| 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 |  | PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer | 1e-7 | -1.748e+01 | 0.0000 | 416.0 | 17.31% | 295.4 | 11.82% | motif file (matrix) |
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| 2 |  | SeqBias: TA-repeat | 1e-7 | -1.711e+01 | 0.0000 | 761.0 | 31.67% | 618.7 | 24.75% | motif file (matrix) |
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| 3 |  | ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer | 1e-7 | -1.691e+01 | 0.0000 | 173.0 | 7.20% | 93.7 | 3.75% | motif file (matrix) |
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| 4 |  | Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer | 1e-6 | -1.456e+01 | 0.0000 | 119.0 | 4.95% | 58.8 | 2.35% | motif file (matrix) |
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| 5 |  | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1e-5 | -1.268e+01 | 0.0002 | 193.0 | 8.03% | 121.5 | 4.86% | motif file (matrix) |
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| 6 |  | PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer | 1e-5 | -1.256e+01 | 0.0002 | 474.0 | 19.73% | 371.9 | 14.87% | motif file (matrix) |
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| 7 |  | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1e-4 | -1.095e+01 | 0.0010 | 227.0 | 9.45% | 156.7 | 6.27% | motif file (matrix) |
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| 8 |  | ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer | 1e-4 | -1.050e+01 | 0.0013 | 138.0 | 5.74% | 83.7 | 3.35% | motif file (matrix) |
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| 9 |  | LHY(Myb)/Seedling-LHY-ChIP-Seq(GSE52175)/Homer | 1e-4 | -1.046e+01 | 0.0013 | 212.0 | 8.82% | 145.9 | 5.84% | motif file (matrix) |
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| 10 |  | Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer | 1e-4 | -1.027e+01 | 0.0013 | 99.0 | 4.12% | 53.3 | 2.13% | motif file (matrix) |
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| 11 |  | Unknown6/Drosophila-Promoters/Homer | 1e-4 | -9.523e+00 | 0.0026 | 175.0 | 7.28% | 117.5 | 4.70% | motif file (matrix) |
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| 12 |  | GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer | 1e-3 | -9.130e+00 | 0.0035 | 233.0 | 9.70% | 169.1 | 6.76% | motif file (matrix) |
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| 13 |  | Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer | 1e-3 | -8.210e+00 | 0.0081 | 155.0 | 6.45% | 105.5 | 4.22% | motif file (matrix) |
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| 14 |  | FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer | 1e-3 | -8.142e+00 | 0.0081 | 150.0 | 6.24% | 101.5 | 4.06% | motif file (matrix) |
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| 15 |  | Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer | 1e-3 | -8.098e+00 | 0.0081 | 23.0 | 0.96% | 5.2 | 0.21% | motif file (matrix) |
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| 16 |  | SeqBias: CG bias | 1e-3 | -7.925e+00 | 0.0087 | 890.0 | 37.04% | 810.3 | 32.41% | motif file (matrix) |
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| 17 |  | EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer | 1e-3 | -7.835e+00 | 0.0090 | 83.0 | 3.45% | 47.6 | 1.90% | motif file (matrix) |
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| 18 |  | FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer | 1e-3 | -7.558e+00 | 0.0112 | 175.0 | 7.28% | 125.4 | 5.02% | motif file (matrix) |
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| 19 |  | Mef2b(MADS)/HEK293-Mef2b.V5-ChIP-Seq(GSE67450)/Homer | 1e-3 | -7.345e+00 | 0.0132 | 144.0 | 5.99% | 99.3 | 3.97% | motif file (matrix) |
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| 20 |  | ZNF136(Zf)/HEK293-ZNF136.GFP-ChIP-Seq(GSE58341)/Homer | 1e-3 | -6.962e+00 | 0.0183 | 17.0 | 0.71% | 3.2 | 0.13% | motif file (matrix) |
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| 21 |  | Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer | 1e-2 | -6.772e+00 | 0.0211 | 32.0 | 1.33% | 12.5 | 0.50% | motif file (matrix) |
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| 22 |  | Etv2(ETS)/ES-ER71-ChIP-Seq(GSE59402)/Homer(0.967) | 1e-2 | -6.529e+00 | 0.0257 | 82.0 | 3.41% | 50.1 | 2.01% | motif file (matrix) |
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| 23 |  | EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer | 1e-2 | -6.419e+00 | 0.0274 | 128.0 | 5.33% | 90.0 | 3.60% | motif file (matrix) |
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| 24 |  | c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer | 1e-2 | -6.188e+00 | 0.0331 | 35.0 | 1.46% | 15.7 | 0.63% | motif file (matrix) |
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| 25 |  | DMRT6(DM)/Testis-DMRT6-ChIP-Seq(GSE60440)/Homer | 1e-2 | -5.977e+00 | 0.0393 | 33.0 | 1.37% | 14.0 | 0.56% | motif file (matrix) |
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| 26 |  | ERE(NR),IR3/MCF7-ERa-ChIP-Seq(Unpublished)/Homer | 1e-2 | -5.844e+00 | 0.0431 | 15.0 | 0.62% | 3.6 | 0.14% | motif file (matrix) |
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| 27 |  | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1e-2 | -5.667e+00 | 0.0496 | 177.0 | 7.37% | 137.0 | 5.48% | motif file (matrix) |
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| 28 |  | E-box/Arabidopsis-Promoters/Homer | 1e-2 | -5.518e+00 | 0.0555 | 36.0 | 1.50% | 17.1 | 0.68% | motif file (matrix) |
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| 29 |  | DMRT1(DM)/Testis-DMRT1-ChIP-Seq(GSE64892)/Homer | 1e-2 | -5.371e+00 | 0.0600 | 41.0 | 1.71% | 21.1 | 0.84% | motif file (matrix) |
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| 30 |  | PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-2 | -5.371e+00 | 0.0600 | 41.0 | 1.71% | 21.8 | 0.87% | motif file (matrix) |
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| 31 |  | Bapx1(Homeobox)/VertebralCol-Bapx1-ChIP-Seq(GSE36672)/Homer | 1e-2 | -5.343e+00 | 0.0600 | 256.0 | 10.65% | 211.4 | 8.45% | motif file (matrix) |
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| 32 |  | Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer | 1e-2 | -4.950e+00 | 0.0857 | 33.0 | 1.37% | 16.4 | 0.65% | motif file (matrix) |
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| 33 |  | Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer | 1e-2 | -4.945e+00 | 0.0857 | 85.0 | 3.54% | 58.3 | 2.33% | motif file (matrix) |
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| 34 |  | c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer | 1e-2 | -4.831e+00 | 0.0908 | 38.0 | 1.58% | 20.8 | 0.83% | motif file (matrix) |
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| 35 |  | Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer | 1e-2 | -4.708e+00 | 0.0998 | 92.0 | 3.83% | 65.7 | 2.63% | motif file (matrix) |
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| 36 |  | SUT1?/SacCer-Promoters/Homer | 1e-2 | -4.705e+00 | 0.0998 | 536.0 | 22.31% | 488.2 | 19.53% | motif file (matrix) |
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