ArticleFrontiers in cell and developmental biology2021
Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data.
Article in Frontiers in cell and developmental biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 18 citations in OpenAlex.
- Less is more: relative rank is more informative than absolute abundance for compositional NGS data.Briefings in functional genomics · 2025Review
- A procedure for DNA methylation assessment in osteoporosis-related gene promoters of umbilical cord blood: A study on the Prospective Epidemiological Research Studies in Iran (PERSIAN) birth cohort.BioImpacts : BI · 2025Article
- Pairwise analysis of gene expression for oral squamous cell carcinoma via a large-scale transcriptome integration.Journal of cellular and molecular medicine · 2024Article
- Co-expression module analysis reveals high expression homogeneity for both coding and non-coding genes in sepsis.BMC genomics · 2023Article
- GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion.Bioinformatics (Oxford, England) · 2023Article
- Iron metabolism-related genes reveal predictive value of acute coronary syndrome.Frontiers in pharmacology · 2022Article
- Blood Circulating miRNA Pairs as a Robust Signature for Early Detection of Esophageal Cancer.Frontiers in oncology · 2021Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bisulfite sequencing is considered as the gold standard approach for measuring DNA methylation, which acts as a pivotal part in regulating a variety of biological processes without changes in DNA sequences. In this study, we introduced the most prevalent methods for processing bisulfite sequencing data and evaluated the consistency of the data acquired from different measurements in liver cancer. Firstly, we introduced three commonly used bisulfite sequencing assays, i.e., reduced-representation bisulfite sequencing (RRBS), whole-genome bisulfite sequencing (WGBS), and targeted bisulfite sequencing (targeted BS). Next, we discussed the principles and compared different methods for alignment, quality assessment, methylation level scoring, and differentially methylated region identification. After that, we screened differential methylated genes in liver cancer through the three bisulfite sequencing assays and evaluated the consistency of their results. Ultimately, we compared bisulfite sequencing to 450 k beadchip and assessed the statistical similarity and functional association of differentially methylated genes (DMGs) among the four assays. Our results demonstrated that the DMGs measured by WGBS, RRBS, targeted BS and 450 k beadchip are consistently hypo-methylated in liver cancer with high functional similarity.
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Registered trials
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