title: An integrated approach to uncover driver genes in breast cancer methylation genomes.
abstract: BACKGROUND
  Cancer cells typically exhibit large-scale aberrant methylation of gene promoters. Some of the genes with promoter methylation alterations play "driver" roles in tumorigenesis, whereas others are only "passengers".
  
  
  RESULTS
  Based on the assumption that promoter methylation alteration of a driver gene may lead to expression alternation of a set of genes associated with cancer pathways, we developed a computational framework for integrating promoter methylation and gene expression data to identify driver methylation aberrations of cancer. Applying this approach to breast cancer data, we identified many novel cancer driver genes and found that some of the identified driver genes were subtype-specific for basal-like, luminal-A and HER2+ subtypes of breast cancer.
  
  
  CONCLUSIONS
  The proposed framework proved effective in identifying cancer driver genes from genome-wide gene methylation and expression data of cancer. These results may provide new molecular targets for potential targeted and selective epigenetic therapy.
authors.affiliation: Bioinformatics Centre, School of Life Science, University of Electronic Science and Technology of China, Chengdu, China.
authors.forename: Xiaopei
authors.initials: X
authors.lastname: Shen
authors.forename: Shan
authors.initials: S
authors.lastname: Li
authors.forename: Lin
authors.initials: L
authors.lastname: Zhang
authors.forename: Hongdong
authors.initials: H
authors.lastname: Li
authors.forename: Guini
authors.initials: G
authors.lastname: Hong
authors.forename: Xianxiao
authors.initials: X
authors.lastname: Zhou
authors.forename: Tingting
authors.initials: T
authors.lastname: Zheng
authors.forename: Wenjing
authors.initials: W
authors.lastname: Zhang
authors.forename: Chunxiang
authors.initials: C
authors.lastname: Hao
authors.forename: Tongwei
authors.initials: T
authors.lastname: Shi
authors.forename: Chunyang
authors.initials: C
authors.lastname: Liu
authors.forename: Zheng
authors.initials: Z
authors.lastname: Guo
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism; D016000:Cluster Analysis; D018899:CpG Islands; D019175:DNA Methylation; D030541:Databases, Genetic; D044127:Epigenesis, Genetic; D057890:Epigenomics; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006801:Humans; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D025941:Protein Interaction Mapping; D015203:Reproducibility of Results