Fig. 4: Metabolic signatures in distinct phases of T cell responses.

a Co-expression cluster of transcriptome and proteome data from CD4 and CD8 T cells. DE mRNA transcripts of each dataset were clustered using mFuzz soft clustering (R package). mRNA or protein intensities at each time point are shown as the mean and the standard error of the mean (SEM) error bars. Number of mRNA/proteins included in each cluster are indicated for CD4 and CD8 T cells, respectively. mRNA transcripts with log2fc > 1.5 or < -1.5 and proteins with log₂fc ≥ 1.0 or ≤ –1.0 were considered as DE. Data is shown as fold change of mRNA and protein intensities in activated T cells relative to 0 h. b Venn diagrams show the overlap of mRNA and protein identified in each cluster between activated CD4 and CD8 T cells. c Enriched KEGG pathways (FDR < 0.05) for co-expression clusters (defined in Fig. 4A) of CD4 and CD8 T cell. d Molecular interaction, reaction, and relation network showing the relationship of the top first 20 enriched KEGG pathways categorized under ‘metabolism’ (FDR < 0.05). The network was generated using all DE mRNA transcripts and proteins. The size of each node directly correlates with the number of genes included. Edges represent sharing of 20% or more genes between two nodes while the thickness of the edge directly correlates with the number of overlapping genes. The number in each colored box indicates the co-expression clusters in Fig. 4a from where the corresponding mRNA transcript/ protein was enriched.