Fig. 5: IREA enables the inference of cytokine activities, immune cell polarization and cell–cell communications based on transcriptomic data.
From: Dictionary of immune responses to cytokines at single-cell resolution
a, Problem statement for cytokine response inference, b, Illustration of the IREA software input and output. Colours in the heatmaps represent different expression values. User input can be gene sets or transcriptome matrices. Blue backgrounds represent cell polarization analysis; orange backgrounds represent cytokine response analysis. c–e, Examples of IREA analysis output on scRNA-seq data collected from cells in the tumour microenvironment following anti-PD-1 treatment relative to control antibody treatment. c, IREA radar plots showing enrichment of macrophage, NK cell and CD8+ T cell polarization states described in Fig. 3. Cytokine drivers of selected polarization states are indicated by arrows. d, IREA cytokine enrichment plot showing the enrichment score (ES) for each of the 86 cytokine responses in NK cells following anti-PD-1 treatment. Bar length represents the ES, shading represents the FDR-adjusted P value (two-sided Wilcoxon rank-sum test), with darker colours representing more significant enrichment (red, enriched in anti-PD-1 treatment, blue, enriched in untreated control). Cytokines with receptors expressed are indicated by black filled boxes. e, Inferred cell–cell communication network mediated by cytokines. For ease of identification, cytokines are plotted from left to right in each segment in the same order as the legend. For clarity, individual cytokine plots following the same visualization scheme are shown on the right and in Extended Data Fig. 12c.
