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. 2020 Jul 22;12(8):2003. doi: 10.3390/cancers12082003

Figure 2.

Figure 2

Deriving Genotype-Tissue Expression (GTEx) gene modules. (A) Multidimensional scaling (MDS) of gene expression of 1086 genes that correlate between NE-DMRs and gene expression in expression data from 53 GTEx tissue samples corresponding to 31 tissue types and cell lines. Prior to MDS, expression was transformed using log10 (RPKM + 1) and mean-centered. For genes with multiple entries, the entry with the highest standard deviation entry was chosen. The different colors represent the modules as defined in (B); (B) Definition of six gene modules based on hierarchical clustering. Modules 1–6 are referred to as follows: (i) early cell cycle/metabolism (n = 193 genes), (ii) proliferation (n = 133 genes), (iii) metabolic process/inconclusive (n = 165 genes), (iv) immune activation/infiltration (n = 197 genes), (v) angiogenesis/TGFb-SMAD (n = 220 genes), and (vi) neurodevelopment/brain (referred to as the neural module, n = 178 genes); (C) Module expression (average of standardized expression of included genes) across GTEx tissue types. Boxplots show the distribution of expression for respective module’s genes in tissue samples according to cell type legend.