Figure 4.

Large-scale network rewiring during T cell dysfunction

(A and B) Venn diagram showing the overlap of nodes (A) or TFs (B) across the four windows. (C) UpSetR plot showing intersection of network edges across the four windows. The number of window-specific edges is marked in red. (D) Boxplots showing JI of TFs in any two windows. Significance of differences across different groups were assessed with an ANOVA test. (E and F) Regulatory rewiring of transcription factor PRDM1 (E) and ID2 (F). The first four groups of targets represent window-specific targets in W1, W2, W3, and W4, respectively, and the last group of genes contained targets that were shared by at least two windows. Representative functions of window-specific groups are shown below the genes. (G) Subnetworks of co-inhibitory receptors (TIGIT, LAG3, PDCD1, HAVCR2, and CTLA4) in each window.