| 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 |  | c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-4 | -1.138e+01 | 0.0030 | 347.0 | 10.81% | 4027.3 | 8.62% | motif file (matrix) |
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| 2 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.034e+00 | 0.0428 | 502.0 | 15.63% | 6315.0 | 13.52% | motif file (matrix) |
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| 3 |  | Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer | 1e-3 | -7.677e+00 | 0.0428 | 307.0 | 9.56% | 3701.1 | 7.92% | motif file (matrix) |
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| 4 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-2 | -6.839e+00 | 0.0707 | 854.0 | 26.60% | 11320.8 | 24.24% | motif file (matrix) |
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| 5 |  | HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer | 1e-2 | -6.347e+00 | 0.0925 | 841.0 | 26.19% | 11189.6 | 23.96% | motif file (matrix) |
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| 6 |  | Sp1(Zf)/Promoter/Homer | 1e-2 | -6.282e+00 | 0.0925 | 80.0 | 2.49% | 825.7 | 1.77% | motif file (matrix) |
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| 7 |  | Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer | 1e-2 | -5.490e+00 | 0.1556 | 774.0 | 24.10% | 10339.7 | 22.14% | motif file (matrix) |
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| 8 |  | Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer | 1e-2 | -5.369e+00 | 0.1556 | 683.0 | 21.27% | 9071.9 | 19.42% | motif file (matrix) |
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