| 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-226 | -5.210e+02 | 0.0000 | 1473.0 | 34.52% | 3101.7 | 14.73% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-176 | -4.072e+02 | 0.0000 | 929.0 | 21.77% | 1647.9 | 7.82% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-69 | -1.594e+02 | 0.0000 | 1976.0 | 46.31% | 7002.1 | 33.25% | motif file (matrix) |
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| 4 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-58 | -1.346e+02 | 0.0000 | 580.0 | 13.59% | 1394.9 | 6.62% | motif file (matrix) |
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| 5 |  | SeqBias: CG-repeat | 1e-46 | -1.074e+02 | 0.0000 | 753.0 | 17.65% | 2176.2 | 10.33% | motif file (matrix) |
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| 6 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-44 | -1.018e+02 | 0.0000 | 428.0 | 10.03% | 1011.8 | 4.80% | motif file (matrix) |
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| 7 |  | SFP1/SacCer-Promoters/Homer | 1e-44 | -1.017e+02 | 0.0000 | 638.0 | 14.95% | 1770.2 | 8.41% | motif file (matrix) |
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| 8 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-42 | -9.885e+01 | 0.0000 | 652.0 | 15.28% | 1840.2 | 8.74% | motif file (matrix) |
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| 9 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-41 | -9.515e+01 | 0.0000 | 403.0 | 9.44% | 954.5 | 4.53% | motif file (matrix) |
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| 10 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-40 | -9.298e+01 | 0.0000 | 1045.0 | 24.49% | 3466.9 | 16.46% | motif file (matrix) |
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| 11 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-39 | -9.138e+01 | 0.0000 | 558.0 | 13.08% | 1529.8 | 7.26% | motif file (matrix) |
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| 12 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-34 | -7.904e+01 | 0.0000 | 379.0 | 8.88% | 944.7 | 4.49% | motif file (matrix) |
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| 13 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-33 | -7.612e+01 | 0.0000 | 462.0 | 10.83% | 1259.9 | 5.98% | motif file (matrix) |
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| 14 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-31 | -7.140e+01 | 0.0000 | 577.0 | 13.52% | 1727.6 | 8.20% | motif file (matrix) |
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| 15 |  | E-box(bHLH)/Promoter/Homer | 1e-28 | -6.552e+01 | 0.0000 | 133.0 | 3.12% | 209.3 | 0.99% | motif file (matrix) |
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| 16 |  | TOD6?/SacCer-Promoters/Homer | 1e-28 | -6.499e+01 | 0.0000 | 358.0 | 8.39% | 940.9 | 4.47% | motif file (matrix) |
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| 17 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-25 | -5.854e+01 | 0.0000 | 1298.0 | 30.42% | 4925.1 | 23.39% | motif file (matrix) |
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| 18 |  | E-box/Arabidopsis-Promoters/Homer | 1e-25 | -5.821e+01 | 0.0000 | 502.0 | 11.76% | 1527.5 | 7.25% | motif file (matrix) |
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| 19 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-25 | -5.765e+01 | 0.0000 | 843.0 | 19.76% | 2934.5 | 13.93% | motif file (matrix) |
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| 20 |  | TATA-box/SacCer-Promoters/Homer | 1e-23 | -5.336e+01 | 0.0000 | 1892.0 | 44.34% | 7760.2 | 36.85% | motif file (matrix) |
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| 21 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-22 | -5.291e+01 | 0.0000 | 416.0 | 9.75% | 1230.0 | 5.84% | motif file (matrix) |
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| 22 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-22 | -5.124e+01 | 0.0000 | 1046.0 | 24.51% | 3888.9 | 18.47% | motif file (matrix) |
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| 23 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-21 | -5.030e+01 | 0.0000 | 930.0 | 21.80% | 3389.7 | 16.09% | motif file (matrix) |
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| 24 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-20 | -4.746e+01 | 0.0000 | 396.0 | 9.28% | 1191.5 | 5.66% | motif file (matrix) |
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| 25 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-18 | -4.369e+01 | 0.0000 | 762.0 | 17.86% | 2736.9 | 13.00% | motif file (matrix) |
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| 26 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-17 | -4.008e+01 | 0.0000 | 128.0 | 3.00% | 266.8 | 1.27% | motif file (matrix) |
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| 27 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-16 | -3.714e+01 | 0.0000 | 770.0 | 18.05% | 2849.1 | 13.53% | motif file (matrix) |
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| 28 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-14 | -3.443e+01 | 0.0000 | 1368.0 | 32.06% | 5598.8 | 26.58% | motif file (matrix) |
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| 29 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-13 | -3.129e+01 | 0.0000 | 749.0 | 17.55% | 2834.3 | 13.46% | motif file (matrix) |
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| 30 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-13 | -3.120e+01 | 0.0000 | 1007.0 | 23.60% | 3991.5 | 18.95% | motif file (matrix) |
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| 31 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-13 | -3.115e+01 | 0.0000 | 529.0 | 12.40% | 1882.2 | 8.94% | motif file (matrix) |
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| 32 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-12 | -2.893e+01 | 0.0000 | 332.0 | 7.78% | 1086.2 | 5.16% | motif file (matrix) |
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| 33 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-11 | -2.610e+01 | 0.0000 | 234.0 | 5.48% | 720.0 | 3.42% | motif file (matrix) |
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| 34 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-10 | -2.470e+01 | 0.0000 | 295.0 | 6.91% | 975.7 | 4.63% | motif file (matrix) |
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| 35 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-10 | -2.449e+01 | 0.0000 | 501.0 | 11.74% | 1843.1 | 8.75% | motif file (matrix) |
pdf |
| 36 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-10 | -2.336e+01 | 0.0000 | 446.0 | 10.45% | 1621.8 | 7.70% | motif file (matrix) |
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| 37 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-9 | -2.138e+01 | 0.0000 | 270.0 | 6.33% | 905.3 | 4.30% | motif file (matrix) |
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| 38 |  | SUT1?/SacCer-Promoters/Homer | 1e-9 | -2.129e+01 | 0.0000 | 2858.0 | 66.98% | 13161.3 | 62.49% | motif file (matrix) |
pdf |
| 39 |  | SeqBias: TA-repeat | 1e-8 | -1.907e+01 | 0.0000 | 3751.0 | 87.91% | 17868.2 | 84.84% | motif file (matrix) |
pdf |
| 40 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-7 | -1.777e+01 | 0.0000 | 1552.0 | 36.37% | 6820.6 | 32.39% | motif file (matrix) |
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| 41 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-7 | -1.766e+01 | 0.0000 | 282.0 | 6.61% | 994.4 | 4.72% | motif file (matrix) |
pdf |
| 42 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-7 | -1.627e+01 | 0.0000 | 143.0 | 3.35% | 442.6 | 2.10% | motif file (matrix) |
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| 43 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-7 | -1.618e+01 | 0.0000 | 140.0 | 3.28% | 431.5 | 2.05% | motif file (matrix) |
pdf |
| 44 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-6 | -1.581e+01 | 0.0000 | 458.0 | 10.73% | 1780.6 | 8.45% | motif file (matrix) |
pdf |
| 45 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-6 | -1.545e+01 | 0.0000 | 122.0 | 2.86% | 367.3 | 1.74% | motif file (matrix) |
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| 46 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-6 | -1.476e+01 | 0.0000 | 683.0 | 16.01% | 2813.1 | 13.36% | motif file (matrix) |
pdf |
| 47 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-6 | -1.449e+01 | 0.0000 | 1361.0 | 31.90% | 5996.5 | 28.47% | motif file (matrix) |
pdf |
| 48 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-5 | -1.220e+01 | 0.0000 | 129.0 | 3.02% | 421.8 | 2.00% | motif file (matrix) |
pdf |
| 49 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-5 | -1.201e+01 | 0.0000 | 210.0 | 4.92% | 758.1 | 3.60% | motif file (matrix) |
pdf |
| 50 |  | RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-5 | -1.177e+01 | 0.0001 | 497.0 | 11.65% | 2028.7 | 9.63% | motif file (matrix) |
pdf |
| 51 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-5 | -1.153e+01 | 0.0001 | 730.0 | 17.11% | 3103.7 | 14.74% | motif file (matrix) |
pdf |
| 52 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-4 | -1.131e+01 | 0.0001 | 95.0 | 2.23% | 294.1 | 1.40% | motif file (matrix) |
pdf |
| 53 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-4 | -1.109e+01 | 0.0001 | 118.0 | 2.77% | 387.9 | 1.84% | motif file (matrix) |
pdf |
| 54 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-4 | -1.041e+01 | 0.0002 | 176.0 | 4.12% | 634.1 | 3.01% | motif file (matrix) |
pdf |
| 55 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-4 | -9.938e+00 | 0.0003 | 118.0 | 2.77% | 398.6 | 1.89% | motif file (matrix) |
pdf |
| 56 |  | PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer | 1e-4 | -9.796e+00 | 0.0004 | 482.0 | 11.30% | 2002.3 | 9.51% | motif file (matrix) |
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| 57 |  | CRE(bZIP)/Promoter/Homer | 1e-4 | -9.524e+00 | 0.0005 | 179.0 | 4.19% | 658.1 | 3.12% | motif file (matrix) |
pdf |
| 58 |  | PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-4 | -9.240e+00 | 0.0006 | 79.0 | 1.85% | 248.8 | 1.18% | motif file (matrix) |
pdf |
| 59 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-3 | -8.854e+00 | 0.0009 | 50.0 | 1.17% | 140.4 | 0.67% | motif file (matrix) |
pdf |
| 60 |  | SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer | 1e-3 | -8.248e+00 | 0.0017 | 270.0 | 6.33% | 1076.4 | 5.11% | motif file (matrix) |
pdf |
| 61 |  | NRF(NRF)/Promoter/Homer | 1e-3 | -8.178e+00 | 0.0018 | 80.0 | 1.87% | 261.1 | 1.24% | motif file (matrix) |
pdf |
| 62 |  | GAGA-repeat/SacCer-Promoters/Homer | 1e-3 | -8.110e+00 | 0.0019 | 3341.0 | 78.30% | 16020.9 | 76.07% | motif file (matrix) |
pdf |
| 63 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.992e+00 | 0.0021 | 949.0 | 22.24% | 4237.5 | 20.12% | motif file (matrix) |
pdf |
| 64 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.818e+00 | 0.0024 | 788.0 | 18.47% | 3480.1 | 16.52% | motif file (matrix) |
pdf |
| 65 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-3 | -7.506e+00 | 0.0033 | 41.0 | 0.96% | 115.6 | 0.55% | motif file (matrix) |
pdf |
| 66 |  | Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer | 1e-2 | -6.752e+00 | 0.0069 | 1590.0 | 37.26% | 7375.7 | 35.02% | motif file (matrix) |
pdf |
| 67 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-2 | -6.434e+00 | 0.0093 | 538.0 | 12.61% | 2349.9 | 11.16% | motif file (matrix) |
pdf |
| 68 |  | Tbet(T-box)/CD8-Tbet-ChIP-Seq(GSE33802)/Homer | 1e-2 | -6.323e+00 | 0.0102 | 1051.0 | 24.63% | 4788.9 | 22.74% | motif file (matrix) |
pdf |
| 69 |  | Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer | 1e-2 | -6.142e+00 | 0.0121 | 202.0 | 4.73% | 812.6 | 3.86% | motif file (matrix) |
pdf |
| 70 |  | TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer | 1e-2 | -6.040e+00 | 0.0132 | 49.0 | 1.15% | 157.0 | 0.75% | motif file (matrix) |
pdf |
| 71 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-2 | -5.953e+00 | 0.0140 | 62.0 | 1.45% | 209.4 | 0.99% | motif file (matrix) |
pdf |
| 72 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-2 | -5.953e+00 | 0.0140 | 62.0 | 1.45% | 209.4 | 0.99% | motif file (matrix) |
pdf |
| 73 |  | AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.842e+00 | 0.0154 | 156.0 | 3.66% | 613.5 | 2.91% | motif file (matrix) |
pdf |
| 74 |  | ERE(NR),IR3/MCF7-ERa-ChIP-Seq(Unpublished)/Homer | 1e-2 | -5.642e+00 | 0.0185 | 113.0 | 2.65% | 428.6 | 2.04% | motif file (matrix) |
pdf |
| 75 |  | GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer | 1e-2 | -5.532e+00 | 0.0204 | 105.0 | 2.46% | 395.4 | 1.88% | motif file (matrix) |
pdf |
| 76 |  | EFL-1(E2F)/cElegans-L1-EFL1-ChIP-Seq(modEncode)/Homer | 1e-2 | -5.461e+00 | 0.0216 | 23.0 | 0.54% | 61.4 | 0.29% | motif file (matrix) |
pdf |
| 77 |  | PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer | 1e-2 | -5.423e+00 | 0.0222 | 30.0 | 0.70% | 87.1 | 0.41% | motif file (matrix) |
pdf |
| 78 |  | Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.206e+00 | 0.0272 | 70.0 | 1.64% | 250.4 | 1.19% | motif file (matrix) |
pdf |
| 79 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-2 | -4.988e+00 | 0.0334 | 41.0 | 0.96% | 133.8 | 0.64% | motif file (matrix) |
pdf |