Fig. 4: CircRNA differential expression analysis after RNase R correction.
From: Accurate quantification of circular RNAs identifies extensive circular isoform switching events
a The correlation of log2 fold change after TRA2B knockdown in RiboMinus and RiboMinus/RNase R-treated libraries. b The schematic workflow of RNase R treatment efficiency correction. Firstly, the BSJ and FSJ reads counts from RiboMinus/RNase R sample were obtained. With the posterior distribution of RNase R enrichment coefficient, the corrected BSJ reads count in RiboMinus sample can be calculated using the equation shown above. c Volcano plot of −log10 p-value (y-axis) against log2 fold change (x-axis) of circRNAs in RiboMinus samples. Size of points indicates DE-score values calculated by CIRIquant. Significantly upregulated and downregulated circRNAs are labeled in red and blue, respectively. d The volcano plot of circRNAs in RiboMinus/RNase R libraries before and after CIRIquant correction. Red and blue nodes represent up and downregulated circRNAs, respectively, with their node sizes representing DE scores. e CircRNA with relatively higher change in prior probability distribution of the number of BSJ reads will have a more significant DE score. Red and gray lines represent posterior distribution of corrected circRNA expression values before and after TRA2B knockdown. f Overlap of significantly differentially expressed circRNAs after and before RNase R correction. The whole and randomly sub-sampled of 50% RiboMinus RNA data are used as control set for RNase R treatment correction in two Venn diagrams. DE-circRNAs are divided into four categories: (I) RiboMinus-specific DE-circRNAs, (II) DE-circRNAs in both RiboMinus and RiboMinus/RNase R-corrected groups, (III) RiboMinus/RNase R-corrected DE-circRNAs, (IV) Dropped DE-circRNAs after RNase R correction. Numbers between the two Venn diagrams show the amount of circRNAs in type III and type IV that can be re-classified into type II when increasing the data size from 50 to 100%. The type III DE-circRNAs are more likely to be re-classified into type II than those in type IV (p-value = 0.02, Chi-squared test), demonstrating the reliability of RNase R correction by CIRIquant.
