Table 4.
Promoter motif gene sets downregulated in mice with postdevelopmental myostatin knockout (GSEA method)
| Motif | Potential Transcription Factor | FDR, % | Gene Set Size | Leading Edge Genes | Leading Edge Genes Differentially Expressed at P < 0.01 |
|---|---|---|---|---|---|
| WWWWNGMCACGTCATYNYW | X-box binding protein 1 (Xbp1) | 0.0 | 47 | 16 | Col1a2, Creb3l1, Sec61a1 |
| GKSRKKCAGMCANCY | Smad4 | 1.0 | 148 | 55 | Col1a2, Notch3, Mylk |
| RYTAAWNNNTGAY | unknown | 1.3 | 36 | 13 | Col16a1 |
| RYAAAKNNNNNNTTGW | unknown | 2.0 | 51 | 28 | none |
| GGCTCYATCAYC | zinc finger and BTB domain containing 6 (Zbtb6) | 2.7 | 136 | 56 | Skil, Sesn3 |
| CCANNAGRKGGC | unknown | 2.9 | 63 | 17 | Eln |
| RTAATNA | POU domain, class 2, transcription factor 1 (Pou2f1) | 3.4 | 142 | 42 | Skil |
| CTGYNNCTYAA | unknown | 3.7 | 49 | 9 | Cercam |
| AAAYWAACM | forkhead box J1 (Foxj1) | 4.7 | 165 | 62 | Itgbl1, Fstl1, Angptl1, Stard13 |
Promoter motifs were defined as 6-base or longer sequences conserved in promoters (within 2 kb of transcription start sites) across different mammalian species (40). Potential transcription factors were derived from the TRANSFAC database, but it is possible that other factors bind to these sequences. Leading edge genes are those that contribute to the enrichment score generated by the gene set enrichment analysis (GSEA) method. Note that most of the leading edge genes are not differentially expressed at nominal P < 0.01.