| 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-226 | -5.207e+02 | 0.0000 | 1485.0 | 34.15% | 3178.3 | 14.61% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-194 | -4.474e+02 | 0.0000 | 947.0 | 21.78% | 1621.8 | 7.45% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-80 | -1.849e+02 | 0.0000 | 2077.0 | 47.76% | 7343.4 | 33.75% | motif file (matrix) |
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| 4 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-62 | -1.437e+02 | 0.0000 | 579.0 | 13.31% | 1369.2 | 6.29% | motif file (matrix) |
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| 5 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-52 | -1.201e+02 | 0.0000 | 657.0 | 15.11% | 1762.1 | 8.10% | motif file (matrix) |
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| 6 |  | SeqBias: CG-repeat | 1e-50 | -1.160e+02 | 0.0000 | 751.0 | 17.27% | 2143.8 | 9.85% | motif file (matrix) |
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| 7 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-46 | -1.063e+02 | 0.0000 | 431.0 | 9.91% | 1015.9 | 4.67% | motif file (matrix) |
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| 8 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-45 | -1.056e+02 | 0.0000 | 417.0 | 9.59% | 970.4 | 4.46% | motif file (matrix) |
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| 9 |  | SFP1/SacCer-Promoters/Homer | 1e-45 | -1.049e+02 | 0.0000 | 661.0 | 15.20% | 1862.9 | 8.56% | motif file (matrix) |
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| 10 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-45 | -1.041e+02 | 0.0000 | 409.0 | 9.40% | 950.0 | 4.37% | motif file (matrix) |
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| 11 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-44 | -1.022e+02 | 0.0000 | 564.0 | 12.97% | 1511.3 | 6.95% | motif file (matrix) |
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| 12 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-44 | -1.021e+02 | 0.0000 | 486.0 | 11.17% | 1227.9 | 5.64% | motif file (matrix) |
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| 13 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-38 | -8.777e+01 | 0.0000 | 1046.0 | 24.05% | 3559.8 | 16.36% | motif file (matrix) |
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| 14 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-37 | -8.541e+01 | 0.0000 | 591.0 | 13.59% | 1711.8 | 7.87% | motif file (matrix) |
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| 15 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-34 | -7.835e+01 | 0.0000 | 867.0 | 19.94% | 2881.9 | 13.25% | motif file (matrix) |
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| 16 |  | E-box/Arabidopsis-Promoters/Homer | 1e-33 | -7.756e+01 | 0.0000 | 518.0 | 11.91% | 1479.9 | 6.80% | motif file (matrix) |
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| 17 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-29 | -6.783e+01 | 0.0000 | 948.0 | 21.80% | 3323.1 | 15.28% | motif file (matrix) |
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| 18 |  | TATA-box/SacCer-Promoters/Homer | 1e-27 | -6.439e+01 | 0.0000 | 1921.0 | 44.17% | 7833.7 | 36.01% | motif file (matrix) |
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| 19 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-26 | -6.121e+01 | 0.0000 | 1062.0 | 24.42% | 3892.8 | 17.89% | motif file (matrix) |
pdf |
| 20 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-26 | -6.061e+01 | 0.0000 | 1296.0 | 29.80% | 4952.7 | 22.77% | motif file (matrix) |
pdf |
| 21 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-25 | -5.953e+01 | 0.0000 | 415.0 | 9.54% | 1198.4 | 5.51% | motif file (matrix) |
pdf |
| 22 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-25 | -5.947e+01 | 0.0000 | 800.0 | 18.40% | 2769.3 | 12.73% | motif file (matrix) |
pdf |
| 23 |  | E-box(bHLH)/Promoter/Homer | 1e-25 | -5.932e+01 | 0.0000 | 132.0 | 3.04% | 224.1 | 1.03% | motif file (matrix) |
pdf |
| 24 |  | TOD6?/SacCer-Promoters/Homer | 1e-25 | -5.869e+01 | 0.0000 | 357.0 | 8.21% | 984.1 | 4.52% | motif file (matrix) |
pdf |
| 25 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-21 | -4.953e+01 | 0.0000 | 1396.0 | 32.10% | 5561.5 | 25.56% | motif file (matrix) |
pdf |
| 26 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-20 | -4.821e+01 | 0.0000 | 126.0 | 2.90% | 237.6 | 1.09% | motif file (matrix) |
pdf |
| 27 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-19 | -4.487e+01 | 0.0000 | 759.0 | 17.45% | 2745.4 | 12.62% | motif file (matrix) |
pdf |
| 28 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-18 | -4.162e+01 | 0.0000 | 776.0 | 17.84% | 2857.7 | 13.14% | motif file (matrix) |
pdf |
| 29 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-15 | -3.632e+01 | 0.0000 | 325.0 | 7.47% | 1010.5 | 4.64% | motif file (matrix) |
pdf |
| 30 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-15 | -3.542e+01 | 0.0000 | 388.0 | 8.92% | 1271.0 | 5.84% | motif file (matrix) |
pdf |
| 31 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-14 | -3.233e+01 | 0.0000 | 514.0 | 11.82% | 1829.5 | 8.41% | motif file (matrix) |
pdf |
| 32 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-13 | -3.088e+01 | 0.0000 | 1002.0 | 23.04% | 4025.1 | 18.50% | motif file (matrix) |
pdf |
| 33 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-12 | -2.891e+01 | 0.0000 | 152.0 | 3.50% | 401.0 | 1.84% | motif file (matrix) |
pdf |
| 34 |  | SUT1?/SacCer-Promoters/Homer | 1e-11 | -2.729e+01 | 0.0000 | 2898.0 | 66.64% | 13383.6 | 61.52% | motif file (matrix) |
pdf |
| 35 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-11 | -2.721e+01 | 0.0000 | 153.0 | 3.52% | 413.6 | 1.90% | motif file (matrix) |
pdf |
| 36 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-11 | -2.665e+01 | 0.0000 | 296.0 | 6.81% | 975.0 | 4.48% | motif file (matrix) |
pdf |
| 37 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-10 | -2.487e+01 | 0.0000 | 1585.0 | 36.45% | 6895.7 | 31.70% | motif file (matrix) |
pdf |
| 38 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-9 | -2.236e+01 | 0.0000 | 425.0 | 9.77% | 1564.5 | 7.19% | motif file (matrix) |
pdf |
| 39 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-9 | -2.192e+01 | 0.0000 | 220.0 | 5.06% | 708.5 | 3.26% | motif file (matrix) |
pdf |
| 40 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-9 | -2.177e+01 | 0.0000 | 268.0 | 6.16% | 905.5 | 4.16% | motif file (matrix) |
pdf |
| 41 |  | SeqBias: TA-repeat | 1e-9 | -2.154e+01 | 0.0000 | 3836.0 | 88.20% | 18486.5 | 84.97% | motif file (matrix) |
pdf |
| 42 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-8 | -2.041e+01 | 0.0000 | 118.0 | 2.71% | 324.1 | 1.49% | motif file (matrix) |
pdf |
| 43 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-8 | -2.038e+01 | 0.0000 | 189.0 | 4.35% | 597.9 | 2.75% | motif file (matrix) |
pdf |
| 44 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-8 | -1.997e+01 | 0.0000 | 467.0 | 10.74% | 1781.0 | 8.19% | motif file (matrix) |
pdf |
| 45 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-8 | -1.986e+01 | 0.0000 | 278.0 | 6.39% | 966.4 | 4.44% | motif file (matrix) |
pdf |
| 46 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-7 | -1.689e+01 | 0.0000 | 491.0 | 11.29% | 1934.5 | 8.89% | motif file (matrix) |
pdf |
| 47 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-6 | -1.583e+01 | 0.0000 | 123.0 | 2.83% | 373.3 | 1.72% | motif file (matrix) |
pdf |
| 48 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-6 | -1.579e+01 | 0.0000 | 693.0 | 15.93% | 2875.2 | 13.22% | motif file (matrix) |
pdf |
| 49 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-6 | -1.570e+01 | 0.0000 | 96.0 | 2.21% | 271.5 | 1.25% | motif file (matrix) |
pdf |
| 50 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-5 | -1.301e+01 | 0.0000 | 52.0 | 1.20% | 127.1 | 0.58% | motif file (matrix) |
pdf |
| 51 |  | TATA-box/Drosophila-Promoters/Homer | 1e-5 | -1.300e+01 | 0.0000 | 214.0 | 4.92% | 773.7 | 3.56% | motif file (matrix) |
pdf |
| 52 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-5 | -1.237e+01 | 0.0000 | 553.0 | 12.72% | 2300.4 | 10.57% | motif file (matrix) |
pdf |
| 53 |  | CRE(bZIP)/Promoter/Homer | 1e-5 | -1.226e+01 | 0.0000 | 187.0 | 4.30% | 667.4 | 3.07% | motif file (matrix) |
pdf |
| 54 |  | NRF(NRF)/Promoter/Homer | 1e-5 | -1.176e+01 | 0.0001 | 82.0 | 1.89% | 244.1 | 1.12% | motif file (matrix) |
pdf |
| 55 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-4 | -1.081e+01 | 0.0001 | 1355.0 | 31.16% | 6161.0 | 28.32% | motif file (matrix) |
pdf |
| 56 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-4 | -1.074e+01 | 0.0001 | 86.0 | 1.98% | 267.3 | 1.23% | motif file (matrix) |
pdf |
| 57 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-4 | -1.067e+01 | 0.0002 | 68.0 | 1.56% | 198.7 | 0.91% | motif file (matrix) |
pdf |
| 58 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-4 | -1.067e+01 | 0.0002 | 68.0 | 1.56% | 198.7 | 0.91% | motif file (matrix) |
pdf |
| 59 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-4 | -1.056e+01 | 0.0002 | 966.0 | 22.21% | 4291.1 | 19.72% | motif file (matrix) |
pdf |
| 60 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-4 | -9.795e+00 | 0.0004 | 39.0 | 0.90% | 97.8 | 0.45% | motif file (matrix) |
pdf |
| 61 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.935e+00 | 0.0008 | 791.0 | 18.19% | 3505.3 | 16.11% | motif file (matrix) |
pdf |
| 62 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-3 | -8.905e+00 | 0.0008 | 117.0 | 2.69% | 410.4 | 1.89% | motif file (matrix) |
pdf |
| 63 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-3 | -8.803e+00 | 0.0009 | 76.0 | 1.75% | 243.7 | 1.12% | motif file (matrix) |
pdf |
| 64 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-3 | -8.799e+00 | 0.0009 | 730.0 | 16.79% | 3219.7 | 14.80% | motif file (matrix) |
pdf |
| 65 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-3 | -8.675e+00 | 0.0010 | 124.0 | 2.85% | 442.7 | 2.03% | motif file (matrix) |
pdf |
| 66 |  | RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-3 | -8.536e+00 | 0.0012 | 484.0 | 11.13% | 2068.4 | 9.51% | motif file (matrix) |
pdf |
| 67 |  | E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.803e+00 | 0.0024 | 255.0 | 5.86% | 1032.0 | 4.74% | motif file (matrix) |
pdf |
| 68 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-3 | -7.782e+00 | 0.0024 | 189.0 | 4.35% | 736.3 | 3.38% | motif file (matrix) |
pdf |
| 69 |  | SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer | 1e-3 | -7.628e+00 | 0.0027 | 275.0 | 6.32% | 1125.0 | 5.17% | motif file (matrix) |
pdf |
| 70 |  | Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer | 1e-3 | -7.224e+00 | 0.0040 | 379.0 | 8.71% | 1612.6 | 7.41% | motif file (matrix) |
pdf |
| 71 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.713e+00 | 0.0066 | 247.0 | 5.68% | 1016.3 | 4.67% | motif file (matrix) |
pdf |
| 72 |  | PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer | 1e-2 | -6.698e+00 | 0.0066 | 461.0 | 10.60% | 2009.9 | 9.24% | motif file (matrix) |
pdf |
| 73 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-2 | -6.687e+00 | 0.0066 | 479.0 | 11.01% | 2094.2 | 9.63% | motif file (matrix) |
pdf |
| 74 |  | X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-2 | -6.458e+00 | 0.0082 | 115.0 | 2.64% | 431.8 | 1.98% | motif file (matrix) |
pdf |
| 75 |  | GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer | 1e-2 | -6.429e+00 | 0.0083 | 101.0 | 2.32% | 371.7 | 1.71% | motif file (matrix) |
pdf |
| 76 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer | 1e-2 | -6.375e+00 | 0.0087 | 41.0 | 0.94% | 124.1 | 0.57% | motif file (matrix) |
pdf |
| 77 |  | GAGA-repeat/SacCer-Promoters/Homer | 1e-2 | -6.269e+00 | 0.0095 | 3382.0 | 77.77% | 16510.4 | 75.89% | motif file (matrix) |
pdf |
| 78 |  | Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer | 1e-2 | -5.967e+00 | 0.0127 | 192.0 | 4.41% | 781.1 | 3.59% | motif file (matrix) |
pdf |
| 79 |  | ELF1(ETS)/Jurkat-ELF1-ChIP-Seq(SRA014231)/Homer | 1e-2 | -5.794e+00 | 0.0149 | 526.0 | 12.09% | 2344.1 | 10.77% | motif file (matrix) |
pdf |
| 80 |  | Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer | 1e-2 | -5.704e+00 | 0.0161 | 1588.0 | 36.51% | 7514.5 | 34.54% | motif file (matrix) |
pdf |
| 81 |  | ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -5.700e+00 | 0.0161 | 49.0 | 1.13% | 161.1 | 0.74% | motif file (matrix) |
pdf |
| 82 |  | TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer | 1e-2 | -5.688e+00 | 0.0161 | 45.0 | 1.03% | 146.0 | 0.67% | motif file (matrix) |
pdf |
| 83 |  | ETS(ETS)/Promoter/Homer | 1e-2 | -5.307e+00 | 0.0231 | 312.0 | 7.17% | 1349.5 | 6.20% | motif file (matrix) |
pdf |
| 84 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.079e+00 | 0.0287 | 36.0 | 0.83% | 114.1 | 0.52% | motif file (matrix) |
pdf |
| 85 |  | GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer | 1e-2 | -5.075e+00 | 0.0287 | 38.0 | 0.87% | 122.4 | 0.56% | motif file (matrix) |
pdf |
| 86 |  | Sp1(Zf)/Promoter/Homer | 1e-2 | -5.018e+00 | 0.0298 | 47.0 | 1.08% | 159.3 | 0.73% | motif file (matrix) |
pdf |
| 87 |  | Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer | 1e-2 | -4.768e+00 | 0.0378 | 96.0 | 2.21% | 372.4 | 1.71% | motif file (matrix) |
pdf |
| 88 |  | PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -4.661e+00 | 0.0416 | 70.0 | 1.61% | 260.3 | 1.20% | motif file (matrix) |
pdf |
| 89 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-2 | -4.656e+00 | 0.0416 | 173.0 | 3.98% | 721.5 | 3.32% | motif file (matrix) |
pdf |