| 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 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-8 | -1.904e+01 | 0.0000 | 112.0 | 7.36% | 38.4 | 2.75% | motif file (matrix) |
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| 2 |  | GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer | 1e-7 | -1.796e+01 | 0.0000 | 231.0 | 15.18% | 119.7 | 8.56% | motif file (matrix) |
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| 3 |  | SeqBias: TA-repeat | 1e-7 | -1.743e+01 | 0.0000 | 389.0 | 25.56% | 241.6 | 17.28% | motif file (matrix) |
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| 4 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-7 | -1.651e+01 | 0.0000 | 128.0 | 8.41% | 52.5 | 3.75% | motif file (matrix) |
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| 5 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-6 | -1.507e+01 | 0.0000 | 23.0 | 1.51% | 0.0 | 0.00% | motif file (matrix) |
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| 6 |  | PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer | 1e-6 | -1.382e+01 | 0.0001 | 214.0 | 14.06% | 118.2 | 8.45% | motif file (matrix) |
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| 7 |  | ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer | 1e-5 | -1.357e+01 | 0.0001 | 156.0 | 10.25% | 77.9 | 5.57% | motif file (matrix) |
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| 8 |  | FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer | 1e-5 | -1.310e+01 | 0.0001 | 99.0 | 6.50% | 40.2 | 2.88% | motif file (matrix) |
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| 9 |  | FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer | 1e-5 | -1.248e+01 | 0.0002 | 94.0 | 6.18% | 38.1 | 2.72% | motif file (matrix) |
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| 10 |  | PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer | 1e-5 | -1.212e+01 | 0.0002 | 253.0 | 16.62% | 153.6 | 10.98% | motif file (matrix) |
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| 11 |  | Unknown2/Drosophila-Promoters/Homer | 1e-5 | -1.154e+01 | 0.0003 | 114.0 | 7.49% | 53.1 | 3.80% | motif file (matrix) |
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| 12 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-4 | -1.066e+01 | 0.0008 | 41.0 | 2.69% | 10.7 | 0.77% | motif file (matrix) |
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| 13 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-4 | -1.052e+01 | 0.0008 | 69.0 | 4.53% | 26.3 | 1.88% | motif file (matrix) |
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| 14 |  | Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer | 1e-4 | -9.879e+00 | 0.0014 | 72.0 | 4.73% | 29.4 | 2.10% | motif file (matrix) |
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| 15 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-4 | -9.869e+00 | 0.0014 | 89.0 | 5.85% | 40.5 | 2.89% | motif file (matrix) |
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| 16 |  | KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer | 1e-4 | -9.780e+00 | 0.0014 | 105.0 | 6.90% | 51.2 | 3.66% | motif file (matrix) |
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| 17 |  | Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer | 1e-4 | -9.543e+00 | 0.0016 | 71.0 | 4.66% | 30.0 | 2.15% | motif file (matrix) |
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| 18 |  | E-box/Arabidopsis-Promoters/Homer | 1e-3 | -8.947e+00 | 0.0028 | 39.0 | 2.56% | 11.9 | 0.85% | motif file (matrix) |
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| 19 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-3 | -8.413e+00 | 0.0045 | 34.0 | 2.23% | 9.5 | 0.68% | motif file (matrix) |
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| 20 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-3 | -8.377e+00 | 0.0045 | 43.0 | 2.83% | 14.4 | 1.03% | motif file (matrix) |
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| 21 |  | PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer | 1e-3 | -8.332e+00 | 0.0045 | 94.0 | 6.18% | 47.0 | 3.36% | motif file (matrix) |
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| 22 |  | Bapx1(Homeobox)/VertebralCol-Bapx1-ChIP-Seq(GSE36672)/Homer | 1e-3 | -8.183e+00 | 0.0049 | 273.0 | 17.94% | 185.6 | 13.27% | motif file (matrix) |
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| 23 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-3 | -7.590e+00 | 0.0085 | 108.0 | 7.10% | 59.7 | 4.27% | motif file (matrix) |
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| 24 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-3 | -7.020e+00 | 0.0144 | 21.0 | 1.38% | 4.8 | 0.34% | motif file (matrix) |
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| 25 |  | CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer | 1e-2 | -6.887e+00 | 0.0158 | 276.0 | 18.13% | 194.7 | 13.93% | motif file (matrix) |
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| 26 |  | Unknown6/Drosophila-Promoters/Homer | 1e-2 | -6.838e+00 | 0.0160 | 77.0 | 5.06% | 39.9 | 2.85% | motif file (matrix) |
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| 27 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-2 | -6.761e+00 | 0.0166 | 88.0 | 5.78% | 47.9 | 3.42% | motif file (matrix) |
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| 28 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-2 | -6.619e+00 | 0.0185 | 35.0 | 2.30% | 12.7 | 0.90% | motif file (matrix) |
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| 29 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -6.010e+00 | 0.0327 | 30.0 | 1.97% | 10.5 | 0.75% | motif file (matrix) |
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| 30 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.504e+00 | 0.0525 | 46.0 | 3.02% | 21.6 | 1.55% | motif file (matrix) |
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| 31 |  | Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.433e+00 | 0.0546 | 155.0 | 10.18% | 103.2 | 7.38% | motif file (matrix) |
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| 32 |  | Nkx3.1(Homeobox)/LNCaP-Nkx3.1-ChIP-Seq(GSE28264)/Homer | 1e-2 | -5.262e+00 | 0.0627 | 207.0 | 13.60% | 146.5 | 10.48% | motif file (matrix) |
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| 33 |  | Mef2d(MADS)/Retina-Mef2d-ChIP-Seq(GSE61391)/Homer | 1e-2 | -5.213e+00 | 0.0639 | 21.0 | 1.38% | 7.0 | 0.50% | motif file (matrix) |
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| 34 |  | Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan_et_al.)/Homer | 1e-2 | -4.900e+00 | 0.0848 | 105.0 | 6.90% | 66.6 | 4.76% | motif file (matrix) |
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| 35 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.811e+00 | 0.0900 | 48.0 | 3.15% | 24.3 | 1.74% | motif file (matrix) |
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| 36 |  | RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer | 1e-2 | -4.771e+00 | 0.0911 | 10.0 | 0.66% | 1.2 | 0.08% | motif file (matrix) |
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