| 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-52 | -1.199e+02 | 0.0000 | 270.0 | 16.75% | 2644.0 | 5.92% | motif file (matrix) |
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| 2 |  | REB1/SacCer-Promoters/Homer | 1e-48 | -1.114e+02 | 0.0000 | 178.0 | 11.04% | 1335.0 | 2.99% | motif file (matrix) |
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| 3 |  | RLR1?/SacCer-Promoters/Homer | 1e-17 | -4.060e+01 | 0.0000 | 319.0 | 19.79% | 5434.7 | 12.17% | motif file (matrix) |
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| 4 |  | SeqBias: GA-repeat | 1e-15 | -3.550e+01 | 0.0000 | 1027.0 | 63.71% | 23996.9 | 53.75% | motif file (matrix) |
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| 5 |  | SeqBias: TA-repeat | 1e-13 | -3.079e+01 | 0.0000 | 972.0 | 60.30% | 22773.3 | 51.01% | motif file (matrix) |
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| 6 |  | SUT1?/SacCer-Promoters/Homer | 1e-12 | -2.876e+01 | 0.0000 | 708.0 | 43.92% | 15716.4 | 35.21% | motif file (matrix) |
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| 7 |  | GAGA-repeat/SacCer-Promoters/Homer | 1e-12 | -2.781e+01 | 0.0000 | 775.0 | 48.08% | 17575.3 | 39.37% | motif file (matrix) |
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| 8 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-8 | -2.028e+01 | 0.0000 | 88.0 | 5.46% | 1214.3 | 2.72% | motif file (matrix) |
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| 9 |  | SeqBias: CG bias | 1e-8 | -1.858e+01 | 0.0000 | 1060.0 | 65.76% | 26286.3 | 58.88% | motif file (matrix) |
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| 10 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-7 | -1.816e+01 | 0.0000 | 64.0 | 3.97% | 810.5 | 1.82% | motif file (matrix) |
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| 11 |  | TATA-box/SacCer-Promoters/Homer | 1e-7 | -1.763e+01 | 0.0000 | 301.0 | 18.67% | 6135.9 | 13.74% | motif file (matrix) |
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| 12 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-7 | -1.727e+01 | 0.0000 | 66.0 | 4.09% | 868.6 | 1.95% | motif file (matrix) |
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| 13 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-7 | -1.712e+01 | 0.0000 | 101.0 | 6.27% | 1569.6 | 3.52% | motif file (matrix) |
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| 14 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-6 | -1.601e+01 | 0.0000 | 86.0 | 5.33% | 1296.7 | 2.90% | motif file (matrix) |
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| 15 |  | SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer | 1e-6 | -1.564e+01 | 0.0000 | 184.0 | 11.41% | 3469.0 | 7.77% | motif file (matrix) |
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| 16 |  | Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer | 1e-6 | -1.466e+01 | 0.0000 | 58.0 | 3.60% | 780.8 | 1.75% | motif file (matrix) |
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| 17 |  | SFP1/SacCer-Promoters/Homer | 1e-5 | -1.260e+01 | 0.0001 | 76.0 | 4.71% | 1202.5 | 2.69% | motif file (matrix) |
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| 18 |  | PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer | 1e-5 | -1.240e+01 | 0.0001 | 137.0 | 8.50% | 2555.0 | 5.72% | motif file (matrix) |
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| 19 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-5 | -1.203e+01 | 0.0001 | 223.0 | 13.83% | 4616.1 | 10.34% | motif file (matrix) |
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| 20 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-5 | -1.163e+01 | 0.0002 | 86.0 | 5.33% | 1451.2 | 3.25% | motif file (matrix) |
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| 21 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-4 | -1.112e+01 | 0.0003 | 67.0 | 4.16% | 1066.0 | 2.39% | motif file (matrix) |
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| 22 |  | TOD6?/SacCer-Promoters/Homer | 1e-4 | -1.089e+01 | 0.0003 | 49.0 | 3.04% | 706.0 | 1.58% | motif file (matrix) |
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| 23 |  | E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer | 1e-4 | -1.013e+01 | 0.0007 | 128.0 | 7.94% | 2471.9 | 5.54% | motif file (matrix) |
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| 24 |  | E-box/Arabidopsis-Promoters/Homer | 1e-4 | -9.325e+00 | 0.0014 | 75.0 | 4.65% | 1308.0 | 2.93% | motif file (matrix) |
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| 25 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-4 | -9.227e+00 | 0.0015 | 60.0 | 3.72% | 986.6 | 2.21% | motif file (matrix) |
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| 26 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-3 | -9.174e+00 | 0.0015 | 145.0 | 9.00% | 2931.7 | 6.57% | motif file (matrix) |
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| 27 |  | DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer | 1e-3 | -8.544e+00 | 0.0028 | 159.0 | 9.86% | 3312.6 | 7.42% | motif file (matrix) |
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| 28 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-3 | -8.505e+00 | 0.0028 | 121.0 | 7.51% | 2404.1 | 5.39% | motif file (matrix) |
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| 29 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-3 | -8.126e+00 | 0.0039 | 214.0 | 13.28% | 4702.4 | 10.53% | motif file (matrix) |
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| 30 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-3 | -7.885e+00 | 0.0049 | 99.0 | 6.14% | 1925.7 | 4.31% | motif file (matrix) |
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| 31 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-3 | -7.816e+00 | 0.0050 | 90.0 | 5.58% | 1720.1 | 3.85% | motif file (matrix) |
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| 32 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.735e+00 | 0.0053 | 21.0 | 1.30% | 250.3 | 0.56% | motif file (matrix) |
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| 33 |  | Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer | 1e-3 | -7.541e+00 | 0.0062 | 87.0 | 5.40% | 1666.7 | 3.73% | motif file (matrix) |
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| 34 |  | Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer | 1e-3 | -7.495e+00 | 0.0063 | 54.0 | 3.35% | 925.6 | 2.07% | motif file (matrix) |
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| 35 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-3 | -7.225e+00 | 0.0081 | 117.0 | 7.26% | 2393.5 | 5.36% | motif file (matrix) |
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| 36 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-3 | -7.041e+00 | 0.0094 | 88.0 | 5.46% | 1718.7 | 3.85% | motif file (matrix) |
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| 37 |  | Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.734e+00 | 0.0124 | 168.0 | 10.42% | 3679.9 | 8.24% | motif file (matrix) |
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| 38 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-2 | -6.266e+00 | 0.0193 | 405.0 | 25.12% | 9849.7 | 22.06% | motif file (matrix) |
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| 39 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-2 | -6.161e+00 | 0.0209 | 223.0 | 13.83% | 5123.2 | 11.48% | motif file (matrix) |
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| 40 |  | SeqBias: CG-repeat | 1e-2 | -6.153e+00 | 0.0209 | 103.0 | 6.39% | 2132.7 | 4.78% | motif file (matrix) |
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| 41 |  | TATA-box/Drosophila-Promoters/Homer | 1e-2 | -6.072e+00 | 0.0218 | 36.0 | 2.23% | 593.2 | 1.33% | motif file (matrix) |
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| 42 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.949e+00 | 0.0240 | 209.0 | 12.97% | 4789.8 | 10.73% | motif file (matrix) |
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| 43 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-2 | -5.872e+00 | 0.0254 | 56.0 | 3.47% | 1044.6 | 2.34% | motif file (matrix) |
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| 44 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-2 | -5.745e+00 | 0.0281 | 77.0 | 4.78% | 1540.0 | 3.45% | motif file (matrix) |
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| 45 |  | c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.659e+00 | 0.0300 | 43.0 | 2.67% | 762.5 | 1.71% | motif file (matrix) |
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| 46 |  | E-box(bHLH)/Promoter/Homer | 1e-2 | -5.044e+00 | 0.0543 | 15.0 | 0.93% | 197.5 | 0.44% | motif file (matrix) |
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| 47 |  | CRE(bZIP)/Promoter/Homer | 1e-2 | -5.032e+00 | 0.0543 | 32.0 | 1.99% | 547.6 | 1.23% | motif file (matrix) |
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| 48 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.994e+00 | 0.0547 | 43.0 | 2.67% | 793.0 | 1.78% | motif file (matrix) |
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| 49 |  | Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer | 1e-2 | -4.872e+00 | 0.0605 | 508.0 | 31.51% | 12825.0 | 28.73% | motif file (matrix) |
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