| 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 | |
| 1 | | Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer | 1e-2 | -6.015e+00 | 0.6448 | 885.0 | 25.80% | 11105.7 | 23.73% | motif file (matrix) | |
| 2 | | NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer | 1e-2 | -5.775e+00 | 0.6448 | 1063.0 | 30.99% | 13502.5 | 28.85% | motif file (matrix) | |
| 3 | | Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer | 1e-2 | -5.216e+00 | 0.6448 | 153.0 | 4.46% | 1691.0 | 3.61% | motif file (matrix) | |
| 4 | | Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer | 1e-2 | -5.054e+00 | 0.6448 | 680.0 | 19.83% | 8498.5 | 18.16% | motif file (matrix) |