Fig. 3

Expression, subcellular fraction enrichment and maturity of cytoplasmic versus nuclear transcripts. a Subcellular fraction enrichment (compartment bias) displayed as normalized cytoplasmic (Cyto) to nuclear (Nuc) expression ratio, of all RNAs that show either cytoplasmic-biased (positive y-axis) or nuclear-biased transcript levels (negative y-axis) at an edgeR-adjusted p-value < 0.001 in at least one of the four biological conditions assayed. For genes showing significant compartment bias in more than one biological condition, data is shown for the condition with the highest FPKM value (Table S2A, columns D and E). Each data point represents one gene showing nuclear or cytoplasmic bias (gene counts shown in table at right). Data are graphed separately for lncRNAs and PCGs in Figure S3A-S3B. b Distributions of FPKM values, and c distribution of subcellular fraction bias values (i.e., differential expression values) for the four indicated sets of subcellular fraction-enriched transcripts. The median fraction bias was 1.8–1.9-fold higher (adjusted p-value < 0.0001) for the nuclear-biased transcripts than for the cytoplasmic-biased transcripts. d Distributions of transcript maturity values (normalized IO/EC read density ratios, from Table S1F) in the cytoplasmic and nuclear fractions (“Fraction”) for multi-exonic lncRNAs and multi-exonic PCGs that show a significant cytoplasmic bias (Cyto) or nuclear bias (Nuc) (“Bias”), or that do not show a significant compartment bias (UB, unbiased). For b, c, and d, median values (black horizontal midline) and IQR (error bars) are indicated; black horizontal lines compare lncRNAs to PCGs within the same fraction, and red horizontal lines compare lncRNAs, or PCGs, between groups, as marked, with ** indicating adjusted p-value < 0.0001. In d, statistical analysis was used to compare Cyto vs UB, and UB vs Nuc, for lncRNAs and PCGs, based on expression data in the cytoplasm or in the nucleus