| 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-200 | -4.623e+02 | 0.0000 | 1369.0 | 35.29% | 3118.5 | 15.47% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-156 | -3.605e+02 | 0.0000 | 835.0 | 21.53% | 1573.4 | 7.81% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-59 | -1.378e+02 | 0.0000 | 1727.0 | 44.52% | 6433.2 | 31.91% | motif file (matrix) |
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| 4 |  | SeqBias: CG-repeat | 1e-52 | -1.216e+02 | 0.0000 | 752.0 | 19.39% | 2209.0 | 10.96% | motif file (matrix) |
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| 5 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-49 | -1.138e+02 | 0.0000 | 544.0 | 14.02% | 1439.8 | 7.14% | motif file (matrix) |
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| 6 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-39 | -9.184e+01 | 0.0000 | 410.0 | 10.57% | 1048.7 | 5.20% | motif file (matrix) |
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| 7 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-38 | -8.867e+01 | 0.0000 | 995.0 | 25.65% | 3483.8 | 17.28% | motif file (matrix) |
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| 8 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-37 | -8.688e+01 | 0.0000 | 524.0 | 13.51% | 1508.7 | 7.48% | motif file (matrix) |
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| 9 |  | SFP1/SacCer-Promoters/Homer | 1e-36 | -8.334e+01 | 0.0000 | 535.0 | 13.79% | 1574.0 | 7.81% | motif file (matrix) |
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| 10 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-36 | -8.300e+01 | 0.0000 | 378.0 | 9.74% | 973.9 | 4.83% | motif file (matrix) |
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| 11 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-36 | -8.297e+01 | 0.0000 | 621.0 | 16.01% | 1923.3 | 9.54% | motif file (matrix) |
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| 12 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-33 | -7.818e+01 | 0.0000 | 452.0 | 11.65% | 1278.9 | 6.34% | motif file (matrix) |
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| 13 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-30 | -7.133e+01 | 0.0000 | 356.0 | 9.18% | 950.2 | 4.71% | motif file (matrix) |
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| 14 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-27 | -6.352e+01 | 0.0000 | 552.0 | 14.23% | 1779.3 | 8.83% | motif file (matrix) |
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| 15 |  | E-box/Arabidopsis-Promoters/Homer | 1e-27 | -6.237e+01 | 0.0000 | 496.0 | 12.79% | 1556.0 | 7.72% | motif file (matrix) |
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| 16 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-26 | -6.102e+01 | 0.0000 | 414.0 | 10.67% | 1234.6 | 6.12% | motif file (matrix) |
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| 17 |  | E-box(bHLH)/Promoter/Homer | 1e-24 | -5.576e+01 | 0.0000 | 124.0 | 3.20% | 219.9 | 1.09% | motif file (matrix) |
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| 18 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-24 | -5.533e+01 | 0.0000 | 745.0 | 19.21% | 2685.1 | 13.32% | motif file (matrix) |
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| 19 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-22 | -5.187e+01 | 0.0000 | 1239.0 | 31.94% | 5017.1 | 24.89% | motif file (matrix) |
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| 20 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-21 | -5.036e+01 | 0.0000 | 806.0 | 20.78% | 3012.0 | 14.94% | motif file (matrix) |
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| 21 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-20 | -4.710e+01 | 0.0000 | 384.0 | 9.90% | 1210.7 | 6.01% | motif file (matrix) |
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| 22 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-20 | -4.619e+01 | 0.0000 | 994.0 | 25.63% | 3931.4 | 19.50% | motif file (matrix) |
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| 23 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-18 | -4.210e+01 | 0.0000 | 875.0 | 22.56% | 3429.6 | 17.01% | motif file (matrix) |
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| 24 |  | TOD6?/SacCer-Promoters/Homer | 1e-18 | -4.209e+01 | 0.0000 | 301.0 | 7.76% | 911.8 | 4.52% | motif file (matrix) |
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| 25 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-17 | -4.110e+01 | 0.0000 | 742.0 | 19.13% | 2829.0 | 14.03% | motif file (matrix) |
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| 26 |  | TATA-box/SacCer-Promoters/Homer | 1e-15 | -3.673e+01 | 0.0000 | 1593.0 | 41.07% | 6995.8 | 34.71% | motif file (matrix) |
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| 27 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-14 | -3.351e+01 | 0.0000 | 120.0 | 3.09% | 280.0 | 1.39% | motif file (matrix) |
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| 28 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-13 | -3.176e+01 | 0.0000 | 516.0 | 13.30% | 1920.1 | 9.53% | motif file (matrix) |
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| 29 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-13 | -3.046e+01 | 0.0000 | 157.0 | 4.05% | 426.6 | 2.12% | motif file (matrix) |
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| 30 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-13 | -2.993e+01 | 0.0000 | 952.0 | 24.54% | 3972.6 | 19.71% | motif file (matrix) |
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| 31 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-11 | -2.755e+01 | 0.0000 | 1276.0 | 32.90% | 5593.7 | 27.75% | motif file (matrix) |
pdf |
| 32 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-9 | -2.270e+01 | 0.0000 | 318.0 | 8.20% | 1148.8 | 5.70% | motif file (matrix) |
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| 33 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-9 | -2.264e+01 | 0.0000 | 691.0 | 17.81% | 2854.5 | 14.16% | motif file (matrix) |
pdf |
| 34 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-9 | -2.152e+01 | 0.0000 | 437.0 | 11.27% | 1693.7 | 8.40% | motif file (matrix) |
pdf |
| 35 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-9 | -2.136e+01 | 0.0000 | 491.0 | 12.66% | 1942.3 | 9.64% | motif file (matrix) |
pdf |
| 36 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-9 | -2.116e+01 | 0.0000 | 219.0 | 5.65% | 739.8 | 3.67% | motif file (matrix) |
pdf |
| 37 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-8 | -2.023e+01 | 0.0000 | 279.0 | 7.19% | 1005.4 | 4.99% | motif file (matrix) |
pdf |
| 38 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-8 | -1.907e+01 | 0.0000 | 260.0 | 6.70% | 935.7 | 4.64% | motif file (matrix) |
pdf |
| 39 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-8 | -1.874e+01 | 0.0000 | 550.0 | 14.18% | 2257.0 | 11.20% | motif file (matrix) |
pdf |
| 40 |  | SUT1?/SacCer-Promoters/Homer | 1e-8 | -1.864e+01 | 0.0000 | 2718.0 | 70.07% | 13264.0 | 65.80% | motif file (matrix) |
pdf |
| 41 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-7 | -1.839e+01 | 0.0000 | 146.0 | 3.76% | 461.2 | 2.29% | motif file (matrix) |
pdf |
| 42 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-7 | -1.774e+01 | 0.0000 | 1482.0 | 38.21% | 6849.6 | 33.98% | motif file (matrix) |
pdf |
| 43 |  | SeqBias: TA-repeat | 1e-7 | -1.765e+01 | 0.0000 | 3345.0 | 86.23% | 16731.7 | 83.00% | motif file (matrix) |
pdf |
| 44 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-7 | -1.703e+01 | 0.0000 | 105.0 | 2.71% | 308.3 | 1.53% | motif file (matrix) |
pdf |
| 45 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-7 | -1.701e+01 | 0.0000 | 281.0 | 7.24% | 1051.8 | 5.22% | motif file (matrix) |
pdf |
| 46 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-6 | -1.575e+01 | 0.0000 | 179.0 | 4.61% | 621.3 | 3.08% | motif file (matrix) |
pdf |
| 47 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-6 | -1.551e+01 | 0.0000 | 117.0 | 3.02% | 366.4 | 1.82% | motif file (matrix) |
pdf |
| 48 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-6 | -1.526e+01 | 0.0000 | 440.0 | 11.34% | 1802.8 | 8.94% | motif file (matrix) |
pdf |
| 49 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-6 | -1.484e+01 | 0.0000 | 1257.0 | 32.41% | 5795.3 | 28.75% | motif file (matrix) |
pdf |
| 50 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-6 | -1.474e+01 | 0.0000 | 119.0 | 3.07% | 380.2 | 1.89% | motif file (matrix) |
pdf |
| 51 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.423e+01 | 0.0000 | 49.0 | 1.26% | 116.2 | 0.58% | motif file (matrix) |
pdf |
| 52 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-5 | -1.343e+01 | 0.0000 | 83.0 | 2.14% | 246.4 | 1.22% | motif file (matrix) |
pdf |
| 53 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-5 | -1.233e+01 | 0.0000 | 662.0 | 17.07% | 2920.8 | 14.49% | motif file (matrix) |
pdf |
| 54 |  | TATA-box/Drosophila-Promoters/Homer | 1e-5 | -1.182e+01 | 0.0001 | 185.0 | 4.77% | 690.4 | 3.42% | motif file (matrix) |
pdf |
| 55 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-4 | -1.061e+01 | 0.0002 | 182.0 | 4.69% | 692.6 | 3.44% | motif file (matrix) |
pdf |
| 56 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-4 | -9.621e+00 | 0.0005 | 565.0 | 14.57% | 2516.2 | 12.48% | motif file (matrix) |
pdf |
| 57 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-4 | -9.493e+00 | 0.0005 | 645.0 | 16.63% | 2910.9 | 14.44% | motif file (matrix) |
pdf |
| 58 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-4 | -9.384e+00 | 0.0006 | 86.0 | 2.22% | 289.4 | 1.44% | motif file (matrix) |
pdf |
| 59 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-3 | -8.658e+00 | 0.0011 | 456.0 | 11.76% | 2012.2 | 9.98% | motif file (matrix) |
pdf |
| 60 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-3 | -8.620e+00 | 0.0012 | 116.0 | 2.99% | 426.0 | 2.11% | motif file (matrix) |
pdf |
| 61 |  | Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer | 1e-3 | -8.139e+00 | 0.0019 | 192.0 | 4.95% | 773.9 | 3.84% | motif file (matrix) |
pdf |
| 62 |  | SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer | 1e-3 | -7.875e+00 | 0.0024 | 253.0 | 6.52% | 1061.2 | 5.26% | motif file (matrix) |
pdf |
| 63 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-3 | -7.746e+00 | 0.0027 | 201.0 | 5.18% | 821.1 | 4.07% | motif file (matrix) |
pdf |
| 64 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-3 | -7.500e+00 | 0.0033 | 495.0 | 12.76% | 2232.6 | 11.08% | motif file (matrix) |
pdf |
| 65 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.354e+00 | 0.0038 | 918.0 | 23.67% | 4335.1 | 21.51% | motif file (matrix) |
pdf |
| 66 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.333e+00 | 0.0038 | 92.0 | 2.37% | 335.7 | 1.67% | motif file (matrix) |
pdf |
| 67 |  | Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer | 1e-3 | -7.080e+00 | 0.0049 | 377.0 | 9.72% | 1670.7 | 8.29% | motif file (matrix) |
pdf |
| 68 |  | CRE(bZIP)/Promoter/Homer | 1e-3 | -7.065e+00 | 0.0049 | 171.0 | 4.41% | 694.2 | 3.44% | motif file (matrix) |
pdf |
| 69 |  | PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer | 1e-2 | -6.457e+00 | 0.0088 | 442.0 | 11.39% | 2003.2 | 9.94% | motif file (matrix) |
pdf |
| 70 |  | GAGA-repeat/SacCer-Promoters/Homer | 1e-2 | -6.456e+00 | 0.0088 | 3003.0 | 77.42% | 15194.0 | 75.38% | motif file (matrix) |
pdf |
| 71 |  | Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.228e+00 | 0.0108 | 124.0 | 3.20% | 492.1 | 2.44% | motif file (matrix) |
pdf |
| 72 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-2 | -5.929e+00 | 0.0143 | 171.0 | 4.41% | 714.5 | 3.54% | motif file (matrix) |
pdf |
| 73 |  | Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer | 1e-2 | -5.751e+00 | 0.0169 | 1490.0 | 38.41% | 7314.8 | 36.29% | motif file (matrix) |
pdf |
| 74 |  | GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer | 1e-2 | -5.551e+00 | 0.0203 | 39.0 | 1.01% | 127.6 | 0.63% | motif file (matrix) |
pdf |
| 75 |  | Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer | 1e-2 | -5.407e+00 | 0.0231 | 96.0 | 2.47% | 377.7 | 1.87% | motif file (matrix) |
pdf |
| 76 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-2 | -5.336e+00 | 0.0242 | 63.0 | 1.62% | 231.8 | 1.15% | motif file (matrix) |
pdf |
| 77 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-2 | -5.336e+00 | 0.0242 | 63.0 | 1.62% | 231.8 | 1.15% | motif file (matrix) |
pdf |
| 78 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-2 | -5.170e+00 | 0.0282 | 111.0 | 2.86% | 449.5 | 2.23% | motif file (matrix) |
pdf |
| 79 |  | TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer | 1e-2 | -4.778e+00 | 0.0412 | 45.0 | 1.16% | 159.3 | 0.79% | motif file (matrix) |
pdf |
| 80 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.769e+00 | 0.0412 | 739.0 | 19.05% | 3541.8 | 17.57% | motif file (matrix) |
pdf |
| 81 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -4.751e+00 | 0.0413 | 35.0 | 0.90% | 117.3 | 0.58% | motif file (matrix) |
pdf |
| 82 |  | RBPJ:Ebox(?,bHLH)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-2 | -4.680e+00 | 0.0438 | 129.0 | 3.33% | 541.7 | 2.69% | motif file (matrix) |
pdf |
| 83 |  | RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-2 | -4.678e+00 | 0.0438 | 451.0 | 11.63% | 2105.3 | 10.44% | motif file (matrix) |
pdf |