| 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 |  | Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer | 1e-6 | -1.510e+01 | 0.0001 | 7093.0 | 19.81% | 6768.6 | 18.77% | motif file (matrix) |
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| 2 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-4 | -1.145e+01 | 0.0014 | 663.0 | 1.85% | 564.0 | 1.56% | motif file (matrix) |
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| 3 |  | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-4 | -1.120e+01 | 0.0014 | 2661.0 | 7.43% | 2475.5 | 6.86% | motif file (matrix) |
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| 4 |  | BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer | 1e-4 | -1.111e+01 | 0.0014 | 5042.0 | 14.08% | 4805.7 | 13.32% | motif file (matrix) |
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| 5 |  | E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer | 1e-4 | -1.098e+01 | 0.0014 | 3896.0 | 10.88% | 3682.0 | 10.21% | motif file (matrix) |
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| 6 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-4 | -1.047e+01 | 0.0014 | 1027.0 | 2.87% | 911.8 | 2.53% | motif file (matrix) |
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| 7 |  | n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer | 1e-4 | -1.037e+01 | 0.0014 | 1348.0 | 3.76% | 1217.3 | 3.38% | motif file (matrix) |
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| 8 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-4 | -1.034e+01 | 0.0014 | 3020.0 | 8.43% | 2834.9 | 7.86% | motif file (matrix) |
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| 9 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-3 | -8.898e+00 | 0.0040 | 838.0 | 2.34% | 743.8 | 2.06% | motif file (matrix) |
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| 10 |  | NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer | 1e-3 | -8.618e+00 | 0.0048 | 1173.0 | 3.28% | 1064.5 | 2.95% | motif file (matrix) |
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| 11 |  | SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer | 1e-3 | -8.184e+00 | 0.0067 | 11019.0 | 30.77% | 10795.0 | 29.93% | motif file (matrix) |
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| 12 |  | CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer | 1e-3 | -8.087e+00 | 0.0068 | 9858.0 | 27.53% | 9638.5 | 26.72% | motif file (matrix) |
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| 13 |  | Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.731e+00 | 0.0089 | 1462.0 | 4.08% | 1350.9 | 3.75% | motif file (matrix) |
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| 14 |  | MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer | 1e-3 | -7.067e+00 | 0.0161 | 2021.0 | 5.64% | 1901.0 | 5.27% | motif file (matrix) |
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| 15 |  | Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-3 | -7.057e+00 | 0.0161 | 1761.0 | 4.92% | 1647.2 | 4.57% | motif file (matrix) |
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| 16 |  | HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer | 1e-3 | -6.957e+00 | 0.0161 | 5250.0 | 14.66% | 5080.7 | 14.09% | motif file (matrix) |
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| 17 |  | GATA3(Zf),DR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer | 1e-2 | -6.869e+00 | 0.0161 | 371.0 | 1.04% | 317.2 | 0.88% | motif file (matrix) |
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| 18 |  | Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer | 1e-2 | -6.728e+00 | 0.0176 | 2685.0 | 7.50% | 2554.5 | 7.08% | motif file (matrix) |
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| 19 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-2 | -6.602e+00 | 0.0189 | 730.0 | 2.04% | 657.5 | 1.82% | motif file (matrix) |
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| 20 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.562e+00 | 0.0189 | 506.0 | 1.41% | 445.4 | 1.23% | motif file (matrix) |
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| 21 |  | CHR(?)/Hela-CellCycle-Expression/Homer | 1e-2 | -6.386e+00 | 0.0212 | 2528.0 | 7.06% | 2405.4 | 6.67% | motif file (matrix) |
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| 22 |  | Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer | 1e-2 | -6.170e+00 | 0.0251 | 1312.0 | 3.66% | 1221.1 | 3.39% | motif file (matrix) |
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| 23 |  | NFY(CCAAT)/Promoter/Homer | 1e-2 | -5.868e+00 | 0.0325 | 2051.0 | 5.73% | 1945.7 | 5.39% | motif file (matrix) |
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| 24 |  | GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer | 1e-2 | -5.806e+00 | 0.0331 | 6264.0 | 17.49% | 6111.9 | 16.95% | motif file (matrix) |
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| 25 |  | HNF6(Homeobox)/Liver-Hnf6-ChIP-Seq(ERP000394)/Homer | 1e-2 | -5.733e+00 | 0.0342 | 2094.0 | 5.85% | 1990.0 | 5.52% | motif file (matrix) |
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| 26 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.711e+00 | 0.0342 | 806.0 | 2.25% | 737.8 | 2.05% | motif file (matrix) |
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| 27 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-2 | -5.681e+00 | 0.0342 | 1126.0 | 3.14% | 1046.3 | 2.90% | motif file (matrix) |
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| 28 |  | YY1(Zf)/Promoter/Homer | 1e-2 | -5.585e+00 | 0.0354 | 107.0 | 0.30% | 82.7 | 0.23% | motif file (matrix) |
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| 29 |  | Otx2(Homeobox)/EpiLC-Otx2-ChIP-Seq(GSE56098)/Homer | 1e-2 | -5.550e+00 | 0.0354 | 3031.0 | 8.46% | 2913.4 | 8.08% | motif file (matrix) |
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| 30 |  | Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer | 1e-2 | -5.331e+00 | 0.0426 | 2306.0 | 6.44% | 2203.6 | 6.11% | motif file (matrix) |
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| 31 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-2 | -5.329e+00 | 0.0426 | 5000.0 | 13.96% | 4866.5 | 13.49% | motif file (matrix) |
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| 32 |  | NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.136e+00 | 0.0485 | 119.0 | 0.33% | 94.8 | 0.26% | motif file (matrix) |
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| 33 |  | GATA3(Zf),DR8/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer | 1e-2 | -4.941e+00 | 0.0572 | 230.0 | 0.64% | 196.1 | 0.54% | motif file (matrix) |
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| 34 |  | Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer | 1e-2 | -4.878e+00 | 0.0591 | 16401.0 | 45.80% | 16287.0 | 45.16% | motif file (matrix) |
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| 35 |  | NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer | 1e-2 | -4.833e+00 | 0.0600 | 129.0 | 0.36% | 104.1 | 0.29% | motif file (matrix) |
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| 36 |  | HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer | 1e-2 | -4.745e+00 | 0.0638 | 566.0 | 1.58% | 515.9 | 1.43% | motif file (matrix) |
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| 37 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-2 | -4.709e+00 | 0.0643 | 2514.0 | 7.02% | 2418.3 | 6.70% | motif file (matrix) |
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| 38 |  | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-2 | -4.703e+00 | 0.0643 | 5647.0 | 15.77% | 5524.9 | 15.32% | motif file (matrix) |
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| 39 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-2 | -4.622e+00 | 0.0666 | 1498.0 | 4.18% | 1421.6 | 3.94% | motif file (matrix) |
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