Validation against RIP-Chip. (a) The distribution of differential RIP-Chip enrichments (PC2 scores) of BCBLl and DG75 for different sets of PAR-CLIP targets. Higher values indicate a stronger enrichment of a gene with RISC in BCBLl than in DG75, and, therefore, a set of KSHV miRNA targets should have a right-shifted distribution of PC2 scores. Genes that have been identified by PARma as well as PARalyzer to be KSHV miRNA targets indeed show such a shift, as well as genes that have only been found by PARma and not by PARalyzer (PARma only). In contrast, genes that are not targets of KSHV miRNAs according to both PARma and PARalyzer do not show a shift. Interestingly, genes found exclusively by PARalyzer and not by PARma are not shifted as well. (b) The P values for the comparisons of PARma to all other methods indicate that PARma not only outperforms PARalyzer but all other methods as well.