Upregulated genes after silencing of PAX3 and PAX3/FKHR in RMS cells. (a) Diagram depicting expression values (fold change scale) of 260 genes upregulated more than twofold in Rh4 cells after 72 h of PAX3-specific siRNA treatment. (b) Expression levels of the same set of genes as in (a) in RD cells. Expression values were calculated in relation to scRNA treatment; levels of upregulation are listed in Supplementary Table 2. (c) Diagram depicting the expression values (fold change scale) of 52 genes (represented by 67 probe sets) involved in muscle development, which are upregulated in Rh4 cells after silencing of PAX3/FKHR for 72 h. Levels of upregulation are listed in Table 2. (d) Diagram depicting the expression values of the same 52 genes as in (c) in RD cells after 72 h of PAX3 silencing. (e and f) Verification of the expression changes of two genes, TNNC2 and MYL1, by qRT–PCR analysis. Fold change values in siRNA compared to scRNA-treated cells are shown. qRT–PCR, quantitative reverse transcription-PCR; RMS, rhabdomyosarcoma; scRNA, scrambled siRNA; siRNA, small interfering RNA.