ArticleMedicine2017
Identification of regulatory role of DNA methylation in colon cancer gene expression via systematic bioinformatics analysis.
Article in Medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 29 citations in OpenAlex.
- Promoter hypermethylation of neural-related genes is compatible with stemness in solid cancers.Epigenetics & chromatin · 2023Article
- Nerves in gastrointestinal cancer: from mechanism to modulations.Nature reviews. Gastroenterology & hepatology · 2022Review
- Identification of Epigenetically Modified Hub Genes and Altered Pathways Associated With Retinoblastoma.Frontiers in cell and developmental biology · 2022Article
- Experiments from unfinished Registered Reports in the Reproducibility Project: Cancer Biology.eLife · 2021Article
- Screening for Colorectal Cancer Leading into a New Decade: The "Roaring '20s" for Epigenetic Biomarkers?Current oncology (Toronto, Ont.) · 2021Review
- The PPARα and PPARγ Epigenetic Landscape in Cancer and Immune and Metabolic Disorders.International journal of molecular sciences · 2021Review
- Integrated bioinformatics identifies the dysregulation induced by aberrant gene methylation in colorectal carcinoma.Genes & diseases · 2021Article
- Identification of DNA methylation markers for early detection of CRC indicates a role for nervous system-related genes in CRC.Clinical epigenetics · 2021Article
- GNAO1 as a Novel Predictive Biomarker for Late Relapse in Hepatocellular Carcinoma.Journal of healthcare engineering · 2021Article
- Identification of hub methylated-CpG sites and associated genes in oral squamous cell carcinoma.Cancer medicine · 2020Article
- Identification of Monotonically Differentially Expressed Genes across Pathologic Stages for Cancers.Journal of oncology · 2020Article
- Epigenetic Clock: DNA Methylation in Aging.Stem cells international · 2020Review
- Construction of a CXC Chemokine-Based Prediction Model for the Prognosis of Colon Cancer.BioMed research international · 2020Article
- Comprehensive analysis identifying aberrant DNA methylation in rectal mucosa from ulcerative colitis patients with neoplasia.Oncotarget · 2018Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Colon cancer arises from the accumulations of genetic and epigenetic changes. Currently, profiles of DNA methylation and gene expression of colon cancer have not been elucidated clearly. This articles aims to characterize the profile of DNA methylation and gene expression of colon cancer systemically, and acquire candidate genes potentially regulated by altered methylation for this disease.Data were downloaded from The Cancer Genome Atlas database. Differentially methylated CpG sites (DMCs) and differentially methylated regions (DMRs) were calculated via COHCAP. Differentially expressed genes (DEGs) were identified by DESeq2. Weighted gene co-expression network analysis (WGCNA) package in R was applied for WGCNA.Data of 275 solid tumor tissues and 19 adjacent tumor tissues of colon cancer were obtained. A total of 1828 DMCs, including 1390 hypermethylated and 438 hypomethylated CpG sites, were identified between tumor and normal groups. A total of 789 DEGs, containing 435 upregulated genes and 354 downregulated genes were observed. It revealed that 8 DMRs-DEGs and 95 DMCs-DEGs pairs were significantly correlated. Furthermore, genes of yellow and brown modules from WGCNA were significantly correlated with tumor/normal status, and significantly enriched in peroxisome proliferator activated receptor signaling pathway, glutamatergic synapse, and neuroactive ligand-receptor interaction. Genes in the above 2 modules were also significantly enriched in DMCs or DMRs-associated genes. Specifically, ADHFE1, HAND2, and GNAO1 were hypermethylated and downregulated in colon cancer, suggesting that the low expression levels of these genes may be regulated by DNA hypermethylation. In addition, the 3 genes were involved in brown module of WGCNA, indicating their important roles in colon cancer.The investigation of the relationship between DNA methylation and gene expression may help to understand the effect of DNA methylation alteration on genes expression, especially gene co-expression network in the development of colon cancer. Genes such as ADHFE1, HAND2, and GNAO1 may be served as potential candidates for diagnosis and therapy targets in colon cancer.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.