Sep 16, 2017

Bioinformatics-Based Identification of Methylated-Differentially Expressed Genes and Related Pathways in Gastric Cancer

Digestive Diseases and Sciences
Hao LiLiping Sun

Abstract

The aim of the study was to identify methylated-differentially expressed genes (MDEGs) in gastric cancer and investigate their potential pathways. Expression profiling (GSE13911 and GSE29272) and methylation profiling (GSE25869 and GSE30601) data were obtained from GEO DataSets. Differentially expressed genes and differentially methylated genes were identified using GEO2R. Gene ontology and pathway enrichment analyses were performed for the MDEGs. Protein-protein interaction (PPI) networks were established by STRING and Cytoscape. Analysis of modules in the PPI networks was performed using MCODE. Further, the hub genes derived from the PPI networks were verified by The Cancer Genome Atlas (TCGA) database and human tissues, with methylation-specific PCR for genes methylation and real-time qPCR for genes expression. A total of 445 genes were identified as hypermethylated, lowly expressed genes (Hyper-LGs), which were enriched in the regulation of system process and channel activity. A total of 129 genes were identified as hypomethylated, highly expressed genes (Hypo-HGs), which were involved in cell adhesion, cell proliferation, and protein binding. Pathway analysis showed that Hyper-LGs were associated with neuroactive ligand-re...Continue Reading

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Mentioned in this Paper

Biological Markers
Real-Time Polymerase Chain Reaction
Channel Activity
Study
Biochemical Pathway
Stromal Cell-Derived Factor 1
Gene Expression Regulation, Neoplastic
Proton Pump Inhibitors
The Cancer Genome Atlas
Protein Binding

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