| 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 |  | BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer | 1e-17 | -3.955e+01 | 0.0000 | 60.0 | 19.67% | 11.0 | 5.98% | motif file (matrix) |
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| 2 |  | Srebp2(HLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer | 1e-15 | -3.618e+01 | 0.0000 | 27.0 | 8.85% | 2.8 | 1.51% | motif file (matrix) |
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| 3 |  | CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski et al.)/Homer | 1e-13 | -3.125e+01 | 0.0000 | 57.0 | 18.69% | 11.7 | 6.34% | motif file (matrix) |
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| 4 |  | E2A-nearPU.1(HLH)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-11 | -2.541e+01 | 0.0000 | 73.0 | 23.93% | 19.3 | 10.50% | motif file (matrix) |
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| 5 |  | Fox:Ebox(Forkhead:HLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer | 1e-7 | -1.708e+01 | 0.0000 | 88.0 | 28.85% | 30.5 | 16.57% | motif file (matrix) |
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| 6 |  | PRDM1/BMI1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer | 1e-7 | -1.678e+01 | 0.0000 | 47.0 | 15.41% | 12.2 | 6.66% | motif file (matrix) |
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| 7 |  | EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer | 1e-5 | -1.292e+01 | 0.0001 | 80.0 | 26.23% | 29.2 | 15.91% | motif file (matrix) |
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| 8 |  | Srebp1a(HLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer | 1e-5 | -1.171e+01 | 0.0003 | 29.0 | 9.51% | 7.2 | 3.94% | motif file (matrix) |
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| 9 |  | Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer | 1e-3 | -8.697e+00 | 0.0046 | 67.0 | 21.97% | 26.7 | 14.51% | motif file (matrix) |
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| 10 |  | Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer | 1e-3 | -8.669e+00 | 0.0046 | 107.0 | 35.08% | 48.0 | 26.09% | motif file (matrix) |
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| 11 |  | Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529/Homer | 1e-3 | -8.314e+00 | 0.0055 | 50.0 | 16.39% | 18.3 | 9.97% | motif file (matrix) |
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| 12 |  | Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer | 1e-3 | -7.782e+00 | 0.0086 | 151.0 | 49.51% | 73.3 | 39.88% | motif file (matrix) |
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| 13 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-3 | -7.594e+00 | 0.0095 | 88.0 | 28.85% | 38.9 | 21.16% | motif file (matrix) |
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| 14 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-3 | -7.459e+00 | 0.0101 | 97.0 | 31.80% | 44.0 | 23.93% | motif file (matrix) |
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| 15 |  | BMYB(HTH)/Hela-BMYB-ChIPSeq(GSE27030)/Homer | 1e-3 | -7.021e+00 | 0.0146 | 96.0 | 31.48% | 44.0 | 23.91% | motif file (matrix) |
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| 16 |  | NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -6.438e+00 | 0.0246 | 118.0 | 38.69% | 56.9 | 30.95% | motif file (matrix) |
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| 17 |  | NF1:FOXA1/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-2 | -6.429e+00 | 0.0246 | 7.0 | 2.30% | 0.5 | 0.27% | motif file (matrix) |
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| 18 |  | Pax8(Paired/Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-2 | -6.369e+00 | 0.0246 | 32.0 | 10.49% | 11.6 | 6.29% | motif file (matrix) |
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| 19 |  | LXRE(NR/DR4)/BLRP(RAW)-LXRb-ChIP-Seq(GSE21512)/Homer | 1e-2 | -6.305e+00 | 0.0246 | 13.0 | 4.26% | 3.0 | 1.64% | motif file (matrix) |
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| 20 |  | E2A(HLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer | 1e-2 | -6.259e+00 | 0.0246 | 96.0 | 31.48% | 44.4 | 24.16% | motif file (matrix) |
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| 21 |  | CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-2 | -6.165e+00 | 0.0246 | 18.0 | 5.90% | 5.6 | 3.03% | motif file (matrix) |
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| 22 |  | Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.128e+00 | 0.0246 | 25.0 | 8.20% | 8.4 | 4.55% | motif file (matrix) |
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| 23 |  | GLI3(Zf)/GLI3-ChIP-Chip(GSE11077)/Homer | 1e-2 | -6.117e+00 | 0.0246 | 10.0 | 3.28% | 2.2 | 1.22% | motif file (matrix) |
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| 24 |  | Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan et al.)/Homer | 1e-2 | -6.049e+00 | 0.0246 | 131.0 | 42.95% | 64.4 | 35.03% | motif file (matrix) |
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| 25 |  | RXR(NR/DR1)/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer | 1e-2 | -5.745e+00 | 0.0315 | 65.0 | 21.31% | 28.4 | 15.44% | motif file (matrix) |
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| 26 |  | TRa(NR)/C17.2-TRa-ChIP-Seq(GSE38347)/Homer | 1e-2 | -5.530e+00 | 0.0375 | 51.0 | 16.72% | 21.7 | 11.81% | motif file (matrix) |
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| 27 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-2 | -5.502e+00 | 0.0375 | 43.0 | 14.10% | 17.1 | 9.31% | motif file (matrix) |
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| 28 |  | ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer | 1e-2 | -5.327e+00 | 0.0427 | 17.0 | 5.57% | 5.3 | 2.90% | motif file (matrix) |
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| 29 |  | Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer | 1e-2 | -5.204e+00 | 0.0466 | 176.0 | 57.70% | 92.2 | 50.13% | motif file (matrix) |
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| 30 |  | Nr5a2(NR)/mES-Nr5a2-ChIP-Seq(GSE19019)/Homer | 1e-2 | -5.015e+00 | 0.0544 | 36.0 | 11.80% | 14.3 | 7.76% | motif file (matrix) |
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| 31 |  | ETS:E-box/HPC7-Scl-ChIP-Seq(GSE22178)/Homer | 1e-2 | -4.960e+00 | 0.0544 | 9.0 | 2.95% | 2.7 | 1.48% | motif file (matrix) |
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| 32 |  | GRE(NR/IR3)/A549-GR-ChIP-Seq(GSE32465)/Homer | 1e-2 | -4.960e+00 | 0.0544 | 9.0 | 2.95% | 2.0 | 1.09% | motif file (matrix) |
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