| 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 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-9 | -2.120e+01 | 0.0000 | 134.0 | 38.62% | 11676.4 | 23.82% | motif file (matrix) |
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| 2 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-6 | -1.388e+01 | 0.0001 | 196.0 | 56.48% | 21366.2 | 43.59% | motif file (matrix) |
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| 3 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-5 | -1.342e+01 | 0.0001 | 183.0 | 52.74% | 19686.6 | 40.16% | motif file (matrix) |
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| 4 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-4 | -1.115e+01 | 0.0009 | 195.0 | 56.20% | 21982.6 | 44.84% | motif file (matrix) |
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| 5 |  | Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer | 1e-3 | -9.110e+00 | 0.0058 | 113.0 | 32.56% | 11618.5 | 23.70% | motif file (matrix) |
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| 6 |  | NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-3 | -7.729e+00 | 0.0194 | 66.0 | 19.02% | 6183.4 | 12.61% | motif file (matrix) |
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| 7 |  | Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-3 | -7.683e+00 | 0.0194 | 137.0 | 39.48% | 15173.0 | 30.95% | motif file (matrix) |
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| 8 |  | c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.609e+00 | 0.0445 | 46.0 | 13.26% | 4097.9 | 8.36% | motif file (matrix) |
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| 9 |  | MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer | 1e-2 | -6.580e+00 | 0.0445 | 113.0 | 32.56% | 12387.3 | 25.27% | motif file (matrix) |
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| 10 |  | JunD(bZIP)/K562-JunD-ChIP-Seq/Homer | 1e-2 | -5.808e+00 | 0.0793 | 17.0 | 4.90% | 1119.9 | 2.28% | motif file (matrix) |
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| 11 |  | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1e-2 | -5.498e+00 | 0.0983 | 120.0 | 34.58% | 13702.7 | 27.95% | motif file (matrix) |
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| 12 |  | CRE(bZIP)/Promoter/Homer | 1e-2 | -5.370e+00 | 0.1024 | 32.0 | 9.22% | 2761.6 | 5.63% | motif file (matrix) |
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| 13 |  | CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.298e+00 | 0.1024 | 80.0 | 23.05% | 8575.7 | 17.49% | motif file (matrix) |
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| 14 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski et al.)/Homer | 1e-2 | -5.008e+00 | 0.1260 | 30.0 | 8.65% | 2607.9 | 5.32% | motif file (matrix) |
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| 15 |  | Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer | 1e-2 | -4.869e+00 | 0.1352 | 160.0 | 46.11% | 19393.8 | 39.56% | motif file (matrix) |
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| 16 |  | Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.717e+00 | 0.1475 | 82.0 | 23.63% | 9033.0 | 18.43% | motif file (matrix) |
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| 17 |  | Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer | 1e-2 | -4.691e+00 | 0.1475 | 48.0 | 13.83% | 4787.3 | 9.77% | motif file (matrix) |
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| 18 |  | ETS:E-box(ETS,bHLH)/HPC7-Scl-ChIP-Seq(GSE22178)/Homer | 1e-2 | -4.612e+00 | 0.1475 | 19.0 | 5.48% | 1477.8 | 3.01% | motif file (matrix) |
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