ArticleJournal of translational medicine2019
Identification of key DNA methylation-driven genes in prostate adenocarcinoma: an integrative analysis of TCGA methylation data.
Article in Journal of translational medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
55 citing papers in PubMed, 2 syntheses or guidelines pooled it, 78 citations in OpenAlex.
- Advances in sequencing and omics studies in prostate cancer: unveiling molecular pathogenesis and clinical applications.Frontiers in oncology · 2024Pooled it
- Bioinformatics analysis of the expression and role of microRNA-221-3p in head and neck squamous cell carcinoma.BMC cancer · 2021Pooled it
- Epigenetic Regulation of the BDNF Gene by Molybdenum in 9 to 11-Year-Old Children: A Targeted Gene DNA Methylation Study.Molecular nutrition & food research · 2026Article
- Vortioxetine enhances the anti-pancreatic cancer efficacy of gemcitabine through reducing MAOB expression.Frontiers in pharmacology · 2026Article
- RTP4 Suppresses Colorectal Cancer Progression via MHC-I-Mediated CD8Journal of cellular and molecular medicine · 2025Article
- The Years 2015-2025 as a Prospective Decade for the Identification of Specific Methylation Biomarkers of Prostate Cancer.Biomolecules · 2025Review
- Extracellular Vesicles as Epigenetic Regulators of Redox Homeostasis: A Systematic Review and Meta-Analysis.Antioxidants (Basel, Switzerland) · 2025Review
- Integrative analysis of DNA methylation and gene expression in skin cutaneous melanoma by bioinformatic approaches.Archives of dermatological research · 2025Article
- Differential DNA Methylation in the Benign and Cancerous Prostate Tissue of African American and European American Men.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2025Article
- Identification of RTP4 facilitating ovarian cancer by bioinformatics analysis and experimental validation.Naunyn-Schmiedeberg's archives of pharmacology · 2025Article
- Causal Relationships Between Neuropathic Pain and Alzheimer's Disease: A Multi-Omics Mendelian Randomization Study with Exploratory Evidence of a Potential Protective Role of Diabetic Neuropathy.Journal of pain research · 2025Article
- 5hmC-profiles in Puerto Rican Hispanic/Latino men with aggressive prostate cancer.Frontiers in oncology · 2025Article
- DNA methylation-driven gene FAM3D promotes colorectal cancer growth via the ATF4-SESN2-mTORC1 pathway.Aging · 2024Article
- A tumour-associated macrophage-based signature for deciphering prognosis and immunotherapy response in prostate cancer.IET systems biology · 2024Article
- Epigenome-wide association study of prostate cancer in African American men identified differentially methylated genes.Cancer medicine · 2024Article
- Article
- Article
- Analysis of the Gene Networks and Pathways Correlated with Tissue Differentiation in Prostate Cancer.International journal of molecular sciences · 2024Article
- Integrative Omics Analysis Reveals Metabolic Features of Ground-Glass Opacity-Associated Lung Cancer.Journal of Cancer · 2024Article
- Multi-Omics Data Analysis Identifies Prognostic Biomarkers across Cancers.Medical sciences (Basel, Switzerland) · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProstate cancer (PCa) remains the second leading cause of deaths due to cancer in the United States in men. The aim of this study was to perform an integrative epigenetic analysis of prostate adenocarcinoma to explore the epigenetic abnormalities involved in the development and progression of prostate adenocarcinoma. The key DNA methylation-driven genes were also identified.
methodsMethylation and RNA-seq data were downloaded for The Cancer Genome Atlas (TCGA). Methylation and gene expression data from TCGA were incorporated and analyzed using MethylMix package. Methylation data from the Gene Expression Omnibus (GEO) were assessed by R package limma to obtain differentially methylated genes. Pathway analysis was performed on genes identified by MethylMix criteria using ConsensusPathDB. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were also applied for the identification of pathways in which DNA methylation-driven genes significantly enriched. The protein-protein interaction (PPI) network and module analysis in Cytoscape software were used to find the hub genes. Two methylation profile (GSE112047 and GSE76938) datasets were utilized to validate screened hub genes. Immunohistochemistry of these hub genes were evaluated by the Human Protein Atlas.
resultsA total of 553 samples in TCGA database, 32 samples in GSE112047 and 136 samples in GSE76938 were included in this study. There were a total of 266 differentially methylated genes were identified by MethylMix. Plus, a total of 369 differentially methylated genes and 594 differentially methylated genes were identified by the R package limma in GSE112047 and GSE76938, respectively. GO term enrichment analysis suggested that DNA methylation-driven genes significantly enriched in oxidation-reduction process, extracellular exosome, electron carrier activity, response to reactive oxygen species, and aldehyde dehydrogenase [NAD(P)+] activity. KEGG pathway analysis found DNA methylation-driven genes significantly enriched in five pathways including drug metabolism-cytochrome P450, phenylalanine metabolism, histidine metabolism, glutathione metabolism, and tyrosine metabolism. The validated hub genes were MAOB and RTP4.
conclusionsMethylated hub genes, including MAOB and RTP4, can be regarded as novel biomarkers for accurate PCa diagnosis and treatment. Further studies are needed to draw more attention to the roles of these hub genes in the occurrence and development of PCa.
Indexed as
Identifiers
What OpenQuestion holds
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.