| 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 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-4 | -1.123e+01 | 0.0035 | 781.0 | 41.81% | 16517.0 | 36.96% | motif file (matrix) |
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| 2 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-4 | -1.110e+01 | 0.0035 | 613.0 | 32.82% | 12642.3 | 28.29% | motif file (matrix) |
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| 3 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-4 | -1.015e+01 | 0.0035 | 1314.0 | 70.34% | 29472.7 | 65.94% | motif file (matrix) |
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| 4 |  | TATA-Box(TBP)/Promoter/Homer | 1e-3 | -9.197e+00 | 0.0067 | 778.0 | 41.65% | 16692.1 | 37.35% | motif file (matrix) |
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| 5 |  | NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-3 | -8.803e+00 | 0.0079 | 556.0 | 29.76% | 11594.8 | 25.94% | motif file (matrix) |
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| 6 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-3 | -7.893e+00 | 0.0164 | 509.0 | 27.25% | 10628.3 | 23.78% | motif file (matrix) |
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| 7 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-3 | -7.782e+00 | 0.0164 | 800.0 | 42.83% | 17400.9 | 38.93% | motif file (matrix) |
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| 8 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-3 | -7.560e+00 | 0.0172 | 260.0 | 13.92% | 5078.4 | 11.36% | motif file (matrix) |
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| 9 |  | Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-3 | -7.539e+00 | 0.0172 | 127.0 | 6.80% | 2236.2 | 5.00% | motif file (matrix) |
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| 10 |  | Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer | 1e-3 | -7.458e+00 | 0.0172 | 799.0 | 42.77% | 17423.6 | 38.98% | motif file (matrix) |
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| 11 |  | Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer | 1e-3 | -7.357e+00 | 0.0172 | 294.0 | 15.74% | 5846.7 | 13.08% | motif file (matrix) |
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| 12 |  | CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer | 1e-3 | -7.197e+00 | 0.0172 | 401.0 | 21.47% | 8257.2 | 18.47% | motif file (matrix) |
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| 13 |  | Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer | 1e-2 | -6.763e+00 | 0.0235 | 1279.0 | 68.47% | 29067.3 | 65.04% | motif file (matrix) |
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| 14 |  | Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer | 1e-2 | -6.378e+00 | 0.0320 | 153.0 | 8.19% | 2863.1 | 6.41% | motif file (matrix) |
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| 15 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.286e+00 | 0.0328 | 797.0 | 42.67% | 17556.0 | 39.28% | motif file (matrix) |
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| 16 |  | Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer | 1e-2 | -6.042e+00 | 0.0392 | 1070.0 | 57.28% | 24106.7 | 53.94% | motif file (matrix) |
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| 17 |  | CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer | 1e-2 | -5.663e+00 | 0.0539 | 1049.0 | 56.16% | 23666.3 | 52.95% | motif file (matrix) |
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| 18 |  | GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer | 1e-2 | -5.627e+00 | 0.0539 | 704.0 | 37.69% | 15474.9 | 34.62% | motif file (matrix) |
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| 19 |  | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1e-2 | -5.494e+00 | 0.0571 | 560.0 | 29.98% | 12134.7 | 27.15% | motif file (matrix) |
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| 20 |  | Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer | 1e-2 | -5.464e+00 | 0.0571 | 163.0 | 8.73% | 3154.1 | 7.06% | motif file (matrix) |
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| 21 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-2 | -5.357e+00 | 0.0593 | 850.0 | 45.50% | 18967.5 | 42.44% | motif file (matrix) |
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| 22 |  | Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer | 1e-2 | -5.289e+00 | 0.0605 | 1520.0 | 81.37% | 35262.4 | 78.90% | motif file (matrix) |
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| 23 |  | Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.253e+00 | 0.0605 | 256.0 | 13.70% | 5226.1 | 11.69% | motif file (matrix) |
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| 24 |  | GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer | 1e-2 | -5.144e+00 | 0.0642 | 127.0 | 6.80% | 2405.2 | 5.38% | motif file (matrix) |
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| 25 |  | Znf263(Zf)/K562-Znf263-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.143e+00 | 0.0642 | 1202.0 | 64.35% | 27457.7 | 61.43% | motif file (matrix) |
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| 26 |  | Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer | 1e-2 | -5.066e+00 | 0.0642 | 929.0 | 49.73% | 20900.5 | 46.76% | motif file (matrix) |
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| 27 |  | Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer | 1e-2 | -4.999e+00 | 0.0660 | 179.0 | 9.58% | 3547.9 | 7.94% | motif file (matrix) |
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| 28 |  | Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer | 1e-2 | -4.855e+00 | 0.0735 | 922.0 | 49.36% | 20774.0 | 46.48% | motif file (matrix) |
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| 29 |  | Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer | 1e-2 | -4.708e+00 | 0.0821 | 409.0 | 21.90% | 8770.6 | 19.62% | motif file (matrix) |
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| 30 |  | PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer | 1e-2 | -4.625e+00 | 0.0863 | 627.0 | 33.57% | 13843.4 | 30.97% | motif file (matrix) |
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| 31 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-2 | -4.625e+00 | 0.0863 | 802.0 | 42.93% | 17965.1 | 40.20% | motif file (matrix) |
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