| 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-220 | -5.084e+02 | 0.0000 | 1515.0 | 35.50% | 3157.6 | 15.62% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-178 | -4.111e+02 | 0.0000 | 959.0 | 22.47% | 1659.2 | 8.21% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-70 | -1.634e+02 | 0.0000 | 2061.0 | 48.29% | 7066.1 | 34.95% | motif file (matrix) |
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| 4 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-50 | -1.152e+02 | 0.0000 | 579.0 | 13.57% | 1421.7 | 7.03% | motif file (matrix) |
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| 5 |  | SeqBias: CG-repeat | 1e-47 | -1.084e+02 | 0.0000 | 789.0 | 18.49% | 2217.2 | 10.97% | motif file (matrix) |
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| 6 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-42 | -9.734e+01 | 0.0000 | 1096.0 | 25.68% | 3499.0 | 17.31% | motif file (matrix) |
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| 7 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-42 | -9.710e+01 | 0.0000 | 576.0 | 13.50% | 1501.3 | 7.43% | motif file (matrix) |
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| 8 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-41 | -9.554e+01 | 0.0000 | 659.0 | 15.44% | 1811.6 | 8.96% | motif file (matrix) |
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| 9 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-40 | -9.404e+01 | 0.0000 | 433.0 | 10.15% | 1020.3 | 5.05% | motif file (matrix) |
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| 10 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-38 | -8.852e+01 | 0.0000 | 406.0 | 9.51% | 954.2 | 4.72% | motif file (matrix) |
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| 11 |  | SFP1/SacCer-Promoters/Homer | 1e-37 | -8.697e+01 | 0.0000 | 639.0 | 14.97% | 1789.4 | 8.85% | motif file (matrix) |
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| 12 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-37 | -8.671e+01 | 0.0000 | 414.0 | 9.70% | 989.3 | 4.89% | motif file (matrix) |
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| 13 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-34 | -7.991e+01 | 0.0000 | 486.0 | 11.39% | 1273.3 | 6.30% | motif file (matrix) |
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| 14 |  | TATA-box/SacCer-Promoters/Homer | 1e-32 | -7.459e+01 | 0.0000 | 2033.0 | 47.63% | 7810.1 | 38.63% | motif file (matrix) |
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| 15 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-28 | -6.535e+01 | 0.0000 | 588.0 | 13.78% | 1741.9 | 8.62% | motif file (matrix) |
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| 16 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-27 | -6.327e+01 | 0.0000 | 1351.0 | 31.65% | 4901.9 | 24.24% | motif file (matrix) |
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| 17 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-25 | -5.979e+01 | 0.0000 | 427.0 | 10.00% | 1177.6 | 5.82% | motif file (matrix) |
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| 18 |  | E-box/Arabidopsis-Promoters/Homer | 1e-24 | -5.747e+01 | 0.0000 | 515.0 | 12.07% | 1520.5 | 7.52% | motif file (matrix) |
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| 19 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-24 | -5.695e+01 | 0.0000 | 882.0 | 20.67% | 2983.7 | 14.76% | motif file (matrix) |
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| 20 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-24 | -5.688e+01 | 0.0000 | 971.0 | 22.75% | 3353.4 | 16.59% | motif file (matrix) |
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| 21 |  | E-box(bHLH)/Promoter/Homer | 1e-23 | -5.476e+01 | 0.0000 | 134.0 | 3.14% | 229.6 | 1.14% | motif file (matrix) |
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| 22 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-23 | -5.326e+01 | 0.0000 | 145.0 | 3.40% | 264.8 | 1.31% | motif file (matrix) |
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| 23 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-21 | -4.968e+01 | 0.0000 | 798.0 | 18.70% | 2712.0 | 13.41% | motif file (matrix) |
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| 24 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-20 | -4.793e+01 | 0.0000 | 1092.0 | 25.59% | 3968.7 | 19.63% | motif file (matrix) |
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| 25 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-20 | -4.625e+01 | 0.0000 | 804.0 | 18.84% | 2772.8 | 13.71% | motif file (matrix) |
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| 26 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-16 | -3.780e+01 | 0.0000 | 412.0 | 9.65% | 1277.7 | 6.32% | motif file (matrix) |
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| 27 |  | TOD6?/SacCer-Promoters/Homer | 1e-16 | -3.707e+01 | 0.0000 | 334.0 | 7.83% | 985.2 | 4.87% | motif file (matrix) |
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| 28 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-15 | -3.492e+01 | 0.0000 | 560.0 | 13.12% | 1892.5 | 9.36% | motif file (matrix) |
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| 29 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-15 | -3.476e+01 | 0.0000 | 1405.0 | 32.92% | 5533.0 | 27.37% | motif file (matrix) |
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| 30 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-14 | -3.445e+01 | 0.0000 | 793.0 | 18.58% | 2865.2 | 14.17% | motif file (matrix) |
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| 31 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-12 | -2.789e+01 | 0.0000 | 1045.0 | 24.48% | 4050.5 | 20.03% | motif file (matrix) |
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| 32 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-11 | -2.752e+01 | 0.0000 | 330.0 | 7.73% | 1047.0 | 5.18% | motif file (matrix) |
pdf |
| 33 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-11 | -2.748e+01 | 0.0000 | 158.0 | 3.70% | 407.7 | 2.02% | motif file (matrix) |
pdf |
| 34 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-11 | -2.571e+01 | 0.0000 | 1653.0 | 38.73% | 6828.6 | 33.77% | motif file (matrix) |
pdf |
| 35 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-11 | -2.561e+01 | 0.0000 | 237.0 | 5.55% | 706.9 | 3.50% | motif file (matrix) |
pdf |
| 36 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-10 | -2.528e+01 | 0.0000 | 161.0 | 3.77% | 430.3 | 2.13% | motif file (matrix) |
pdf |
| 37 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-10 | -2.508e+01 | 0.0000 | 290.0 | 6.79% | 913.3 | 4.52% | motif file (matrix) |
pdf |
| 38 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-10 | -2.359e+01 | 0.0000 | 308.0 | 7.22% | 997.8 | 4.94% | motif file (matrix) |
pdf |
| 39 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-9 | -2.175e+01 | 0.0000 | 311.0 | 7.29% | 1027.7 | 5.08% | motif file (matrix) |
pdf |
| 40 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-9 | -2.144e+01 | 0.0000 | 128.0 | 3.00% | 336.4 | 1.66% | motif file (matrix) |
pdf |
| 41 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-9 | -2.127e+01 | 0.0000 | 113.0 | 2.65% | 285.7 | 1.41% | motif file (matrix) |
pdf |
| 42 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-8 | -2.046e+01 | 0.0000 | 459.0 | 10.75% | 1646.0 | 8.14% | motif file (matrix) |
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| 43 |  | SUT1?/SacCer-Promoters/Homer | 1e-8 | -1.971e+01 | 0.0000 | 2917.0 | 68.35% | 12958.7 | 64.09% | motif file (matrix) |
pdf |
| 44 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-7 | -1.676e+01 | 0.0000 | 201.0 | 4.71% | 642.9 | 3.18% | motif file (matrix) |
pdf |
| 45 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-7 | -1.667e+01 | 0.0000 | 61.0 | 1.43% | 134.9 | 0.67% | motif file (matrix) |
pdf |
| 46 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-7 | -1.639e+01 | 0.0000 | 507.0 | 11.88% | 1908.4 | 9.44% | motif file (matrix) |
pdf |
| 47 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-6 | -1.560e+01 | 0.0000 | 1426.0 | 33.41% | 6023.5 | 29.79% | motif file (matrix) |
pdf |
| 48 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-6 | -1.534e+01 | 0.0000 | 481.0 | 11.27% | 1814.9 | 8.98% | motif file (matrix) |
pdf |
| 49 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-6 | -1.512e+01 | 0.0000 | 712.0 | 16.68% | 2820.7 | 13.95% | motif file (matrix) |
pdf |
| 50 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-6 | -1.464e+01 | 0.0000 | 593.0 | 13.89% | 2309.5 | 11.42% | motif file (matrix) |
pdf |
| 51 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-5 | -1.343e+01 | 0.0000 | 77.0 | 1.80% | 203.4 | 1.01% | motif file (matrix) |
pdf |
| 52 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-5 | -1.343e+01 | 0.0000 | 77.0 | 1.80% | 203.4 | 1.01% | motif file (matrix) |
pdf |
| 53 |  | SeqBias: TA-repeat | 1e-5 | -1.311e+01 | 0.0000 | 3791.0 | 88.82% | 17480.0 | 86.46% | motif file (matrix) |
pdf |
| 54 |  | NRF(NRF)/Promoter/Homer | 1e-5 | -1.282e+01 | 0.0000 | 96.0 | 2.25% | 275.0 | 1.36% | motif file (matrix) |
pdf |
| 55 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-5 | -1.189e+01 | 0.0000 | 121.0 | 2.84% | 376.8 | 1.86% | motif file (matrix) |
pdf |
| 56 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-4 | -1.128e+01 | 0.0001 | 45.0 | 1.05% | 105.3 | 0.52% | motif file (matrix) |
pdf |
| 57 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-4 | -9.767e+00 | 0.0004 | 129.0 | 3.02% | 427.5 | 2.11% | motif file (matrix) |
pdf |
| 58 |  | TATA-box/Drosophila-Promoters/Homer | 1e-4 | -9.757e+00 | 0.0004 | 215.0 | 5.04% | 777.4 | 3.84% | motif file (matrix) |
pdf |
| 59 |  | Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer | 1e-4 | -9.708e+00 | 0.0004 | 217.0 | 5.08% | 786.5 | 3.89% | motif file (matrix) |
pdf |
| 60 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-3 | -8.977e+00 | 0.0008 | 738.0 | 17.29% | 3080.7 | 15.24% | motif file (matrix) |
pdf |
| 61 |  | CRE(bZIP)/Promoter/Homer | 1e-2 | -6.470e+00 | 0.0098 | 185.0 | 4.33% | 701.8 | 3.47% | motif file (matrix) |
pdf |
| 62 |  | Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer | 1e-2 | -6.324e+00 | 0.0112 | 1645.0 | 38.54% | 7355.0 | 36.38% | motif file (matrix) |
pdf |
| 63 |  | E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.968e+00 | 0.0157 | 269.0 | 6.30% | 1073.4 | 5.31% | motif file (matrix) |
pdf |
| 64 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-2 | -5.848e+00 | 0.0175 | 491.0 | 11.50% | 2061.4 | 10.20% | motif file (matrix) |
pdf |
| 65 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.557e+00 | 0.0230 | 596.0 | 13.96% | 2544.5 | 12.58% | motif file (matrix) |
pdf |
| 66 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-2 | -5.555e+00 | 0.0230 | 181.0 | 4.24% | 700.8 | 3.47% | motif file (matrix) |
pdf |
| 67 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-2 | -5.549e+00 | 0.0230 | 184.0 | 4.31% | 713.1 | 3.53% | motif file (matrix) |
pdf |
| 68 |  | ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -5.284e+00 | 0.0289 | 49.0 | 1.15% | 156.7 | 0.78% | motif file (matrix) |
pdf |
| 69 |  | ZNF692(Zf)/HEK293-ZNF692.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -5.118e+00 | 0.0336 | 55.0 | 1.29% | 181.4 | 0.90% | motif file (matrix) |
pdf |
| 70 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.106e+00 | 0.0336 | 976.0 | 22.87% | 4301.6 | 21.28% | motif file (matrix) |
pdf |
| 71 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.061e+00 | 0.0345 | 192.0 | 4.50% | 757.4 | 3.75% | motif file (matrix) |
pdf |
| 72 |  | PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.061e+00 | 0.0345 | 77.0 | 1.80% | 270.3 | 1.34% | motif file (matrix) |
pdf |
| 73 |  | GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer | 1e-2 | -4.989e+00 | 0.0361 | 39.0 | 0.91% | 120.3 | 0.59% | motif file (matrix) |
pdf |
| 74 |  | SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer | 1e-2 | -4.955e+00 | 0.0369 | 268.0 | 6.28% | 1092.3 | 5.40% | motif file (matrix) |
pdf |
| 75 |  | PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer | 1e-2 | -4.733e+00 | 0.0454 | 30.0 | 0.70% | 88.2 | 0.44% | motif file (matrix) |
pdf |
| 76 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.714e+00 | 0.0457 | 804.0 | 18.84% | 3526.1 | 17.44% | motif file (matrix) |
pdf |
| 77 |  | X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-2 | -4.634e+00 | 0.0488 | 118.0 | 2.76% | 447.5 | 2.21% | motif file (matrix) |
pdf |
| 78 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.631e+00 | 0.0488 | 263.0 | 6.16% | 1078.3 | 5.33% | motif file (matrix) |
pdf |