Fig. 3: Clustering and functional analysis displays regional AT/RT proteomic maps in the tumour microenvironment at 833 µm spatial resolution.

a H&E Image of AT/RT tissue (n = 1). b Map of cluster assignment based on hierarchical clustering and the dynamic tree cut algorithm (spatially-unaware). c UMAP embedding of data coloured by cluster assignment in b. d Enriched MSigDB Hallmark gene sets within marker proteins of clusters shown in the cluster map. Enriched MSigDB Hallmark gene sets within marker proteins (two-sided Wilcox test, Benjamini-Hochberg multiple testing correction threshold of 1%) of clusters shown in the cluster map. Significantly enriched hallmarks (one-sided hypergeometric test, Benjamini-Hochberg multiple testing correction threshold of 5%) for each cluster are indicated by the presence of circles. The size and colour of the circles represent the number of proteins contributing to that term and the adjusted p value of the enrichment, respectively. e Cluster-map of AT/RT tissue generated by Affinity Network Fusion. This clustering is spatially-aware, meaning the relative spatial locations of samples and protein abundance values are used to generate the clusters. f UMAP embedding of data coloured by ANF cluster assignment in e. g Enriched MSigDB Hallmark gene sets within marker proteins of clusters shown in the cluster map generated by ANF, as in d. Source data are provided as a Source Data file.