| 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 |  | Oct2(POU/Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer | 1e-4 | -1.087e+01 | 0.0047 | 7.0 | 1.17% | 1.2 | 0.16% | motif file (matrix) |
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| 2 |  | RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer | 1e-4 | -9.548e+00 | 0.0088 | 21.0 | 3.51% | 10.1 | 1.34% | motif file (matrix) |
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| 3 |  | Tcf12(HLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-3 | -7.555e+00 | 0.0429 | 19.0 | 3.18% | 10.8 | 1.44% | motif file (matrix) |
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| 4 |  | Oct4(POU/Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-3 | -7.158e+00 | 0.0479 | 9.0 | 1.51% | 3.5 | 0.47% | motif file (matrix) |
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| 5 |  | Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-3 | -7.046e+00 | 0.0479 | 31.0 | 5.18% | 21.2 | 2.80% | motif file (matrix) |
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| 6 |  | NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -6.618e+00 | 0.0548 | 5.0 | 0.84% | 1.7 | 0.22% | motif file (matrix) |
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| 7 |  | Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer | 1e-2 | -6.466e+00 | 0.0548 | 28.0 | 4.68% | 19.2 | 2.55% | motif file (matrix) |
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| 8 |  | TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -6.370e+00 | 0.0548 | 14.0 | 2.34% | 7.4 | 0.98% | motif file (matrix) |
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| 9 |  | Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer | 1e-2 | -5.977e+00 | 0.0693 | 11.0 | 1.84% | 5.5 | 0.72% | motif file (matrix) |
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| 10 |  | bZIP:IRF/Th17-BatF-ChIP-Seq(GSE39756)/Homer | 1e-2 | -5.785e+00 | 0.0756 | 8.0 | 1.34% | 3.2 | 0.42% | motif file (matrix) |
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| 11 |  | HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer | 1e-2 | -5.169e+00 | 0.1166 | 6.0 | 1.00% | 2.4 | 0.31% | motif file (matrix) |
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| 12 |  | Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-2 | -5.169e+00 | 0.1166 | 6.0 | 1.00% | 2.6 | 0.34% | motif file (matrix) |
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| 13 |  | CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer | 1e-2 | -5.104e+00 | 0.1166 | 37.0 | 6.19% | 30.1 | 3.99% | motif file (matrix) |
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| 14 |  | Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer | 1e-2 | -4.742e+00 | 0.1341 | 4.0 | 0.67% | 0.6 | 0.08% | motif file (matrix) |
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| 15 |  | HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer | 1e-2 | -4.742e+00 | 0.1341 | 4.0 | 0.67% | 1.5 | 0.20% | motif file (matrix) |
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| 16 |  | PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer | 1e-2 | -4.742e+00 | 0.1341 | 4.0 | 0.67% | 1.9 | 0.26% | motif file (matrix) |
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