| 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 |  | Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer | 1e-5 | -1.182e+01 | 0.0019 | 2508.0 | 54.88% | 23439.3 | 51.67% | motif file (matrix) |
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| 2 |  | Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer | 1e-4 | -9.951e+00 | 0.0063 | 2073.0 | 45.36% | 19275.5 | 42.49% | motif file (matrix) |
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| 3 |  | Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer | 1e-3 | -8.148e+00 | 0.0255 | 742.0 | 16.24% | 6537.4 | 14.41% | motif file (matrix) |
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| 4 |  | ISRE(IRF)/ThioMac-LPS-Expression(GSE23622)/Homer | 1e-2 | -6.321e+00 | 0.1187 | 75.0 | 1.64% | 520.3 | 1.15% | motif file (matrix) |
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| 5 |  | RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer | 1e-2 | -5.209e+00 | 0.2888 | 47.0 | 1.03% | 312.7 | 0.69% | motif file (matrix) |
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| 6 |  | Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer | 1e-2 | -4.931e+00 | 0.3177 | 1038.0 | 22.71% | 9623.1 | 21.21% | motif file (matrix) |
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| 7 |  | GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer | 1e-2 | -4.730e+00 | 0.3329 | 97.0 | 2.12% | 748.7 | 1.65% | motif file (matrix) |
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| 8 |  | IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer | 1e-2 | -4.718e+00 | 0.3329 | 155.0 | 3.39% | 1265.6 | 2.79% | motif file (matrix) |
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| 9 |  | EBNA1(EBV virus)/Raji-EBNA1-ChIP-Seq(GSE30709)/Homer | 1e-2 | -4.678e+00 | 0.3329 | 13.0 | 0.28% | 60.2 | 0.13% | motif file (matrix) |
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