Research Paper Volume 12, Issue 6 pp 4970—4995

Integrative analysis of DNA methylation and gene expression reveals distinct hepatocellular carcinoma subtypes with therapeutic implications

Figure 1. Identification of HCC subclasses based on integrated transcriptome and methylation data of MDGs. (A) Consensus matrix for k = 2 to k = 5. (B) Silhouette values under corresponding k values. (C) T-SNE analysis of mRNA expression data from tumor samples included in the cluster analysis (D) OS and RFS of 4 HCC subclasses. Statistical significance of differences was determined by Log-rank test. (E) Heatmaps show the expression and methylation level of 401 MDGs in HCC subclasses. 401 MDGs were divided into 4 groups, including metabolism associated MDGs, immune associated MDGs, putative methylation driven TSGs and other MDGs. HCC: hepatocellular carcinoma; MDG: methylation driven gene; t-SNE: t-distributed stochastic neighbor embedding; OS: overall survival; RFS: recurrence free survival; TSG: tumor suppressor genes.