| 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-211 | -4.862e+02 | 0.0000 | 1360.0 | 34.33% | 3178.5 | 14.56% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-182 | -4.198e+02 | 0.0000 | 871.0 | 21.99% | 1623.6 | 7.44% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-83 | -1.915e+02 | 0.0000 | 1887.0 | 47.64% | 7152.8 | 32.76% | motif file (matrix) |
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| 4 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-66 | -1.533e+02 | 0.0000 | 555.0 | 14.01% | 1381.3 | 6.33% | motif file (matrix) |
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| 5 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-57 | -1.326e+02 | 0.0000 | 623.0 | 15.73% | 1743.0 | 7.98% | motif file (matrix) |
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| 6 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-55 | -1.284e+02 | 0.0000 | 417.0 | 10.53% | 976.2 | 4.47% | motif file (matrix) |
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| 7 |  | SeqBias: CG-repeat | 1e-53 | -1.227e+02 | 0.0000 | 730.0 | 18.43% | 2239.3 | 10.26% | motif file (matrix) |
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| 8 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-48 | -1.117e+02 | 0.0000 | 530.0 | 13.38% | 1480.8 | 6.78% | motif file (matrix) |
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| 9 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-47 | -1.100e+02 | 0.0000 | 385.0 | 9.72% | 934.9 | 4.28% | motif file (matrix) |
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| 10 |  | SFP1/SacCer-Promoters/Homer | 1e-43 | -1.008e+02 | 0.0000 | 592.0 | 14.95% | 1795.0 | 8.22% | motif file (matrix) |
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| 11 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-43 | -9.970e+01 | 0.0000 | 449.0 | 11.34% | 1223.8 | 5.61% | motif file (matrix) |
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| 12 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-42 | -9.770e+01 | 0.0000 | 367.0 | 9.27% | 920.9 | 4.22% | motif file (matrix) |
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| 13 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-41 | -9.622e+01 | 0.0000 | 553.0 | 13.96% | 1661.5 | 7.61% | motif file (matrix) |
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| 14 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-40 | -9.304e+01 | 0.0000 | 982.0 | 24.79% | 3589.5 | 16.44% | motif file (matrix) |
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| 15 |  | E-box/Arabidopsis-Promoters/Homer | 1e-35 | -8.227e+01 | 0.0000 | 489.0 | 12.35% | 1483.0 | 6.79% | motif file (matrix) |
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| 16 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-34 | -8.000e+01 | 0.0000 | 397.0 | 10.02% | 1122.0 | 5.14% | motif file (matrix) |
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| 17 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-30 | -6.987e+01 | 0.0000 | 788.0 | 19.89% | 2900.1 | 13.28% | motif file (matrix) |
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| 18 |  | E-box(bHLH)/Promoter/Homer | 1e-29 | -6.819e+01 | 0.0000 | 124.0 | 3.13% | 201.2 | 0.92% | motif file (matrix) |
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| 19 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-29 | -6.689e+01 | 0.0000 | 875.0 | 22.09% | 3338.2 | 15.29% | motif file (matrix) |
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| 20 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-27 | -6.300e+01 | 0.0000 | 1194.0 | 30.14% | 4938.6 | 22.62% | motif file (matrix) |
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| 21 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-25 | -5.964e+01 | 0.0000 | 738.0 | 18.63% | 2768.2 | 12.68% | motif file (matrix) |
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| 22 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-24 | -5.715e+01 | 0.0000 | 978.0 | 24.69% | 3944.4 | 18.07% | motif file (matrix) |
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| 23 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-24 | -5.655e+01 | 0.0000 | 138.0 | 3.48% | 274.5 | 1.26% | motif file (matrix) |
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| 24 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-23 | -5.452e+01 | 0.0000 | 723.0 | 18.25% | 2751.7 | 12.60% | motif file (matrix) |
pdf |
| 25 |  | TATA-box/SacCer-Promoters/Homer | 1e-23 | -5.444e+01 | 0.0000 | 1728.0 | 43.63% | 7816.1 | 35.80% | motif file (matrix) |
pdf |
| 26 |  | TOD6?/SacCer-Promoters/Homer | 1e-22 | -5.292e+01 | 0.0000 | 318.0 | 8.03% | 963.6 | 4.41% | motif file (matrix) |
pdf |
| 27 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-20 | -4.767e+01 | 0.0000 | 373.0 | 9.42% | 1231.0 | 5.64% | motif file (matrix) |
pdf |
| 28 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-17 | -4.124e+01 | 0.0000 | 1256.0 | 31.71% | 5568.9 | 25.51% | motif file (matrix) |
pdf |
| 29 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-17 | -3.929e+01 | 0.0000 | 691.0 | 17.45% | 2776.5 | 12.72% | motif file (matrix) |
pdf |
| 30 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-15 | -3.585e+01 | 0.0000 | 310.0 | 7.83% | 1053.2 | 4.82% | motif file (matrix) |
pdf |
| 31 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-15 | -3.480e+01 | 0.0000 | 494.0 | 12.47% | 1896.8 | 8.69% | motif file (matrix) |
pdf |
| 32 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-14 | -3.418e+01 | 0.0000 | 927.0 | 23.40% | 4012.2 | 18.38% | motif file (matrix) |
pdf |
| 33 |  | SUT1?/SacCer-Promoters/Homer | 1e-13 | -3.126e+01 | 0.0000 | 2660.0 | 67.15% | 13402.0 | 61.38% | motif file (matrix) |
pdf |
| 34 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-13 | -3.028e+01 | 0.0000 | 143.0 | 3.61% | 398.7 | 1.83% | motif file (matrix) |
pdf |
| 35 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-12 | -2.981e+01 | 0.0000 | 149.0 | 3.76% | 424.3 | 1.94% | motif file (matrix) |
pdf |
| 36 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-12 | -2.887e+01 | 0.0000 | 217.0 | 5.48% | 709.9 | 3.25% | motif file (matrix) |
pdf |
| 37 |  | SeqBias: TA-repeat | 1e-12 | -2.819e+01 | 0.0000 | 3479.0 | 87.83% | 18296.2 | 83.80% | motif file (matrix) |
pdf |
| 38 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-10 | -2.423e+01 | 0.0000 | 254.0 | 6.41% | 910.3 | 4.17% | motif file (matrix) |
pdf |
| 39 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-10 | -2.336e+01 | 0.0000 | 265.0 | 6.69% | 968.7 | 4.44% | motif file (matrix) |
pdf |
| 40 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-9 | -2.278e+01 | 0.0000 | 416.0 | 10.50% | 1677.3 | 7.68% | motif file (matrix) |
pdf |
| 41 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-9 | -2.169e+01 | 0.0000 | 1433.0 | 36.18% | 6892.9 | 31.57% | motif file (matrix) |
pdf |
| 42 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-9 | -2.095e+01 | 0.0000 | 273.0 | 6.89% | 1030.8 | 4.72% | motif file (matrix) |
pdf |
| 43 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-8 | -2.055e+01 | 0.0000 | 96.0 | 2.42% | 269.9 | 1.24% | motif file (matrix) |
pdf |
| 44 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-8 | -1.972e+01 | 0.0000 | 175.0 | 4.42% | 603.0 | 2.76% | motif file (matrix) |
pdf |
| 45 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-8 | -1.934e+01 | 0.0000 | 114.0 | 2.88% | 348.3 | 1.60% | motif file (matrix) |
pdf |
| 46 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-8 | -1.912e+01 | 0.0000 | 1249.0 | 31.53% | 5982.1 | 27.40% | motif file (matrix) |
pdf |
| 47 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-7 | -1.632e+01 | 0.0000 | 427.0 | 10.78% | 1828.0 | 8.37% | motif file (matrix) |
pdf |
| 48 |  | CRE(bZIP)/Promoter/Homer | 1e-7 | -1.614e+01 | 0.0000 | 182.0 | 4.59% | 668.3 | 3.06% | motif file (matrix) |
pdf |
| 49 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-6 | -1.562e+01 | 0.0000 | 116.0 | 2.93% | 383.9 | 1.76% | motif file (matrix) |
pdf |
| 50 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-6 | -1.550e+01 | 0.0000 | 431.0 | 10.88% | 1862.4 | 8.53% | motif file (matrix) |
pdf |
| 51 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-5 | -1.238e+01 | 0.0000 | 114.0 | 2.88% | 402.3 | 1.84% | motif file (matrix) |
pdf |
| 52 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-5 | -1.195e+01 | 0.0000 | 49.0 | 1.24% | 134.4 | 0.62% | motif file (matrix) |
pdf |
| 53 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-4 | -1.151e+01 | 0.0001 | 41.0 | 1.04% | 106.8 | 0.49% | motif file (matrix) |
pdf |
| 54 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-4 | -1.101e+01 | 0.0001 | 613.0 | 15.48% | 2878.1 | 13.18% | motif file (matrix) |
pdf |
| 55 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-4 | -1.019e+01 | 0.0003 | 185.0 | 4.67% | 754.7 | 3.46% | motif file (matrix) |
pdf |
| 56 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-4 | -9.894e+00 | 0.0003 | 482.0 | 12.17% | 2235.1 | 10.24% | motif file (matrix) |
pdf |
| 57 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-4 | -9.852e+00 | 0.0004 | 44.0 | 1.11% | 126.2 | 0.58% | motif file (matrix) |
pdf |
| 58 |  | PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer | 1e-4 | -9.734e+00 | 0.0004 | 427.0 | 10.78% | 1959.5 | 8.98% | motif file (matrix) |
pdf |
| 59 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-4 | -9.397e+00 | 0.0005 | 115.0 | 2.90% | 437.6 | 2.00% | motif file (matrix) |
pdf |
| 60 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-4 | -9.233e+00 | 0.0006 | 867.0 | 21.89% | 4257.9 | 19.50% | motif file (matrix) |
pdf |
| 61 |  | TATA-box/Drosophila-Promoters/Homer | 1e-3 | -9.196e+00 | 0.0006 | 184.0 | 4.65% | 764.7 | 3.50% | motif file (matrix) |
pdf |
| 62 |  | Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer | 1e-3 | -9.018e+00 | 0.0008 | 293.0 | 7.40% | 1301.3 | 5.96% | motif file (matrix) |
pdf |
| 63 |  | NRF(NRF)/Promoter/Homer | 1e-3 | -8.897e+00 | 0.0008 | 81.0 | 2.04% | 289.5 | 1.33% | motif file (matrix) |
pdf |
| 64 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-3 | -8.678e+00 | 0.0010 | 68.0 | 1.72% | 234.4 | 1.07% | motif file (matrix) |
pdf |
| 65 |  | Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer | 1e-3 | -8.656e+00 | 0.0010 | 181.0 | 4.57% | 758.3 | 3.47% | motif file (matrix) |
pdf |
| 66 |  | RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-3 | -8.588e+00 | 0.0011 | 435.0 | 10.98% | 2028.6 | 9.29% | motif file (matrix) |
pdf |
| 67 |  | GAGA-repeat/SacCer-Promoters/Homer | 1e-3 | -8.567e+00 | 0.0011 | 3062.0 | 77.30% | 16346.0 | 74.87% | motif file (matrix) |
pdf |
| 68 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.002e+00 | 0.0019 | 225.0 | 5.68% | 984.6 | 4.51% | motif file (matrix) |
pdf |
| 69 |  | ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer | 1e-3 | -7.984e+00 | 0.0019 | 47.0 | 1.19% | 150.1 | 0.69% | motif file (matrix) |
pdf |
| 70 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.793e+00 | 0.0023 | 711.0 | 17.95% | 3485.2 | 15.96% | motif file (matrix) |
pdf |
| 71 |  | GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer | 1e-3 | -7.555e+00 | 0.0029 | 40.0 | 1.01% | 124.6 | 0.57% | motif file (matrix) |
pdf |
| 72 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-3 | -7.527e+00 | 0.0029 | 642.0 | 16.21% | 3132.3 | 14.35% | motif file (matrix) |
pdf |
| 73 |  | GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer | 1e-3 | -7.205e+00 | 0.0039 | 97.0 | 2.45% | 380.7 | 1.74% | motif file (matrix) |
pdf |
| 74 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-3 | -7.041e+00 | 0.0046 | 36.0 | 0.91% | 111.5 | 0.51% | motif file (matrix) |
pdf |
| 75 |  | Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer | 1e-2 | -6.879e+00 | 0.0053 | 86.0 | 2.17% | 334.0 | 1.53% | motif file (matrix) |
pdf |
| 76 |  | PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer | 1e-2 | -6.673e+00 | 0.0064 | 29.0 | 0.73% | 85.9 | 0.39% | motif file (matrix) |
pdf |
| 77 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-2 | -6.635e+00 | 0.0066 | 71.0 | 1.79% | 267.2 | 1.22% | motif file (matrix) |
pdf |
| 78 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-2 | -6.600e+00 | 0.0067 | 56.0 | 1.41% | 200.6 | 0.92% | motif file (matrix) |
pdf |
| 79 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-2 | -6.600e+00 | 0.0067 | 56.0 | 1.41% | 200.6 | 0.92% | motif file (matrix) |
pdf |
| 80 |  | Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer | 1e-2 | -6.217e+00 | 0.0096 | 1425.0 | 35.98% | 7377.6 | 33.79% | motif file (matrix) |
pdf |
| 81 |  | X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-2 | -6.156e+00 | 0.0101 | 104.0 | 2.63% | 427.0 | 1.96% | motif file (matrix) |
pdf |
| 82 |  | E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.031e+00 | 0.0113 | 229.0 | 5.78% | 1045.9 | 4.79% | motif file (matrix) |
pdf |
| 83 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-2 | -4.977e+00 | 0.0322 | 412.0 | 10.40% | 2017.3 | 9.24% | motif file (matrix) |
pdf |
| 84 |  | NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer | 1e-2 | -4.878e+00 | 0.0351 | 56.0 | 1.41% | 218.5 | 1.00% | motif file (matrix) |
pdf |
| 85 |  | Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer | 1e-2 | -4.776e+00 | 0.0384 | 342.0 | 8.63% | 1659.4 | 7.60% | motif file (matrix) |
pdf |
| 86 |  | ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer | 1e-2 | -4.748e+00 | 0.0390 | 107.0 | 2.70% | 464.8 | 2.13% | motif file (matrix) |
pdf |