| 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-233 | -5.386e+02 | 0.0000 | 1510.0 | 34.23% | 3043.5 | 14.52% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-203 | -4.697e+02 | 0.0000 | 979.0 | 22.19% | 1578.4 | 7.53% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-75 | -1.731e+02 | 0.0000 | 2103.0 | 47.68% | 7170.2 | 34.21% | motif file (matrix) |
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| 4 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-54 | -1.262e+02 | 0.0000 | 578.0 | 13.10% | 1370.7 | 6.54% | motif file (matrix) |
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| 5 |  | SeqBias: CG-repeat | 1e-52 | -1.215e+02 | 0.0000 | 783.0 | 17.75% | 2121.8 | 10.12% | motif file (matrix) |
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| 6 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-42 | -9.690e+01 | 0.0000 | 431.0 | 9.77% | 1003.2 | 4.79% | motif file (matrix) |
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| 7 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-39 | -9.016e+01 | 0.0000 | 1069.0 | 24.23% | 3452.8 | 16.47% | motif file (matrix) |
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| 8 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-38 | -8.939e+01 | 0.0000 | 408.0 | 9.25% | 959.7 | 4.58% | motif file (matrix) |
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| 9 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-38 | -8.839e+01 | 0.0000 | 638.0 | 14.46% | 1780.9 | 8.50% | motif file (matrix) |
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| 10 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-36 | -8.341e+01 | 0.0000 | 392.0 | 8.89% | 932.7 | 4.45% | motif file (matrix) |
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| 11 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-35 | -8.243e+01 | 0.0000 | 562.0 | 12.74% | 1536.7 | 7.33% | motif file (matrix) |
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| 12 |  | SFP1/SacCer-Promoters/Homer | 1e-35 | -8.202e+01 | 0.0000 | 635.0 | 14.40% | 1809.6 | 8.63% | motif file (matrix) |
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| 13 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-34 | -8.056e+01 | 0.0000 | 482.0 | 10.93% | 1258.5 | 6.00% | motif file (matrix) |
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| 14 |  | TATA-box/SacCer-Promoters/Homer | 1e-31 | -7.288e+01 | 0.0000 | 2058.0 | 46.66% | 7950.9 | 37.93% | motif file (matrix) |
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| 15 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-24 | -5.663e+01 | 0.0000 | 1331.0 | 30.17% | 4901.2 | 23.38% | motif file (matrix) |
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| 16 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-24 | -5.648e+01 | 0.0000 | 569.0 | 12.90% | 1738.8 | 8.30% | motif file (matrix) |
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| 17 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-24 | -5.575e+01 | 0.0000 | 422.0 | 9.57% | 1187.8 | 5.67% | motif file (matrix) |
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| 18 |  | E-box/Arabidopsis-Promoters/Homer | 1e-23 | -5.453e+01 | 0.0000 | 499.0 | 11.31% | 1484.2 | 7.08% | motif file (matrix) |
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| 19 |  | TOD6?/SacCer-Promoters/Homer | 1e-21 | -5.045e+01 | 0.0000 | 348.0 | 7.89% | 950.3 | 4.53% | motif file (matrix) |
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| 20 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-21 | -4.990e+01 | 0.0000 | 854.0 | 19.36% | 2946.8 | 14.06% | motif file (matrix) |
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| 21 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-21 | -4.918e+01 | 0.0000 | 800.0 | 18.14% | 2730.1 | 13.03% | motif file (matrix) |
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| 22 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-20 | -4.817e+01 | 0.0000 | 1081.0 | 24.51% | 3925.5 | 18.73% | motif file (matrix) |
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| 23 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-20 | -4.746e+01 | 0.0000 | 136.0 | 3.08% | 257.0 | 1.23% | motif file (matrix) |
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| 24 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-20 | -4.724e+01 | 0.0000 | 953.0 | 21.61% | 3391.9 | 16.18% | motif file (matrix) |
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| 25 |  | E-box(bHLH)/Promoter/Homer | 1e-18 | -4.336e+01 | 0.0000 | 120.0 | 2.72% | 222.2 | 1.06% | motif file (matrix) |
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| 26 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-16 | -3.703e+01 | 0.0000 | 790.0 | 17.91% | 2826.1 | 13.48% | motif file (matrix) |
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| 27 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-12 | -2.981e+01 | 0.0000 | 328.0 | 7.44% | 1022.0 | 4.88% | motif file (matrix) |
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| 28 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-12 | -2.937e+01 | 0.0000 | 388.0 | 8.80% | 1261.5 | 6.02% | motif file (matrix) |
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| 29 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-12 | -2.861e+01 | 0.0000 | 548.0 | 12.42% | 1918.1 | 9.15% | motif file (matrix) |
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| 30 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-12 | -2.812e+01 | 0.0000 | 1392.0 | 31.56% | 5603.1 | 26.73% | motif file (matrix) |
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| 31 |  | KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer | 1e-12 | -2.793e+01 | 0.0000 | 236.0 | 5.35% | 687.3 | 3.28% | motif file (matrix) |
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| 32 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-11 | -2.759e+01 | 0.0000 | 159.0 | 3.60% | 411.3 | 1.96% | motif file (matrix) |
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| 33 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer | 1e-10 | -2.492e+01 | 0.0000 | 1013.0 | 22.97% | 3969.3 | 18.94% | motif file (matrix) |
pdf |
| 34 |  | ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer | 1e-10 | -2.488e+01 | 0.0000 | 303.0 | 6.87% | 968.2 | 4.62% | motif file (matrix) |
pdf |
| 35 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-9 | -2.207e+01 | 0.0000 | 735.0 | 16.66% | 2802.6 | 13.37% | motif file (matrix) |
pdf |
| 36 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-9 | -2.192e+01 | 0.0000 | 146.0 | 3.31% | 398.5 | 1.90% | motif file (matrix) |
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| 37 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-8 | -2.058e+01 | 0.0000 | 1632.0 | 37.00% | 6860.0 | 32.73% | motif file (matrix) |
pdf |
| 38 |  | SUT1?/SacCer-Promoters/Homer | 1e-8 | -2.045e+01 | 0.0000 | 2954.0 | 66.97% | 13133.4 | 62.66% | motif file (matrix) |
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| 39 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-8 | -1.971e+01 | 0.0000 | 277.0 | 6.28% | 915.8 | 4.37% | motif file (matrix) |
pdf |
| 40 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-8 | -1.967e+01 | 0.0000 | 101.0 | 2.29% | 253.4 | 1.21% | motif file (matrix) |
pdf |
| 41 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-7 | -1.800e+01 | 0.0000 | 438.0 | 9.93% | 1596.9 | 7.62% | motif file (matrix) |
pdf |
| 42 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-7 | -1.775e+01 | 0.0000 | 119.0 | 2.70% | 327.2 | 1.56% | motif file (matrix) |
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| 43 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-7 | -1.731e+01 | 0.0000 | 291.0 | 6.60% | 997.3 | 4.76% | motif file (matrix) |
pdf |
| 44 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-7 | -1.703e+01 | 0.0000 | 481.0 | 10.90% | 1792.9 | 8.55% | motif file (matrix) |
pdf |
| 45 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-7 | -1.640e+01 | 0.0000 | 772.0 | 17.50% | 3066.1 | 14.63% | motif file (matrix) |
pdf |
| 46 |  | GAGA-repeat/Arabidopsis-Promoters/Homer | 1e-7 | -1.632e+01 | 0.0000 | 503.0 | 11.40% | 1897.2 | 9.05% | motif file (matrix) |
pdf |
| 47 |  | ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.593e+01 | 0.0000 | 59.0 | 1.34% | 131.5 | 0.63% | motif file (matrix) |
pdf |
| 48 |  | TATA-box/Drosophila-Promoters/Homer | 1e-6 | -1.579e+01 | 0.0000 | 235.0 | 5.33% | 789.0 | 3.76% | motif file (matrix) |
pdf |
| 49 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-6 | -1.502e+01 | 0.0000 | 590.0 | 13.38% | 2295.5 | 10.95% | motif file (matrix) |
pdf |
| 50 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-5 | -1.202e+01 | 0.0000 | 128.0 | 2.90% | 403.0 | 1.92% | motif file (matrix) |
pdf |
| 51 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-4 | -1.131e+01 | 0.0001 | 701.0 | 15.89% | 2862.3 | 13.66% | motif file (matrix) |
pdf |
| 52 |  | NRF(NRF)/Promoter/Homer | 1e-4 | -1.099e+01 | 0.0001 | 93.0 | 2.11% | 278.2 | 1.33% | motif file (matrix) |
pdf |
| 53 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-4 | -1.006e+01 | 0.0003 | 71.0 | 1.61% | 203.8 | 0.97% | motif file (matrix) |
pdf |
| 54 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-4 | -1.006e+01 | 0.0003 | 71.0 | 1.61% | 203.8 | 0.97% | motif file (matrix) |
pdf |
| 55 |  | E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer | 1e-4 | -9.833e+00 | 0.0004 | 120.0 | 2.72% | 392.9 | 1.87% | motif file (matrix) |
pdf |
| 56 |  | E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer | 1e-4 | -9.763e+00 | 0.0004 | 185.0 | 4.19% | 655.7 | 3.13% | motif file (matrix) |
pdf |
| 57 |  | Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer | 1e-4 | -9.558e+00 | 0.0005 | 1002.0 | 22.72% | 4269.8 | 20.37% | motif file (matrix) |
pdf |
| 58 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-4 | -9.269e+00 | 0.0006 | 1393.0 | 31.58% | 6078.4 | 29.00% | motif file (matrix) |
pdf |
| 59 |  | CRE(bZIP)/Promoter/Homer | 1e-4 | -9.246e+00 | 0.0006 | 187.0 | 4.24% | 671.0 | 3.20% | motif file (matrix) |
pdf |
| 60 |  | SeqBias: TA-repeat | 1e-3 | -8.311e+00 | 0.0016 | 3871.0 | 87.76% | 18016.6 | 85.95% | motif file (matrix) |
pdf |
| 61 |  | E2F(E2F)/Hela-CellCycle-Expression/Homer | 1e-3 | -7.944e+00 | 0.0022 | 123.0 | 2.79% | 424.5 | 2.03% | motif file (matrix) |
pdf |
| 62 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-3 | -7.457e+00 | 0.0036 | 41.0 | 0.93% | 111.4 | 0.53% | motif file (matrix) |
pdf |
| 63 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.448e+00 | 0.0036 | 275.0 | 6.23% | 1072.3 | 5.12% | motif file (matrix) |
pdf |
| 64 |  | Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.317e+00 | 0.0040 | 820.0 | 18.59% | 3511.7 | 16.75% | motif file (matrix) |
pdf |
| 65 |  | SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer | 1e-3 | -6.976e+00 | 0.0056 | 283.0 | 6.42% | 1116.9 | 5.33% | motif file (matrix) |
pdf |
| 66 |  | NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -6.832e+00 | 0.0063 | 38.0 | 0.86% | 105.0 | 0.50% | motif file (matrix) |
pdf |
| 67 |  | Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer | 1e-2 | -6.662e+00 | 0.0074 | 106.0 | 2.40% | 370.8 | 1.77% | motif file (matrix) |
pdf |
| 68 |  | Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer | 1e-2 | -6.648e+00 | 0.0074 | 207.0 | 4.69% | 794.4 | 3.79% | motif file (matrix) |
pdf |
| 69 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.359e+00 | 0.0097 | 203.0 | 4.60% | 782.2 | 3.73% | motif file (matrix) |
pdf |
| 70 |  | Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer | 1e-2 | -6.149e+00 | 0.0118 | 1648.0 | 37.36% | 7396.6 | 35.29% | motif file (matrix) |
pdf |
| 71 |  | GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer | 1e-2 | -6.040e+00 | 0.0130 | 38.0 | 0.86% | 109.8 | 0.52% | motif file (matrix) |
pdf |
| 72 |  | PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer | 1e-2 | -5.813e+00 | 0.0161 | 31.0 | 0.70% | 85.6 | 0.41% | motif file (matrix) |
pdf |
| 73 |  | NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer | 1e-2 | -5.762e+00 | 0.0167 | 62.0 | 1.41% | 203.6 | 0.97% | motif file (matrix) |
pdf |
| 74 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-2 | -5.738e+00 | 0.0168 | 75.0 | 1.70% | 256.0 | 1.22% | motif file (matrix) |
pdf |
| 75 |  | RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-2 | -5.646e+00 | 0.0182 | 483.0 | 10.95% | 2037.5 | 9.72% | motif file (matrix) |
pdf |
| 76 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-2 | -5.552e+00 | 0.0198 | 495.0 | 11.22% | 2094.9 | 9.99% | motif file (matrix) |
pdf |
| 77 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-2 | -5.465e+00 | 0.0213 | 185.0 | 4.19% | 721.6 | 3.44% | motif file (matrix) |
pdf |
| 78 |  | Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.261e+00 | 0.0258 | 68.0 | 1.54% | 232.9 | 1.11% | motif file (matrix) |
pdf |
| 79 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-2 | -5.125e+00 | 0.0291 | 535.0 | 12.13% | 2289.1 | 10.92% | motif file (matrix) |
pdf |
| 80 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.085e+00 | 0.0299 | 591.0 | 13.40% | 2545.5 | 12.14% | motif file (matrix) |
pdf |
| 81 |  | ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer | 1e-2 | -4.994e+00 | 0.0324 | 50.0 | 1.13% | 163.0 | 0.78% | motif file (matrix) |
pdf |
| 82 |  | HEB(bHLH)/mES-Heb-ChIP-Seq(GSE53233)/Homer | 1e-2 | -4.834e+00 | 0.0375 | 899.0 | 20.38% | 3969.2 | 18.94% | motif file (matrix) |
pdf |
| 83 |  | Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.669e+00 | 0.0437 | 33.0 | 0.75% | 100.5 | 0.48% | motif file (matrix) |
pdf |