Profiling of immune related genes silenced in EBV-positive gastric carcinoma identified novel restriction factors of human gammaherpesviruses
Fig 2
DNA methylation analysis of IRGs in EBVaGC.
(A) Heat map showed the hierarchical clustering of all differentially methylated (DE) IRGs, comparing between EBV-positive (right, red) and EBV-negative (left, blue) GC samples. (B) Venn diagram showed the number of DE IRGs (grey circle) for both down-regulated IRGs (left, blue circle) and up-regulated IRGs (right, red circle). (C) (Left panel) Bar graph showed the proportion of methylated and unmethylated genes in deregulated IRG and non-IRG groups. (Right panel) Stacked bar graph showed the distribution of methylated CpG probes at different regions, including TSS1500 (orange), TSS200 (green), 5’UTR (purple), 3’UTR (light green), gene body (pink), and 1st Exon (blue), for up-regulated and down-regulated IRGs in EBVaGC. TSS200: 200bp upstream of transcription start site (TSS); TSS1500: 200-1500bp upstream of TSS. Proportion of each regions in the whole array is included. (D) Manhattan plot showed the chromosomal localization (x-axis) and log-base of adjusted p-value (y-axis) of all differentially methylated IRGs in EBVaGC. Examples of top methylated IRGs were annotated. (E) Circos diagram of all IRGs in EBVaGC depicts the methylation pattern in the outer circle (hypomethylated or hypermethylated gene position is displayed as blue or red respectively), and the transcriptional pattern in the inner circle (down-regulated or up-regulated gene position is displayed as blue or red respectively).
