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pmid:31423235
DNA methylation profiling identifies potentially significant epigenetically-regulated genes in glioblastoma multiforme.
Shifeng Kan · Song Chai · Wenhua Chen · Bo Yu
Oncology letters · 2019 doi:10.3892/ol.2019.10512
Paper
complete
Experiment
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Data
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Analysis
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Execution
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Complete file
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The current study was conducted to identify differentially methylated genes (DMGs) between GBM and normal controls, and to improve our understanding of GBM at the epigenetic level. The DNA methylation profile of GBM was downloaded from the Gene Expression Omnibus (GEO) database using the accession number GSE50923. The MethyAnalysis package was applied to identify DMGs between GBM and controls, which were then analyzed by functional enrichment analysis. Protein-protein interaction (PPI) networks were constructed using the hypermethylated and hypomethylated genes. Finally, transcription factors (TFs) that can regulate the hypermethylated and hypomethylated genes were predicted, followed by construction of transcriptional regulatory networks. Furthermore, another relevant dataset, GSE22867, was downloaded from the GEO database for data validation. A total of 476 hypermethylated and 850 hypomethylated genes were identified, which were mainly associated with the functions of 'G-protein-coupled receptors ligand binding', 'cytokine activity', 'cytokine-cytokine receptor interaction', and 'D-glutamine and D-glutamate metabolism'. The hypermethylated gene neuropeptide Y (NPY) and the hypomethylated gene tumor necrosis factor (TNF) demonstrated high degrees in the PPI network. Forkhead box protein A1 (FOXA1), potassium voltage-gated channel subfamily C member 3 (KCNC3) and caspase-8 (CASP8) exhibited high degrees in the transcriptional regulatory networks. In addition, the methylation profiles of NPY, TNF, FOXA1, KCNC3 and CASP8 were confirmed by another dataset. 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{"label": "Table II.", "caption": "Top five GO terms enriched by hypermethylated genes and hypomethylated genes.", "rows": [["A, Hypermethylated genes"], [""], ["GO ID", "GO term", "P-value"], ["Biological process", "", ""], ["GO:0048856", "Anatomical structure development", "3.19×10−8"], ["GO:0032502", "Developmental process", "4.06×10−8"], ["GO:0044707", "Single-multicellular organism process", "4.85×10−8"], ["GO:0032501", "Multicellular organismal process", "8.26×10−8"], ["GO:0007275", "Multicellular organismal development", "3.47×10−7"], ["Molecular function", "", ""], ["GO:0003700", "Sequence-specific DNA binding transcription factor activity", "5.04×10−9"], ["GO:0001071", "Nucleic acid binding transcription factor activity", "5.51×10−9"], ["GO:0043565", "Sequence-specific DNA binding", "1.76×10−8"], ["GO:0044212", "Transcription regulatory region DNA binding", "6.04×10−7"], ["GO:0000975", "Regulatory region DNA binding", "9.99×10−7"], ["Cellular component", "", ""], 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