| 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)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-5 | -1.377e+01 | 0.0004 | 133.0 | 8.65% | 66.0 | 4.43% | motif file (matrix) |
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| 2 |  | PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer | 1e-5 | -1.324e+01 | 0.0004 | 256.0 | 16.66% | 161.3 | 10.82% | motif file (matrix) |
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| 3 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-5 | -1.307e+01 | 0.0004 | 118.0 | 7.68% | 56.7 | 3.80% | motif file (matrix) |
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| 4 |  | FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer | 1e-5 | -1.200e+01 | 0.0006 | 116.0 | 7.55% | 57.1 | 3.83% | motif file (matrix) |
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| 5 |  | PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer | 1e-4 | -1.149e+01 | 0.0008 | 288.0 | 18.74% | 194.4 | 13.05% | motif file (matrix) |
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| 6 |  | SeqBias: TA-repeat | 1e-4 | -1.062e+01 | 0.0016 | 430.0 | 27.98% | 321.5 | 21.58% | motif file (matrix) |
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| 7 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-4 | -1.059e+01 | 0.0016 | 19.0 | 1.24% | 1.5 | 0.10% | motif file (matrix) |
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| 8 |  | TOD6?/SacCer-Promoters/Homer | 1e-4 | -9.323e+00 | 0.0043 | 17.0 | 1.11% | 1.9 | 0.13% | motif file (matrix) |
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| 9 |  | Brn1(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer | 1e-3 | -8.189e+00 | 0.0119 | 39.0 | 2.54% | 13.9 | 0.93% | motif file (matrix) |
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| 10 |  | E-box/Arabidopsis-Promoters/Homer | 1e-3 | -7.963e+00 | 0.0135 | 24.0 | 1.56% | 5.5 | 0.37% | motif file (matrix) |
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| 11 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-3 | -7.837e+00 | 0.0139 | 96.0 | 6.25% | 53.6 | 3.59% | motif file (matrix) |
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| 12 |  | ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer | 1e-3 | -7.837e+00 | 0.0139 | 117.0 | 7.61% | 69.0 | 4.63% | motif file (matrix) |
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| 13 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-3 | -7.448e+00 | 0.0173 | 14.0 | 0.91% | 1.6 | 0.11% | motif file (matrix) |
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| 14 |  | Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer | 1e-3 | -7.434e+00 | 0.0173 | 70.0 | 4.55% | 35.3 | 2.37% | motif file (matrix) |
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| 15 |  | GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer | 1e-3 | -6.973e+00 | 0.0242 | 163.0 | 10.61% | 109.7 | 7.36% | motif file (matrix) |
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| 16 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-3 | -6.964e+00 | 0.0242 | 31.0 | 2.02% | 10.8 | 0.72% | motif file (matrix) |
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| 17 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-3 | -6.954e+00 | 0.0242 | 20.0 | 1.30% | 4.7 | 0.32% | motif file (matrix) |
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| 18 |  | Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer | 1e-2 | -6.568e+00 | 0.0302 | 15.0 | 0.98% | 2.7 | 0.18% | motif file (matrix) |
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| 19 |  | FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer | 1e-2 | -6.443e+00 | 0.0324 | 97.0 | 6.31% | 59.0 | 3.96% | motif file (matrix) |
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| 20 |  | Sox15(HMG)/CPA-Sox15-ChIP-Seq(GSE62909)/Homer | 1e-2 | -6.344e+00 | 0.0340 | 73.0 | 4.75% | 40.2 | 2.70% | motif file (matrix) |
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| 21 |  | Oct6(POU,Homeobox)/NPC-Oct6-ChIP-Seq(GSE35496)/Homer | 1e-2 | -6.177e+00 | 0.0383 | 46.0 | 2.99% | 21.8 | 1.46% | motif file (matrix) |
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| 22 |  | LHY(Myb)/Seedling-LHY-ChIP-Seq(GSE52175)/Homer | 1e-2 | -6.071e+00 | 0.0406 | 123.0 | 8.00% | 80.6 | 5.41% | motif file (matrix) |
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| 23 |  | SeqBias: G/A bias | 1e-2 | -6.051e+00 | 0.0406 | 1511.0 | 98.31% | 1440.2 | 96.65% | motif file (matrix) |
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| 24 |  | Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer | 1e-2 | -5.980e+00 | 0.0408 | 41.0 | 2.67% | 19.0 | 1.27% | motif file (matrix) |
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| 25 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.873e+00 | 0.0436 | 83.0 | 5.40% | 49.9 | 3.35% | motif file (matrix) |
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| 26 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-2 | -5.805e+00 | 0.0448 | 36.0 | 2.34% | 15.4 | 1.03% | motif file (matrix) |
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| 27 |  | GAGA-repeat/SacCer-Promoters/Homer | 1e-2 | -5.684e+00 | 0.0488 | 319.0 | 20.75% | 251.5 | 16.88% | motif file (matrix) |
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| 28 |  | DMRT1(DM)/Testis-DMRT1-ChIP-Seq(GSE64892)/Homer | 1e-2 | -5.299e+00 | 0.0691 | 22.0 | 1.43% | 7.8 | 0.52% | motif file (matrix) |
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| 29 |  | Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.287e+00 | 0.0691 | 36.0 | 2.34% | 16.6 | 1.11% | motif file (matrix) |
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| 30 |  | Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.221e+00 | 0.0697 | 43.0 | 2.80% | 22.0 | 1.48% | motif file (matrix) |
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| 31 |  | DMRT6(DM)/Testis-DMRT6-ChIP-Seq(GSE60440)/Homer | 1e-2 | -5.055e+00 | 0.0796 | 18.0 | 1.17% | 5.7 | 0.38% | motif file (matrix) |
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| 32 |  | caudal(Homeobox)/Drosophila-Embryos-ChIP-Chip(modEncode)/Homer | 1e-2 | -5.046e+00 | 0.0796 | 82.0 | 5.34% | 52.0 | 3.49% | motif file (matrix) |
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| 33 |  | Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-2 | -5.038e+00 | 0.0796 | 92.0 | 5.99% | 59.4 | 3.99% | motif file (matrix) |
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| 34 |  | Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer | 1e-2 | -4.945e+00 | 0.0810 | 61.0 | 3.97% | 35.6 | 2.39% | motif file (matrix) |
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| 35 |  | STAT5(Stat)/mCD4+-Stat5-ChIP-Seq(GSE12346)/Homer | 1e-2 | -4.876e+00 | 0.0844 | 21.0 | 1.37% | 7.7 | 0.52% | motif file (matrix) |
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