| 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-13 | -3.061e+01 | 0.0000 | 198.0 | 25.29% | 3940.4 | 15.00% | motif file (matrix) |
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| 2 |  | Pit1(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer | 1e-13 | -3.060e+01 | 0.0000 | 375.0 | 47.89% | 9162.8 | 34.89% | motif file (matrix) |
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| 3 |  | Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer | 1e-13 | -3.014e+01 | 0.0000 | 223.0 | 28.48% | 4648.3 | 17.70% | motif file (matrix) |
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| 4 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-9 | -2.207e+01 | 0.0000 | 70.0 | 8.94% | 1026.8 | 3.91% | motif file (matrix) |
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| 5 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-7 | -1.682e+01 | 0.0000 | 37.0 | 4.73% | 446.0 | 1.70% | motif file (matrix) |
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| 6 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-7 | -1.682e+01 | 0.0000 | 37.0 | 4.73% | 446.0 | 1.70% | motif file (matrix) |
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| 7 |  | NRF(NRF)/Promoter/Homer | 1e-6 | -1.548e+01 | 0.0000 | 27.0 | 3.45% | 280.5 | 1.07% | motif file (matrix) |
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| 8 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-6 | -1.418e+01 | 0.0000 | 99.0 | 12.64% | 2003.4 | 7.63% | motif file (matrix) |
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| 9 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-6 | -1.390e+01 | 0.0000 | 56.0 | 7.15% | 930.4 | 3.54% | motif file (matrix) |
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| 10 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo et al.)/Homer | 1e-5 | -1.293e+01 | 0.0001 | 85.0 | 10.86% | 1691.7 | 6.44% | motif file (matrix) |
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| 11 |  | p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer | 1e-5 | -1.238e+01 | 0.0001 | 54.0 | 6.90% | 931.9 | 3.55% | motif file (matrix) |
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| 12 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-5 | -1.191e+01 | 0.0001 | 188.0 | 24.01% | 4667.0 | 17.77% | motif file (matrix) |
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| 13 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-4 | -1.143e+01 | 0.0002 | 285.0 | 36.40% | 7692.6 | 29.29% | motif file (matrix) |
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| 14 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-3 | -9.148e+00 | 0.0020 | 65.0 | 8.30% | 1339.7 | 5.10% | motif file (matrix) |
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| 15 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.576e+00 | 0.0090 | 42.0 | 5.36% | 811.7 | 3.09% | motif file (matrix) |
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| 16 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-3 | -7.271e+00 | 0.0115 | 81.0 | 10.34% | 1884.0 | 7.17% | motif file (matrix) |
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| 17 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.977e+00 | 0.0394 | 59.0 | 7.54% | 1350.0 | 5.14% | motif file (matrix) |
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| 18 |  | Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer | 1e-2 | -5.940e+00 | 0.0394 | 238.0 | 30.40% | 6801.8 | 25.90% | motif file (matrix) |
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| 19 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.915e+00 | 0.0394 | 89.0 | 11.37% | 2213.3 | 8.43% | motif file (matrix) |
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