| 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 | -5.229e+02 | 0.0000 | 1484.0 | 35.21% | 3153.9 | 15.09% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-174 | -4.017e+02 | 0.0000 | 921.0 | 21.85% | 1646.3 | 7.88% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-76 | -1.761e+02 | 0.0000 | 1986.0 | 47.12% | 6954.6 | 33.28% | motif file (matrix) |
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| 4 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-59 | -1.378e+02 | 0.0000 | 580.0 | 13.76% | 1387.0 | 6.64% | motif file (matrix) |
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| 5 |  | SFP1/SacCer-Promoters/Homer | 1e-48 | -1.117e+02 | 0.0000 | 646.0 | 15.33% | 1753.6 | 8.39% | motif file (matrix) |
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| 6 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-46 | -1.077e+02 | 0.0000 | 428.0 | 10.15% | 991.6 | 4.74% | motif file (matrix) |
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| 7 |  | SeqBias: CG-repeat | 1e-46 | -1.060e+02 | 0.0000 | 762.0 | 18.08% | 2231.7 | 10.68% | motif file (matrix) |
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| 8 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-43 | -1.000e+02 | 0.0000 | 406.0 | 9.63% | 948.8 | 4.54% | motif file (matrix) |
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| 9 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-42 | -9.746e+01 | 0.0000 | 638.0 | 15.14% | 1804.3 | 8.63% | motif file (matrix) |
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| 10 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-40 | -9.306e+01 | 0.0000 | 547.0 | 12.98% | 1486.6 | 7.11% | motif file (matrix) |
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| 11 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-39 | -9.004e+01 | 0.0000 | 1045.0 | 24.79% | 3509.3 | 16.79% | motif file (matrix) |
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| 12 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-35 | -8.160e+01 | 0.0000 | 467.0 | 11.08% | 1253.1 | 6.00% | motif file (matrix) |
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| 13 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-32 | -7.499e+01 | 0.0000 | 373.0 | 8.85% | 947.2 | 4.53% | motif file (matrix) |
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| 14 |  | E-box/Arabidopsis-Promoters/Homer | 1e-29 | -6.891e+01 | 0.0000 | 506.0 | 12.00% | 1476.9 | 7.07% | motif file (matrix) |
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| 15 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-29 | -6.803e+01 | 0.0000 | 418.0 | 9.92% | 1148.4 | 5.50% | motif file (matrix) |
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| 16 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-29 | -6.705e+01 | 0.0000 | 566.0 | 13.43% | 1723.7 | 8.25% | motif file (matrix) |
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| 17 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-28 | -6.646e+01 | 0.0000 | 813.0 | 19.29% | 2738.0 | 13.10% | motif file (matrix) |
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| 18 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-25 | -5.955e+01 | 0.0000 | 147.0 | 3.49% | 265.0 | 1.27% | motif file (matrix) |
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| 19 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-23 | -5.492e+01 | 0.0000 | 827.0 | 19.62% | 2908.7 | 13.92% | motif file (matrix) |
pdf |
| 20 |  | E-box(bHLH)/Promoter/Homer | 1e-22 | -5.265e+01 | 0.0000 | 130.0 | 3.08% | 234.2 | 1.12% | motif file (matrix) |
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| 21 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-22 | -5.226e+01 | 0.0000 | 913.0 | 21.66% | 3309.2 | 15.83% | motif file (matrix) |
pdf |
| 22 |  | TOD6?/SacCer-Promoters/Homer | 1e-22 | -5.220e+01 | 0.0000 | 333.0 | 7.90% | 925.3 | 4.43% | motif file (matrix) |
pdf |
| 23 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-21 | -5.020e+01 | 0.0000 | 1271.0 | 30.15% | 4936.7 | 23.62% | motif file (matrix) |
pdf |
| 24 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-21 | -4.873e+01 | 0.0000 | 412.0 | 9.77% | 1250.7 | 5.98% | motif file (matrix) |
pdf |
| 25 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-20 | -4.756e+01 | 0.0000 | 1045.0 | 24.79% | 3949.9 | 18.90% | motif file (matrix) |
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| 26 |  | TATA-box/SacCer-Promoters/Homer | 1e-20 | -4.723e+01 | 0.0000 | 1840.0 | 43.65% | 7648.8 | 36.60% | motif file (matrix) |
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| 27 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-17 | -3.983e+01 | 0.0000 | 545.0 | 12.93% | 1866.1 | 8.93% | motif file (matrix) |
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| 28 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-16 | -3.859e+01 | 0.0000 | 760.0 | 18.03% | 2801.3 | 13.40% | motif file (matrix) |
pdf |
| 29 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-14 | -3.449e+01 | 0.0000 | 463.0 | 10.98% | 1577.5 | 7.55% | motif file (matrix) |
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| 30 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-13 | -3.154e+01 | 0.0000 | 1322.0 | 31.36% | 5462.6 | 26.14% | motif file (matrix) |
pdf |
| 31 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-13 | -3.080e+01 | 0.0000 | 239.0 | 5.67% | 708.5 | 3.39% | motif file (matrix) |
pdf |
| 32 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-13 | -3.030e+01 | 0.0000 | 135.0 | 3.20% | 330.9 | 1.58% | motif file (matrix) |
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| 33 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-12 | -2.981e+01 | 0.0000 | 1008.0 | 23.91% | 4038.6 | 19.32% | motif file (matrix) |
pdf |
| 34 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-12 | -2.902e+01 | 0.0000 | 159.0 | 3.77% | 421.6 | 2.02% | motif file (matrix) |
pdf |
| 35 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-12 | -2.883e+01 | 0.0000 | 281.0 | 6.67% | 887.7 | 4.25% | motif file (matrix) |
pdf |
| 36 |  | SUT1?/SacCer-Promoters/Homer | 1e-12 | -2.807e+01 | 0.0000 | 2869.0 | 68.07% | 13130.3 | 62.83% | motif file (matrix) |
pdf |
| 37 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-12 | -2.769e+01 | 0.0000 | 325.0 | 7.71% | 1074.2 | 5.14% | motif file (matrix) |
pdf |
| 38 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-12 | -2.766e+01 | 0.0000 | 497.0 | 11.79% | 1795.1 | 8.59% | motif file (matrix) |
pdf |
| 39 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-10 | -2.384e+01 | 0.0000 | 297.0 | 7.05% | 996.6 | 4.77% | motif file (matrix) |
pdf |
| 40 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-9 | -2.287e+01 | 0.0000 | 151.0 | 3.58% | 428.6 | 2.05% | motif file (matrix) |
pdf |
| 41 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-8 | -2.071e+01 | 0.0000 | 109.0 | 2.59% | 287.6 | 1.38% | motif file (matrix) |
pdf |
| 42 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-7 | -1.834e+01 | 0.0000 | 706.0 | 16.75% | 2861.1 | 13.69% | motif file (matrix) |
pdf |
| 43 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-7 | -1.802e+01 | 0.0000 | 130.0 | 3.08% | 381.9 | 1.83% | motif file (matrix) |
pdf |
| 44 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-7 | -1.747e+01 | 0.0000 | 57.0 | 1.35% | 124.5 | 0.60% | motif file (matrix) |
pdf |
| 45 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-7 | -1.733e+01 | 0.0000 | 280.0 | 6.64% | 994.6 | 4.76% | motif file (matrix) |
pdf |
| 46 |  | NRF(NRF)/Promoter/Homer | 1e-7 | -1.664e+01 | 0.0000 | 99.0 | 2.35% | 274.7 | 1.31% | motif file (matrix) |
pdf |
| 47 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-7 | -1.634e+01 | 0.0000 | 566.0 | 13.43% | 2263.1 | 10.83% | motif file (matrix) |
pdf |
| 48 |  | PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer | 1e-6 | -1.574e+01 | 0.0000 | 41.0 | 0.97% | 80.4 | 0.38% | motif file (matrix) |
pdf |
| 49 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-6 | -1.493e+01 | 0.0000 | 680.0 | 16.13% | 2809.6 | 13.44% | motif file (matrix) |
pdf |
| 50 |  | SeqBias: TA-repeat | 1e-6 | -1.452e+01 | 0.0000 | 3678.0 | 87.26% | 17678.6 | 84.59% | motif file (matrix) |
pdf |
| 51 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-5 | -1.368e+01 | 0.0000 | 190.0 | 4.51% | 658.9 | 3.15% | motif file (matrix) |
pdf |
| 52 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-5 | -1.352e+01 | 0.0000 | 1341.0 | 31.81% | 5957.8 | 28.51% | motif file (matrix) |
pdf |
| 53 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-5 | -1.241e+01 | 0.0000 | 125.0 | 2.97% | 405.6 | 1.94% | motif file (matrix) |
pdf |
| 54 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-5 | -1.164e+01 | 0.0001 | 435.0 | 10.32% | 1759.6 | 8.42% | motif file (matrix) |
pdf |
| 55 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-5 | -1.158e+01 | 0.0001 | 1517.0 | 35.99% | 6867.1 | 32.86% | motif file (matrix) |
pdf |
| 56 |  | CRE(bZIP)/Promoter/Homer | 1e-4 | -1.050e+01 | 0.0002 | 196.0 | 4.65% | 721.2 | 3.45% | motif file (matrix) |
pdf |
| 57 |  | TATA-box/Drosophila-Promoters/Homer | 1e-4 | -1.006e+01 | 0.0003 | 203.0 | 4.82% | 757.4 | 3.62% | motif file (matrix) |
pdf |
| 58 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-4 | -9.710e+00 | 0.0004 | 590.0 | 14.00% | 2512.7 | 12.02% | motif file (matrix) |
pdf |
| 59 |  | Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer | 1e-4 | -9.308e+00 | 0.0006 | 201.0 | 4.77% | 759.5 | 3.63% | motif file (matrix) |
pdf |
| 60 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-4 | -9.287e+00 | 0.0006 | 188.0 | 4.46% | 703.8 | 3.37% | motif file (matrix) |
pdf |
| 61 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-3 | -8.688e+00 | 0.0011 | 124.0 | 2.94% | 438.6 | 2.10% | motif file (matrix) |
pdf |
| 62 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-3 | -8.374e+00 | 0.0014 | 66.0 | 1.57% | 205.2 | 0.98% | motif file (matrix) |
pdf |
| 63 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-3 | -8.374e+00 | 0.0014 | 66.0 | 1.57% | 205.2 | 0.98% | motif file (matrix) |
pdf |
| 64 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-3 | -8.152e+00 | 0.0017 | 192.0 | 4.56% | 737.2 | 3.53% | motif file (matrix) |
pdf |
| 65 |  | GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer | 1e-3 | -8.043e+00 | 0.0019 | 42.0 | 1.00% | 116.7 | 0.56% | motif file (matrix) |
pdf |
| 66 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-3 | -8.021e+00 | 0.0019 | 678.0 | 16.09% | 2970.9 | 14.22% | motif file (matrix) |
pdf |
| 67 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.900e+00 | 0.0021 | 95.0 | 2.25% | 326.4 | 1.56% | motif file (matrix) |
pdf |
| 68 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-3 | -7.824e+00 | 0.0023 | 482.0 | 11.44% | 2059.4 | 9.85% | motif file (matrix) |
pdf |
| 69 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.333e+00 | 0.0037 | 778.0 | 18.46% | 3465.6 | 16.58% | motif file (matrix) |
pdf |
| 70 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-3 | -6.921e+00 | 0.0055 | 42.0 | 1.00% | 123.7 | 0.59% | motif file (matrix) |
pdf |
| 71 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.608e+00 | 0.0074 | 945.0 | 22.42% | 4289.4 | 20.52% | motif file (matrix) |
pdf |
| 72 |  | RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-2 | -6.432e+00 | 0.0086 | 480.0 | 11.39% | 2088.3 | 9.99% | motif file (matrix) |
pdf |
| 73 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-2 | -6.398e+00 | 0.0088 | 515.0 | 12.22% | 2254.0 | 10.79% | motif file (matrix) |
pdf |
| 74 |  | Sp1(Zf)/Promoter/Homer | 1e-2 | -6.238e+00 | 0.0102 | 52.0 | 1.23% | 167.2 | 0.80% | motif file (matrix) |
pdf |
| 75 |  | Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer | 1e-2 | -6.051e+00 | 0.0122 | 368.0 | 8.73% | 1577.1 | 7.55% | motif file (matrix) |
pdf |
| 76 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-2 | -6.018e+00 | 0.0124 | 75.0 | 1.78% | 263.1 | 1.26% | motif file (matrix) |
pdf |
| 77 |  | Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.967e+00 | 0.0129 | 34.0 | 0.81% | 99.3 | 0.48% | motif file (matrix) |
pdf |
| 78 |  | ETS(ETS)/Promoter/Homer | 1e-2 | -5.532e+00 | 0.0196 | 313.0 | 7.43% | 1336.1 | 6.39% | motif file (matrix) |
pdf |
| 79 |  | Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer | 1e-2 | -5.195e+00 | 0.0272 | 191.0 | 4.53% | 785.9 | 3.76% | motif file (matrix) |
pdf |
| 80 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.192e+00 | 0.0272 | 38.0 | 0.90% | 120.5 | 0.58% | motif file (matrix) |
pdf |
| 81 |  | AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.172e+00 | 0.0272 | 148.0 | 3.51% | 592.3 | 2.83% | motif file (matrix) |
pdf |
| 82 |  | GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer | 1e-2 | -5.096e+00 | 0.0289 | 99.0 | 2.35% | 377.5 | 1.81% | motif file (matrix) |
pdf |
| 83 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-2 | -4.886e+00 | 0.0352 | 81.0 | 1.92% | 302.2 | 1.45% | motif file (matrix) |
pdf |
| 84 |  | PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -4.863e+00 | 0.0356 | 73.0 | 1.73% | 268.5 | 1.28% | motif file (matrix) |
pdf |
| 85 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-2 | -4.705e+00 | 0.0412 | 39.0 | 0.93% | 128.2 | 0.61% | motif file (matrix) |
pdf |