Genome-wide DNA methylation profiling in 40 breast cancer cell lines

Leng Han, Siyuan Zheng, Shuying Sun, Tim Hm Huang, Zhongming Zhao

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations


DNA methylation plays important roles in gene regulation and functions. Aberrant methylation, either hypomethylation or hypermethylation, has been reported to cause various diseases, especially cancers. Breast cancer ranked the fifth according to the number of cancer deaths in the world. To systematically characterize the epigenetic modification in breast cancer, we examined the genome-wide methylation profiling in 40 breast cancer cell lines. We identified a gene signature consisting of 345 differentially methylated genes, which could be used to discriminate estrogen receptor (ER)-negative and ER-positive breast cancer cell lines. This gene signature is promising for diagnosis and therapies of breast cancer. In the follow up functional analysis of this gene signature, three enriched networks could be highlighted. Interestingly, one of these networks contained estrogen receptor, implying its functional importance of ER-centric module. Finally, we examined the correlation between methylation and expression of these breast cancer cell lines. Very few genes showed significant correlation, suggesting that gene expression regulated by methylation is a complex biological process.

Original languageEnglish (US)
Title of host publicationAdvanced Intelligent Computing Theories and Applications - 6th International Conference on Intelligent Computing, ICIC 2010, Proceedings
Number of pages8
StatePublished - 2010
Externally publishedYes
Event6th International Conference on Intelligent Computing, ICIC 2010 - Changsha, China
Duration: Aug 18 2010Aug 21 2010

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6215 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Other6th International Conference on Intelligent Computing, ICIC 2010


  • breast cancer
  • estrogen receptor
  • expression
  • methylation
  • network

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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