MDDM: A Resource for Differential Methylation in Cancer

Differential DNA methylation has been linked to cancer mainly due to silencing of tumor-suppressor genes. Recent surge in research on epigenomics in cancer has produced tremendous amount of published literature, but till date there is no resource that collates all the information and represents it in an easily accessible and immediately use- ful form. In an effort to alleviate this problem, we propose a curated database MDDM, containing information about genes differentially methylated in cancer of various tissues. We present the database, its schema and sample queries on this database which cover the experimental methods, results in terms of sensitivity and specificity on particular tissues and cell lines. We also discuss the MDDM environment that is trying to pull information from various related resources. We propose a workflow and usage scenario for our MDDM environment to support a study for finding the role in gene regulation via DNA methyl binding proteins for breast can- cer. In our usage scenario, we used the MSP primers re- ported in various studies to find the genomic area detected to be differentially methylated. These areas were searched for consensus sequence patterns for various methyl binding proteins to detect their potential binding and hence deter- mine role in regulation of differential expression