Table 3.
Summary of the results for human muscle expression data
| TM-1 | TM-2 | TM-3,4,5 | |
|---|---|---|---|
| TREMOR | • 19 TM-1s detected. | • 87 TM-2s detected | • 218 TM-3s detected. SRF, MEF-2 and MyoD are included in 119, 41 and 19 |
| • The top 2 TM-2s were SRF and MEF-2. | • 21 included SRF, 11 included MEF-2 and 7 included MyoD. | • Most core muscle TFs tend to group with non-core TFs in a TM. | |
| • MyoD was at rank 4. | • Rank-1 TM-2 is (SRF MEF-2). | • Rank 16 TM-3 is (SRF MEF-2 SMAD). | |
| • We did not detect SP1, probably because it is a ubiquitous signal. TEF-1 had a P-value of 0.06 and was thus not detected as significant. | • Rank-8 TM-2includes the two SRF PWMs (see text). | • Rank 28 TM-3 is (SRF MEF-2 MyoD). | |
| • Seven of the remaining 14 TFs have evidence of involvement in muscle gene regulation: SMAD (54), SREBP (55), p53 (56), PBX (57), Hox-1.3 (58) (this reference implicated Hox factors in general), COMP1 (59) (Myogenin interacts with COMP1), GATA-4. | • TEF-1 is part of a significant TM-2 SRF and with SMAD. | • 244 TM-4s detected. SRF, MEF-2 and MyoD are part of 177, 75 and 17 TM-3s. | |
| • Additional factor RREB was also detected previously by oPOSSUM2 in a slightly different dataset (13). | • 283 TM-5s detected. SRF is part of 232. | ||
| • TEF-1 yielded a P-value of 0.06 and missed detection | |||
| OPOSSUM2 | TM-2 | TM-3 | |
| • 293 TM-2s detected. SRF, MEF-2 and Myf (same as MyoD) were part of 37, 42 and 37. Compare with TREMOR above. | • In our dataset, 764 TM-3s were detected TMs. | ||
| • See text for additional comparative discussion | • In the original oPPOSSUM2 publication, using three different muscle datasets, the authors have reported top 5 TM-2 in each dataset. Greater than half of these were detected by TREMOR, notably (YY1 SRF), (YY1 Myf), (SRF E47) and (SRF MEF-2). | ||
| CREME | With the default setting, CREME did not yield any TMs. However, at the least stringent setting it detected 1 TM-2—(SRF SRF). TREMOR also detected a size-2 TM with two SRF motifs, in addition to several others. | ||
For oPOSSUM2 and CREME, the results are compared to TREMOR. Unless otherwise specified, for TREMOR we only mention the TMs whose P-values were lower than the lowest P-value for the corresponding randomly permuted set (see text).