| 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 |  | EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer | 1e-6 | -1.444e+01 | 0.0002 | 74.0 | 11.92% | 23.6 | 6.67% | motif file (matrix) |
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| 2 |  | E2A(HLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer | 1e-5 | -1.225e+01 | 0.0007 | 59.0 | 9.50% | 18.3 | 5.19% | motif file (matrix) |
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| 3 |  | SEP3(MADS)/Arabidoposis-Flower-Sep3-ChIP-Seq/Homer | 1e-5 | -1.170e+01 | 0.0008 | 51.0 | 8.21% | 15.8 | 4.48% | motif file (matrix) |
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| 4 |  | MyoD(HLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer | 1e-4 | -1.047e+01 | 0.0021 | 29.0 | 4.67% | 7.8 | 2.22% | motif file (matrix) |
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| 5 |  | PAX5(Paired/Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-4 | -1.011e+01 | 0.0025 | 23.0 | 3.70% | 6.0 | 1.69% | motif file (matrix) |
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| 6 |  | CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-4 | -9.325e+00 | 0.0045 | 9.0 | 1.45% | 1.1 | 0.31% | motif file (matrix) |
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| 7 |  | PAX5-shortForm(Paired/Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer | 1e-3 | -8.156e+00 | 0.0124 | 12.0 | 1.93% | 2.1 | 0.58% | motif file (matrix) |
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| 8 |  | ERE(NR/IR3)/MCF7-ERa-ChIP-Seq(Unpublished)/Homer | 1e-3 | -7.660e+00 | 0.0143 | 8.0 | 1.29% | 0.0 | 0.00% | motif file (matrix) |
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| 9 |  | GATA-IR4(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer | 1e-3 | -7.660e+00 | 0.0143 | 8.0 | 1.29% | 0.0 | 0.00% | motif file (matrix) |
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| 10 |  | HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer | 1e-3 | -7.660e+00 | 0.0143 | 8.0 | 1.29% | 1.1 | 0.32% | motif file (matrix) |
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| 11 |  | Tcf12(HLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer | 1e-2 | -6.608e+00 | 0.0372 | 34.0 | 5.48% | 11.3 | 3.21% | motif file (matrix) |
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| 12 |  | Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer | 1e-2 | -6.303e+00 | 0.0462 | 24.0 | 3.86% | 7.8 | 2.19% | motif file (matrix) |
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| 13 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-2 | -5.917e+00 | 0.0627 | 59.0 | 9.50% | 23.3 | 6.58% | motif file (matrix) |
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| 14 |  | RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer | 1e-2 | -5.756e+00 | 0.0685 | 28.0 | 4.51% | 9.3 | 2.63% | motif file (matrix) |
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| 15 |  | Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer | 1e-2 | -5.400e+00 | 0.0912 | 32.0 | 5.15% | 11.8 | 3.34% | motif file (matrix) |
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| 16 |  | Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529/Homer | 1e-2 | -4.970e+00 | 0.1315 | 29.0 | 4.67% | 10.3 | 2.92% | motif file (matrix) |
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| 17 |  | SeqBias: A/T bias | 1e-2 | -4.943e+00 | 0.1315 | 588.0 | 94.69% | 325.7 | 92.13% | motif file (matrix) |
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| 18 |  | Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1e-2 | -4.902e+00 | 0.1315 | 22.0 | 3.54% | 8.0 | 2.26% | motif file (matrix) |
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| 19 |  | FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer | 1e-2 | -4.882e+00 | 0.1315 | 135.0 | 21.74% | 63.2 | 17.88% | motif file (matrix) |
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| 20 |  | Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer | 1e-2 | -4.732e+00 | 0.1334 | 33.0 | 5.31% | 12.1 | 3.43% | motif file (matrix) |
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| 21 |  | NFkB-p65-Rel(RHD)/LPS-exp(GSE23622)/Homer | 1e-2 | -4.684e+00 | 0.1334 | 6.0 | 0.97% | 0.0 | 0.00% | motif file (matrix) |
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| 22 |  | RBPJ:Ebox/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-2 | -4.684e+00 | 0.1334 | 6.0 | 0.97% | 1.7 | 0.47% | motif file (matrix) |
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| 23 |  | ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer | 1e-2 | -4.684e+00 | 0.1334 | 6.0 | 0.97% | 1.2 | 0.33% | motif file (matrix) |
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| 24 |  | TATA-box/Drosophila-Promoters/Homer | 1e-2 | -4.684e+00 | 0.1334 | 6.0 | 0.97% | 1.3 | 0.38% | motif file (matrix) |
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| 25 |  | ETS(ETS)/Promoter/Homer | 1e-2 | -4.643e+00 | 0.1334 | 35.0 | 5.64% | 13.3 | 3.77% | motif file (matrix) |
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| 26 |  | GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer | 1e-2 | -4.608e+00 | 0.1334 | 9.0 | 1.45% | 2.5 | 0.70% | motif file (matrix) |
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