Fig. 6: Classification of liver cancer samples and prediction of patient survival based on the expression of genes in TCGA liver tumor tissues with a nearby liver-tumor specific plasma cfDNA DMR.
From: Tumor detection by analysis of both symmetric- and hemi-methylation of plasma cell-free DNA
a An outline to identify genes having at least one liver cancer cfDNA DMR within 20Kb from their promoters and whose expression in TCGA liver tumor tissue samples being associated with patient survival. b sscf-MeDIP-seq density at DMRs close to the 150 genes with at least one cfDNA DMR nearby. The z-score, represented by color, is log2 (RPKM) of sscf-MeDIP-Seq signals. A “Hyper DMR” refers to a gene with at least one hyper-methylated cfDNA DMR nearby, A “Hypo DMR” is defined as a gene with a hypo-methylated cfDNA DMR nearby. c Classification of 371 liver tumors in the TCGA-LIHC cohort based on expression of the 150 marker genes identified above. Patients are classified into two clusters. The color represents the z-score of log2 (RPKM) of RNA-seq signals of 150 genes in 371 liver cancer samples. d Kaplan–Meier survival analysis of 371 liver cancer patients separated into two clusters as in (c). P value is calculated by log rank test. Note that the software did not provide the exact p value when it is smaller than 0.0001.
