ArticleScientific reports2015
CellMethy: Identification of a focal concordantly methylated pattern of CpGs revealed wide differences between normal and cancer tissues.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells.Genome biology · 2021Article
- Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis.Nature biomedical engineering · 2021Article
- Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data.BMC genomics · 2019Article
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10 authors.
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Abstract
DNA methylation patterns may serve as a key in determining cell phenotypes and functions. Adjacent CpG patterns may provide insight into methylation functional mechanisms. Some regions display different DNA methylation patterns between normal and cancer tissues, but the same average methylation level. Here, we developed a method (CellMethy) to infer a region in which all CpGs exhibit concordant methylation (CM) and to quantify the extent of CM in the region. Using simulation data, CellMethy showed high performance in discovering the concordant methylation patterns (AUC = 0.89). CellMethy was then applied to RRBS data including 11 normal tissues and 12 tumors. We found that the extent of CM exhibited wider differentials among tissues than did the average methylation levels from the CM regions, with 45% of CM regions occurring specifically in one tissue and mainly in tumors. Then, we identified CM regions through genome wide bisulfite sequencing (GWBS) data on breast cancer. Approximately 82% of CM regions revealed a significantly different extent of CM between cancer and normal tissues. CellMethy can accurately describe concordantly methylated regions, and the results suggest that CM might also serve as a stable marker of cell sub-populations.
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