Supplementary Figure Legends
Supplementary Figure 1. Unsupervised hierarchical clustering of gene expression
distinguishes fusion-positive from fusion-negative rhabdomyosarcoma. Each individual
sample is shown in one column with the 33 fusion-positive rhabdomyosarcoma cases
labeled red and the 25 fusion-negative rhabdomyosarcoma cases labeled blue above
the heat map.
Supplementary Figure 2. The overall correlation between promoter methylation and
gene expression in rhabdomyosarcoma samples.
Supplementary Figure 3. Expression of genes from the 11-gene methylation signature
in 58 rhabdomyosarcoma samples assayed by expression arrays. Asterisks denote
statistical difference at a P value of <0.05. Abbreviations: FP, fusion-positive
rhabdomyosarcoma; FN, fusion-negative rhabdomyosarcoma.
Supplementary Figure 4. Relative position of the CpG sites examined by 27K
methylation array (shown in red) and pyrosequencing (shown in green). The first and
second exons are shown as solid boxes, and the transcription start site is indicated by a
horizontal arrow. CpG sites in the region are shown by short vertical lines. The scale at
the bottom indicates genomic positions on the designated chromosomes. Abbreviation:
pyro, pryosequencing.
1