Fig. 2: Cross-regulation hierarchies within cytokines.
From: Systematic investigation of cytokine signaling activity at the tissue and single-cell levels
a, Differential expression of target cytokines (x axis) in response to primary cytokines (y axis). Each dot represents a treatment profile. Blue solid points are profiles that pass quality controls, with numbers labeled on the top of box plots. The thick line represents the median value. The bottom and top of the boxes are the 25th and 75th percentiles (interquartile range). The whiskers encompass 1.5 times the interquartile range. The P value, testing whether group values are different from zero, was calculated using the two-sided Wilcoxon signed-rank test. b, Inter-cytokine regulation hierarchy. Between each pair of regulators (x axis) and targets (y axis), the logFC values are the medians among profiles that passed our quality controls. The plot only includes regulators and targets with at least one logFC value that was larger than two. The upper heat map includes target ligands, and the lower part includes target receptors with ligands in brackets. The NF-κB and interferon transcriptional groups are labeled with boxes. c, Differential logFC values of GZMA, GZMB and PRF1 upon TGF-β1 treatment, shown by violin plots, smoothed by a kernel density estimator. Each dot represents an independent profile. The P value, testing whether the T cell group values are different from zero, was calculated using the two-sided Wilcoxon signed-rank test (n = 11 independent treatment profiles for each gene). d, Perforin intracellular levels measured by flow cytometry upon TGF-β1 treatment in human primary CD8+ T cells. The x axis shows the signal intensity. The y axis shows the T cell fraction with modal normalization, scaling the maximum y axis to 100%. The vertical line indicates the percentage of T cells with signal intensity above the gate threshold (Extended Data Fig. 2d). e, Granzyme and perforin protein levels upon TGF-β treatment in human and mouse CD8+ T cells. The mean percentage of T cells with an intensity above the gate threshold is shown, with standard deviations as error bars (n = 3 cell culture replicates per condition). The two-sided Wilcoxon rank-sum test was used to compare groups.
