| 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-209 | -4.812e+02 | 0.0000 | 1579.0 | 35.95% | 3132.3 | 16.61% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-173 | -4.002e+02 | 0.0000 | 948.0 | 21.58% | 1496.6 | 7.93% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-79 | -1.841e+02 | 0.0000 | 2059.0 | 46.88% | 6230.5 | 33.03% | motif file (matrix) |
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| 4 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-60 | -1.393e+02 | 0.0000 | 658.0 | 14.98% | 1433.3 | 7.60% | motif file (matrix) |
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| 5 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-49 | -1.143e+02 | 0.0000 | 458.0 | 10.43% | 922.6 | 4.89% | motif file (matrix) |
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| 6 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-47 | -1.084e+02 | 0.0000 | 487.0 | 11.09% | 1031.6 | 5.47% | motif file (matrix) |
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| 7 |  | SeqBias: CG-repeat | 1e-45 | -1.052e+02 | 0.0000 | 877.0 | 19.97% | 2329.9 | 12.35% | motif file (matrix) |
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| 8 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-45 | -1.048e+02 | 0.0000 | 641.0 | 14.59% | 1533.6 | 8.13% | motif file (matrix) |
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| 9 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-43 | -1.000e+02 | 0.0000 | 1179.0 | 26.84% | 3453.8 | 18.31% | motif file (matrix) |
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| 10 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-43 | -9.937e+01 | 0.0000 | 733.0 | 16.69% | 1868.0 | 9.90% | motif file (matrix) |
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| 11 |  | SFP1/SacCer-Promoters/Homer | 1e-42 | -9.759e+01 | 0.0000 | 652.0 | 14.85% | 1607.0 | 8.52% | motif file (matrix) |
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| 12 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-37 | -8.714e+01 | 0.0000 | 544.0 | 12.39% | 1305.6 | 6.92% | motif file (matrix) |
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| 13 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-36 | -8.425e+01 | 0.0000 | 432.0 | 9.84% | 962.6 | 5.10% | motif file (matrix) |
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| 14 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-34 | -7.991e+01 | 0.0000 | 669.0 | 15.23% | 1764.2 | 9.35% | motif file (matrix) |
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| 15 |  | E-box/Arabidopsis-Promoters/Homer | 1e-31 | -7.199e+01 | 0.0000 | 592.0 | 13.48% | 1549.8 | 8.22% | motif file (matrix) |
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| 16 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-30 | -7.099e+01 | 0.0000 | 498.0 | 11.34% | 1239.6 | 6.57% | motif file (matrix) |
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| 17 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-27 | -6.272e+01 | 0.0000 | 957.0 | 21.79% | 2930.4 | 15.54% | motif file (matrix) |
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| 18 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-25 | -5.825e+01 | 0.0000 | 1213.0 | 27.62% | 3951.2 | 20.95% | motif file (matrix) |
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| 19 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-25 | -5.787e+01 | 0.0000 | 1050.0 | 23.91% | 3327.7 | 17.64% | motif file (matrix) |
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| 20 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-25 | -5.776e+01 | 0.0000 | 483.0 | 11.00% | 1266.1 | 6.71% | motif file (matrix) |
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| 21 |  | E-box(bHLH)/Promoter/Homer | 1e-24 | -5.729e+01 | 0.0000 | 143.0 | 3.26% | 224.2 | 1.19% | motif file (matrix) |
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| 22 |  | TOD6?/SacCer-Promoters/Homer | 1e-23 | -5.412e+01 | 0.0000 | 379.0 | 8.63% | 940.6 | 4.99% | motif file (matrix) |
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| 23 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-21 | -5.000e+01 | 0.0000 | 1483.0 | 33.77% | 5115.9 | 27.12% | motif file (matrix) |
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| 24 |  | TATA-box/SacCer-Promoters/Homer | 1e-21 | -4.985e+01 | 0.0000 | 1931.0 | 43.97% | 6950.1 | 36.85% | motif file (matrix) |
pdf |
| 25 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-21 | -4.878e+01 | 0.0000 | 867.0 | 19.74% | 2723.9 | 14.44% | motif file (matrix) |
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| 26 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-19 | -4.554e+01 | 0.0000 | 149.0 | 3.39% | 272.6 | 1.45% | motif file (matrix) |
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| 27 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-18 | -4.277e+01 | 0.0000 | 894.0 | 20.36% | 2888.4 | 15.31% | motif file (matrix) |
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| 28 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-16 | -3.830e+01 | 0.0000 | 1160.0 | 26.41% | 3978.4 | 21.09% | motif file (matrix) |
pdf |
| 29 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-13 | -3.113e+01 | 0.0000 | 1532.0 | 34.88% | 5587.3 | 29.62% | motif file (matrix) |
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| 30 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-12 | -2.991e+01 | 0.0000 | 851.0 | 19.38% | 2876.7 | 15.25% | motif file (matrix) |
pdf |
| 31 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-12 | -2.833e+01 | 0.0000 | 178.0 | 4.05% | 428.9 | 2.27% | motif file (matrix) |
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| 32 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-12 | -2.810e+01 | 0.0000 | 378.0 | 8.61% | 1115.9 | 5.92% | motif file (matrix) |
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| 33 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-10 | -2.338e+01 | 0.0000 | 599.0 | 13.64% | 1988.4 | 10.54% | motif file (matrix) |
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| 34 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-9 | -2.253e+01 | 0.0000 | 654.0 | 14.89% | 2211.0 | 11.72% | motif file (matrix) |
pdf |
| 35 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-9 | -2.226e+01 | 0.0000 | 340.0 | 7.74% | 1031.3 | 5.47% | motif file (matrix) |
pdf |
| 36 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-9 | -2.083e+01 | 0.0000 | 270.0 | 6.15% | 792.8 | 4.20% | motif file (matrix) |
pdf |
| 37 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-8 | -2.068e+01 | 0.0000 | 300.0 | 6.83% | 901.3 | 4.78% | motif file (matrix) |
pdf |
| 38 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-8 | -2.033e+01 | 0.0000 | 174.0 | 3.96% | 462.1 | 2.45% | motif file (matrix) |
pdf |
| 39 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-8 | -2.017e+01 | 0.0000 | 330.0 | 7.51% | 1015.0 | 5.38% | motif file (matrix) |
pdf |
| 40 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-8 | -1.864e+01 | 0.0000 | 818.0 | 18.62% | 2915.5 | 15.46% | motif file (matrix) |
pdf |
| 41 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-7 | -1.790e+01 | 0.0000 | 572.0 | 13.02% | 1959.3 | 10.39% | motif file (matrix) |
pdf |
| 42 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-7 | -1.755e+01 | 0.0000 | 265.0 | 6.03% | 804.3 | 4.26% | motif file (matrix) |
pdf |
| 43 |  | SUT1?/SacCer-Promoters/Homer | 1e-7 | -1.744e+01 | 0.0000 | 3173.0 | 72.24% | 12914.4 | 68.46% | motif file (matrix) |
pdf |
| 44 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-6 | -1.569e+01 | 0.0000 | 689.0 | 15.69% | 2454.9 | 13.01% | motif file (matrix) |
pdf |
| 45 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-6 | -1.552e+01 | 0.0000 | 567.0 | 12.91% | 1976.4 | 10.48% | motif file (matrix) |
pdf |
| 46 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-6 | -1.530e+01 | 0.0000 | 101.0 | 2.30% | 251.5 | 1.33% | motif file (matrix) |
pdf |
| 47 |  | CRE(bZIP)/Promoter/Homer | 1e-6 | -1.479e+01 | 0.0000 | 227.0 | 5.17% | 693.3 | 3.68% | motif file (matrix) |
pdf |
| 48 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-6 | -1.453e+01 | 0.0000 | 500.0 | 11.38% | 1730.0 | 9.17% | motif file (matrix) |
pdf |
| 49 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-5 | -1.374e+01 | 0.0000 | 1758.0 | 40.03% | 6896.0 | 36.56% | motif file (matrix) |
pdf |
| 50 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-5 | -1.325e+01 | 0.0000 | 59.0 | 1.34% | 129.2 | 0.68% | motif file (matrix) |
pdf |
| 51 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-5 | -1.262e+01 | 0.0000 | 222.0 | 5.05% | 697.5 | 3.70% | motif file (matrix) |
pdf |
| 52 |  | SeqBias: TA-repeat | 1e-5 | -1.244e+01 | 0.0000 | 3807.0 | 86.68% | 15895.8 | 84.27% | motif file (matrix) |
pdf |
| 53 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-5 | -1.236e+01 | 0.0000 | 135.0 | 3.07% | 387.0 | 2.05% | motif file (matrix) |
pdf |
| 54 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-5 | -1.234e+01 | 0.0000 | 120.0 | 2.73% | 334.4 | 1.77% | motif file (matrix) |
pdf |
| 55 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-5 | -1.156e+01 | 0.0001 | 107.0 | 2.44% | 295.5 | 1.57% | motif file (matrix) |
pdf |
| 56 |  | NRF(NRF)/Promoter/Homer | 1e-4 | -1.146e+01 | 0.0001 | 112.0 | 2.55% | 313.8 | 1.66% | motif file (matrix) |
pdf |
| 57 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-4 | -1.132e+01 | 0.0001 | 132.0 | 3.01% | 384.4 | 2.04% | motif file (matrix) |
pdf |
| 58 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-4 | -1.044e+01 | 0.0002 | 118.0 | 2.69% | 342.8 | 1.82% | motif file (matrix) |
pdf |
| 59 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-4 | -9.584e+00 | 0.0005 | 1481.0 | 33.72% | 5853.2 | 31.03% | motif file (matrix) |
pdf |
| 60 |  | TATA-box/Drosophila-Promoters/Homer | 1e-4 | -9.249e+00 | 0.0006 | 219.0 | 4.99% | 726.4 | 3.85% | motif file (matrix) |
pdf |
| 61 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-3 | -8.996e+00 | 0.0008 | 591.0 | 13.46% | 2195.7 | 11.64% | motif file (matrix) |
pdf |
| 62 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-3 | -8.940e+00 | 0.0008 | 758.0 | 17.26% | 2874.6 | 15.24% | motif file (matrix) |
pdf |
| 63 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-3 | -8.929e+00 | 0.0008 | 193.0 | 4.39% | 632.8 | 3.35% | motif file (matrix) |
pdf |
| 64 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-3 | -8.474e+00 | 0.0013 | 131.0 | 2.98% | 407.7 | 2.16% | motif file (matrix) |
pdf |
| 65 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-3 | -8.461e+00 | 0.0013 | 78.0 | 1.78% | 218.5 | 1.16% | motif file (matrix) |
pdf |
| 66 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-3 | -8.461e+00 | 0.0013 | 78.0 | 1.78% | 218.5 | 1.16% | motif file (matrix) |
pdf |
| 67 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-3 | -7.524e+00 | 0.0031 | 489.0 | 11.13% | 1818.6 | 9.64% | motif file (matrix) |
pdf |
| 68 |  | RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-3 | -7.327e+00 | 0.0037 | 547.0 | 12.45% | 2057.3 | 10.91% | motif file (matrix) |
pdf |
| 69 |  | Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer | 1e-2 | -6.812e+00 | 0.0062 | 461.0 | 10.50% | 1722.4 | 9.13% | motif file (matrix) |
pdf |
| 70 |  | AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.649e+00 | 0.0072 | 197.0 | 4.49% | 679.3 | 3.60% | motif file (matrix) |
pdf |
| 71 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -6.434e+00 | 0.0088 | 49.0 | 1.12% | 133.4 | 0.71% | motif file (matrix) |
pdf |
| 72 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-2 | -6.261e+00 | 0.0103 | 142.0 | 3.23% | 474.3 | 2.51% | motif file (matrix) |
pdf |
| 73 |  | PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer | 1e-2 | -6.254e+00 | 0.0103 | 517.0 | 11.77% | 1963.7 | 10.41% | motif file (matrix) |
pdf |
| 74 |  | ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -5.791e+00 | 0.0160 | 56.0 | 1.28% | 162.5 | 0.86% | motif file (matrix) |
pdf |
| 75 |  | Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.620e+00 | 0.0187 | 74.0 | 1.68% | 229.0 | 1.21% | motif file (matrix) |
pdf |
| 76 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-2 | -5.531e+00 | 0.0202 | 50.0 | 1.14% | 143.9 | 0.76% | motif file (matrix) |
pdf |
| 77 |  | Unknown1(NR/Ini-like)/Drosophila-Promoters/Homer | 1e-2 | -5.443e+00 | 0.0218 | 176.0 | 4.01% | 617.2 | 3.27% | motif file (matrix) |
pdf |
| 78 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.131e+00 | 0.0293 | 289.0 | 6.58% | 1070.8 | 5.68% | motif file (matrix) |
pdf |
| 79 |  | PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer | 1e-2 | -5.122e+00 | 0.0293 | 37.0 | 0.84% | 101.8 | 0.54% | motif file (matrix) |
pdf |
| 80 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.068e+00 | 0.0305 | 1067.0 | 24.29% | 4282.0 | 22.70% | motif file (matrix) |
pdf |
| 81 |  | Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer | 1e-2 | -4.835e+00 | 0.0380 | 228.0 | 5.19% | 833.9 | 4.42% | motif file (matrix) |
pdf |
| 82 |  | p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer | 1e-2 | -4.745e+00 | 0.0410 | 223.0 | 5.08% | 815.7 | 4.32% | motif file (matrix) |
pdf |
| 83 |  | ETS(ETS)/Promoter/Homer | 1e-2 | -4.712e+00 | 0.0419 | 366.0 | 8.33% | 1391.1 | 7.37% | motif file (matrix) |
pdf |
| 84 |  | Unknown3/Arabidopsis-Promoters/Homer | 1e-2 | -4.696e+00 | 0.0421 | 556.0 | 12.66% | 2169.0 | 11.50% | motif file (matrix) |
pdf |
| 85 |  | ZSCAN22(Zf)/HEK293-ZSCAN22.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -4.640e+00 | 0.0440 | 15.0 | 0.34% | 32.7 | 0.17% | motif file (matrix) |
pdf |