Table 2.
TFBS motifs associated preferentially with FSHD up- vs. downregulated genes in myotubes.
| No. of genes with the motif from 826 promoter regionsa | p-value: skewing of up- or dnreg. | Prominent functional annotationb | ||||
|---|---|---|---|---|---|---|
| TFBS motif | FSH upreg. | FSH dnreg. | Upreg./dnreg. | FSH upreg. | FSH dnreg. | |
| MEF2A | 39 | 101 | 0.4 | < 0.0001 | PI3K signaling, 8 genes | muscle phenotype, 16 genes |
| E4BP4 | 16 | 42 | 0.4 | 0.008 | cell adhesion, 5 genes, GO:0007155 | none |
| PPARG | 100 | 43 | 2.3 | 0.0001 | extracellular matrix, 13 genes, GO:0031012; arachidonic acid, 15 genes | cardiac hypertrophy, 7 genes |
| p53 | 84 | 37 | 2.3 | 0.0009 | inflammation, 29 genes; superoxide, 29 genes | Activation of cAMP-dependent PKA, 5 genes |
aPredicted transcription factor binding site motifs (TFBS) in the upstream (promoter) region for 403 and 423 genes that displayed the strongest up- or downregulation (p < 0.01), respectively, in FSHD vs. control myotubes. These sites were identified by GeneCards http://genecards.org and were analyzed by Chi-square tests for association with FSHD up- vs. downregulation in myotubes. Of the 126 TFBS scored, the four shown in this table had the strongest association with either FSHD up- or downregulated genes. For PPARG, PPARG1 and PPARG2 motifs were pooled.
bFunctional annotation from GeneDecks http://genecards.org