ArticleWorld journal of gastroenterology2019
Identification of differentially expressed genes regulated by methylation in colon cancer based on bioinformatics analysis.
Article in World journal of gastroenterology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 50 citations in OpenAlex.
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- Identification of MAD2L1 as a novel biomarker for hepatoblastoma through bioinformatics and machine learning approaches.Frontiers in oncology · 2025Article
- Methods in DNA methylation array dataset analysis: A review.Computational and structural biotechnology journal · 2024Review
- Engineered Immunologic Niche Monitors Checkpoint Blockade Response and Probes Mechanisms of Resistance.Immunomedicine · 2024Article
- Machine learning-based identification of proteomic markers in colorectal cancer using UK Biobank data.Frontiers in oncology · 2024Article
- Promoter hypermethylation of neural-related genes is compatible with stemness in solid cancers.Epigenetics & chromatin · 2023Article
- Identifying Genes that Affect Differentiation of Human Neural Stem Cells and Myelination of Mature Oligodendrocytes.Cellular and molecular neurobiology · 2023Article
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- Identifying Tumor-Associated Genes from Bilayer Networks of DNA Methylation Sites and RNAs.Life (Basel, Switzerland) · 2022Article
- Methylated DNA markers for plasma detection of ovarian cancer: Discovery, validation, and clinical feasibility.Gynecologic oncology · 2022Article
- DNA methylation and miRNA expression in colon adenomas compared with matched normal colon mucosa and carcinomas.International journal of experimental pathology · 2022Article
- The prognostic effect of PNN in digestive tract cancers and its correlation with the tumor immune landscape in colon adenocarcinoma.Journal of clinical laboratory analysis · 2022Article
- Network Pharmacology and Data Mining Approach Reveal the Medication Rule of Traditional Chinese Medicine in the Treatment of Premenstrual Syndrome/Premenstrual Dysphoric Disorder.Frontiers in pharmacology · 2022Article
- Article
- SOCS2 is a potential prognostic marker that suppresses the viability of hepatocellular carcinoma cells.Oncology letters · 2021Article
- Cysteine metabolic circuitries: druggable targets in cancer.British journal of cancer · 2021Review
- A Review of DUSP26: Structure, Regulation and Relevance in Human Disease.International journal of molecular sciences · 2021Review
- Colon Cancer-Related Genes Identification and Function Study Based on Single-Cell Multi-Omics Integration.Frontiers in cell and developmental biology · 2021Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA methylation, acknowledged as a key modification in the field of epigenetics, regulates gene expression at the transcriptional level. Aberrant methylation in DNA regulatory regions could upregulate oncogenes and downregulate tumor suppressor genes without changing the sequences. However, studies of methylation in the control of gene expression are still inadequate. In the present research, we performed bioinformatics analysis to clarify the function of methylation and supply candidate methylation-related biomarkers and drivers for colon cancer.
aimTo identify and analyze methylation-regulated differentially expressed genes (MeDEGs) in colon cancer by bioinformatics analysis.
methodsWe downloaded RNA expression profiles, Illumina Human Methylation 450K BeadChip data, and clinical data of colon cancer from The Cancer Genome Atlas project. MeDEGs were identified by analyzing the gene expression and methylation levels using the edgeR and limma package in R software. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed in the DAVID database and KEGG Orthology-Based Annotation System 3.0, respectively. We then conducted Kaplan-Meier survival analysis to explore the relationship between methylation and expression and prognosis. Gene set enrichment analysis (GSEA) and investigation of protein-protein interactions (PPI) were performed to clarify the function of prognosis-related genes.
resultsA total of 5 up-regulated and 81 down-regulated genes were identified as MeDEGs. GO and KEGG pathway analyses indicated that MeDEGs were enriched in multiple cancer-related terms. Furthermore, Kaplan-Meier survival analysis showed that the prognosis was negatively associated with the methylation status of glial cell-derived neurotrophic factor (GDNF) and reelin (RELN). In PPI networks, GDNF and RELN interact with neural cell adhesion molecule 1. Besides, GDNF can interact with GDNF family receptor alpha (GFRA1), GFRA2, GFRA3, and RET. RELN can interact with RAFAH1B1, disabled homolog 1, very low-density lipoprotein receptor, lipoprotein receptor-related protein 8, and NMDA 2B. Based on GSEA, hypermethylation of GDNF and RELN were both significantly associated with pathways including "RNA degradation," "ribosome," "mismatch repair," "cell cycle" and "base excision repair."
conclusionAberrant DNA methylation plays an important role in colon cancer progression. MeDEGs that are associated with the overall survival of patients may be potential targets in tumor diagnosis and treatment.
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