| 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 | | Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer | 1e-2 | -5.473e+00 | 1.0000 | 349.0 | 19.26% | 8083.1 | 16.88% | motif file (matrix) | |
| 2 | | Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer | 1e-2 | -5.052e+00 | 1.0000 | 655.0 | 36.15% | 15970.4 | 33.35% | motif file (matrix) |