Fig. 4: SimiC captures complex regulatory dynamics within CAR T cells (CD8+ CAR T cell dataset52).
From: SimiC enables the inference of complex gene regulatory dynamics across cell phenotypes
a Comparison of the authority scores for each target gene in the two phenotypes IP and D12. We observe an increment of the authority score in D12 as compared to IP (Wilcoxon rank test, FDR < 0.05). b Network representing the weighted regulons of the transcription factors MYC and RUNX3 for the considered phenotypes IP and D12. The color of the edges linking the TFs with their corresponding target genes indicates whether the regulation is positive (yellow) or negative (blue), and the width of the edge corresponds to its strength (i.e., the inferred weight). Regulon activity score distribution for the two different phenotypes IP and D12 for MYC (c), RUNX3 (d), and EOMES (e) regulons. tSNE plots showing the CAR T cells at IP (top) and D12 (bottom) colored by their MYC (f), RUNX3 (g), and EOMES (h) regulon activity score. The peak of activity of the MYC regulon is observed at IP, while at D12 it gets progressively turned off. The RUNX3 regulon has its peak of activity after tumor recognition at D12, while its activity gets turned off once cells get exhausted at D12. Finally, the EOMES regulon gets more active once CAR T cells get exhausted after tumor recognition on D12.
