Fig. 3

GSEA and Motif Activity Analysis. Pathway analysis in samples of Huh-7 cells grown for 7 days on polystyrene coated cell culture plates (Control), Matrigel (1.5 mg/ml, 3.0 mg/ml or 6.0 mg/ml) or Collagen (0.5 mg/ml and 1.0 mg/ml) basement membrane matrices. a Heatmap summarizing the enrichment of KEGG pathways among genes ranked by expression changes in cells grown on a basement membrane matrix in comparison to Control cultured cells. A pathway was included in the heatmap if it was significantly enriched for at least one condition. FDR < 0.05 was chosen as significance threshold. b Activities of the 5 most active motifs in Collagen culture condition. c Activity of the top motif in the Matrigel culture condition. Each dot corresponds to one sample. Samples are grouped by conditions. Z-scores indicate the contribution of regulatory motifs associated with TF(s) to explaining gene expression changes