Fig. 3

Co-occurrence of A-to-I RNA editing sites in Alu elements detected by L-GIREMI. a Genomic context of A-to-I RNA editing sites identified in the AD sample or GM12878 cells. b Number of RNA editing sites in Alu repeats or otherwise. c Cumulative distribution for the Gini index of Alu repeats calculated via read-specific editing ratio. Shuffled data were generated for comparison (Methods), which led to significantly lower Gini index values than the original data (p < 0.001 for both data sets, KS test). d Cumulative distribution of mutual information of pairs of editing sites or pairs of SNPs in the same gene. Compared to the shuffled controls, both editing sites and SNPs show higher levels of linkage (p < 0.001 for all comparisons, KS test) although the latter were associated with much higher mutual information