Figure 2

The details of four identified A-to-I editing sites in miRNAs. (A) to (D) are schematic views of hsa-miR-378b, hsa-miR-497, hsa-miR-6503 and hsa-let-7a-2, respectively. In part (A) to (D), the upper panel shows the total number of reads (vertical axis) aligned to positions (horizontal axis) of the precursors of miRNAs, the central panel shows the number of reads that do not match the reference precursor sequences of miRNAs, the lower panel shows - log10 of the multiple-test corrected P-value (with Benjamini and Hochberg [39] method) of the editing or mutation sites. The meaning of different colors in the central and lower panels are given at the lower right corner. (E) to (H) are the reads supporting hsa-miR-378b_53_A_g, hsa-miR-497_83_A_g, hsa-miR-6503_59_A_g and hsa-let-7a-a_28_A_g, respectively. In part (E) to (H), the lower case nucleotides in the reads mean the mismatched nucleotides that are generated in editing or mutation events; and the upper case nucleotides in the precursors mean the mature miRNAs. The three columns after a read are the original number of this read in the library, the length of the read, and the weight of this read at this locus calculated by the cross mapping algorithm [11]. The percentage values after the name of editing site are the percentage of edited or mutated reads. The lines below the pre-miRNA sequences are the secondary structures predicted with RNAfold [36], and numbers in the parent thesis mean the minimum free energy in k-cal/mol. In all parts, the names of the sequencing profiles are shown in the parenthesis after the name of the editing sites.