| 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 |  | RUNX(Runt)/HPC7-Runx1-ChIP-Seq(GSE22178)/Homer | 1e-38 | -8.818e+01 | 0.0000 | 353.0 | 29.59% | 6951.1 | 14.76% | motif file (matrix) |
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| 2 |  | RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer | 1e-26 | -6.147e+01 | 0.0000 | 356.0 | 29.84% | 8060.4 | 17.11% | motif file (matrix) |
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| 3 |  | RUNX-AML(Runt)/CD4+-PolII-ChIP-Seq(Barski et al.)/Homer | 1e-26 | -6.095e+01 | 0.0000 | 313.0 | 26.24% | 6739.0 | 14.30% | motif file (matrix) |
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| 4 |  | RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer | 1e-26 | -6.018e+01 | 0.0000 | 407.0 | 34.12% | 9776.1 | 20.75% | motif file (matrix) |
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| 5 |  | Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer | 1e-7 | -1.741e+01 | 0.0000 | 211.0 | 17.69% | 5752.8 | 12.21% | motif file (matrix) |
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| 6 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-5 | -1.238e+01 | 0.0002 | 281.0 | 23.55% | 8650.2 | 18.36% | motif file (matrix) |
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| 7 |  | Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer | 1e-5 | -1.168e+01 | 0.0003 | 276.0 | 23.13% | 8548.4 | 18.15% | motif file (matrix) |
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| 8 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-4 | -1.094e+01 | 0.0006 | 233.0 | 19.53% | 7094.5 | 15.06% | motif file (matrix) |
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| 9 |  | Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer | 1e-4 | -1.077e+01 | 0.0006 | 407.0 | 34.12% | 13485.1 | 28.62% | motif file (matrix) |
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| 10 |  | NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer | 1e-4 | -9.395e+00 | 0.0022 | 279.0 | 23.39% | 8933.6 | 18.96% | motif file (matrix) |
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| 11 |  | Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-3 | -9.143e+00 | 0.0026 | 348.0 | 29.17% | 11512.1 | 24.44% | motif file (matrix) |
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| 12 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-3 | -8.609e+00 | 0.0040 | 220.0 | 18.44% | 6897.9 | 14.64% | motif file (matrix) |
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| 13 |  | Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan et al.)/Homer | 1e-3 | -8.534e+00 | 0.0040 | 460.0 | 38.56% | 15838.6 | 33.62% | motif file (matrix) |
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| 14 |  | AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.329e+00 | 0.0046 | 374.0 | 31.35% | 12609.9 | 26.77% | motif file (matrix) |
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| 15 |  | MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer | 1e-3 | -8.185e+00 | 0.0049 | 301.0 | 25.23% | 9908.4 | 21.03% | motif file (matrix) |
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| 16 |  | Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer | 1e-3 | -7.671e+00 | 0.0077 | 382.0 | 32.02% | 13019.0 | 27.64% | motif file (matrix) |
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| 17 |  | Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-3 | -7.521e+00 | 0.0084 | 403.0 | 33.78% | 13839.2 | 29.38% | motif file (matrix) |
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| 18 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-3 | -7.485e+00 | 0.0084 | 151.0 | 12.66% | 4578.6 | 9.72% | motif file (matrix) |
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| 19 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-3 | -7.128e+00 | 0.0111 | 127.0 | 10.65% | 3779.6 | 8.02% | motif file (matrix) |
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| 20 |  | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1e-2 | -6.433e+00 | 0.0212 | 108.0 | 9.05% | 3193.3 | 6.78% | motif file (matrix) |
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| 21 |  | BMYB(HTH)/Hela-BMYB-ChIP-Seq(GSE27030)/Homer | 1e-2 | -6.392e+00 | 0.0212 | 383.0 | 32.10% | 13283.0 | 28.20% | motif file (matrix) |
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| 22 |  | Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer | 1e-2 | -6.309e+00 | 0.0218 | 732.0 | 61.36% | 26931.7 | 57.17% | motif file (matrix) |
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| 23 |  | Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer | 1e-2 | -6.269e+00 | 0.0218 | 351.0 | 29.42% | 12093.7 | 25.67% | motif file (matrix) |
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| 24 |  | AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer | 1e-2 | -6.170e+00 | 0.0230 | 453.0 | 37.97% | 16004.5 | 33.97% | motif file (matrix) |
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| 25 |  | AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.980e+00 | 0.0267 | 166.0 | 13.91% | 5294.2 | 11.24% | motif file (matrix) |
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| 26 |  | Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer | 1e-2 | -5.942e+00 | 0.0267 | 506.0 | 42.41% | 18100.1 | 38.42% | motif file (matrix) |
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| 27 |  | HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer | 1e-2 | -5.672e+00 | 0.0337 | 144.0 | 12.07% | 4546.0 | 9.65% | motif file (matrix) |
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| 28 |  | NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -5.414e+00 | 0.0420 | 488.0 | 40.91% | 17517.1 | 37.18% | motif file (matrix) |
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| 29 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-2 | -5.414e+00 | 0.0420 | 83.0 | 6.96% | 2435.6 | 5.17% | motif file (matrix) |
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| 30 |  | Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer | 1e-2 | -5.337e+00 | 0.0423 | 66.0 | 5.53% | 1865.5 | 3.96% | motif file (matrix) |
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| 31 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-2 | -5.258e+00 | 0.0443 | 143.0 | 11.99% | 4565.8 | 9.69% | motif file (matrix) |
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| 32 |  | CHR(?)/Hela-CellCycle-Expression/Homer | 1e-2 | -5.125e+00 | 0.0491 | 130.0 | 10.90% | 4117.1 | 8.74% | motif file (matrix) |
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| 33 |  | MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer | 1e-2 | -5.040e+00 | 0.0518 | 354.0 | 29.67% | 12449.6 | 26.43% | motif file (matrix) |
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| 34 |  | Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer | 1e-2 | -4.924e+00 | 0.0565 | 502.0 | 42.08% | 18174.7 | 38.58% | motif file (matrix) |
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| 35 |  | Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski et al.)/Homer | 1e-2 | -4.913e+00 | 0.0565 | 93.0 | 7.80% | 2834.4 | 6.02% | motif file (matrix) |
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| 36 |  | TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer | 1e-2 | -4.883e+00 | 0.0565 | 216.0 | 18.11% | 7290.7 | 15.48% | motif file (matrix) |
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| 37 |  | TEAD2(TEA)/Py2T-Tead2-ChIP-Seq(GSE55709)/Homer | 1e-2 | -4.817e+00 | 0.0577 | 137.0 | 11.48% | 4410.7 | 9.36% | motif file (matrix) |
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| 38 |  | Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer | 1e-2 | -4.664e+00 | 0.0655 | 234.0 | 19.61% | 7999.7 | 16.98% | motif file (matrix) |
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