Analysis of distribution of DNA methylation in kidney-renal-clear-cell-carcinoma specific genes using entropy

DNA Methylation is an epigenetic phenomenon in which methyl groups are added to the cytosines, thereby altering the physio-chemical properties of the DNA region and influencing gene expression. Aberrant DNA methylation in a set of genes or across the genome results in many epigenetic diseases including cancer. In this paper, we use entropy to analyze the extent and distribution of DNA methylation in Tumor Suppressor Genes (TSG's) and Oncogenes related to a specific type of cancer (viz.) KIRC (Kidney-renal-clear-cell-carcinoma). We apply various mathematical transformations to enhance the different regions in DNA methylation distribution and compare the resultant entropies for healthy and tumor samples. We also obtain the sensitivity and specificity of classification for the different mathematical transformations. Our findings show that it is not just the measure of methylation, but the distribution of the methylation levels in the genes that are significant in cancer.