Fig. 5

Correlation of the gene expression profiles of HuH7 cells, HepG2 cells and primary human hepatocytes (PHH) grown in 2D (standard culture for cell lines and Collagen/Matrigel ‘sandwich’ culture for PHH) and 3D (low-adherence plates to promote cell aggregation) conditions. a-c Pairwise correlation of the gene expression levels in different cell types grown in 2D culture. d-f Pairwise correlation of the gene expression levels in different cell types grown in 3D culture. The RNA-seq data came from the publicly available ERX2636883 record from the SRA database. ‘r’ indicates the value of the Pearson correlation coefficient. Black dashed lines correspond to directions of the highest variance (for comparison), with the slope ‘s’ and intercept ‘i’. g-i Correlation of gene expression changes in HuH7 cells, HepG2 cells and primary human hepatocytes (PHH) grown in 3D in comparison to 2D conditions. g HepG2 cells vs. HuH7 cells. h HepG2 cells vs. PHH cells. i HuH7 cells vs. PHH cells. The publicly available data set ERX2636883 from the SRA database was used for the analysis. ‘r’ indicates the value of the Pearson correlation coefficient. Black dashed lines correspond to directions of the highest variance for comparisons, with the slope ‘s’ and intercept ‘i’