| 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 |  | Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-3 | -7.683e+00 | 0.1133 | 61.0 | 2.96% | 63.1 | 1.87% | motif file (matrix) |
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| 2 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-2 | -6.905e+00 | 0.1234 | 195.0 | 9.46% | 255.3 | 7.58% | motif file (matrix) |
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| 3 |  | Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.934e+00 | 0.2171 | 31.0 | 1.50% | 29.3 | 0.87% | motif file (matrix) |
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| 4 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-2 | -5.801e+00 | 0.2171 | 401.0 | 19.45% | 576.3 | 17.12% | motif file (matrix) |
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| 5 |  | EBNA1(EBV virus)/Raji-EBNA1-ChIP-Seq(GSE30709)/Homer | 1e-2 | -5.625e+00 | 0.2171 | 4.0 | 0.19% | 0.8 | 0.02% | motif file (matrix) |
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| 6 |  | Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-2 | -5.462e+00 | 0.2171 | 48.0 | 2.33% | 52.9 | 1.57% | motif file (matrix) |
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| 7 |  | YY1(Zf)/Promoter/Homer | 1e-2 | -5.375e+00 | 0.2171 | 12.0 | 0.58% | 8.7 | 0.26% | motif file (matrix) |
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