Changes in gene expression after PAX3/FKHR silencing and identification of PAX3/FKHR target genes in aRMS cells. (a) Diagram depicting normalized expression values (log 10 scale) of 16221 filtered genes as measured in Rh4 cells after 0, 24, 48 and 72 h of treatment with PAX3-specific siRNA. Each line represents the expression of one gene. (b) Diagram depicting the overlap between a PAX3(7)/FKHR-specific gene signature derived from aRMS biopsies and genes downregulated by PAX3-specific siRNA treatment in Rh4 cells: 51 genes are present in both signatures. (c) Temporal changes of expression levels of the 51 genes identified in (b) in Rh4 cells after 0, 24, 48 and 72 h of treatment with PAX3-specific siRNA or scRNA. (d) Graphic representation depicting the ontology of the 51 potential PAX3/FKHR target genes identified in (b). A complete list of the functions as well as downregulation levels of the 51 genes is shown in Table 1. aRMS, alveolar RMS; RMS, rhabdomyosarcoma; scRNA, scrambled siRNA; siRNA, small interfering RNA.