Fig. 5. Th1-recall is characterised by the upregulation of a select few genes.

A UMAP of PbTII cells after scVI integration of naïve and primary Th1 scRNA-seq data from Soon et al.²³. with Th1-recall scRNA-seq in this study (open circles) coloured according to pseudotime values (after 1-dimensional BGPLVM)—apparent Th1-recall trajectory indicated with an arrow. B (Left) Venn diagrams showing overlap in lists of differentially expressed genes (Bayes factor > 3) from peak Th1-primary (relative to naïve PbTIIs), compared to peak Th1-recall (relative to naïve PbTIIs). (Right) Summary of gene ontology enrichment analysis of biological processes associated with genes common or unique to each comparison; Fisher’s exact test used to identify over-represented GO terms. C Sankey plot schematic summarising dynamics of 1319 genes initially upregulated in Th1-primary cells (compared to naïve PbTIIs), as cells proceed to memory and then to peak Th1-recall (Up: upregulated, Down: downregulated, Stable: no significant change; at each stage in reference to the preceding stage). Full list of all 60 genes upregulated from Th1-memory to recall is shown on the right.