Fig. 3
From: Comprehensive analysis of normal adjacent to tumor transcriptomes
Upregulated genes in NAT compared with healthy. a Overall, 2451 genes were upregulated in NAT compared with healthy across all tissue types. Of those, 660 were found in more than one tissue site, 223 in more than two (x-fold more than expected by random) and 98 in more than three (x-fold). The chord diagram shows the vast amount of shared genes among all tissue types. b Boxplot of the expression levels of ATP5E, an example of a gene that is consistently upregulated in NAT compared with healthy. No significant difference is observed between NAT and tumor. c STRING analysis of protein–protein interactions of the 98 genes, corresponding to 91 proteins, upregulated in NAT compared with healthy in at least four tissue types. A total of 180 edges are found between 57 of the genes (other genes not shown). Only 30 are expected by chance (Poisson approximation p-value < 1 × 10−20). Thickness of edges indicates confidence. We observed four clusters with three or more genes cluster 1: cell division; cluster 2: immune response; cluster 3: cellular stimuli; cluster 4: ATP. d Gene-set enrichment analysis (GSEA) of the hallmark gene sets using NAT vs. healthy differential expression. NES are presented, but only for significant comparisons (FDR < 1%). Otherwise, the color of the cell is white. Only gene sets significant in at least one tissue site are presented. The full data is in Supplementary Data 3. Inflammatory response-related pathways are generally enriched in NAT in most tissue types (red). On the other hand, the NAT tissue tends to not express normal development pathways such as myogenesis and adipogenesis (blue)
