Fig. 4

Significantly upregulated genes in neoplastic vs. non-neoplastic tissues compartments (N = 10). a, b Volcano plot of upregulated genes in the expression-based tissue compartment, and morphological-based tissue compartment. Genes which show a high significance and/or high fold change between the neoplastic and non-neoplastic tissue compartments are labelled by name. Genes belonging to different biological processes are marked with different symbols in different colours to achieve an overview of relevant processes upregulated in neoplastic tissue compartments. Each dot represents an individual gene, a two-sided paired t-test is used for statistical testing with a significance level α = 0.05 (horizontal line). c List of all significantly upregulated genes in the expression-based tissue compartment. Red labelled genes were only found significantly differential expressed in the expression-based tissue compartment. Black labelled genes are concordant between expression- and morphological-based tissue compartments. d Diagram of the amount of genes upregulated in the expression-based and the morphological tissue compartment. e List of all significantly upregulated genes in the morphological tissue compartment. TA stromal cells = tumour associated stromal cells, EMT = epithelial–mesenchymal transition. The 8 identified genes for the tumor gene signature are highlighted in yellow