Fig. 2

miRDeep* putative miRNAs and miRBase miRNAs. This Venn diagram depicts the overlap between two sets of hairpin miRNAs. The first is the set of miRDeep* results after score-filtering (86.13) and filtering to remove exons and sRNAs, using annotation files from gencode v19 and matching by genomic locations with the intersect function from bedtools v2.22.1. This set of 454 miRDeep* results overlaps the set of miRBase v20 hairpin miRNAs, also filtered for exons and sRNAs with the same method. As seen in the Venn diagram, the majority of the score and exon/sRNA filtered miRDeep* results exist within the miRBase database. The 99 that do not are the final putative novel miRNAs of this study. (*) The total number of filtered miRBase hairpin miRNAs is not the sum of the intersection and the remaining miRBase set because the miRBase and miRDeep* hairpin miRNAs do not have a one-to-one relationship. Twenty-two of the miRDeep* set overlap two members of the miRBase set, and eight of the miRBase set overlap two members of the miRDeep* set. In this Venn diagram we have displayed that 355 of the 454 filtered miRDeep* hairpin miRNA predictions overlap at least one filtered miRBase v20 hairpin miRNA, and 1138 of 1507 filtered miRBase v20 hairpin miRNAs overlap zero filtered miRDeep* hairpin miRNA predictions