Fig. 4

Coexpression analysis of all TAM samples. a Correlation based heatmap of gene clusters (I, II and III; 265, 222 and 139 genes, respectively) defined by coexpression analysis of genes with the highest variance across all TAM samples, followed by hierarchical clustering (see Additional file 3: Figure S4 for a dendrogram). b Hierarchical clustering of patients based on the genes identified in panel (a). c Overlap of genes in clusters I - IV with signatures A and B identified by PCA. d Functional annotation of cluster I (blue), cluster II (green) and cluster III (red) genes by gene ontology (GO) enrichment analysis. p values are plotted against fold enrichment. Only specific non-redundant terms with p values <0.0001 and enrichment >3 are shown. e Expression of cluster I genes (n = 120; genewise normalized TPM values) in subgroup A (red) and B (blue) samples. f As panel (e), but for cluster II genes (n = 223). g As panel (e), but for cluster III genes (n = 148). Boxes show the upper and lower quartiles, whiskers the 95% confidence intervals (CI), and horizontal lines the median