| 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 |  | Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer | 1e-7 | -1.628e+01 | 0.0000 | 39.0 | 18.06% | 11.1 | 7.15% | motif file (matrix) |
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| 2 |  | Nanog(Homeobox)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-6 | -1.544e+01 | 0.0000 | 102.0 | 47.22% | 47.1 | 30.43% | motif file (matrix) |
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| 3 |  | IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.526e+01 | 0.0000 | 11.0 | 5.09% | 1.9 | 1.24% | motif file (matrix) |
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| 4 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-4 | -1.055e+01 | 0.0016 | 41.0 | 18.98% | 16.0 | 10.33% | motif file (matrix) |
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| 5 |  | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1e-4 | -9.779e+00 | 0.0028 | 24.0 | 11.11% | 7.8 | 5.06% | motif file (matrix) |
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| 6 |  | ERE(NR/IR3)/MCF7-ERa-ChIP-Seq(Unpublished)/Homer | 1e-4 | -9.224e+00 | 0.0040 | 8.0 | 3.70% | 1.1 | 0.73% | motif file (matrix) |
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| 7 |  | ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer | 1e-3 | -8.794e+00 | 0.0053 | 23.0 | 10.65% | 7.4 | 4.78% | motif file (matrix) |
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| 8 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-3 | -8.661e+00 | 0.0053 | 44.0 | 20.37% | 18.5 | 11.92% | motif file (matrix) |
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| 9 |  | Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer | 1e-3 | -8.160e+00 | 0.0078 | 78.0 | 36.11% | 39.5 | 25.50% | motif file (matrix) |
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| 10 |  | Gata4(Zf)/Heart-Gata4-ChIP-Seq(GSE35151)/Homer | 1e-3 | -7.794e+00 | 0.0101 | 26.0 | 12.04% | 9.5 | 6.17% | motif file (matrix) |
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| 11 |  | RBPJ:Ebox/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-3 | -7.434e+00 | 0.0132 | 7.0 | 3.24% | 1.8 | 1.14% | motif file (matrix) |
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| 12 |  | Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer | 1e-3 | -7.423e+00 | 0.0132 | 15.0 | 6.94% | 4.9 | 3.17% | motif file (matrix) |
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| 13 |  | Unknown-ESC-element/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-3 | -7.161e+00 | 0.0147 | 17.0 | 7.87% | 5.7 | 3.70% | motif file (matrix) |
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| 14 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-3 | -6.978e+00 | 0.0164 | 25.0 | 11.57% | 9.8 | 6.34% | motif file (matrix) |
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| 15 |  | Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer | 1e-2 | -6.829e+00 | 0.0177 | 66.0 | 30.56% | 34.0 | 21.94% | motif file (matrix) |
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| 16 |  | Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer | 1e-2 | -6.738e+00 | 0.0182 | 34.0 | 15.74% | 14.0 | 9.06% | motif file (matrix) |
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| 17 |  | PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -6.708e+00 | 0.0182 | 12.0 | 5.56% | 3.8 | 2.44% | motif file (matrix) |
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| 18 |  | BMYB(HTH)/Hela-BMYB-ChIPSeq(GSE27030)/Homer | 1e-2 | -6.608e+00 | 0.0184 | 32.0 | 14.81% | 13.1 | 8.46% | motif file (matrix) |
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| 19 |  | Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer | 1e-2 | -6.198e+00 | 0.0250 | 16.0 | 7.41% | 5.0 | 3.26% | motif file (matrix) |
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| 20 |  | Max(HLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.198e+00 | 0.0250 | 16.0 | 7.41% | 5.4 | 3.47% | motif file (matrix) |
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| 21 |  | STAT6/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer | 1e-2 | -6.126e+00 | 0.0250 | 18.0 | 8.33% | 6.6 | 4.25% | motif file (matrix) |
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| 22 |  | STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer | 1e-2 | -6.126e+00 | 0.0250 | 18.0 | 8.33% | 6.3 | 4.10% | motif file (matrix) |
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| 23 |  | Pax8(Paired/Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-2 | -6.087e+00 | 0.0250 | 9.0 | 4.17% | 2.4 | 1.53% | motif file (matrix) |
pdf |
| 24 |  | Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.776e+00 | 0.0305 | 6.0 | 2.78% | 0.5 | 0.33% | motif file (matrix) |
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| 25 |  | Srebp1a(HLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.776e+00 | 0.0305 | 6.0 | 2.78% | 1.7 | 1.09% | motif file (matrix) |
pdf |
| 26 |  | TRa(NR)/C17.2-TRa-ChIP-Seq(GSE38347)/Homer | 1e-2 | -5.591e+00 | 0.0353 | 11.0 | 5.09% | 3.6 | 2.32% | motif file (matrix) |
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| 27 |  | Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer | 1e-2 | -4.857e+00 | 0.0708 | 8.0 | 3.70% | 2.5 | 1.64% | motif file (matrix) |
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| 28 |  | BMAL1(HLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-2 | -4.653e+00 | 0.0809 | 39.0 | 18.06% | 19.7 | 12.75% | motif file (matrix) |
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| 29 |  | GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer | 1e-2 | -4.653e+00 | 0.0809 | 39.0 | 18.06% | 19.7 | 12.72% | motif file (matrix) |
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