Extended Data Fig. 4: Further differential gene and pathway analysis on each cluster.
From: Endothelial sensing of AHR ligands regulates intestinal homeostasis
a, Dot plots showing top 20 DE genes for remaining 5 clusters (other 6 in Fig. 2e). + and – indicate ligand- and vehicle- treated conditions respectively. Colour intensity represents average expression level, dot size – average % expression of each gene. Genes relating to canonical AHR pathway, or proliferation in bold. b, UpSet plots showing DE gene overlaps between each cluster, within BEC (top) or LEC (bottom) supercluster. Black connecting lines in columns represent all possible overlaps, intersection size the number of shared genes in each overlap. Total DE genes for each cluster shown in right bars. Coloured bars at top of plot indicate number of overlaps within range. Only genes expressed in all BEC or LEC clusters were included in this analysis. c, Venn diagram showing overlap between DE genes shared in all BEC and DE genes shared across all LEC. d,e, Heatmaps to compare DE gene expression across clusters. Heatmaps show DE gene expression (as log2 fold-change compared to vehicle only) in either shared genes in all parent BEC/LEC clusters (d), or top 5 unique genes for each cluster (e). Numbers to right of unique gene heatmaps indicate total number of unique DE genes within each cluster. f, As in Fig. 2e, Top 5 enriched genesets (GO Biological Processes) in 5 remaining clusters (red – upregulated geneset, blue – downregulated geneset). P values calculated by Wilcoxon Rank Sum tests.
