Figure 3. Genome wide integrative analysis of gene under-expression, DNA copy number loss and promoter DNA hypermethylation in esophageal adenocarcinoma.

Circos plots that demonstrate gene expression versus copy number that have the same directional changes. Gene expression and copy number vs methylation have opposite directional changes. DNA copy number loss/deletions are more frequent than copy number gain/amplification as shown in Fig. 2. While some chromosomes such as 3, 4, 5, 10, 14, 16, 17, and 19 displayed more copy number losses, other chromosomes such as 2, 13, 20, and X showed fewer copy number losses. DNA hypermethylation was more frequent in chromosomes 1, 17 and 19. Overall, data shows the complexity of gene regulation through genetic and epigenetic mechanisms.