09 May 2018 : Laboratory Research
Identification of Core Genes and Key Pathways via Integrated Analysis of Gene Expression and DNA Methylation Profiles in Bladder CancerYongzhen Zhang1BCE*, Liang Fang1F, Yuanwei Zang1D, Zhonghua Xu1AG
Med Sci Monit 2018; 24: LBR3024-3033
BACKGROUND: Bladder cancer (BC) is the most common urological malignant tumor. In BC, aberrant DNA methylation is believed to be associated with carcinogenesis. Therefore, the identification of key genes and pathways could help determine the potential molecular mechanisms of BC development.
MATERIAL AND METHODS: Microarray data on gene expression and gene methylation were downloaded from the Gene Expression Omnibus (GEO) database. Abnormal methylated/expressed genes were analyzed by GEO2R and statistical software R. Gene Ontology term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the DAVID database and KOBAS 3.0. STRING and Cytoscape software were used to construct protein–protein interaction (PPI) networks and analyze modules of the PPI network.
RESULTS: A total of 71 hypomethylated/upregulated genes were significantly enriched in cell–cell adhesion and blood vessel development. KEGG pathway analysis highlighted p53 signaling and metabolic pathways. Five core genes in the PPI network were determined: CDH1, DDOST, CASP8, DHX15, and PTPRF. Additionally, 89 hypermethylated/downregulated genes were found. These genes were enriched mostly in cell adhesion and signal transduction. KEGG pathway analysis revealed enrichment in focal adhesion. The top 5 core genes in the PPI network were GNG4, ADCY9, NPY, ADRA2B, and PENK. We found most of the core genes were also significantly altered in the Cancer Genome Atlas database.
CONCLUSIONS: Abnormal methylated/expressed genes and key signaling pathways involved in BC were identified through integrated bioinformatics analysis. In the future, these genes may serve as biomarkers for diagnosis and therapeutic targets in BC.
Keywords: Computational Biology
01 March 2024 : EditorialEditorial: First Regulatory Approvals for CRISPR-Cas9 Therapeutic Gene Editing for Sickle Cell Disease and Transfusion-Dependent β-Thalassemia
Med Sci Monit 2024; 30:e944204
23 Feb 2024 : Clinical ResearchEarly Mobilization in Pediatric Critical Care: Exploring the Gap Between Theory and Practice in Saudi Arabia
Med Sci Monit In Press; DOI: 10.12659/MSM.942467
01 Feb 2024 : Review articleEnhancing Patient Adherence to Newly-Prescribed Medicine for Chronic Diseases: A Comprehensive Review and C...
Med Sci Monit In Press; DOI: 10.12659/MSM.942923
10 Jan 2024 : Clinical ResearchEfficacy of Bakri Intrauterine Balloon in Managing Postpartum Hemorrhage: A Comparative Analysis of Vaginal...
Med Sci Monit In Press; DOI: 10.12659/MSM.943072
Most Viewed Current Articles
16 May 2023 : Clinical ResearchElectrophysiological Testing for an Auditory Processing Disorder and Reading Performance in 54 School Stude...
Med Sci Monit 2023; 29:e940387
17 Jan 2024 : Review articleVaccination Guidelines for Pregnant Women: Addressing COVID-19 and the Omicron Variant
Med Sci Monit 2024; 30:e942799
14 Dec 2022 : Clinical ResearchPrevalence and Variability of Allergen-Specific Immunoglobulin E in Patients with Elevated Tryptase Levels
Med Sci Monit 2022; 28:e937990