Fig. 4: Human and murine T_MIC cells share transcriptional features and show enrichment of effector-related genes.

See also Supplemental Fig. 5 and Supplemental Fig. 6. Colonic human CD161^hi and murine DN T cells as well as several control populations were sorted and subjected to bulk RNA sequencing. The depicted analyses were performed after filtering for non- and lowly expressed genes. A Principal component analysis was performed on the 866 most variable genes (IQR > 0.75); plotted are the scores of the first two principal components (PC). Genes were obtained from a merged dataset consisting of human and murine T-cell populations derived from experiments described in this study or obtained from Immgen as indicated. Human and murine datasets were merged based on orthologue genes. B Loading analysis of the principal components from A, illustrating the contribution of genes encoding cytokine receptors to the overall variance described by PC1 and 2. C Analysis showing the top 20 Gene Ontology (GO) terms enriched in the genes positively contributing to PC2 from A. For the highlighted GO terms, the respective top 20 genes from PC2 are shown. D–F GSEA plots depicting the enrichment of the three indicated GO terms in human (CD161^hi CD4) and murine (DN) T_MIC cells compared to their respective control populations. NES = normalized enrichment score. Statistics: GO-term enrichment was tested by a one-tailed version of Fisher’s exact test implemented in the clusterprofiler R package and p values were multiple hypothesis testing by the Benjamini–Hochberg method (C). GSEA p-values were derived from an adaptive multi-level split Monte Carlo scheme implemented in the fgsea R package and adjusted for multiple hypothesis testing by the Benjamini–Hochberg method (D–F). Source data are provided as a Source Data file.