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Cancer Cell International
Published in: Cancer Cell International 1/2019

Open Access 01-12-2019 | Biomarkers | Primary research

Identification of DNA methylation-driven genes in esophageal squamous cell carcinoma: a study based on The Cancer Genome Atlas

Authors: Tong Lu, Di Chen, Yuanyong Wang, Xiao Sun, Shicheng Li, Shuncheng Miao, Yang Wo, Yanting Dong, Xiaoliang Leng, Wenxing Du, Wenjie Jiao

Published in: Cancer Cell International | Issue 1/2019

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Abstract

Background

Aberrant DNA methylations are significantly associated with esophageal squamous cell carcinoma (ESCC). In this study, we aimed to investigate the DNA methylation-driven genes in ESCC by integrative bioinformatics analysis.

Methods

Data of DNA methylation and transcriptome profiling were downloaded from TCGA database. DNA methylation-driven genes were obtained by methylmix R package. David database and ConsensusPathDB were used to perform gene ontology (GO) analysis and pathway analysis, respectively. Survival R package was used to analyze overall survival analysis of methylation-driven genes.

Results

Totally 26 DNA methylation-driven genes were identified by the methylmix, which were enriched in molecular function of DNA binding and transcription factor activity. Then, ABCD1, SLC5A10, SPIN3, ZNF69, and ZNF608 were recognized as significant independent prognostic biomarkers from 26 methylation-driven genes. Additionally, a further integrative survival analysis, which combined methylation and gene expression data, was identified that ABCD1, CCDC8, FBXO17 were significantly associated with patients’ survival. Also, multiple aberrant methylation sites were found to be correlated with gene expression.

Conclusion

In summary, we studied the DNA methylation-driven genes in ESCC by bioinformatics analysis, offering better understand of molecular mechanisms of ESCC and providing potential biomarkers precision treatment and prognosis detection.
Appendix
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Metadata
Title
Identification of DNA methylation-driven genes in esophageal squamous cell carcinoma: a study based on The Cancer Genome Atlas
Authors
Tong Lu
Di Chen
Yuanyong Wang
Xiao Sun
Shicheng Li
Shuncheng Miao
Yang Wo
Yanting Dong
Xiaoliang Leng
Wenxing Du
Wenjie Jiao
Publication date
01-12-2019
Publisher
BioMed Central
Keyword
Biomarkers
Published in
Cancer Cell International / Issue 1/2019
Electronic ISSN: 1475-2867
DOI
https://doi.org/10.1186/s12935-019-0770-9

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