Mar 15, 2019

Combined analysis and validation for DNA methylation and gene expression profiles associated with prostate cancer

Cancer Cell International
Yanqiu TongShixiong Deng

Abstract

Prostate cancer (PCa) is a malignancy cause of cancer deaths and frequently diagnosed in male. This study aimed to identify tumor suppressor genes, hub genes and their pathways by combined bioinformatics analysis. A combined analysis method was used for two types of microarray datasets (DNA methylation and gene expression profiles) from the Gene Expression Omnibus (GEO). Differentially methylated genes (DMGs) were identified by the R package minfi and differentially expressed genes (DEGs) were screened out via the R package limma. A total of 4451 DMGs and 1509 DEGs, identified with nine overlaps between DMGs, DEGs and tumor suppressor genes, were screened for candidate tumor suppressor genes. All these nine candidate tumor suppressor genes were validated by TCGA (The Cancer Genome Atlas) database and Oncomine database. And then, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed by DAVID (Database for Annotation, Visualization and Integrated Discovery) database. Protein-protein interaction (PPI) network was constructed by STRING and visualized in Cytoscape. At last, Kaplan-Meier analysis was performed to validate these genes. The candidate tumor suppressor genes ...Continue Reading

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Mentioned in this Paper

Biological Markers
Study
Biochemical Pathway
Candidate Tumor Suppressor Gene
FUBP1 protein, human
Proton Pump Inhibitors
The Cancer Genome Atlas
Laboratory Procedures
Tumor Suppressor Genes
Fibroblast growth factor 13

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