Twelve tumors (n=6 with 12q13-q14 amplification; n=6 without 12q13-q14 amplification) were selected from 57 cases reported in a previous study (9 (link)). Criteria for selection included PAX3-FOXO1 expression, prior analysis by copy number arrays (9 (link)), and availability of RNA. Oligonucleotide microarray expression analysis was performed on the 12 selected cases using the Affymetrix GeneChip Human Gene 1.0 ST Array at the University of Pennsylvania Microarray Facility. We defined a gene as overexpressed in a sample if its expression level was >1 standard deviation (SD) from the mean expression level of that gene across all samples. More stringent analysis was also performed by defining overexpression as >2 SD from the mean. The total number of overexpressed genes in each sample was used as a relative measure of E2F pathway activation. Additional details are described in Supplemental methods.