Figure 2
DE-TAR overlap with genomic annotation. (A,B) Overlaps in nucleotides between DE-TARs and different annotation categories. Log2 transformed odds ratios and their 95% confidence interval for the respective annotation dataset are shown (annotations are described in detail in Additional file 1: Table S28). To assess the significance of the observed overlap, 100 lists containing random intervals from the genome controlling for repeat content and DE-TAR length were sampled. Odds ratios of observed versus randomized relative overlaps were calculated and tested using Fisher’s exact test for significant enrichment or depletion. *** indicates P<0.001 for the observed versus random nucleotide overlaps, ** P<0.01 and * P<0.05. Results are shown for DE-TARs that overlap annotated protein-coding genes (A) (additional annotations are shown in Additional file 1: Figure S10) and bona fide non-coding DE-TARs that overlap with several classes of experimentally verified and predicted ncRNAs (B) (additional annotations shown in Additional file 1: Figure S11). For the detailed output of Fisher’s exact tests refer to Additional file 1: Tables S4 and S6. (C) Fraction of nucleotides in intergenic bona fide non-coding DE-TARs overlapping with known long ncRNAs (large intergenic non-coding RNAs and transcripts of unknown protein-coding potential as identified in [30], Gencode v12 long ncRNAs, lncRNAs found in the Long Non-Coding RNA Database (lncRNAdb, [49]) and ncRNAs found in chromatin [50]), short RNAs (UCSC sno/miRNA track), conserved secondary structures (Evofold[45], RNAz[44, 51] and SISSIz[52]) and novel transcribed nucleotides. CAR, chromatin-associated RNA; CC, cell cycle; CDS, coding sequence; lncRNA, long ncRNA; ncRNA, non-protein-coding RNA; UTR, untranslated region.