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 webcite 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 webcite

Tsumagari et al. BMC Medical Genomics 2011 4:67   doi:10.1186/1755-8794-4-67

Open Data