| 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 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-3 | -8.996e+00 | 0.0479 | 49.0 | 2.00% | 20.2 | 0.78% | motif file (matrix) |
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| 2 |  | PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer | 1e-3 | -8.393e+00 | 0.0479 | 460.0 | 18.81% | 389.8 | 15.09% | motif file (matrix) |
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| 3 |  | FOXA1:AR(Forkhead,NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer | 1e-3 | -8.362e+00 | 0.0479 | 17.0 | 0.70% | 2.6 | 0.10% | motif file (matrix) |
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| 4 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-2 | -6.586e+00 | 0.1334 | 171.0 | 6.99% | 128.5 | 4.97% | motif file (matrix) |
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| 5 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.748e+00 | 0.2467 | 32.0 | 1.31% | 14.5 | 0.56% | motif file (matrix) |
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| 6 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-2 | -5.737e+00 | 0.2467 | 201.0 | 8.22% | 160.9 | 6.23% | motif file (matrix) |
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| 7 |  | FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer | 1e-2 | -5.504e+00 | 0.2467 | 154.0 | 6.30% | 118.5 | 4.59% | motif file (matrix) |
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| 8 |  | MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer | 1e-2 | -5.141e+00 | 0.2832 | 17.0 | 0.70% | 5.3 | 0.21% | motif file (matrix) |
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| 9 |  | Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer | 1e-2 | -4.789e+00 | 0.3577 | 50.0 | 2.04% | 30.6 | 1.18% | motif file (matrix) |
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| 10 |  | E-box/Arabidopsis-Promoters/Homer | 1e-2 | -4.688e+00 | 0.3577 | 25.0 | 1.02% | 11.5 | 0.45% | motif file (matrix) |
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| 11 |  | IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer | 1e-2 | -4.613e+00 | 0.3577 | 116.0 | 4.74% | 88.3 | 3.42% | motif file (matrix) |
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