Differential splicing between CD4
subtypes. (A) Schematic illustrating expression of major and minor mRNA transcript isoforms by alternative splicing of a single gene. (B) Distribution of relative expression (MISO percent spliced in, PSI, values) of major and minor isoforms for protein coding genes in Th1 cells with two (top), three (middle), and four (bottom) annotated isoforms. The data represent the top 25% most highly expressed genes with multiple isoforms, such that most of these isoforms are classified as highly expressed (HE) genes. (C) For each pairwise comparison between subtypes, protein-coding genes that do not exhibit differential gene expression but that do express different major splice isoforms (referred to as transcript switching) were found. Distributions of the number of genes that exhibit any transcript switching (left) or at least a two-fold switch (right) for all pairwise comparisons between CD4+ subtypes are shown. (D) Relative expression (PSI) of switched transcripts at their high levels (left) and low levels (right) for each switch event across all comparisons.