| 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 |  | HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer | 1e-8 | -1.885e+01 | 0.0000 | 236.0 | 35.22% | 11727.3 | 25.26% | motif file (matrix) |
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| 2 |  | Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer | 1e-7 | -1.666e+01 | 0.0000 | 105.0 | 15.67% | 4261.2 | 9.18% | motif file (matrix) |
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| 3 |  | c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-6 | -1.391e+01 | 0.0001 | 70.0 | 10.45% | 2631.9 | 5.67% | motif file (matrix) |
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| 4 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-6 | -1.382e+01 | 0.0001 | 99.0 | 14.78% | 4191.8 | 9.03% | motif file (matrix) |
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| 5 |  | Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer | 1e-5 | -1.364e+01 | 0.0001 | 75.0 | 11.19% | 2912.9 | 6.27% | motif file (matrix) |
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| 6 |  | CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer | 1e-5 | -1.327e+01 | 0.0001 | 123.0 | 18.36% | 5607.8 | 12.08% | motif file (matrix) |
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| 7 |  | NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-5 | -1.305e+01 | 0.0001 | 84.0 | 12.54% | 3442.7 | 7.42% | motif file (matrix) |
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| 8 |  | Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer | 1e-5 | -1.192e+01 | 0.0002 | 128.0 | 19.10% | 6060.7 | 13.06% | motif file (matrix) |
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| 9 |  | Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer | 1e-5 | -1.178e+01 | 0.0002 | 340.0 | 50.75% | 19667.0 | 42.37% | motif file (matrix) |
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| 10 |  | JunD(bZIP)/K562-JunD-ChIP-Seq/Homer | 1e-4 | -1.063e+01 | 0.0006 | 26.0 | 3.88% | 715.0 | 1.54% | motif file (matrix) |
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| 11 |  | NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-4 | -1.029e+01 | 0.0008 | 299.0 | 44.63% | 17193.2 | 37.04% | motif file (matrix) |
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| 12 |  | HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer | 1e-4 | -1.009e+01 | 0.0009 | 77.0 | 11.49% | 3342.8 | 7.20% | motif file (matrix) |
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| 13 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-4 | -9.903e+00 | 0.0010 | 70.0 | 10.45% | 2974.4 | 6.41% | motif file (matrix) |
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| 14 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-4 | -9.659e+00 | 0.0012 | 105.0 | 15.67% | 4995.1 | 10.76% | motif file (matrix) |
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| 15 |  | Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer | 1e-4 | -9.618e+00 | 0.0012 | 404.0 | 60.30% | 24551.9 | 52.89% | motif file (matrix) |
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| 16 |  | NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-3 | -8.604e+00 | 0.0030 | 174.0 | 25.97% | 9380.5 | 20.21% | motif file (matrix) |
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| 17 |  | ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer | 1e-3 | -8.105e+00 | 0.0047 | 281.0 | 41.94% | 16460.2 | 35.46% | motif file (matrix) |
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| 18 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-3 | -7.905e+00 | 0.0054 | 119.0 | 17.76% | 6084.7 | 13.11% | motif file (matrix) |
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| 19 |  | CRE(bZIP)/Promoter/Homer | 1e-3 | -7.733e+00 | 0.0061 | 45.0 | 6.72% | 1824.5 | 3.93% | motif file (matrix) |
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| 20 |  | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1e-3 | -7.484e+00 | 0.0074 | 202.0 | 30.15% | 11394.4 | 24.55% | motif file (matrix) |
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| 21 |  | HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer | 1e-3 | -7.180e+00 | 0.0096 | 52.0 | 7.76% | 2257.9 | 4.86% | motif file (matrix) |
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| 22 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-3 | -7.103e+00 | 0.0099 | 115.0 | 17.16% | 5971.5 | 12.86% | motif file (matrix) |
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| 23 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-3 | -7.037e+00 | 0.0101 | 129.0 | 19.25% | 6846.7 | 14.75% | motif file (matrix) |
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| 24 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-3 | -7.030e+00 | 0.0101 | 49.0 | 7.31% | 2107.5 | 4.54% | motif file (matrix) |
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| 25 |  | Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer | 1e-2 | -6.851e+00 | 0.0112 | 287.0 | 42.84% | 17167.2 | 36.98% | motif file (matrix) |
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| 26 |  | NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-2 | -6.477e+00 | 0.0156 | 42.0 | 6.27% | 1779.9 | 3.83% | motif file (matrix) |
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| 27 |  | Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer | 1e-2 | -6.359e+00 | 0.0169 | 101.0 | 15.07% | 5240.1 | 11.29% | motif file (matrix) |
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| 28 |  | EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer | 1e-2 | -6.118e+00 | 0.0208 | 114.0 | 17.01% | 6083.7 | 13.11% | motif file (matrix) |
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| 29 |  | Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer | 1e-2 | -6.061e+00 | 0.0212 | 196.0 | 29.25% | 11327.2 | 24.40% | motif file (matrix) |
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| 30 |  | HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer | 1e-2 | -5.949e+00 | 0.0229 | 128.0 | 19.10% | 6990.4 | 15.06% | motif file (matrix) |
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| 31 |  | Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer | 1e-2 | -5.945e+00 | 0.0229 | 43.0 | 6.42% | 1888.1 | 4.07% | motif file (matrix) |
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| 32 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski et al.)/Homer | 1e-2 | -5.935e+00 | 0.0229 | 38.0 | 5.67% | 1614.3 | 3.48% | motif file (matrix) |
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| 33 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.306e+00 | 0.0397 | 61.0 | 9.10% | 3001.1 | 6.46% | motif file (matrix) |
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| 34 |  | Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer | 1e-2 | -5.225e+00 | 0.0418 | 286.0 | 42.69% | 17549.4 | 37.80% | motif file (matrix) |
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| 35 |  | Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer | 1e-2 | -5.182e+00 | 0.0424 | 195.0 | 29.10% | 11484.3 | 24.74% | motif file (matrix) |
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| 36 |  | USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer | 1e-2 | -5.174e+00 | 0.0424 | 84.0 | 12.54% | 4406.0 | 9.49% | motif file (matrix) |
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| 37 |  | MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer | 1e-2 | -5.062e+00 | 0.0452 | 134.0 | 20.00% | 7560.5 | 16.29% | motif file (matrix) |
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| 38 |  | Brachyury(T-box)/Mesoendoderm-Brachyury-ChIP-exo(GSE54963)/Homer | 1e-2 | -5.049e+00 | 0.0452 | 58.0 | 8.66% | 2861.1 | 6.16% | motif file (matrix) |
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| 39 |  | IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer | 1e-2 | -4.627e+00 | 0.0662 | 33.0 | 4.93% | 1473.3 | 3.17% | motif file (matrix) |
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