CancerEpiDB: A database for DNA methylated genes in cancer

Epigenetic refers to the reversible functional modifications of the genome that do not correlate to changes in the DNA sequence. These modifications are caused by changes in the chro-matin structure, DNA methylation and histone modification. DNA methylation occurs in and out of CpG islands, and affects the transcription factors (TFs). The TFs affect the downstream genes by activating or silencing them. This is observed in all the complex diseases. The DNA methylated genes are further classified as hyper and hypo methylated genes. Most of the oncogenes are DNA methylated. This database is developed using the available data in THE CANCER GENOME ATLAS (TCGA) and the significant DNA methylated genes identified were validated using literature. For this database a comprehensive methodology based on the DNA methylated genes in and out of CpG islands was developed. The objective of the database is fivefold - (i) Identification of stage-specific DNA methylated genes across cancers (ii) Classification of DNA methylated genes as hyper and hypo methylated (iii) Annotating the DNA methylated genes with their biological properties like Gene Ontology, Pathway, and Disease association (iv) Identifying the environmental factors associated with the DNA methylated genes (v) Identifying the interactome of the DNA methylated gene based on the BioGRID interaction and expressed genes from TCGA, this gives an overview of existing and new interactions that can be validated by the researcher. The database is complemented by Web interface for searching, browsing and interactions. CancerEpiDB provides an initial attempt to create a comprehensive resource of epigenetic genes in cancer. CancerEpiDB is available at (http://regen.informatics.iupui.edu/cgi-bin/epigenetics/DEVenv/index.php).