Table 1.
Primary and cofactor motifs found by DREME in 13 mES cell ChIP-seq datasets
| TF | Peaks | m | r | Cofactor motifs |
|---|---|---|---|---|
| CTCF | 39609 | 29 | 1 | Myc, STAT3, GABPA |
| cMyc | 3422 | 12 | 1 | STAT3, Egr1 |
| E2f1 | 20699 | 25 | 2a | STAT3, Myc, Klf4, Fox, |
| CREB/ATF | ||||
| Esrrb | 21647 | 29 | 1 | Klf4, Sox2, STAT3, Oct4, Myc, |
| Rxra, Zic3, Ewsr1 | ||||
| Klf4 | 10875 | 26 | 1 | STAT3, Esrrb, Sox2, Oct4, Sp1, |
| Gata3, Myc, Zfp161 | ||||
| Nanog | 10343 | 24 | 4a | Sox2, Oct4, Zic3, Klf4, Elf5, |
| Esrrb, Tead1 | ||||
| nMyc | 7182 | 21 | 1 | STAT3, Smad1, CREB/ATF, |
| Sfpib | ||||
| Oct4 | 3761 | 17 | 1 | Sox2, Klf4, CREB/ATF, Esrrb |
| STAT3 | 2546 | 13 | 1 | Klf4, Esrrb, Sox2, Oct4, Myc, |
| Sp1, Irf4 | ||||
| Smad1 | 1126 | 10 | No | Sox2, Oct4, Esrrb, Zic3, Klf4, |
| Zfp740 | ||||
| Sox2 | 4526 | 19 | 1 | Oct4, Klf4, STAT3, Zic3, Esrrb |
| Tcfcp2l1 | 26910 | 33 | 1 | STAT3, Klf4, Esrrb, Egr1, Sox2, |
| Oct4, Fox, Myc, Sp1, Tead1, | ||||
| CREB/ATF | ||||
| Zfx | 10338 | 20 | 1 | STAT3, Myc, Esrrb |
Columns show the name of the ChIP-ed TF; the number of ChIP-seq peaks; the number of significant motifs (m) found by DREME (E < 0.05); the rank (r) of the ChIP-ed TF's motif; and cofactor motifs found. Cofactor TFs are listed in the order of DREME significance and in bold font if they are 1 of the 12 pluripotency TFs. Only the cofactor TF family name is given when several family members match the DREME motif (e.g. ‘Myc’).
aSee text for discussion of E2f1 and Nanog motifs.