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- Title
Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer.
- Authors
Je-Gun Joung; Dokyoon Kim; Kyung Hwa Kim; Ju Han Kim
- 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.
- Subjects
DNA methylation; STATISTICAL methods in gene expression; OVARIAN cancer; CARCINOGENESIS; HUMAN carcinogenesis; GENETIC regulation; MATHEMATICAL models
- Publication
Journal of the American Medical Informatics Association, 2013, Vol 20, Issue 4, p637
- ISSN
1067-5027
- Publication type
Article
- DOI
10.1136/amiajnl-2012-001571