| 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 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-14 | -3.452e+01 | 0.0000 | 22.0 | 20.56% | 1049.7 | 2.12% | motif file (matrix) |
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| 2 |  | Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer | 1e-13 | -3.182e+01 | 0.0000 | 22.0 | 20.56% | 1200.7 | 2.42% | motif file (matrix) |
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| 3 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-11 | -2.677e+01 | 0.0000 | 31.0 | 28.97% | 3340.4 | 6.75% | motif file (matrix) |
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| 4 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-11 | -2.613e+01 | 0.0000 | 48.0 | 44.86% | 8100.4 | 16.36% | motif file (matrix) |
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| 5 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-11 | -2.566e+01 | 0.0000 | 55.0 | 51.40% | 10548.1 | 21.30% | motif file (matrix) |
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| 6 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-10 | -2.369e+01 | 0.0000 | 51.0 | 47.66% | 9666.9 | 19.52% | motif file (matrix) |
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| 7 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-10 | -2.326e+01 | 0.0000 | 50.0 | 46.73% | 9438.9 | 19.06% | motif file (matrix) |
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| 8 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-8 | -2.033e+01 | 0.0000 | 32.0 | 29.91% | 4593.8 | 9.28% | motif file (matrix) |
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| 9 |  | Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-8 | -1.892e+01 | 0.0000 | 24.0 | 22.43% | 2809.9 | 5.67% | motif file (matrix) |
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| 10 |  | X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-7 | -1.732e+01 | 0.0000 | 17.0 | 15.89% | 1514.4 | 3.06% | motif file (matrix) |
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| 11 |  | Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer | 1e-6 | -1.609e+01 | 0.0000 | 22.0 | 20.56% | 2768.0 | 5.59% | motif file (matrix) |
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| 12 |  | OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-4 | -1.128e+01 | 0.0003 | 20.0 | 18.69% | 3148.0 | 6.36% | motif file (matrix) |
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| 13 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-4 | -1.081e+01 | 0.0004 | 51.0 | 47.66% | 14094.0 | 28.46% | motif file (matrix) |
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| 14 |  | NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-4 | -1.029e+01 | 0.0006 | 69.0 | 64.49% | 22208.7 | 44.85% | motif file (matrix) |
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| 15 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-4 | -1.010e+01 | 0.0007 | 29.0 | 27.10% | 6223.5 | 12.57% | motif file (matrix) |
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| 16 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-3 | -9.008e+00 | 0.0020 | 74.0 | 69.16% | 25347.4 | 51.19% | motif file (matrix) |
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| 17 |  | Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer | 1e-3 | -8.557e+00 | 0.0030 | 8.0 | 7.48% | 726.4 | 1.47% | motif file (matrix) |
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| 18 |  | Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer | 1e-3 | -7.248e+00 | 0.0104 | 45.0 | 42.06% | 13524.5 | 27.31% | motif file (matrix) |
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| 19 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-3 | -7.236e+00 | 0.0104 | 68.0 | 63.55% | 23641.8 | 47.74% | motif file (matrix) |
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| 20 |  | Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer | 1e-2 | -6.673e+00 | 0.0167 | 67.0 | 62.62% | 23570.5 | 47.60% | motif file (matrix) |
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| 21 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-2 | -6.560e+00 | 0.0178 | 68.0 | 63.55% | 24122.7 | 48.72% | motif file (matrix) |
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| 22 |  | Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -6.102e+00 | 0.0269 | 28.0 | 26.17% | 7510.3 | 15.17% | motif file (matrix) |
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| 23 |  | Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.009e+00 | 0.0282 | 7.0 | 6.54% | 843.4 | 1.70% | motif file (matrix) |
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| 24 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-2 | -5.957e+00 | 0.0282 | 10.0 | 9.35% | 1606.2 | 3.24% | motif file (matrix) |
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| 25 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-2 | -5.957e+00 | 0.0282 | 10.0 | 9.35% | 1606.2 | 3.24% | motif file (matrix) |
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| 26 |  | NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.854e+00 | 0.0291 | 7.0 | 6.54% | 867.6 | 1.75% | motif file (matrix) |
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| 27 |  | E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer | 1e-2 | -5.644e+00 | 0.0346 | 53.0 | 49.53% | 17994.9 | 36.34% | motif file (matrix) |
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| 28 |  | GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer | 1e-2 | -5.420e+00 | 0.0417 | 17.0 | 15.89% | 3918.4 | 7.91% | motif file (matrix) |
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| 29 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-2 | -5.374e+00 | 0.0422 | 28.0 | 26.17% | 7897.4 | 15.95% | motif file (matrix) |
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