Figure 3
Differentially expressed genes (DEG) between HFGC and LFGC. (A,B) (Left panel of each) A heatmap shows the expression of DEG between HFGC and LFGC of Thai HCC (A) and Thai iCCA (B) Samples are represented in columns, grouped by HFGC and LFGC, and up- or down-regulated genes are represented in rows. (Right panel of each) Enrichment plots based on the 93 upregulated genes and 104 down-regulated genes are shown in the upper and lower panel, respectively. Normalized enrichment scores (NES) and FDR for each gene set were noted. (C,D) GO analysis performed based on the DEGs of Thai HCC and Thai iCCA, respectively. The −log10 (p-value) is shown in orange and blue bars for up- and down-regulated genes, respectively. (E) Venn diagrams show the overlapping genes between DEG of Thai HCC and of Thai iCCA. Up- and down-regulated genes are analyzed separately. (F) Heatmaps show the ssGSEA of Thai HCC (left) and Thai iCCA (right) based on the gene sets derived from the biological process (BP) gene sets in Molecular Signatures Database (MSigDB database v5.2). The overlapping gene sets significantly enriched in both Thai HCC and Thai iCCA are shown. The P-value from the Kolmogorov-Smirnov (ks) test was transformed in -log scale and used in the plot. Samples were in columns according to the increasing order of FGC value and the log-transformed p-value for each gene set is represented in rows.
