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Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer.


ABSTRACT: Aberrant DNA methylation of CpG islands, CpG island shores and first exons is known to play a key role in the altered gene expression patterns in all human cancers. To date, a systematic study on the effect of DNA methylation on gene expression using high resolution data has not been reported. In this study, we conducted an integrated analysis of MethylCap-sequencing data and Affymetrix gene expression microarray data for 30 breast cancer cell lines representing different breast tumor phenotypes. As well-developed methods for the integrated analysis do not currently exist, we created a series of four different analysis methods. On the computational side, our goal is to develop methylome data analysis protocols for the integrated analysis of DNA methylation and gene expression data on the genome scale. On the cancer biology side, we present comprehensive genome-wide methylome analysis results for differentially methylated regions and their potential effect on gene expression in 30 breast cancer cell lines representing three molecular phenotypes, luminal, basal A and basal B. Our integrated analysis demonstrates that methylation status of different genomic regions may play a key role in establishing transcriptional patterns in molecular subtypes of human breast cancer.

SUBMITTER: Rhee JK 

PROVIDER: S-EPMC3794600 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

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Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer.

Rhee Je-Keun JK   Kim Kwangsoo K   Chae Heejoon H   Evans Jared J   Yan Pearlly P   Zhang Byoung-Tak BT   Gray Joe J   Spellman Paul P   Huang Tim H-M TH   Nephew Kenneth P KP   Kim Sun S  

Nucleic acids research 20130724 18


Aberrant DNA methylation of CpG islands, CpG island shores and first exons is known to play a key role in the altered gene expression patterns in all human cancers. To date, a systematic study on the effect of DNA methylation on gene expression using high resolution data has not been reported. In this study, we conducted an integrated analysis of MethylCap-sequencing data and Affymetrix gene expression microarray data for 30 breast cancer cell lines representing different breast tumor phenotypes  ...[more]

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