| 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-190 | -4.396e+02 | 0.0000 | 1323.0 | 35.36% | 3096.3 | 15.64% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-155 | -3.577e+02 | 0.0000 | 800.0 | 21.38% | 1501.1 | 7.58% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-59 | -1.364e+02 | 0.0000 | 1617.0 | 43.22% | 6052.3 | 30.56% | motif file (matrix) |
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| 4 |  | SFP1/SacCer-Promoters/Homer | 1e-48 | -1.122e+02 | 0.0000 | 559.0 | 14.94% | 1534.9 | 7.75% | motif file (matrix) |
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| 5 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-48 | -1.111e+02 | 0.0000 | 542.0 | 14.49% | 1474.1 | 7.44% | motif file (matrix) |
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| 6 |  | SeqBias: CG-repeat | 1e-43 | -1.004e+02 | 0.0000 | 746.0 | 19.94% | 2366.3 | 11.95% | motif file (matrix) |
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| 7 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-37 | -8.633e+01 | 0.0000 | 368.0 | 9.84% | 939.2 | 4.74% | motif file (matrix) |
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| 8 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-36 | -8.395e+01 | 0.0000 | 525.0 | 14.03% | 1560.4 | 7.88% | motif file (matrix) |
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| 9 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-35 | -8.104e+01 | 0.0000 | 963.0 | 25.74% | 3479.9 | 17.57% | motif file (matrix) |
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| 10 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-33 | -7.751e+01 | 0.0000 | 388.0 | 10.37% | 1058.7 | 5.35% | motif file (matrix) |
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| 11 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-33 | -7.628e+01 | 0.0000 | 604.0 | 16.15% | 1938.9 | 9.79% | motif file (matrix) |
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| 12 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-29 | -6.895e+01 | 0.0000 | 352.0 | 9.41% | 966.3 | 4.88% | motif file (matrix) |
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| 13 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-29 | -6.748e+01 | 0.0000 | 437.0 | 11.68% | 1309.6 | 6.61% | motif file (matrix) |
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| 14 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-27 | -6.358e+01 | 0.0000 | 549.0 | 14.68% | 1802.0 | 9.10% | motif file (matrix) |
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| 15 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-25 | -5.929e+01 | 0.0000 | 402.0 | 10.75% | 1221.4 | 6.17% | motif file (matrix) |
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| 16 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-25 | -5.895e+01 | 0.0000 | 1258.0 | 33.63% | 5118.2 | 25.85% | motif file (matrix) |
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| 17 |  | E-box/Arabidopsis-Promoters/Homer | 1e-23 | -5.409e+01 | 0.0000 | 485.0 | 12.96% | 1604.1 | 8.10% | motif file (matrix) |
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| 18 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-22 | -5.072e+01 | 0.0000 | 793.0 | 21.20% | 3008.6 | 15.19% | motif file (matrix) |
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| 19 |  | TOD6?/SacCer-Promoters/Homer | 1e-20 | -4.709e+01 | 0.0000 | 309.0 | 8.26% | 927.3 | 4.68% | motif file (matrix) |
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| 20 |  | E-box(bHLH)/Promoter/Homer | 1e-20 | -4.633e+01 | 0.0000 | 119.0 | 3.18% | 235.2 | 1.19% | motif file (matrix) |
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| 21 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-19 | -4.577e+01 | 0.0000 | 864.0 | 23.10% | 3398.2 | 17.16% | motif file (matrix) |
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| 22 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-19 | -4.559e+01 | 0.0000 | 990.0 | 26.46% | 3999.1 | 20.19% | motif file (matrix) |
pdf |
| 23 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-19 | -4.512e+01 | 0.0000 | 749.0 | 20.02% | 2869.3 | 14.49% | motif file (matrix) |
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| 24 |  | TATA-box/SacCer-Promoters/Homer | 1e-19 | -4.440e+01 | 0.0000 | 1507.0 | 40.28% | 6568.8 | 33.17% | motif file (matrix) |
pdf |
| 25 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-16 | -3.698e+01 | 0.0000 | 124.0 | 3.31% | 284.8 | 1.44% | motif file (matrix) |
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| 26 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-15 | -3.674e+01 | 0.0000 | 370.0 | 9.89% | 1259.9 | 6.36% | motif file (matrix) |
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| 27 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-15 | -3.495e+01 | 0.0000 | 705.0 | 18.85% | 2791.6 | 14.10% | motif file (matrix) |
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| 28 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-14 | -3.357e+01 | 0.0000 | 945.0 | 25.26% | 3957.8 | 19.99% | motif file (matrix) |
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| 29 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-12 | -2.919e+01 | 0.0000 | 1260.0 | 33.68% | 5592.7 | 28.24% | motif file (matrix) |
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| 30 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-11 | -2.566e+01 | 0.0000 | 507.0 | 13.55% | 1993.3 | 10.07% | motif file (matrix) |
pdf |
| 31 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-10 | -2.506e+01 | 0.0000 | 324.0 | 8.66% | 1171.6 | 5.92% | motif file (matrix) |
pdf |
| 32 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-10 | -2.467e+01 | 0.0000 | 684.0 | 18.28% | 2842.9 | 14.36% | motif file (matrix) |
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| 33 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-10 | -2.455e+01 | 0.0000 | 156.0 | 4.17% | 466.3 | 2.35% | motif file (matrix) |
pdf |
| 34 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-9 | -2.281e+01 | 0.0000 | 251.0 | 6.71% | 875.3 | 4.42% | motif file (matrix) |
pdf |
| 35 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-9 | -2.199e+01 | 0.0000 | 276.0 | 7.38% | 992.6 | 5.01% | motif file (matrix) |
pdf |
| 36 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-8 | -1.944e+01 | 0.0000 | 224.0 | 5.99% | 791.9 | 4.00% | motif file (matrix) |
pdf |
| 37 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-7 | -1.831e+01 | 0.0000 | 143.0 | 3.82% | 459.0 | 2.32% | motif file (matrix) |
pdf |
| 38 |  | SUT1?/SacCer-Promoters/Homer | 1e-7 | -1.800e+01 | 0.0000 | 2644.0 | 70.68% | 13155.5 | 66.43% | motif file (matrix) |
pdf |
| 39 |  | SeqBias: TA-repeat | 1e-7 | -1.796e+01 | 0.0000 | 3154.0 | 84.31% | 16004.6 | 80.82% | motif file (matrix) |
pdf |
| 40 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-7 | -1.757e+01 | 0.0000 | 649.0 | 17.35% | 2799.3 | 14.14% | motif file (matrix) |
pdf |
| 41 |  | CRE(bZIP)/Promoter/Homer | 1e-7 | -1.743e+01 | 0.0000 | 194.0 | 5.19% | 681.4 | 3.44% | motif file (matrix) |
pdf |
| 42 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-7 | -1.703e+01 | 0.0000 | 429.0 | 11.47% | 1755.5 | 8.87% | motif file (matrix) |
pdf |
| 43 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-6 | -1.605e+01 | 0.0000 | 1432.0 | 38.28% | 6774.3 | 34.21% | motif file (matrix) |
pdf |
| 44 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.597e+01 | 0.0000 | 271.0 | 7.24% | 1039.9 | 5.25% | motif file (matrix) |
pdf |
| 45 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-6 | -1.548e+01 | 0.0000 | 633.0 | 16.92% | 2763.4 | 13.95% | motif file (matrix) |
pdf |
| 46 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-6 | -1.523e+01 | 0.0000 | 461.0 | 12.32% | 1937.5 | 9.78% | motif file (matrix) |
pdf |
| 47 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-6 | -1.518e+01 | 0.0000 | 416.0 | 11.12% | 1724.1 | 8.71% | motif file (matrix) |
pdf |
| 48 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-5 | -1.375e+01 | 0.0000 | 211.0 | 5.64% | 796.2 | 4.02% | motif file (matrix) |
pdf |
| 49 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-5 | -1.340e+01 | 0.0000 | 112.0 | 2.99% | 369.2 | 1.86% | motif file (matrix) |
pdf |
| 50 |  | REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer | 1e-5 | -1.328e+01 | 0.0000 | 5.0 | 0.13% | 1.3 | 0.01% | motif file (matrix) |
pdf |
| 51 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-5 | -1.254e+01 | 0.0000 | 1208.0 | 32.29% | 5726.7 | 28.92% | motif file (matrix) |
pdf |
| 52 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-5 | -1.217e+01 | 0.0000 | 166.0 | 4.44% | 614.5 | 3.10% | motif file (matrix) |
pdf |
| 53 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-5 | -1.183e+01 | 0.0001 | 498.0 | 13.31% | 2182.2 | 11.02% | motif file (matrix) |
pdf |
| 54 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-5 | -1.178e+01 | 0.0001 | 77.0 | 2.06% | 238.7 | 1.21% | motif file (matrix) |
pdf |
| 55 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-4 | -1.151e+01 | 0.0001 | 101.0 | 2.70% | 339.0 | 1.71% | motif file (matrix) |
pdf |
| 56 |  | Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer | 1e-4 | -1.041e+01 | 0.0002 | 380.0 | 10.16% | 1640.3 | 8.28% | motif file (matrix) |
pdf |
| 57 |  | NRF(NRF)/Promoter/Homer | 1e-4 | -1.034e+01 | 0.0002 | 95.0 | 2.54% | 324.8 | 1.64% | motif file (matrix) |
pdf |
| 58 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-4 | -1.014e+01 | 0.0003 | 42.0 | 1.12% | 112.6 | 0.57% | motif file (matrix) |
pdf |
| 59 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-4 | -9.997e+00 | 0.0003 | 122.0 | 3.26% | 444.6 | 2.25% | motif file (matrix) |
pdf |
| 60 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-4 | -9.993e+00 | 0.0003 | 111.0 | 2.97% | 396.1 | 2.00% | motif file (matrix) |
pdf |
| 61 |  | Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer | 1e-4 | -9.868e+00 | 0.0003 | 192.0 | 5.13% | 761.4 | 3.84% | motif file (matrix) |
pdf |
| 62 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-4 | -9.639e+00 | 0.0004 | 432.0 | 11.55% | 1909.5 | 9.64% | motif file (matrix) |
pdf |
| 63 |  | TATA-box/Drosophila-Promoters/Homer | 1e-4 | -9.364e+00 | 0.0005 | 166.0 | 4.44% | 649.7 | 3.28% | motif file (matrix) |
pdf |
| 64 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-3 | -9.136e+00 | 0.0007 | 176.0 | 4.70% | 698.5 | 3.53% | motif file (matrix) |
pdf |
| 65 |  | RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-3 | -9.134e+00 | 0.0007 | 461.0 | 12.32% | 2063.1 | 10.42% | motif file (matrix) |
pdf |
| 66 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-3 | -8.930e+00 | 0.0008 | 176.0 | 4.70% | 701.4 | 3.54% | motif file (matrix) |
pdf |
| 67 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-3 | -8.516e+00 | 0.0012 | 122.0 | 3.26% | 461.2 | 2.33% | motif file (matrix) |
pdf |
| 68 |  | Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer | 1e-3 | -7.640e+00 | 0.0027 | 1442.0 | 38.55% | 7115.2 | 35.93% | motif file (matrix) |
pdf |
| 69 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-3 | -7.566e+00 | 0.0029 | 522.0 | 13.95% | 2407.7 | 12.16% | motif file (matrix) |
pdf |
| 70 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.467e+00 | 0.0032 | 885.0 | 23.66% | 4245.0 | 21.44% | motif file (matrix) |
pdf |
| 71 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.302e+00 | 0.0037 | 236.0 | 6.31% | 1012.0 | 5.11% | motif file (matrix) |
pdf |
| 72 |  | GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer | 1e-3 | -7.259e+00 | 0.0038 | 41.0 | 1.10% | 125.5 | 0.63% | motif file (matrix) |
pdf |
| 73 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.245e+00 | 0.0038 | 89.0 | 2.38% | 329.2 | 1.66% | motif file (matrix) |
pdf |
| 74 |  | Sp1(Zf)/Promoter/Homer | 1e-3 | -7.008e+00 | 0.0047 | 46.0 | 1.23% | 147.5 | 0.74% | motif file (matrix) |
pdf |
| 75 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-3 | -6.973e+00 | 0.0048 | 721.0 | 19.27% | 3428.7 | 17.31% | motif file (matrix) |
pdf |
| 76 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-2 | -6.180e+00 | 0.0105 | 43.0 | 1.15% | 141.0 | 0.71% | motif file (matrix) |
pdf |
| 77 |  | PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer | 1e-2 | -5.782e+00 | 0.0155 | 28.0 | 0.75% | 83.4 | 0.42% | motif file (matrix) |
pdf |
| 78 |  | PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer | 1e-2 | -5.492e+00 | 0.0204 | 434.0 | 11.60% | 2031.7 | 10.26% | motif file (matrix) |
pdf |
| 79 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-2 | -5.425e+00 | 0.0216 | 73.0 | 1.95% | 279.5 | 1.41% | motif file (matrix) |
pdf |
| 80 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-2 | -5.381e+00 | 0.0223 | 451.0 | 12.06% | 2120.1 | 10.71% | motif file (matrix) |
pdf |
| 81 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.063e+00 | 0.0302 | 37.0 | 0.99% | 125.6 | 0.63% | motif file (matrix) |
pdf |
| 82 |  | SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer | 1e-2 | -5.055e+00 | 0.0302 | 236.0 | 6.31% | 1061.8 | 5.36% | motif file (matrix) |
pdf |
| 83 |  | Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer | 1e-2 | -4.798e+00 | 0.0384 | 1136.0 | 30.37% | 5659.0 | 28.58% | motif file (matrix) |
pdf |
| 84 |  | MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer | 1e-2 | -4.756e+00 | 0.0396 | 99.0 | 2.65% | 408.1 | 2.06% | motif file (matrix) |
pdf |
| 85 |  | ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer | 1e-2 | -4.705e+00 | 0.0412 | 112.0 | 2.99% | 470.5 | 2.38% | motif file (matrix) |
pdf |