Supplementary Figure 4: Characterization of unannotated transcripts.

(a) Dot plots depicting the comparison of the MiTranscriptome with reference transcripts from RefSeq, UCSC or GENCODE. Precision (blue), precision for the subset of transcripts overlapping annotated transcripts (light blue) and sensitivity (orange) are plotted for each comparison. (b) Dot plots comparing the base-wise, splice-site and splicing pattern precision and sensitivity of MiTranscriptome and GENCODE using lncRNAs from RefSeq (left) or Cabili et al. (right). (c) Bar plots comparing the numbers of unannotated transcripts versus different classes of annotated transcripts for each of the 18 cohorts. Top, stacked bar plot showing annotated ncRNAs (red), pseudogenes (cyan), read-throughs (purple) and protein-coding genes (blue). Bottom, bar plot showing unannotated transcripts (pink).