ArticlePloS one2013
An integrated approach to uncover driver genes in breast cancer methylation genomes.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Identification of Genes Universally Differentially Expressed in Gastric Cancer.BioMed research international · 2021Article
- Identifying primary site of lung-limited Cancer of unknown primary based on relative gene expression orderings.BMC cancer · 2019Article
- Epigenomics alternations and dynamic transcriptional changes in responses to 5-fluorouracil stimulation reveal mechanisms of acquired drug resistance of colorectal cancer cells.The pharmacogenomics journal · 2018Article
- Tumorigenic Cell Reprogramming and Cancer Plasticity: Interplay between Signaling, Microenvironment, and Epigenetics.Stem cells international · 2018Review
- Article
- Individualized analysis reveals CpG sites with methylation aberrations in almost all lung adenocarcinoma tissues.Journal of translational medicine · 2017Article
- Expression of human endogenous retrovirus-K is strongly associated with the basal-like breast cancer phenotype.Scientific reports · 2017Article
- Multi-omics landscapes of colorectal cancer subtypes discriminated by an individualized prognostic signature for 5-fluorouracil-based chemotherapy.Oncogenesis · 2016Article
- Article
- Identification of Novel Breast Cancer Subtype-Specific Biomarkers by Integrating Genomics Analysis of DNA Copy Number Aberrations and miRNA-mRNA Dual Expression Profiling.BioMed research international · 2015Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCancer 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".
resultsBased 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.
conclusionThe 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.
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