Fig. 5.

Common Gene expression Signatures of Putative Liver CSCs. (A) Unsupervised hierachial cluster analysis of SP and non-SP fractions from Huh7, WRL68 and KMCH cell lines after zebularine treatment. A common gene expression signature of 617 differentially expressed genes from three SP-ZEB fractions identified by Bootstrap t-test (P-values ≤ 0.05 and fold-change ≥1.5). Note clear separation of SP (red) and non-SP (green) cells into 2 clusters. (B) GSEA based on two previously published gene sets: Adult tissue stem cell genes(23) and upregulated genes of the HB-signature.(24) For the adult tissue stem module available homologue genes were used. Results demonstrate enrichment of both gene sets in SP-ZEB cells. Enrichment score (ES) reflects degree of over-representation for each group at the peak of the entire set. Statistical significance calculated by nominal P-value of the ES by using an empirical phenotype-based permutation test. False positives are calculated by the false discovery rate (FDR).(C) Top 5 functional networks for the SP-ZEB-signature.