| 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 |  | RARg(NR)/ES-RARg-ChIP-Seq(GSE30538)/Homer | 1e-3 | -8.266e+00 | 0.0633 | 79.0 | 0.96% | 206.9 | 0.64% | motif file (matrix) |
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| 2 |  | PAX5(Paired/Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-3 | -7.546e+00 | 0.0650 | 919.0 | 11.22% | 3290.8 | 10.11% | motif file (matrix) |
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| 3 |  | Pax8(Paired/Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-3 | -7.337e+00 | 0.0650 | 858.0 | 10.48% | 3065.9 | 9.42% | motif file (matrix) |
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| 4 |  | OCT4-SOX2-TCF-NANOG((POU/Homeobox/HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.267e+00 | 0.3172 | 444.0 | 5.42% | 1562.2 | 4.80% | motif file (matrix) |
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| 5 |  | ETS:E-box/HPC7-Scl-ChIP-Seq(GSE22178)/Homer | 1e-2 | -5.130e+00 | 0.3172 | 248.0 | 3.03% | 837.4 | 2.57% | motif file (matrix) |
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