif file (matrix) |
pdf |
| 77 |  | GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer | 1e-2 | -5.393e+00 | 0.0229 | 101.0 | 2.36% | 387.4 | 1.80% | motif file (matrix) |
pdf |
| 78 |  | ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer | 1e-2 | -5.250e+00 | 0.0260 | 108.0 | 2.52% | 420.2 | 1.95% | motif file (matrix) |
pdf |
| 79 |  | RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-2 | -5.223e+00 | 0.0264 | 469.0 | 10.94% | 2104.4 | 9.76% | motif file (matrix) |
pdf |
| 80 |  | PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer | 1e-2 | -4.948e+00 | 0.0343 | 29.0 | 0.68% | 88.7 | 0.41% | motif file (matrix) |
pdf |
| 81 |  | NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer | 1e-2 | -4.870e+00 | 0.0367 | 60.0 | 1.40% | 216.9 | 1.01% | motif file (matrix) |
pdf |
| 82 |  | Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer | 1e-2 | -4.728e+00 | 0.0417 | 301.0 | 7.02% | 1321.3 | 6.13% | motif file (matrix) |
pdf |