Fig. 2

GO analysis of genes associated with the growth of Huh-7 on Matrigel and Collagen matrices. Principal component analysis (PCA) of the RNA-Seq data set prepared for samples of Huh-7 cells grown for 7 days on polystyrene coated cell culture plates (Control), or on Matrigel (1.5 mg/ml, 3.0 mg/ml or 6.0 mg/ml), or on Collagen (0.5 mg/ml and 1.0 mg/ml) basement membrane matrices. a Loadings of samples on PC1. b Loadings of samples on PC2. Each dot corresponds to one sample. Samples are grouped by conditions. The numbers associated with the principal components indicate the fraction of the variance in transcript expression that is explained by the corresponding principal component. c Gene ontology (GO) analysis of genes aligned with PC1. Positive and negative correlation coefficients are indicated as “neg. Cor.” or “pos. Cor.”, respectively. d GO analysis of genes aligned with PC2. GO analysis was performed with DAVID [16]. Numbers on the top of bar plots indicate the number of genes used for the GO analysis. Top 20 enriched GO terms were visualized. As a significance threshold for the enrichment, we considered p-value < 0.01 (dashed red lines)