ArticleFrontiers in oncology2021
Identification of Methylation-Regulated Differentially Expressed Genes and Related Pathways in Hepatocellular Carcinoma: A Study Based on TCGA Database and Bioinformatics Analysis.
Article in Frontiers in oncology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Article
- Identification of potential DNA methylation biomarkers related to diagnosis in patients with bladder cancer through integrated bioinformatic analysis.BMC urology · 2023Article
- The coagulation-related genes for prognosis and tumor microenvironment in pancreatic ductal adenocarcinoma.BMC cancer · 2023Article
- Targeted DNA demethylation of the ZNF334 promoter inhibits colorectal cancer growth.Cell death & disease · 2023Article
- Bioinformatics Analysis IdentifiesDisease markers · 2023Article
- lncRNA-AC079061.1/VIPR1 axis may suppress the development of hepatocellular carcinoma: a bioinformatics analysis and experimental validation.Journal of translational medicine · 2022Article
- Crosstalk of Redox-Related Subtypes, Establishment of a Prognostic Model and Immune Responses in Endometrial Carcinoma.Cancers · 2022Article
- Molecular subtypes, clinical significance, and tumor immune landscape of angiogenesis-related genes in ovarian cancer.Frontiers in oncology · 2022Article
- Review
- PROZ May Serve as a Prognostic Biomarker for Early Hepatocellular Carcinoma.International journal of general medicine · 2021Article
- Exploration of Ziziphi Spinosae Semen in Treating Insomnia Based on Network Pharmacology Strategy.Evidence-based complementary and alternative medicine : eCAM · 2021Article
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4 authors.
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Abstract
backgroundIn recent years, DNA methylation modification has been shown to be a critical mechanism in the field of epigenetics.
methodsHepatocellular carcinoma (HCC) data were obtained from The Cancer Genome Atlas project, including RNA expression profiles, Illumina Human Methylation 450K BeadChip data, clinical information, and pathological features. Then, differentially expressed genes (DEGs) and differentially methylated genes were identified using R software. Methylation-regulated DEGs (MeDEGs) were further analyzed using Spearman's correlation analysis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using the DAVID database and ClueGO in Cytoscape software. Kaplan-Meier survival analysis explored the relationship between methylation, expression of MeDEGs, and survival time. Gene set enrichment analysis (GSEA) was conducted to predict the function of prognosis-related MeDEGs.
resultsA total of nine up-regulated and 72 down-regulated MeDEGs were identified. GO and KEGG pathway analyses results indicated that multiple cancer-related terms were enriched. Kaplan-Meier survival analysis showed that the methylation status of four MeDEGs (CTF1, FZD8, PDK4, and ZNF334) was negatively associated with overall survival. Moreover, the methylation status of CDF1 and PDK4 was identified as an independent prognostic factor. According to GSEA, hypermethylation of prognosis-related MeDEGs was enriched in pathways that included "Spliceosome", "Cell cycle", "RNA degradation", "RNA polymerase", "DNA replication", "Mismatch repair", "Base excision repair", "Nucleotide excision repair", "Homologous recombination", "Protein export", and "Pyrimidine metabolism".
conclusionsAberrant DNA methylation plays a critical role in malignant progression of HCC. Prognosis-related MeDEGs identified in this research may be potential biomarkers and targets in diagnosis and treatment.
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