Fig. 2: Cytokines induce cell type specific gene expression programs in CD4+ T cells.
a PCA plot from the full transcriptome and proteome of TN and TM cells following five days of cytokine stimulations. Only stimulated cells were included in this analysis. PCA plots were derived using 20 naive and 21 memory T cells samples RNAseq and 18 naive and 17 memory T cells for proteomics. b Gene expression changes at the RNA and protein levels from pairwise comparisons between cytokine-stimulated cells and Th0-stimulated cells. Up-regulated genes are in red and down-regulated genes are in blue. Different shades indicate different fold-change thresholds. c Selection of significantly enriched pathways (with enrichment scores > 0.7 in at least one cytokine condition) estimated using differentially expressed genes and proteins with the 1D enrichment method. Colors correspond to the enrichment score estimated for each pathway. For the pathways and conditions indicated in light gray, not enough genes were detected to reliably estimate enrichment scores (NAs). d Volcano plots highlighting significant differences in gene and protein expression between Th17 and iTreg-stimulated TN and TM cells. Red indicates expression upregulation in iTreg with respect to Th17-stimulation, blue indicates expression upregulation in Th17 with respect to iTreg-stimulation. Labels were added to IL17, FOXP3 and the top 20 most differentially expressed genes. e Cell state-specific gene signatures defined using jointly RNA and protein expression. Colours encode normalized (Z-scored) gene and protein expression levels. Example genes for each signature are labelled. Source data are provided as a Source Data file.
