Fig. 4: There is a continuous gradient of transcriptomic states along the G0/G1 path to senescence. | Nature Communications

Fig. 4: There is a continuous gradient of transcriptomic states along the G0/G1 path to senescence.

From: Single-cell RNA sequencing reveals a quiescence-senescence continuum and distinct senotypes following chemotherapy

Fig. 4

A Top 5 up- and down-regulated genes for cluster 3 (shallow quiescence) vs. senescent cells (clusters 4, 9, 12) and cluster 7 (quiescence-senescence transition) vs. senescent cells. Color corresponds to the average scaled expression. B GSEA pathway analysis for results from the DGE analysis in A. Top 8 pathways (ranked by p.adjusted) are shown. Cluster 7 had no significantly downregulated pathways. For full pathway names, see Supplementary Data 1. C Distribution of module scores by cluster for leading-edge genes in two selected up- and down-regulated pathways for quiescent cluster 3 vs. senescent cells. D UMAP with cells colored by progress along pseudotime trajectory. Trajectory branches are visualized separately as Trajectory 1 and Trajectory 2. E Etoposide dose distribution of cells over pseudotime. F Log-normalized expression of select top senescent markers over pseudotime. Cells colored by cluster. Loess fit visualized in blue. G Left: Module scores for grouped biological processes over pseudotime (see methods). Scores for one select up- and down-regulated pathway group over pseudotime are shown as single-cell data. Cells colored by cluster. Loess fit in blue. Right: Heatmap of all pathway groups over pseudotime. Color represents the Loess fit value for each module score vs. pseudotime scatter plot for the pathways listed along the y-axis. Module scores were rescaled for visualization on the same scale.

Back to article page