Fig. 4: Proteomic map clustering defines functional layers at the tumour periphery at 350 µm spatial resolution. | Nature Communications

Fig. 4: Proteomic map clustering defines functional layers at the tumour periphery at 350 µm spatial resolution.

From: Deep topographic proteomics of a human brain tumour

Fig. 4

a H&E image of AT/RT tissue (representative from three independent experiments). b Map of cluster assignment based on hierarchical clustering and the dynamic tree cut algorithm (spatially-unaware). Cluster 3 corresponds to brain/tumour interface. Cluster 1 corresponds to solid tumour. Clusters 4,7 & 5 correspond to the transition between solid tumour and brain/tumour interface. c UMAP embedding of data coloured by cluster assignment in b. d Volcano plot of clusters 3 against cluster 1 from b. Significance was calculated using a two-sided t-test, p-values were corrected for multiple testing using Benjamini-Hochberg 5% FDR threshold. The horizontal dashed line represents an FDR of 5%. The vertical dashed line represents –/+ 2-fold-change. e GSEA of clusters 1 and 3 from b. Gene set membership is indicated by colouring the cell with that protein’s log2 fold-change. Source data are provided as a Source Data file.

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