| 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 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-25 | -5.889e+01 | 0.0000 | 467.0 | 24.66% | 4298.2 | 15.30% | motif file (matrix) |
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| 2 |  | Pit1(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer | 1e-20 | -4.811e+01 | 0.0000 | 837.0 | 44.19% | 9457.3 | 33.66% | motif file (matrix) |
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| 3 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-18 | -4.212e+01 | 0.0000 | 149.0 | 7.87% | 990.7 | 3.53% | motif file (matrix) |
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| 4 |  | Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer | 1e-18 | -4.186e+01 | 0.0000 | 497.0 | 26.24% | 5069.1 | 18.04% | motif file (matrix) |
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| 5 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-16 | -3.692e+01 | 0.0000 | 83.0 | 4.38% | 429.7 | 1.53% | motif file (matrix) |
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| 6 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-16 | -3.692e+01 | 0.0000 | 83.0 | 4.38% | 429.7 | 1.53% | motif file (matrix) |
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| 7 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-14 | -3.263e+01 | 0.0000 | 695.0 | 36.69% | 8003.4 | 28.49% | motif file (matrix) |
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| 8 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-12 | -2.834e+01 | 0.0000 | 128.0 | 6.76% | 952.4 | 3.39% | motif file (matrix) |
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| 9 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo et al.)/Homer | 1e-10 | -2.505e+01 | 0.0000 | 191.0 | 10.08% | 1709.6 | 6.08% | motif file (matrix) |
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| 10 |  | Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer | 1e-10 | -2.435e+01 | 0.0000 | 340.0 | 17.95% | 3556.0 | 12.66% | motif file (matrix) |
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| 11 |  | p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer | 1e-10 | -2.387e+01 | 0.0000 | 122.0 | 6.44% | 955.8 | 3.40% | motif file (matrix) |
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| 12 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-8 | -1.948e+01 | 0.0000 | 202.0 | 10.67% | 1969.7 | 7.01% | motif file (matrix) |
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| 13 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-7 | -1.695e+01 | 0.0000 | 403.0 | 21.28% | 4644.9 | 16.53% | motif file (matrix) |
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| 14 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-6 | -1.566e+01 | 0.0000 | 93.0 | 4.91% | 776.3 | 2.76% | motif file (matrix) |
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| 15 |  | NRF(NRF)/Promoter/Homer | 1e-6 | -1.502e+01 | 0.0000 | 49.0 | 2.59% | 323.7 | 1.15% | motif file (matrix) |
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| 16 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-5 | -1.256e+01 | 0.0001 | 135.0 | 7.13% | 1337.6 | 4.76% | motif file (matrix) |
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| 17 |  | GATA3(Zf),DR8/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer | 1e-5 | -1.240e+01 | 0.0001 | 45.0 | 2.38% | 315.4 | 1.12% | motif file (matrix) |
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| 18 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-4 | -1.151e+01 | 0.0001 | 130.0 | 6.86% | 1305.9 | 4.65% | motif file (matrix) |
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| 19 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.032e+00 | 0.0045 | 192.0 | 10.14% | 2225.3 | 7.92% | motif file (matrix) |
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| 20 |  | Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer | 1e-2 | -6.577e+00 | 0.0184 | 256.0 | 13.52% | 3165.2 | 11.27% | motif file (matrix) |
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| 21 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-2 | -6.074e+00 | 0.0289 | 160.0 | 8.45% | 1893.8 | 6.74% | motif file (matrix) |
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| 22 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-2 | -5.438e+00 | 0.0522 | 31.0 | 1.64% | 273.8 | 0.97% | motif file (matrix) |
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