Fig. 4: Transcriptional reprogramming of praja2-silenced GBM cells.

a MA-plot from RNA-Seq data analysis showing the transcriptome differences after praja2 silencing in U87 cells, compared to control. Red dots represent upregulated transcripts with fold-change ≥1.5 and adjusted p value ≤0.10, while blue dots represent downregulated transcripts with fold-change ≤−1.5 and adjusted p value ≤0.10. Gray dots represent those transcripts with −1.5< fold-change <1.5 and/or with an adjusted p value >0.10. The x-axis represents the log2 of mean expression, while the y-axis represents the log2 fold-change, as computed by DESeq2. Dashed lines highlight the fold-change cutoff of ≥1.5 or ≤−1.5. b Histogram showing the distribution of adjusted p values for the 725 differentially expressed genes. More than 81.5% of differentially expressed genes are associated with an adjusted p value ≤ 0.05. c Histogram showing NES (normalized enrichment score) values of the molecular signatures statistically significant (FDR ≤0.25) involving the differentially expressed transcripts, as computed by the GSEA tool. d Heatmap summarizing expression data for the differentially expressed transcripts involved in the molecular signature of indicated pathways, as computed with GSEA, in siPraja2 versus siRNAc conditions. Normalized expression values in log2 scale and centered on the median value. Immunoblot analysis of praja2 in siRNA-transfected U87MG cells before RNA preparation is also shown. e IPA upstream regulator analysis of master upstream regulatory factors (PPARGC1A, PPARGC1B, and NRF1) on their target genes. Data were expressed as the ratio of the normalized read counts in siPraja2 vs siRNAc samples.