| 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 |  | Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer | 1e-207 | -4.783e+02 | 0.0000 | 18674.0 | 23.52% | 15188.2 | 19.10% | motif file (matrix) |
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| 2 |  | Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer | 1e-200 | -4.617e+02 | 0.0000 | 17462.0 | 21.99% | 14127.3 | 17.77% | motif file (matrix) |
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| 3 |  | GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer | 1e-104 | -2.396e+02 | 0.0000 | 32278.0 | 40.65% | 29342.5 | 36.91% | motif file (matrix) |
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| 4 |  | CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer | 1e-76 | -1.767e+02 | 0.0000 | 40675.0 | 51.22% | 38101.3 | 47.93% | motif file (matrix) |
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| 5 |  | E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-74 | -1.709e+02 | 0.0000 | 33539.0 | 42.24% | 31051.9 | 39.06% | motif file (matrix) |
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| 6 |  | E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer | 1e-72 | -1.666e+02 | 0.0000 | 33392.0 | 42.05% | 30938.1 | 38.92% | motif file (matrix) |
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| 7 |  | THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer | 1e-64 | -1.484e+02 | 0.0000 | 15335.0 | 19.31% | 13519.3 | 17.01% | motif file (matrix) |
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| 8 |  | LXRE(NR),DR4/RAW-LXRb.biotin-ChIP-Seq(GSE21512)/Homer | 1e-61 | -1.410e+02 | 0.0000 | 7344.0 | 9.25% | 6073.3 | 7.64% | motif file (matrix) |
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| 9 |  | Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer | 1e-59 | -1.376e+02 | 0.0000 | 14933.0 | 18.81% | 13203.5 | 16.61% | motif file (matrix) |
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| 10 |  | Nkx3.1(Homeobox)/LNCaP-Nkx3.1-ChIP-Seq(GSE28264)/Homer | 1e-59 | -1.367e+02 | 0.0000 | 39473.0 | 49.71% | 37222.2 | 46.82% | motif file (matrix) |
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| 11 |  | Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer | 1e-57 | -1.332e+02 | 0.0000 | 45550.0 | 57.36% | 43348.7 | 54.53% | motif file (matrix) |
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| 12 |  | Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer | 1e-48 | -1.127e+02 | 0.0000 | 51789.0 | 65.22% | 49845.7 | 62.70% | motif file (matrix) |
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| 13 |  | Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer | 1e-37 | -8.641e+01 | 0.0000 | 9281.0 | 11.69% | 8167.7 | 10.27% | motif file (matrix) |
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| 14 |  | Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer | 1e-34 | -8.006e+01 | 0.0000 | 11187.0 | 14.09% | 10022.8 | 12.61% | motif file (matrix) |
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| 15 |  | Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer | 1e-34 | -8.003e+01 | 0.0000 | 35743.0 | 45.01% | 34054.9 | 42.84% | motif file (matrix) |
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| 16 |  | KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer | 1e-31 | -7.264e+01 | 0.0000 | 22749.0 | 28.65% | 21295.5 | 26.79% | motif file (matrix) |
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| 17 |  | Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer | 1e-31 | -7.264e+01 | 0.0000 | 15463.0 | 19.47% | 14195.2 | 17.86% | motif file (matrix) |
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| 18 |  | Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer | 1e-22 | -5.201e+01 | 0.0000 | 54918.0 | 69.16% | 53684.0 | 67.53% | motif file (matrix) |
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| 19 |  | EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer | 1e-19 | -4.538e+01 | 0.0000 | 5007.0 | 6.31% | 4407.7 | 5.54% | motif file (matrix) |
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| 20 |  | p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer | 1e-18 | -4.323e+01 | 0.0000 | 5513.0 | 6.94% | 4900.1 | 6.16% | motif file (matrix) |
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| 21 |  | Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer | 1e-17 | -4.088e+01 | 0.0000 | 6249.0 | 7.87% | 5617.9 | 7.07% | motif file (matrix) |
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| 22 |  | Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer | 1e-16 | -3.862e+01 | 0.0000 | 44439.0 | 55.96% | 43308.9 | 54.48% | motif file (matrix) |
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| 23 |  | CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-15 | -3.476e+01 | 0.0000 | 2202.0 | 2.77% | 1856.0 | 2.33% | motif file (matrix) |
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| 24 |  | NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer | 1e-14 | -3.225e+01 | 0.0000 | 17201.0 | 21.66% | 16343.4 | 20.56% | motif file (matrix) |
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| 25 |  | Reverb(NR),DR2/RAW-Reverba.biotin-ChIP-Seq(GSE45914)/Homer | 1e-13 | -3.014e+01 | 0.0000 | 3520.0 | 4.43% | 3112.9 | 3.92% | motif file (matrix) |
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| 26 |  | Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer | 1e-11 | -2.721e+01 | 0.0000 | 2833.0 | 3.57% | 2486.9 | 3.13% | motif file (matrix) |
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| 27 |  | Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer | 1e-11 | -2.559e+01 | 0.0000 | 4624.0 | 5.82% | 4197.1 | 5.28% | motif file (matrix) |
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| 28 |  | Srebp1a(bHLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer | 1e-7 | -1.818e+01 | 0.0000 | 5657.0 | 7.12% | 5268.9 | 6.63% | motif file (matrix) |
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| 29 |  | Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer | 1e-7 | -1.698e+01 | 0.0000 | 8899.0 | 11.21% | 8440.4 | 10.62% | motif file (matrix) |
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| 30 |  | FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong et al.)/Homer | 1e-6 | -1.527e+01 | 0.0000 | 5903.0 | 7.43% | 5545.0 | 6.97% | motif file (matrix) |
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| 31 |  | Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer | 1e-6 | -1.522e+01 | 0.0000 | 36048.0 | 45.40% | 35385.7 | 44.51% | motif file (matrix) |
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| 32 |  | Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-6 | -1.406e+01 | 0.0000 | 2782.0 | 3.50% | 2544.0 | 3.20% | motif file (matrix) |
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| 33 |  | MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer | 1e-5 | -1.328e+01 | 0.0000 | 3292.0 | 4.15% | 3041.1 | 3.83% | motif file (matrix) |
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| 34 |  | YY1(Zf)/Promoter/Homer | 1e-5 | -1.299e+01 | 0.0000 | 791.0 | 1.00% | 670.5 | 0.84% | motif file (matrix) |
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| 35 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-5 | -1.282e+01 | 0.0000 | 7038.0 | 8.86% | 6687.4 | 8.41% | motif file (matrix) |
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| 36 |  | Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer | 1e-4 | -1.085e+01 | 0.0001 | 3303.0 | 4.16% | 3080.8 | 3.88% | motif file (matrix) |
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| 37 |  | c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-4 | -1.042e+01 | 0.0002 | 5134.0 | 6.47% | 4867.0 | 6.12% | motif file (matrix) |
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| 38 |  | VDR(NR),DR3/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer | 1e-4 | -9.822e+00 | 0.0004 | 2689.0 | 3.39% | 2499.1 | 3.14% | motif file (matrix) |
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| 39 |  | CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer | 1e-4 | -9.220e+00 | 0.0007 | 7872.0 | 9.91% | 7571.3 | 9.52% | motif file (matrix) |
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| 40 |  | Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer | 1e-3 | -9.193e+00 | 0.0007 | 5093.0 | 6.41% | 4846.6 | 6.10% | motif file (matrix) |
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| 41 |  | Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer | 1e-3 | -9.020e+00 | 0.0008 | 497.0 | 0.63% | 420.9 | 0.53% | motif file (matrix) |
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| 42 |  | Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer | 1e-3 | -8.987e+00 | 0.0008 | 24827.0 | 31.27% | 24379.1 | 30.67% | motif file (matrix) |
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| 43 |  | NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer | 1e-3 | -8.593e+00 | 0.0011 | 6370.0 | 8.02% | 6108.9 | 7.68% | motif file (matrix) |
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| 44 |  | CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer | 1e-3 | -7.427e+00 | 0.0036 | 9653.0 | 12.16% | 9368.5 | 11.78% | motif file (matrix) |
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| 45 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-3 | -7.292e+00 | 0.0040 | 9695.0 | 12.21% | 9413.5 | 11.84% | motif file (matrix) |
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| 46 |  | p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer | 1e-3 | -7.124e+00 | 0.0045 | 1149.0 | 1.45% | 1047.8 | 1.32% | motif file (matrix) |
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| 47 |  | p53(p53)/Saos-p53-ChIP-Seq/Homer | 1e-3 | -7.124e+00 | 0.0045 | 1149.0 | 1.45% | 1047.8 | 1.32% | motif file (matrix) |
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| 48 |  | p53(p53)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-3 | -6.941e+00 | 0.0053 | 460.0 | 0.58% | 397.7 | 0.50% | motif file (matrix) |
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| 49 |  | NFkB-p50,p52(RHD)/Monocyte-p50-ChIP-Chip(Schreiber et al.)/Homer | 1e-2 | -6.204e+00 | 0.0109 | 1520.0 | 1.91% | 1413.6 | 1.78% | motif file (matrix) |
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| 50 |  | Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer | 1e-2 | -6.132e+00 | 0.0115 | 9219.0 | 11.61% | 8974.8 | 11.29% | motif file (matrix) |
pdf |
| 51 |  | ERE(NR),IR3/MCF7-ERa-ChIP-Seq(Unpublished)/Homer | 1e-2 | -5.964e+00 | 0.0133 | 3605.0 | 4.54% | 3447.8 | 4.34% | motif file (matrix) |
pdf |
| 52 |  | Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.848e+00 | 0.0146 | 454.0 | 0.57% | 398.5 | 0.50% | motif file (matrix) |
pdf |
| 53 |  | NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.801e+00 | 0.0151 | 578.0 | 0.73% | 515.8 | 0.65% | motif file (matrix) |
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| 54 |  | Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer | 1e-2 | -5.693e+00 | 0.0165 | 22530.0 | 28.37% | 22214.0 | 27.94% | motif file (matrix) |
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| 55 |  | Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer | 1e-2 | -5.185e+00 | 0.0269 | 6269.0 | 7.89% | 6085.0 | 7.65% | motif file (matrix) |
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| 56 |  | MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer | 1e-2 | -5.158e+00 | 0.0271 | 8704.0 | 10.96% | 8493.5 | 10.68% | motif file (matrix) |
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| 57 |  | bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer | 1e-2 | -4.760e+00 | 0.0397 | 3881.0 | 4.89% | 3743.0 | 4.71% | motif file (matrix) |
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