Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer

J Am Med Inform Assoc. Jul-Aug 2013;20(4):637-42. doi: 10.1136/amiajnl-2012-001571. Epub 2013 Apr 18.

Abstract

Objective: DNA methylation, a regulator of gene expression, plays an important role in diverse biological processes including developmental process, carcinogenesis and aging. In particular, aberrant DNA methylation has been largely observed in several types of cancers. Currently, it is important to extract disease-specific gene sets associated with the regulation of DNA methylation.

Materials and methods: Here we propose a novel approach to find the minimum regulatory units of genes, co-methylated and co-expressed gene pairs (MEGP) that are highly correlated gene pairs between DNA methylation and gene expression showing the co-regulatory relationship. To evaluate whether our method is applicable to extract disease-associated genes, we applied our method to a large-scale dataset from the Cancer Genome Atlas extracting significantly associated MEGP and analyzed their functional correlation.

Results: We observed that many MEGP physically interacted with each other and showed high semantic similarity with gene ontology terms. Furthermore, we performed gene set enrichment tests to identify how they are correlated in a complex biological process. Our MEGP were highly enriched in the biological pathway associated with ovarian cancers.

Conclusions: Our approach is useful for discovering coordinated epigenetic markers associated with specific diseases.

Keywords: Cancer Gene; DNA Methylation; Gene Expression Profile; Ovarian Cancer; Protein Interaction Maps.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods
  • DNA Methylation*
  • Female
  • Gene Expression Profiling / methods
  • Gene Expression*
  • Genes / physiology*
  • Humans
  • Mathematical Concepts
  • Ovarian Neoplasms / genetics*