| 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-61 | -1.406e+02 | 0.0000 | 264.0 | 69.29% | 13902.0 | 28.24% | motif file (matrix) |
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| 2 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-49 | -1.138e+02 | 0.0000 | 331.0 | 86.88% | 25038.0 | 50.87% | motif file (matrix) |
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| 3 |  | Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer | 1e-48 | -1.124e+02 | 0.0000 | 240.0 | 62.99% | 13154.6 | 26.72% | motif file (matrix) |
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| 4 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-42 | -9.862e+01 | 0.0000 | 314.0 | 82.41% | 23739.1 | 48.23% | motif file (matrix) |
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| 5 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-39 | -9.112e+01 | 0.0000 | 307.0 | 80.58% | 23407.0 | 47.55% | motif file (matrix) |
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| 6 |  | Oct4:Sox17(POU,Homeobox,HMG)/F9-Sox17-ChIP-Seq(GSE44553)/Homer | 1e-10 | -2.425e+01 | 0.0000 | 51.0 | 13.39% | 2316.9 | 4.71% | motif file (matrix) |
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| 7 |  | c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-6 | -1.399e+01 | 0.0000 | 58.0 | 15.22% | 3833.1 | 7.79% | motif file (matrix) |
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| 8 |  | Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer | 1e-5 | -1.242e+01 | 0.0001 | 61.0 | 16.01% | 4324.5 | 8.79% | motif file (matrix) |
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| 9 |  | Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer | 1e-4 | -9.626e+00 | 0.0019 | 99.0 | 25.98% | 8852.1 | 17.98% | motif file (matrix) |
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| 10 |  | Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer | 1e-4 | -9.521e+00 | 0.0019 | 76.0 | 19.95% | 6348.1 | 12.90% | motif file (matrix) |
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| 11 |  | JunD(bZIP)/K562-JunD-ChIP-Seq/Homer | 1e-3 | -9.202e+00 | 0.0024 | 20.0 | 5.25% | 977.1 | 1.98% | motif file (matrix) |
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| 12 |  | Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer | 1e-3 | -8.386e+00 | 0.0050 | 133.0 | 34.91% | 13109.8 | 26.63% | motif file (matrix) |
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| 13 |  | IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer | 1e-3 | -8.217e+00 | 0.0055 | 71.0 | 18.64% | 6074.0 | 12.34% | motif file (matrix) |
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| 14 |  | GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer | 1e-3 | -7.444e+00 | 0.0110 | 48.0 | 12.60% | 3793.6 | 7.71% | motif file (matrix) |
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| 15 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-3 | -7.267e+00 | 0.0123 | 49.0 | 12.86% | 3928.9 | 7.98% | motif file (matrix) |
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| 16 |  | NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -6.555e+00 | 0.0235 | 48.0 | 12.60% | 3958.1 | 8.04% | motif file (matrix) |
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| 17 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.106e+00 | 0.0346 | 38.0 | 9.97% | 3004.9 | 6.10% | motif file (matrix) |
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| 18 |  | Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer | 1e-2 | -6.067e+00 | 0.0346 | 38.0 | 9.97% | 3011.2 | 6.12% | motif file (matrix) |
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| 19 |  | Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer | 1e-2 | -5.775e+00 | 0.0431 | 19.0 | 4.99% | 1204.7 | 2.45% | motif file (matrix) |
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| 20 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-2 | -5.477e+00 | 0.0552 | 48.0 | 12.60% | 4183.2 | 8.50% | motif file (matrix) |
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| 21 |  | Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan et al.)/Homer | 1e-2 | -5.287e+00 | 0.0636 | 220.0 | 57.74% | 25123.8 | 51.04% | motif file (matrix) |
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| 22 |  | Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer | 1e-2 | -5.186e+00 | 0.0671 | 151.0 | 39.63% | 16394.3 | 33.31% | motif file (matrix) |
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| 23 |  | Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer | 1e-2 | -5.144e+00 | 0.0671 | 80.0 | 21.00% | 7867.1 | 15.98% | motif file (matrix) |
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| 24 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.123e+00 | 0.0671 | 58.0 | 15.22% | 5368.7 | 10.91% | motif file (matrix) |
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| 25 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-2 | -5.116e+00 | 0.0671 | 72.0 | 18.90% | 6954.9 | 14.13% | motif file (matrix) |
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| 26 |  | GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer | 1e-2 | -4.810e+00 | 0.0827 | 27.0 | 7.09% | 2110.2 | 4.29% | motif file (matrix) |
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