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Fig. 3 | BMC Biology

Fig. 3

From: Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

Fig. 3

Differential gene and protein expression analysis during iTreg polarization. Differential expression was modeled over time (activation effect) and specific for iTreg induction (group effect). Group abbreviations: G01, Unstimulated naïve CD4+ T cells; G02, Mock-stimulated cells; G03, iTreg TGF-β; G04, iTreg TGF-β + ATRA; G05, iTreg TGF-β + ATRA + Rapa; G06, iTreg TGF-β + butyrate; G07, unstimulated nTreg. a DEGs in iTreg groups compared to Mock control in at least one time point or at baseline are counted. Number of DEGs in each condition or shared between iTreg conditions (see color code) is indicated and proportional to the circle size; numbers in parentheses are exclusive DEGs per condition. b DEPs in iTreg conditions compared to control are counted. Numbers of exclusive DEPs (in parentheses) or shared in the two iTreg conditions are shown. The number of (c) DEGs (FDR < 0.01) or (d) DEPs (FDR < 0.05) is shown for each of the indicated coefficients (grey-black: activation effect; red, blue: group effect) on a statistical model with time as a discrete factor. e A heatmap of RNA and protein data is shown for the genes detected at both levels. The expression is shown as separate RNA (regularized log (rlog)-transformed counts) or protein (log2R) z-score (blue: low; red: high). Black bars to the left indicate differential expression. Hierarchical clustering was performed separately for the indicated four blocks using RNA and protein data and clusters were obtained for the DEG and DEP blocks (see Methods). A, B, D: Donor 1, 2, 3; S01–S05: TMT set. Colored bars on the right show the relative fraction of the cellular compartments for the proteins with available data. Histograms show the distribution of the Spearman correlation; green line marks the median value

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