Fig. 3
Identification of a common set of genes in the B16 variants. A Venn diagram showing that there are 104 genes whose expression is highly significantly different from B16-F0 in all tissue derived B16 cells (> log2 two-fold difference, p < 0.05, FDR < 0.05), B heatmap showing the expression of the 104 genes in every sample of 4th generation B16 cells. (log2 normalized counts re-scaled from 0 to 1). Hierarchical clustering of rows and columns is based on the 1-Pearson correlation coefficient metric and average linkage method. Boxed genes are differentially expressed in human metastatic melanoma; genes in blue are associated with upregulation of the KRAS signaling pathway, C association of the 104 genes with Reactome, Gene Ontology and Wikipathways databases (log10P < − 3.5): R-MMU-1474244, Extracellular matrix organization; GO:0051962, positive regulation of nervous system development; GO:0042447, hormone catabolic process; GO:0051152, positive regulation of smooth muscle cell differentiation; GO:0030199, collagen fibril organization; GO:0060749, mammary gland alveolus development; WP3625, Tyrobp causal network in microglia; GO:0006935, chemotaxis, D dot plots of normalized transcript counts of potential hub genes among the 104 genes, based on a String PPI network (0.9 confidence limit)