Fig. 2
Global transcriptomic analysis gives a ‘bird’s-eye’ view of iTreg polarization and temporal gene expression architecture. a Self-organizing map (SOM) analysis of transcriptome data from Mock-stimulated (control) or iTreg cells induced by the indicated protocols shows the topology of the polarization at the transcript level. The panels are pseudo-colored SOMs from different time points (0, 2, 6, 24, and 48 h, and 6 days). The colors correspond to the average RNA expression levels (z-score) of the genes contained on each hexagonal cell (blue: low, red: high). The effect of the activation is predominant, but treatment differences become evident after 1 day of culture. b Principal component analysis differentiates the samples on the basis of the activation time and treatment; ellipses highlight samples from the same time point. Arrows correspond to selected gene signatures that correlate significantly with the first three principal components (PCs) (p < 10− 6 in either PC1, PC2 or PC3; Additional file 2: Table S1) and belonging to different functional categories (red: Treg vs. Tcon; blue: T cell activation; cyan: TGF-β treatment). PC scores are shown on the bottom and left axes, while top and right axes show the Pearson coefficient of each gene signature with the corresponding PC. The text on the bottom specifies the reference for each numbered signature (Additional file 2: Table S1)