Extended Data Fig. 9: Analysis of independent ST datasets.
a-h, HCC-5-A (Wu et al.). i-n, HCC-R1 (Wang et al.). o-t, HCC-4-L (Wu et al.). a,i and o, Spatial feature plots of the signature score of VIMhigh macrophages (left panel) and Tregs (right panel). b,j and p, Unbiased clustering of ST spots and violin plots showing the signature scores of VIMhigh macrophages (upper panel) and Tregs (lower panel) in clusters. The red rectangle highlighted the cluster with high signature scores of both VIMhigh macrophages and Tregs. c-e, k-l and q-r, The Spearman correlation (two-sided) between the signature scores of VIMhigh macrophages and Tregs in highlighted clusters in Extended Data Fig. 8b,j,p respectively. f-h, m-n and s-t, Gene set enrichment analysis (GSEA) on the signature genes of the highlighted clusters in Extended Data Fig. 8b,j,p respectively. The top 7 pathways were displayed. Two-sided Wilcox tests.
