| 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 |  | Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer | 1e-5 | -1.163e+01 | 0.0035 | 91.0 | 2.38% | 44.9 | 1.13% | motif file (matrix) |
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| 2 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-3 | -8.536e+00 | 0.0380 | 258.0 | 6.76% | 194.2 | 4.86% | motif file (matrix) |
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| 3 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-3 | -8.212e+00 | 0.0380 | 298.0 | 7.81% | 232.6 | 5.83% | motif file (matrix) |
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| 4 |  | GABPA(ETS)/Jurkat-GABPa-ChIP-Seq(GSE17954)/Homer | 1e-3 | -7.209e+00 | 0.0716 | 98.0 | 2.57% | 61.2 | 1.53% | motif file (matrix) |
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| 5 |  | FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer | 1e-3 | -6.919e+00 | 0.0765 | 245.0 | 6.42% | 191.4 | 4.80% | motif file (matrix) |
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| 6 |  | Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.669e+00 | 0.0819 | 129.0 | 3.38% | 89.3 | 2.24% | motif file (matrix) |
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| 7 |  | ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer | 1e-2 | -5.939e+00 | 0.1457 | 122.0 | 3.20% | 86.2 | 2.16% | motif file (matrix) |
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| 8 |  | PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.862e+00 | 0.1457 | 41.0 | 1.07% | 20.2 | 0.50% | motif file (matrix) |
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| 9 |  | ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer | 1e-2 | -5.755e+00 | 0.1457 | 174.0 | 4.56% | 133.9 | 3.35% | motif file (matrix) |
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| 10 |  | PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.720e+00 | 0.1457 | 198.0 | 5.19% | 155.7 | 3.90% | motif file (matrix) |
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| 11 |  | Brn1(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer | 1e-2 | -5.471e+00 | 0.1481 | 80.0 | 2.10% | 52.0 | 1.30% | motif file (matrix) |
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| 12 |  | Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer | 1e-2 | -5.079e+00 | 0.2009 | 121.0 | 3.17% | 89.9 | 2.25% | motif file (matrix) |
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| 13 |  | SeqBias: GA-repeat | 1e-2 | -4.986e+00 | 0.2035 | 1270.0 | 33.27% | 1223.7 | 30.65% | motif file (matrix) |
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| 14 |  | Unknown6/Drosophila-Promoters/Homer | 1e-2 | -4.918e+00 | 0.2035 | 278.0 | 7.28% | 235.6 | 5.90% | motif file (matrix) |
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| 15 |  | PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer | 1e-2 | -4.878e+00 | 0.2035 | 699.0 | 18.31% | 647.1 | 16.21% | motif file (matrix) |
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| 16 |  | THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer | 1e-2 | -4.872e+00 | 0.2035 | 57.0 | 1.49% | 35.5 | 0.89% | motif file (matrix) |
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| 17 |  | FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer | 1e-2 | -4.754e+00 | 0.2035 | 212.0 | 5.55% | 174.3 | 4.37% | motif file (matrix) |
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