Extended Data Fig. 4: Increased inflammatory pathways in APC validation set.

a. Barplot of the number of Differentially Expressed Genes (DEG) for each severity group (Healthy versus moderate and severe patients; moderate versus healthy and severe; severe versus healthy and moderate). Up-regulated (logFoldChange > 0.25) genes are shown in black, down-regulated (logFoldChange < −0.25) genes are shown in grey; b. Heatmap representation of top up-regulated genes in severe APC from the validation set, as compared to moderate and healthy groups, z-score values of average expression levels of cells per severity group is color coded; Comparative analysis of enriched pathways from the upregulated genes in moderate or severe (c) APC as compared to healthy cells, as well as pairwise comparison of upregulated genes in moderate compared to severe (shown in pink), up-regulated genes in severe compared to moderate (shown in yellow) (d); horizontal axis displays the adjusted p-values (-log10), e. Representation of ranked genes by descendant order according to their absolute log Fold Change (log FC), upregulated in moderate as compared to severe (plot in red), upregulated in severe APC as compared to moderate (plot in blue).Top genes, with an absolute value of logFC above 0.5 are shown. Validation set included: n=2 HC, n= 4 moderate and n=9 severe samples from a total of 2 healthy donors, 2 moderate and 6 severe patients. The two-sided Wilcoxon Rank-Sum test was used for comparison, P-values were adjusted to multiple testing using ‘Bonferroni’ correction; and only genes with adjusted-P Values < 0.05 were considered.