Fig. 4

Combined analysis of differential gene expression and AltTEM in tappAS. a From left to right: intersections of differential module results: DIU with and without minor isoform filtering (eliminates isoforms with gene proportion of expression < 0.1) of DE vs DIU and DIU vs DCU and major isoform switching vs no switching. Numbers and vertical bar heights indicate the number of genes in each group. b Total usage change (i.e., expression redistribution between isoforms) vs log-transformed values of gene expression fold change between cell types. Genes with a major isoform switch are represented in orange. Labels are assigned to genes with the highest total usage change, indicating also whether they undergo major isoform switching. c From left to right: gene, transcript, and protein-level expression charts for the Cntn1 gene in the two conditions in our system (NPC and OPC, each containing two replicates—squares indicate replicate expression, points indicate mean replicate expression), and tappAS graphical representation of its transcript-level annotation. While there are no changes in the gene expression level (not DE), the gene presents differential isoform usage. Two alternative isoforms present the inclusion of a uORF due to an alternative TSS. d Multi-dimensional gene set enrichment analysis of genes ranked by DE and DIU significance level. Nodes correspond to GO terms obtained by selecting representatives of the top enriched GO term clusters. Pie chart area represents DE (blue) and DIU (orange) regulation measured by relative -log10(p value) of the enrichment test, and node size represents the number of genes annotated for each GO term