Fig. 1.

Pathways are differentially expressed between cell lines and their tissues of origin. a Number of differentially expressed genes (absolute log₂ fold change >2 and FDR < 0.05) using voom on paired samples. b Results of GSEA reported based on the log₁₀(FDR) significance scale, with one group in red and the other one in blue. The 15 pathways most significantly differentially expressed between each cell line and its tissue of origin. c Pathways enriched for at least two group comparisons (FDR < 0.05). The pathways differentially expressed between the tissues that are also differentially expressed between the cell lines (preserved pathways) are highlighted in red and blue. Pathways over-expressed in both cell lines compared to their tissues of origin are highlighted in yellow. Rows are ordered by hierarchical clustering of the enrichment significance values, log₁₀(FDR). To represent the FDR significance in the heatmap, the color was saturated at 1.1 × 10⁻⁴. The exact reported FDR can be found in Additional file 2