Fig. 4

Analysis of RNA seq data by Principal Component Analysis (PCA) and gene set enrichment analysis (GSEA) from samples of control, photon (6 Gy; 24 h) and ¹²C-ion (2 Gy; 24 h) irradiation or DHT treatment (20 nM; 24 h). A PCA Biplot of the mRNAs including all samples. The principal component 1 (PC1) covers 58.9% (x-axes) and PC2 covers 10% (y-axes) of the multidimensional data sets of the detected mRNA targets (n > 10⁴). The samples of LNCaP or DU145 cells are grouped as control, photons, ¹²C-ions or DHT, as indicated by different colors and symbols (see legend). The n-number of controls is n = 9 for LNCaP and n = 6 DU145 since the respective matched control values (n = 3) were merged. The samples are encircled by a line representing the 95% confidence interval (95% CI) for each group. The loading vectors (light blue) represent several selected altered genes and indicate their contribution to PC1 or PC2. (B-E) Gene set enrichment analyses (GSEA) of enrichment score (ES) and false discovery rate (FDR) are displayed as volcano plots (ES vs. − log FDR). In GSEA, ES-values are considered as significant if FDR < 0.25 and p < 0.05. The dotted line at (− log FDR = 0.602) corresponds to FDR = 0.25, meaning that the ES values above this line have an FDR < 0.25. Here, these gene sets have nominal p-values < 0.01 (see supplementary information) and therefore the ES-values above the dotted line represent significant ES-values. The critical ES-values of the treatments are displayed with respect to different gene sets: B Amundson-DNA-damage-response-TP53 (TP53-DNA-damage) for photons and ¹²C-ions; C WP-G1-to S-cell cycle-control (G1-S-Cell cycle) photons and ¹²C-ions; D WP-DNA-repair pathway full network (FN-DNA-Repair) for photons and ¹²C-ions. In E the Hallmark Androgen Response (HM-AR) in DHT-treated LNCaP cells is compared with photon and ¹²C-ion irradiated LNCaP cells. In E, the gene sets shown in B–D are analyzed with respect to DHT treatment. In F, the ES values of FN-DNA-repair are correlated with those of other DNA-repair modes particularly, DNA-repair-homologue-recombination (HR-DNA-repair), non-homologue-end-joining (NHEJ-DNA-repair), mismatch repair-DNA-repair (MM-DNA-repair) and AR-targeted DNA-repair (AR-DNA-repair). The symbols refer to the DNA-repair mode (see inset table). Treatments and cells are indicated LNCaP (LN) and DU145 (DU)