Figure 2 from The Proteogenomics of Prostate Cancer Radioresistance

Transcriptomic signatures of cancer-related genes in radioresistant cells. A, The differences in RNA abundances of driver cancer genes. The most abundant transcript out of all transcripts per gene was taken for visualization. B–C, The differences in RNA abundances of affected driver gene, compared to their abundance differences at the protein level. B, Differences between CF-resistant cells and the parental cells. C, Differences between HF-resistant cells and the parental cells. D, The RNA abundance profile of cancer hallmark genes in CF-resistant cells is distinct from HF-resistant cells and the parental profiles, which are relatively similar. The heatmap presents normalized counts of RNA isoforms that were significantly differentially abundant in CF-resistant cells compared to HF. Red, high abundance; blue, low abundance. For visualization, RNA abundances as a function of log₁₀ were converted to z-scores. E, Enrichment analysis of hallmark gene sets. The dot size represents the enrichment score and the dot color represents the directionality: for CF vs. PAR, HF vs. PAR, and HF vs. CF tests, orange represents upregulation toward CF-resistant cells, HF-resistant cells, and HF-resistant cells. F, The differences in RNA abundances of the lncRNA UCA1, the miRNAs 200c-3P and 200b-3P, and ZEB2 (the target of the miRNAs 200c-3P and 200b-3P). For UCA1 transcripts, the small letters represent different isoforms. In A and F, the dot size represents the log₂ (fold change) size and the dot color represents the directionality: for CF vs. PAR, HF vs. PAR, and HF vs. CF tests, red represents upregulation toward CF-resistant cells, HF-resistant cells, and HF-resistant cells. For all figures , three RNA-seq replicates were used for the radioresistant cell lines and two for the parental line. In B–C, three replicates were used for all cell types.