Figure 5

Genomic organization of DE-macroRNAs. (A) Schematic representation of the algorithm used to identify macroRNAs resembling the example in Figure 3A. DE and expressed intervals identified by TileShuffle are summarized as the density of positive nucleotides. Local maxima are identified and the density curve is ‘flooded’ to 50% of the local maximum to identify the boundaries of the region. Overlapping regions are merged and for each region a score based on coverage by positive nucleotides and silhouette is calculated. (B) Computationally identified macroRNAs with a score > 10,000 were manually inspected to discard false positives, which are typically long protein-coding genes with many exons interspersed by small introns. Identified DE-macroRNAs fall into different genomic categories: intergenic (IG), overlapping exons (E), overlapping non-coding exons (EN), located in introns (I), joint start but different end as coding RNA (ES) and presumed primary transcript (P). (C) DE-macroRNA examples for the E, EN, ES, I and P cases. The IG case is illustrated in Figure 3A. Only z-scores and selected transcript isoforms are shown. CC, cell cycle; E, overlapping exons; EN, overlapping non-coding exons; ES, joint start but different end as coding RNA; I, located in introns; IG, intergenic; kB, kilobase; Nr, number; P, presumed primary transcript; STAT3, signal transducer and activator of transcription-3.