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Fig. 5 | BMC Biology

Fig. 5

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

Fig. 5

Treg factors represent hubs in a core network of known and novel genes with regulatory potential. A hub-centered approach was employed to reconstruct a gene co-expression network and the temporal rewiring of the nodes. a Hubs were defined as TFs which were DEGs and DEPs (see Methods). Numbers correspond to the counts of selected features at each step. A heatmap shows the relative gene (rlog counts) and protein (log2R) expression (z-score) for the hubs differentially expressed in iTregs (G03: TGF-β and/or G05: TGF-β + ATRA + Rapa). Abbreviations and color codes as in Fig. 3. Black boxes to the left of the heatmap indicate whether the given TF is differentially expressed over time (‘hub.time’) or in iTregs (‘Hub.G03’ or ‘Hub.G05’) in at least one time point; the gene has a known role in T cells or specifically Tregs (‘Known.in.T’ or ‘Known.in.Treg’). b Two networks were reverse-engineered using the early or late time point samples, then, a rewiring score was calculated for each node by comparing them (see Methods, Additional file 1: Figure S6b, c, Additional file 5: Table S4). Shown is the sub-network of nodes that were modeled as DEGs in all four iTreg conditions, in addition to FOXP3. A triangle marks TFs. Light blue nodes correspond to the hubs and their size is proportional to the rewiring score. A green continuous line marks the edges with support from a TF:target gene network built from ENCODE data (see Methods). Unconnected nodes are not displayed

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