| 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 |  | MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer | 1e-13 | -3.194e+01 | 0.0000 | 453.0 | 47.14% | 339.6 | 35.17% | motif file (matrix) |
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| 2 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-13 | -3.115e+01 | 0.0000 | 789.0 | 82.10% | 691.4 | 71.62% | motif file (matrix) |
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| 3 |  | TATA-Box(TBP)/Promoter/Homer | 1e-10 | -2.421e+01 | 0.0000 | 424.0 | 44.12% | 327.2 | 33.89% | motif file (matrix) |
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| 4 |  | Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer | 1e-7 | -1.822e+01 | 0.0000 | 530.0 | 55.15% | 445.4 | 46.13% | motif file (matrix) |
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| 5 |  | TEAD2(TEA)/Py2T-Tead2-ChIP-Seq(GSE55709)/Homer | 1e-7 | -1.676e+01 | 0.0000 | 194.0 | 20.19% | 134.8 | 13.96% | motif file (matrix) |
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| 6 |  | Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-7 | -1.647e+01 | 0.0000 | 494.0 | 51.40% | 414.7 | 42.95% | motif file (matrix) |
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| 7 |  | SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer | 1e-7 | -1.614e+01 | 0.0000 | 926.0 | 96.36% | 891.0 | 92.28% | motif file (matrix) |
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| 8 |  | Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.474e+01 | 0.0000 | 118.0 | 12.28% | 74.1 | 7.67% | motif file (matrix) |
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| 9 |  | TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer | 1e-6 | -1.396e+01 | 0.0000 | 215.0 | 22.37% | 158.0 | 16.37% | motif file (matrix) |
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| 10 |  | CArG(MADS)/PUER-Srf-ChIP-Seq(Sullivan et al.)/Homer | 1e-5 | -1.373e+01 | 0.0000 | 121.0 | 12.59% | 78.8 | 8.16% | motif file (matrix) |
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| 11 |  | PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer | 1e-5 | -1.243e+01 | 0.0001 | 220.0 | 22.89% | 167.0 | 17.29% | motif file (matrix) |
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| 12 |  | Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer | 1e-5 | -1.211e+01 | 0.0001 | 355.0 | 36.94% | 292.7 | 30.32% | motif file (matrix) |
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| 13 |  | Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer | 1e-4 | -1.119e+01 | 0.0003 | 201.0 | 20.92% | 152.8 | 15.83% | motif file (matrix) |
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| 14 |  | PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer | 1e-4 | -1.114e+01 | 0.0003 | 47.0 | 4.89% | 24.2 | 2.50% | motif file (matrix) |
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| 15 |  | MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer | 1e-4 | -1.075e+01 | 0.0004 | 507.0 | 52.76% | 445.4 | 46.14% | motif file (matrix) |
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| 16 |  | TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer | 1e-4 | -1.046e+01 | 0.0005 | 301.0 | 31.32% | 247.0 | 25.58% | motif file (matrix) |
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| 17 |  | Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer | 1e-4 | -1.023e+01 | 0.0006 | 536.0 | 55.78% | 476.7 | 49.38% | motif file (matrix) |
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| 18 |  | Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer | 1e-4 | -9.912e+00 | 0.0007 | 107.0 | 11.13% | 73.7 | 7.63% | motif file (matrix) |
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| 19 |  | NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer | 1e-4 | -9.267e+00 | 0.0013 | 365.0 | 37.98% | 311.9 | 32.30% | motif file (matrix) |
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| 20 |  | ETS:E-box(ETS,bHLH)/HPC7-Scl-ChIP-Seq(GSE22178)/Homer | 1e-3 | -9.122e+00 | 0.0014 | 40.0 | 4.16% | 21.9 | 2.27% | motif file (matrix) |
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| 21 |  | NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer | 1e-3 | -9.090e+00 | 0.0014 | 259.0 | 26.95% | 211.7 | 21.92% | motif file (matrix) |
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| 22 |  | GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer | 1e-3 | -8.608e+00 | 0.0022 | 46.0 | 4.79% | 26.5 | 2.75% | motif file (matrix) |
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| 23 |  | Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer | 1e-3 | -8.443e+00 | 0.0025 | 661.0 | 68.78% | 612.0 | 63.39% | motif file (matrix) |
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| 24 |  | Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo et al.)/Homer | 1e-3 | -8.434e+00 | 0.0025 | 340.0 | 35.38% | 290.7 | 30.11% | motif file (matrix) |
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| 25 |  | Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer | 1e-3 | -8.421e+00 | 0.0025 | 478.0 | 49.74% | 425.1 | 44.03% | motif file (matrix) |
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| 26 |  | Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer | 1e-3 | -8.202e+00 | 0.0028 | 464.0 | 48.28% | 413.0 | 42.78% | motif file (matrix) |
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| 27 |  | AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer | 1e-3 | -7.869e+00 | 0.0037 | 846.0 | 88.03% | 812.7 | 84.18% | motif file (matrix) |
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| 28 |  | Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer | 1e-3 | -7.413e+00 | 0.0057 | 184.0 | 19.15% | 147.4 | 15.26% | motif file (matrix) |
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| 29 |  | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-3 | -7.231e+00 | 0.0066 | 157.0 | 16.34% | 123.7 | 12.82% | motif file (matrix) |
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| 30 |  | HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson et al.)/Homer | 1e-3 | -7.223e+00 | 0.0066 | 29.0 | 3.02% | 15.3 | 1.59% | motif file (matrix) |
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| 31 |  | Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer | 1e-3 | -6.917e+00 | 0.0084 | 57.0 | 5.93% | 37.6 | 3.90% | motif file (matrix) |
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| 32 |  | IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer | 1e-2 | -6.391e+00 | 0.0138 | 51.0 | 5.31% | 33.1 | 3.43% | motif file (matrix) |
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| 33 |  | Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer | 1e-2 | -6.384e+00 | 0.0138 | 478.0 | 49.74% | 434.2 | 44.97% | motif file (matrix) |
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| 34 |  | bZIP:IRF(bZIP,IRF)/Th17-BatF-ChIP-Seq(GSE39756)/Homer | 1e-2 | -6.331e+00 | 0.0138 | 143.0 | 14.88% | 113.6 | 11.76% | motif file (matrix) |
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| 35 |  | Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer | 1e-2 | -6.286e+00 | 0.0140 | 566.0 | 58.90% | 523.1 | 54.18% | motif file (matrix) |
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| 36 |  | Znf263(Zf)/K562-Znf263-ChIP-Seq(GSE31477)/Homer | 1e-2 | -6.069e+00 | 0.0170 | 757.0 | 78.77% | 722.1 | 74.79% | motif file (matrix) |
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| 37 |  | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-2 | -6.063e+00 | 0.0170 | 164.0 | 17.07% | 133.3 | 13.81% | motif file (matrix) |
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| 38 |  | NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma et al.)/Homer | 1e-2 | -5.872e+00 | 0.0196 | 56.0 | 5.83% | 38.9 | 4.03% | motif file (matrix) |
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| 39 |  | PRDM1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.773e+00 | 0.0210 | 191.0 | 19.88% | 159.7 | 16.54% | motif file (matrix) |
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| 40 |  | RBPJ:Ebox(?,bHLH)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-2 | -5.771e+00 | 0.0210 | 177.0 | 18.42% | 146.4 | 15.17% | motif file (matrix) |
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| 41 |  | STAT6(Stat)/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer | 1e-2 | -5.750e+00 | 0.0210 | 178.0 | 18.52% | 147.3 | 15.26% | motif file (matrix) |
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| 42 |  | Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer | 1e-2 | -5.622e+00 | 0.0227 | 372.0 | 38.71% | 333.4 | 34.53% | motif file (matrix) |
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| 43 |  | Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer | 1e-2 | -5.438e+00 | 0.0267 | 141.0 | 14.67% | 114.1 | 11.81% | motif file (matrix) |
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| 44 |  | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.315e+00 | 0.0295 | 63.0 | 6.56% | 45.3 | 4.69% | motif file (matrix) |
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| 45 |  | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-2 | -5.175e+00 | 0.0332 | 128.0 | 13.32% | 103.8 | 10.75% | motif file (matrix) |
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| 46 |  | Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer | 1e-2 | -5.123e+00 | 0.0342 | 217.0 | 22.58% | 186.3 | 19.29% | motif file (matrix) |
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| 47 |  | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1e-2 | -5.024e+00 | 0.0370 | 246.0 | 25.60% | 214.4 | 22.21% | motif file (matrix) |
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| 48 |  | Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer | 1e-2 | -5.020e+00 | 0.0370 | 270.0 | 28.10% | 237.9 | 24.64% | motif file (matrix) |
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| 49 |  | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-2 | -4.956e+00 | 0.0379 | 85.0 | 8.84% | 65.2 | 6.75% | motif file (matrix) |
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| 50 |  | Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer | 1e-2 | -4.901e+00 | 0.0393 | 49.0 | 5.10% | 34.1 | 3.53% | motif file (matrix) |
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| 51 |  | EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer | 1e-2 | -4.857e+00 | 0.0402 | 141.0 | 14.67% | 116.6 | 12.07% | motif file (matrix) |
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| 52 |  | FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong et al.)/Homer | 1e-2 | -4.639e+00 | 0.0491 | 200.0 | 20.81% | 172.5 | 17.87% | motif file (matrix) |
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| 53 |  | Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer | 1e-2 | -4.607e+00 | 0.0497 | 572.0 | 59.52% | 538.6 | 55.79% | motif file (matrix) |
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