Fig. 5
Interaction network of immunotherapy-related genes. Genes that after post hoc testing showed i) significant regulation in the same direction in the two comparisons of irMyositis against Mi2 and TIF1γ subtypes, and ii) opposite regulation or insignificant DGE, in the two comparisons of Mi2 and TIF1γ subtypes against NDC were selected and defined as irDEGs. Next, directional interactions from Reactome pathways containing irDEGs, (PD-L1), PDCD1 (PD-1), or CTLA4 were extracted. The depicted directed network consists of all-pairs shortest paths (APSPs) between such genes within the selected pathways. Genes included in the nCounter PanCancer Immune Profiling Panel are depicted by pie charts, while genes excluded from the analysis due to close-to-noise expression levels are depicted as dashed circles (see Methods for details). Each sector of the pie chart represents a pairwise DGE analysis between NDC, TIF1γ, Mi2, and irMyositis subtypes. Stroke color of pie charts represents the average gene expression across subtypes with respect to the pan-gene interquartile expression (IQR). Nodes of genes not included in the panel are minimized. CD274, PDCD1, CTLA4, and their neighbors are highlighted by red labels. Reactome annotation for the interaction types are depicted by the color and type of edge lines and the network is laid out using a force-directed algorithm in which stronger and weaker forces reflect intracellular and extracellular interactions (see Methods for details).
