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. 2024 Apr 5;12:RP91729. doi: 10.7554/eLife.91729

Figure 4. Endothelial cell (EC)-activating perturbations in vitro elicit EC subtype-specific transcriptional responses.

(A) Upset plots of up- and downregulated differentially expressed genes (DEGs) across EC subtypes with siERG (gray), IL1B (pink), and TGFB2 (blue). Upset plots visualize intersections between sets in a matrix, where the columns of the matrix correspond to the sets, and the rows correspond to the intersections. Intersection size represents the number of genes at each intersection. (B) Pathway enrichment analysis (PEA) for EC3-4 up- and downregulated DEGs with TGFB2 compared to control media. (C) PEA for EC2-4 up- and downregulated DEGs with IL1B compared to control media. (D) PEA for EC1-4 up- and downregulated DEGs with siERG compared to siSCR. (E) PEA comparing up- and downregulated DEGs that are mutually exclusive and shared between IL1B and siERG in EC3.

Figure 4.

Figure 4—figure supplement 1. Profiles of shared peaks and motif enrichments across endothelial subtypes.

Figure 4—figure supplement 1.

(A) Upset plot of induced peaks for siERG (gray), IL1B (pink), and TGFB2 (blue) across EC1, EC2, EC3, and EC4. Upset plots visualize intersections between sets in a matrix, where the columns of the matrix correspond to the sets, and the rows correspond to the intersections. Intersection size represents the number of genes at each intersection. (B) Heatmap of top motifs enriched in IL1B-induced peaks. Top transcription factors (TFs) for each EC subtype are selected based on ascending p-value. Rows (TFs) and columns (EC subtype) are clustered based on enrichment score (ES). (C) Heatmap of top motifs enriched in siERG-induced peaks. (D), Heatmap of top motifs enriched in TGFB2-induced peaks.