Figure 3. Biological pathways enriched in exhausted CD4⁺ T cells.

(A) Enriched gene sets in exhausted versus effector or memory CD4⁺ T cells using GSEA analysis and the MSigDB C2 curated gene sets. (B) GSEA of exhausted versus memory CD4⁺ or CD8⁺ T cells with an IFN-I transcriptional signature (Agarwal et al., 2009). (C) Heatmap of IFN responsive genes differentially expressed by exhausted CD4⁺ T cells (over naïve). (D) The core exhausted signature shared in CD4⁺ and CD8⁺ T cells (see also Table S3). Networks identified and their score from Ingenuity pathway analysis are shown. (E) Ingenuity pathway analysis of the main network associated with both exhausted CD4⁺ and CD8⁺ T cells. Figure 3, see also Figure S3 and Table S2 and S3.