Figure 2.

Tissue-dependent exon usage is widespread in the human genome. Panels (A–C) show data from subset A of the GTEx data. The same plots using data from subsets B and C can be found in Supplementary Figures S12 and S14. (A) Similar to a volcano-plot, this figure shows statistical significance (P-value on −log₁₀ scale) versus effect size (tissue score) of our tissue-dependence test for each exonic region of the human genome. The solid red lines show the thresholds used in this study to call an exonic region tissue-dependent. The P-value threshold 4.28 · 10⁻² corresponds to an adjusted P-value of 0.1 according to the Benjamini–Hochberg method to control FDR. (B) Histogram of the fraction of exonic regions within each gene that are subject to TDU (X-axis). The Y-axis shows the number of genes. (C) Similar to Panel B, but expressed in terms of fraction of base-pairs within a gene affected by TDU. (D) Exemplary data from four out of nine tissues of individual 131XE from subset B. Shown is RNA-seq coverage (Y-axis) plots along genomic coordinates (X-axis) at the locus of the gene EPB41L4B on chromosome 9. The lower panel shows the transcript annotations for this gene. Skin and thyroid express short isoforms, while tibial nerve and skeletal muscle express longer isoforms.