Fig. 5: The characteristics of fibroblasts and endothelial cells in nccRCC TME.

A tSNE plot of four subsets of fibroblasts; B Violin plot of specific markers of each subgroup in fibroblasts; C Heatmap of expression regulated by transcription factors estimated by SCENIC among the three clusters; red color represents active TFs. D tSNE plot of seven subsets of Endothelial cells; and the distribution of tumor-derived and normal-derived endothelials; E Volcano plot of upregulated and downregulated genes between tumor-derived and normal-derived macrophages (logFC > 1.15, p < 1e−5); upregulated genes are colored in red, and downregulated genes are colored in blue. F Violin plot of specific markers of tumor-derived and normal-derived macrophages; G Differentiation trajectory of macrophages in nccRCC, with each color coded for pseudotime (top) and clusters (bottom); H GSEA revealed pathways enriched in tumor-derived macrophages, FDR < 0.05 was considered as significantly enriched. I The pathways network of tumor-derived macrophages. J GSVA results of pathways enriched in each cell cluster, and most cancer-associated pathways upregulated in tumor-derived macrophages (C1 and C4).