For example, module 3 contained 139/331 genes upregulated in alveolar compared to embryonic rhabdomyosarcoma, 27/48 genes that were downregulated when FOXO1-PAX3 was altered with RNA interference, and 22/64 genes previously associated with cell line differences related to PAX3 and PAX7 fusions (Table 4 and Table S4). This evidence concerns the gene PAX3 and rhabdomyosarcoma.