| 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 |  | Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer | 1e-10 | -2.320e+01 | 0.0000 | 1167.0 | 18.54% | 6541.5 | 15.55% | motif file (matrix) |
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| 2 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo et al.)/Homer | 1e-8 | -1.925e+01 | 0.0000 | 643.0 | 10.22% | 3431.4 | 8.16% | motif file (matrix) |
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| 3 |  | AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer | 1e-6 | -1.594e+01 | 0.0000 | 2916.0 | 46.34% | 18130.1 | 43.10% | motif file (matrix) |
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| 4 |  | Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer | 1e-6 | -1.583e+01 | 0.0000 | 623.0 | 9.90% | 3395.0 | 8.07% | motif file (matrix) |
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| 5 |  | AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer | 1e-6 | -1.491e+01 | 0.0000 | 1266.0 | 20.12% | 7438.4 | 17.68% | motif file (matrix) |
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| 6 |  | EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer | 1e-6 | -1.484e+01 | 0.0000 | 1233.0 | 19.59% | 7231.1 | 17.19% | motif file (matrix) |
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| 7 |  | AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer | 1e-5 | -1.201e+01 | 0.0002 | 978.0 | 15.54% | 5725.2 | 13.61% | motif file (matrix) |
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| 8 |  | Pit1(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer | 1e-5 | -1.192e+01 | 0.0002 | 569.0 | 9.04% | 3174.2 | 7.55% | motif file (matrix) |
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| 9 |  | NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-4 | -1.067e+01 | 0.0007 | 532.0 | 8.45% | 2984.7 | 7.09% | motif file (matrix) |
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| 10 |  | Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer | 1e-3 | -9.167e+00 | 0.0028 | 1432.0 | 22.76% | 8763.9 | 20.83% | motif file (matrix) |
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| 11 |  | PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer | 1e-3 | -8.962e+00 | 0.0031 | 230.0 | 3.65% | 1199.6 | 2.85% | motif file (matrix) |
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| 12 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-3 | -7.241e+00 | 0.0158 | 355.0 | 5.64% | 2001.9 | 4.76% | motif file (matrix) |
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| 13 |  | Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer | 1e-3 | -7.086e+00 | 0.0170 | 1328.0 | 21.10% | 8209.0 | 19.51% | motif file (matrix) |
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| 14 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-3 | -6.963e+00 | 0.0178 | 1009.0 | 16.03% | 6153.0 | 14.63% | motif file (matrix) |
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| 15 |  | HNF4a(NR),DR1/HepG2-HNF4a-ChIP-Seq(GSE25021)/Homer | 1e-2 | -6.870e+00 | 0.0183 | 304.0 | 4.83% | 1699.0 | 4.04% | motif file (matrix) |
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| 16 |  | GATA3(Zf),DR8/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer | 1e-2 | -6.817e+00 | 0.0183 | 53.0 | 0.84% | 224.5 | 0.53% | motif file (matrix) |
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| 17 |  | RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-2 | -6.432e+00 | 0.0250 | 960.0 | 15.26% | 5867.3 | 13.95% | motif file (matrix) |
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| 18 |  | PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer | 1e-2 | -5.973e+00 | 0.0374 | 1422.0 | 22.60% | 8892.4 | 21.14% | motif file (matrix) |
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| 19 |  | FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong et al.)/Homer | 1e-2 | -5.505e+00 | 0.0565 | 355.0 | 5.64% | 2061.4 | 4.90% | motif file (matrix) |
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| 20 |  | Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer | 1e-2 | -5.440e+00 | 0.0573 | 422.0 | 6.71% | 2484.7 | 5.91% | motif file (matrix) |
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| 21 |  | NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer | 1e-2 | -5.272e+00 | 0.0645 | 441.0 | 7.01% | 2611.5 | 6.21% | motif file (matrix) |
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| 22 |  | NFkB-p50,p52(RHD)/Monocyte-p50-ChIP-Chip(Schreiber et al.)/Homer | 1e-2 | -5.228e+00 | 0.0645 | 151.0 | 2.40% | 814.3 | 1.94% | motif file (matrix) |
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| 23 |  | Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer | 1e-2 | -5.180e+00 | 0.0646 | 234.0 | 3.72% | 1321.8 | 3.14% | motif file (matrix) |
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| 24 |  | Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer | 1e-2 | -4.982e+00 | 0.0755 | 100.0 | 1.59% | 516.2 | 1.23% | motif file (matrix) |
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| 25 |  | Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer | 1e-2 | -4.726e+00 | 0.0936 | 479.0 | 7.61% | 2877.3 | 6.84% | motif file (matrix) |
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