Figure 5

Identify the T cell differentiation programmes that are disturbed in Stat3 -KO by CCA. The Stat3 dataset was analysed by CCA using the Th dataset as explanatory variables. (a) CCA biplot showing the relationships between samples (see legend) and Th differentiation programmes (arrows). Percentage indicates that of the variance accounted for by the inertia of the axis. (b) CCA triplot showing samples (see legend in (a)), Th differentiation programmes (arrows), and genes (small grey closed circles). (c) Gene plot of the CCA solution in (a) and (b) showing the ‘Th17-signature genes’ and the CCA top-ranked genes (2% top genes in Axis 1) only. Genes in the intersection of these two gene lists are shown as ‘Both’ in the legend. (d, e) CCA sample scores using (d) Th17/iTreg and (e) Th2/Th1 differentiation variables. Differentially expressed genes by the explanatory dataset (the Th dataset) were selected by false discovery rate (FDR) <0.01, and fold change (top/bottom 1%) in the comparison of Th2 and Th17, or that of Th1 and iTreg. (f) Heatmap analysis of the top-ranked genes in (c). Gene expression of those genes in the Stat3 dataset (left) and that in the Th dataset (right) were separately analysed by heatmap analysis, while clustering column (samples) only. Genes were ordered according to the CCA Axis 1 score. See Colour Key for expression levels.