| 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-227 | -5.248e+02 | 0.0000 | 1488.0 | 34.04% | 3048.0 | 14.51% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-197 | -4.548e+02 | 0.0000 | 963.0 | 22.03% | 1585.3 | 7.55% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-71 | -1.651e+02 | 0.0000 | 2089.0 | 47.79% | 7259.4 | 34.57% | motif file (matrix) |
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| 4 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-53 | -1.231e+02 | 0.0000 | 570.0 | 13.04% | 1372.0 | 6.53% | motif file (matrix) |
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| 5 |  | SeqBias: CG-repeat | 1e-47 | -1.085e+02 | 0.0000 | 755.0 | 17.27% | 2117.7 | 10.08% | motif file (matrix) |
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| 6 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-45 | -1.048e+02 | 0.0000 | 1084.0 | 24.80% | 3435.1 | 16.36% | motif file (matrix) |
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| 7 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-45 | -1.037e+02 | 0.0000 | 657.0 | 15.03% | 1781.0 | 8.48% | motif file (matrix) |
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| 8 |  | SFP1/SacCer-Promoters/Homer | 1e-40 | -9.392e+01 | 0.0000 | 655.0 | 14.99% | 1830.8 | 8.72% | motif file (matrix) |
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| 9 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-40 | -9.242e+01 | 0.0000 | 401.0 | 9.17% | 933.1 | 4.44% | motif file (matrix) |
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| 10 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-38 | -8.860e+01 | 0.0000 | 417.0 | 9.54% | 1004.1 | 4.78% | motif file (matrix) |
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| 11 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-37 | -8.705e+01 | 0.0000 | 402.0 | 9.20% | 960.9 | 4.58% | motif file (matrix) |
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| 12 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-33 | -7.645e+01 | 0.0000 | 548.0 | 12.54% | 1538.7 | 7.33% | motif file (matrix) |
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| 13 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-32 | -7.470e+01 | 0.0000 | 469.0 | 10.73% | 1258.8 | 5.99% | motif file (matrix) |
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| 14 |  | TATA-box/SacCer-Promoters/Homer | 1e-32 | -7.375e+01 | 0.0000 | 2057.0 | 47.06% | 8028.6 | 38.23% | motif file (matrix) |
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| 15 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-29 | -6.906e+01 | 0.0000 | 588.0 | 13.45% | 1738.1 | 8.28% | motif file (matrix) |
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| 16 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-25 | -5.957e+01 | 0.0000 | 1326.0 | 30.34% | 4899.6 | 23.33% | motif file (matrix) |
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| 17 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-24 | -5.724e+01 | 0.0000 | 865.0 | 19.79% | 2950.0 | 14.05% | motif file (matrix) |
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| 18 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-24 | -5.603e+01 | 0.0000 | 968.0 | 22.15% | 3394.2 | 16.16% | motif file (matrix) |
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| 19 |  | E-box/Arabidopsis-Promoters/Homer | 1e-23 | -5.510e+01 | 0.0000 | 496.0 | 11.35% | 1485.8 | 7.08% | motif file (matrix) |
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| 20 |  | E-box(bHLH)/Promoter/Homer | 1e-21 | -5.059e+01 | 0.0000 | 126.0 | 2.88% | 221.4 | 1.05% | motif file (matrix) |
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| 21 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-21 | -5.006e+01 | 0.0000 | 408.0 | 9.33% | 1186.7 | 5.65% | motif file (matrix) |
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| 22 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-21 | -4.870e+01 | 0.0000 | 137.0 | 3.13% | 258.1 | 1.23% | motif file (matrix) |
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| 23 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-21 | -4.850e+01 | 0.0000 | 1073.0 | 24.55% | 3931.5 | 18.72% | motif file (matrix) |
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| 24 |  | TOD6?/SacCer-Promoters/Homer | 1e-20 | -4.645e+01 | 0.0000 | 338.0 | 7.73% | 949.3 | 4.52% | motif file (matrix) |
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| 25 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-18 | -4.287e+01 | 0.0000 | 774.0 | 17.71% | 2721.5 | 12.96% | motif file (matrix) |
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| 26 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-17 | -4.133e+01 | 0.0000 | 410.0 | 9.38% | 1258.1 | 5.99% | motif file (matrix) |
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| 27 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-16 | -3.859e+01 | 0.0000 | 787.0 | 18.01% | 2826.3 | 13.46% | motif file (matrix) |
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| 28 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-15 | -3.501e+01 | 0.0000 | 336.0 | 7.69% | 1022.4 | 4.87% | motif file (matrix) |
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| 29 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-14 | -3.300e+01 | 0.0000 | 765.0 | 17.50% | 2803.6 | 13.35% | motif file (matrix) |
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| 30 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-13 | -3.037e+01 | 0.0000 | 1389.0 | 31.78% | 5611.1 | 26.72% | motif file (matrix) |
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| 31 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-12 | -2.954e+01 | 0.0000 | 237.0 | 5.42% | 688.0 | 3.28% | motif file (matrix) |
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| 32 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-12 | -2.775e+01 | 0.0000 | 307.0 | 7.02% | 969.2 | 4.62% | motif file (matrix) |
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| 33 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-11 | -2.575e+01 | 0.0000 | 1006.0 | 23.02% | 3968.8 | 18.90% | motif file (matrix) |
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| 34 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-10 | -2.493e+01 | 0.0000 | 1637.0 | 37.45% | 6861.5 | 32.67% | motif file (matrix) |
pdf |
| 35 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-10 | -2.384e+01 | 0.0000 | 148.0 | 3.39% | 398.5 | 1.90% | motif file (matrix) |
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| 36 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-9 | -2.301e+01 | 0.0000 | 105.0 | 2.40% | 253.7 | 1.21% | motif file (matrix) |
pdf |
| 37 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-9 | -2.213e+01 | 0.0000 | 149.0 | 3.41% | 412.2 | 1.96% | motif file (matrix) |
pdf |
| 38 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-8 | -2.047e+01 | 0.0000 | 297.0 | 6.79% | 998.7 | 4.76% | motif file (matrix) |
pdf |
| 39 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-8 | -1.939e+01 | 0.0000 | 514.0 | 11.76% | 1918.5 | 9.14% | motif file (matrix) |
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| 40 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-8 | -1.912e+01 | 0.0000 | 507.0 | 11.60% | 1892.6 | 9.01% | motif file (matrix) |
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| 41 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-8 | -1.893e+01 | 0.0000 | 120.0 | 2.75% | 327.9 | 1.56% | motif file (matrix) |
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| 42 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-7 | -1.829e+01 | 0.0000 | 481.0 | 11.00% | 1793.8 | 8.54% | motif file (matrix) |
pdf |
| 43 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-7 | -1.763e+01 | 0.0000 | 774.0 | 17.71% | 3085.9 | 14.69% | motif file (matrix) |
pdf |
| 44 |  | SeqBias: TA-repeat | 1e-7 | -1.715e+01 | 0.0000 | 3885.0 | 88.88% | 18088.4 | 86.13% | motif file (matrix) |
pdf |
| 45 |  | SUT1?/SacCer-Promoters/Homer | 1e-7 | -1.710e+01 | 0.0000 | 2897.0 | 66.28% | 13094.7 | 62.35% | motif file (matrix) |
pdf |
| 46 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.549e+01 | 0.0000 | 58.0 | 1.33% | 131.7 | 0.63% | motif file (matrix) |
pdf |
| 47 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-6 | -1.501e+01 | 0.0000 | 263.0 | 6.02% | 920.5 | 4.38% | motif file (matrix) |
pdf |
| 48 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-6 | -1.410e+01 | 0.0000 | 420.0 | 9.61% | 1596.3 | 7.60% | motif file (matrix) |
pdf |
| 49 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-5 | -1.379e+01 | 0.0000 | 706.0 | 16.15% | 2860.0 | 13.62% | motif file (matrix) |
pdf |
| 50 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-5 | -1.213e+01 | 0.0000 | 1402.0 | 32.08% | 6093.3 | 29.02% | motif file (matrix) |
pdf |
| 51 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-5 | -1.184e+01 | 0.0001 | 45.0 | 1.03% | 104.1 | 0.50% | motif file (matrix) |
pdf |
| 52 |  | NRF(NRF)/Promoter/Homer | 1e-4 | -1.116e+01 | 0.0001 | 92.0 | 2.10% | 276.9 | 1.32% | motif file (matrix) |
pdf |
| 53 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-4 | -1.100e+01 | 0.0001 | 124.0 | 2.84% | 401.9 | 1.91% | motif file (matrix) |
pdf |
| 54 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-4 | -9.847e+00 | 0.0004 | 70.0 | 1.60% | 203.1 | 0.97% | motif file (matrix) |
pdf |
| 55 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-4 | -9.847e+00 | 0.0004 | 70.0 | 1.60% | 203.1 | 0.97% | motif file (matrix) |
pdf |
| 56 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-4 | -9.612e+00 | 0.0005 | 44.0 | 1.01% | 111.1 | 0.53% | motif file (matrix) |
pdf |
| 57 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-3 | -9.133e+00 | 0.0007 | 557.0 | 12.74% | 2299.2 | 10.95% | motif file (matrix) |
pdf |
| 58 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-3 | -8.813e+00 | 0.0010 | 124.0 | 2.84% | 423.5 | 2.02% | motif file (matrix) |
pdf |
| 59 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.329e+00 | 0.0016 | 983.0 | 22.49% | 4269.3 | 20.33% | motif file (matrix) |
pdf |
| 60 |  | CRE(bZIP)/Promoter/Homer | 1e-3 | -8.271e+00 | 0.0016 | 182.0 | 4.16% | 670.3 | 3.19% | motif file (matrix) |
pdf |
| 61 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-3 | -8.141e+00 | 0.0018 | 178.0 | 4.07% | 655.0 | 3.12% | motif file (matrix) |
pdf |
| 62 |  | TATA-box/Drosophila-Promoters/Homer | 1e-3 | -7.532e+00 | 0.0033 | 208.0 | 4.76% | 792.0 | 3.77% | motif file (matrix) |
pdf |
| 63 |  | GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer | 1e-3 | -7.395e+00 | 0.0038 | 40.0 | 0.92% | 109.6 | 0.52% | motif file (matrix) |
pdf |
| 64 |  | PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer | 1e-3 | -7.254e+00 | 0.0043 | 33.0 | 0.75% | 85.3 | 0.41% | motif file (matrix) |
pdf |
| 65 |  | Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer | 1e-3 | -7.156e+00 | 0.0046 | 207.0 | 4.74% | 794.2 | 3.78% | motif file (matrix) |
pdf |
| 66 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-3 | -6.969e+00 | 0.0055 | 111.0 | 2.54% | 391.6 | 1.86% | motif file (matrix) |
pdf |
| 67 |  | Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer | 1e-2 | -6.530e+00 | 0.0084 | 480.0 | 10.98% | 2020.1 | 9.62% | motif file (matrix) |
pdf |
| 68 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.286e+00 | 0.0106 | 200.0 | 4.58% | 779.3 | 3.71% | motif file (matrix) |
pdf |
| 69 |  | SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer | 1e-2 | -6.218e+00 | 0.0112 | 277.0 | 6.34% | 1118.4 | 5.33% | motif file (matrix) |
pdf |
| 70 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.160e+00 | 0.0117 | 802.0 | 18.35% | 3508.2 | 16.71% | motif file (matrix) |
pdf |
| 71 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-2 | -5.802e+00 | 0.0165 | 174.0 | 3.98% | 675.9 | 3.22% | motif file (matrix) |
pdf |
| 72 |  | NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer | 1e-2 | -5.281e+00 | 0.0274 | 60.0 | 1.37% | 202.3 | 0.96% | motif file (matrix) |
pdf |
| 73 |  | Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer | 1e-2 | -5.264e+00 | 0.0274 | 1618.0 | 37.02% | 7382.0 | 35.15% | motif file (matrix) |
pdf |
| 74 |  | PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.244e+00 | 0.0276 | 71.0 | 1.62% | 247.9 | 1.18% | motif file (matrix) |
pdf |
| 75 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.146e+00 | 0.0300 | 260.0 | 5.95% | 1067.7 | 5.08% | motif file (matrix) |
pdf |
| 76 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-2 | -4.909e+00 | 0.0376 | 72.0 | 1.65% | 255.9 | 1.22% | motif file (matrix) |
pdf |
| 77 |  | Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer | 1e-2 | -4.764e+00 | 0.0429 | 378.0 | 8.65% | 1609.3 | 7.66% | motif file (matrix) |
pdf |
| 78 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-2 | -4.697e+00 | 0.0452 | 40.0 | 0.92% | 128.1 | 0.61% | motif file (matrix) |
pdf |
| 79 |  | RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-2 | -4.672e+00 | 0.0458 | 470.0 | 10.75% | 2032.6 | 9.68% | motif file (matrix) |
pdf |