| 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 |  | STAT5(Stat)/mCD4+-Stat5-ChIP-Seq(GSE12346)/Homer | 1e-10 | -2.339e+01 | 0.0000 | 995.0 | 4.47% | 1014.3 | 3.64% | motif file (matrix) |
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| 2 |  | STAT6(Stat)/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer | 1e-6 | -1.567e+01 | 0.0000 | 1518.0 | 6.82% | 1670.1 | 5.99% | motif file (matrix) |
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| 3 |  | Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer | 1e-6 | -1.521e+01 | 0.0000 | 2582.0 | 11.61% | 2942.2 | 10.55% | motif file (matrix) |
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| 4 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-6 | -1.449e+01 | 0.0000 | 4077.0 | 18.33% | 4761.8 | 17.08% | motif file (matrix) |
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| 5 |  | STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer | 1e-5 | -1.154e+01 | 0.0005 | 2452.0 | 11.02% | 2828.6 | 10.15% | motif file (matrix) |
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| 6 |  | LXRE(NR),DR4/RAW-LXRb.biotin-ChIP-Seq(GSE21512)/Homer | 1e-4 | -1.069e+01 | 0.0010 | 414.0 | 1.86% | 422.5 | 1.52% | motif file (matrix) |
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| 7 |  | ZNF711(Zf)/SHSY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer | 1e-4 | -1.052e+01 | 0.0010 | 2721.0 | 12.23% | 3167.3 | 11.36% | motif file (matrix) |
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| 8 |  | ZFX(Zf)/mES-Zfx-ChIP-Seq(GSE11431)/Homer | 1e-4 | -1.030e+01 | 0.0011 | 1892.0 | 8.50% | 2168.2 | 7.78% | motif file (matrix) |
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| 9 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-3 | -8.958e+00 | 0.0038 | 600.0 | 2.70% | 646.1 | 2.32% | motif file (matrix) |
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| 10 |  | Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer | 1e-3 | -8.606e+00 | 0.0048 | 2347.0 | 10.55% | 2740.8 | 9.83% | motif file (matrix) |
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| 11 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-3 | -7.181e+00 | 0.0183 | 699.0 | 3.14% | 776.1 | 2.78% | motif file (matrix) |
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| 12 |  | BMYB(HTH)/Hela-BMYB-ChIP-Seq(GSE27030)/Homer | 1e-3 | -7.043e+00 | 0.0192 | 3267.0 | 14.69% | 3889.8 | 13.95% | motif file (matrix) |
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| 13 |  | THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer | 1e-2 | -6.833e+00 | 0.0219 | 1054.0 | 4.74% | 1202.8 | 4.31% | motif file (matrix) |
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| 14 |  | Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer | 1e-2 | -6.607e+00 | 0.0255 | 2360.0 | 10.61% | 2788.0 | 10.00% | motif file (matrix) |
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| 15 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-2 | -6.352e+00 | 0.0307 | 4308.0 | 19.36% | 5184.4 | 18.60% | motif file (matrix) |
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| 16 |  | CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer | 1e-2 | -6.046e+00 | 0.0391 | 2176.0 | 9.78% | 2572.1 | 9.23% | motif file (matrix) |
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| 17 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-2 | -5.804e+00 | 0.0468 | 2080.0 | 9.35% | 2459.3 | 8.82% | motif file (matrix) |
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| 18 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-2 | -5.583e+00 | 0.0552 | 433.0 | 1.95% | 476.8 | 1.71% | motif file (matrix) |
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| 19 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.502e+00 | 0.0567 | 996.0 | 4.48% | 1149.0 | 4.12% | motif file (matrix) |
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| 20 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-2 | -5.376e+00 | 0.0611 | 3483.0 | 15.66% | 4189.1 | 15.03% | motif file (matrix) |
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| 21 |  | Hnf1(Homeobox)/Liver-Foxa2-Chip-Seq(GSE25694)/Homer | 1e-2 | -5.317e+00 | 0.0617 | 569.0 | 2.56% | 639.9 | 2.30% | motif file (matrix) |
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| 22 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.286e+00 | 0.0617 | 919.0 | 4.13% | 1058.2 | 3.80% | motif file (matrix) |
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| 23 |  | Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer | 1e-2 | -5.131e+00 | 0.0679 | 1918.0 | 8.62% | 2273.4 | 8.16% | motif file (matrix) |
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| 24 |  | HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer | 1e-2 | -5.102e+00 | 0.0679 | 4325.0 | 19.44% | 5235.6 | 18.78% | motif file (matrix) |
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| 25 |  | STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer | 1e-2 | -4.980e+00 | 0.0726 | 762.0 | 3.43% | 873.4 | 3.13% | motif file (matrix) |
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| 26 |  | GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer | 1e-2 | -4.866e+00 | 0.0782 | 4837.0 | 21.74% | 5875.0 | 21.08% | motif file (matrix) |
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| 27 |  | Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer | 1e-2 | -4.724e+00 | 0.0868 | 5437.0 | 24.44% | 6623.5 | 23.76% | motif file (matrix) |
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| 28 |  | EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer | 1e-2 | -4.671e+00 | 0.0882 | 1768.0 | 7.95% | 2098.7 | 7.53% | motif file (matrix) |
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