Table 3.
PWMs enriched among specific groups of targets
| Binding factors-motif name | p value | No. of hitsa |
|---|---|---|
| Total MRF and MEF2 targets | ||
| Group A. MyoD targets | ||
| E-box motif | 3.64E-21 to 5.01E-06 | 64 to 119 |
| MEF2 | 0.0018148 | 65 |
| SRF | 0.0021653 | 43 |
| TEAD/TEF family | 0.0033224 | 89 |
| ATF-2 and c-Jun | 0.005934 | 59 |
| Group B. Myogenin targets | ||
| E-box motif | 1.02E-34 to 2.41E-06 | 57 to 108 |
| SRF | 0.0004 | 40 |
| HNF2 | 0.0006 | 40 |
| MEF2 | 0.0007 | 62 |
| Nuclear hormone receptors (PR and GR) | 0.0024 | 41 |
| Group C. MEF2 targets | ||
| TEAD/TEF family | 4.77E-06 | 20 |
| MEF2 | 0.0002 | 16 |
| E-box motif | 0.0002 | 23 |
| Ikaros 2 | 0.0004 | 25 |
| CREB | 0.0080 | 6 |
| Zic and Gli factors | 0.0046 | 23 |
| Condition-specific binding sites | ||
| Group D. Targets of MyoD in GM but not in MT | ||
| NFE2L2 | 0.0004 | 29 |
| S8/Prrx2 | 0.0008 | 18 |
| ATF-2 and c-Jun | 0.0009 | 17 |
| Pax8 | 0.0028 | 29 |
| E-box motif | 0.0050 | 21 |
| Group E. Targets of MyoD in MT but not in GM | ||
| Ikaros 2 | 0.0008 | 21 |
| NF-κB | 0.0021 | 10 |
| Nuclear hormone receptors (PR and GR) | 0.0043 | 13 |
| Factor-specific binding sites | ||
| Group F. Bound in MT by MyoD but not by myogenin | ||
| Nuclear hormone receptors (PR and GR) | 8.92E-06 | 14 |
| Pou2f1/Octamer factor 1 | 0.0010 | 8 |
| Nkx2.1/Thyroid transcription factor 1 | 0.0027 | 18 |
| E4F1 | 0.0058 | 8 |
| NFE2L2 | 0.0080 | 19 |
| peroxisome proliferator activated receptor | 0.0094 | 8 |
| Group G. Bound in MT by myogenin but not by MyoD | ||
| E-box | 7.31E-18 | 54 |
| HNF-2 | 0.0003 | 24 |
| aryl hydrocarbon/dioxin receptor | 0.0004 | 23 |
| Zic and Gli factors | 0.0010 to 0.0014 | 47 to 53 |
| Expression-specific binding sites | ||
| Group H. Bound by MyoD and induced during differentiation | ||
| TEAD/TEF family | 0.0001 | 28 |
| SRF | 0.0003 | 16 |
| Retinoid and thyroid hormones receptors | 0.0030 | 19 |
| Zic and Gli factors | 0.0048 | 29 |
| MEF2 | 0.0052 | 22 |
| Group I. Bound by MyoD but not induced during differentiation | ||
| X-box binding protein 1 | 0.0038 | 63 |
| Myc | 0.0050 to 0.0074 | 7 to 26 |
| Pax8 | 0.0089 | 68 |
| Group J. Bound by myogenin and induced during differentiation | ||
| HNF-2 | 2.58E-06 | 17 |
| Nuclear hormone receptors (PR and GR) | 8.32E-05 | 37 |
| Smad proteins | 0.0001 to 0.0036 | 5 to 31 |
| TEAD/TEF family | 0.0005 | 29 |
| Zic and Gli factors | 0.0013 to 0.0069 | 33 to 37 |
| SRF | 0.0019 | 15 |
| MEF2 | 0.0022 to 0.0063 | 13 to 22 |
| COUP-TF1/NR2F1 | 0.0036 | 28 |
| Six1 homeobox transcription factor | 0.0093 | 35 |
| Group K. Bound by myogenin but not induced during differentiation | ||
| Tfcp2/Ubp1 | 5.43E-10 | 48 |
| Interferon Regulatory Factor 2 | 0.0007 | 7 |
| Olf1 (Olfactory Receptor) | 0.0044 | 10 |
| NF-KB | 0.0063 | 16 |
| Copeb, ZNF148, Sp6, KLF13 (CACCC motif) | 0.0070 | 6 |
Enrichment of transcription factor-binding site matrices in the promotor sequences (−1750 to 250 relative to transcription start site) of target genes was analyzed using the CREME algorithm (Sharan et al. 2003b). For the factor- and condition-specific PWMs, only those specific to the indicated sets that have a p-value <0.01 are shown. Not all redundant matrices (e.g., similar E-box motif PWMs) are shown. We indicate (in bold type) binding factors discovered in this study as MRF or MEF2 targets.
a
Number of different sequences with at least one occurrence of the motif.