Integrated analysis of DNA methylation and mRNA expression profiles to identify key genes in head and neck squamous cell carcinoma.

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In the present study, methylation microarray dataset (GSE87053) and gene expression microarray dataset (GSE23558) were downloaded from GEO database and analyzed through R language. A total of 255 hypermethylated-downregulated genes and 114 hypomethylated-upregulated genes were finally identified. Functional enrichment analyses were performed and a comprehensive protein-protein interaction (PPI) network was constructed. Subsequently, the top ten hub genes selected by Cytoscape software were subjected to further analyses. It was illustrated that the expression level of CSF2, CTLA4, ETS1, PIK3CD, and CFTR was intimately associated with HNSCC. Survival analysis suggested that CTLA4 and FGFR2 could serve as effective independent prognostic biomarkers for HNSCC patients. Overall, our study lay a groundwork for further investigation into the underlying molecular mechanisms in HNSCC carcinogenesis, providing potential biomarkers and therapeutic targets for HNSCC.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier survival analysis was utilized to explore the association of hub gene expression with HNSCC patient survival using log‐rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31894857", "locator": "sections[10] \"Statistical analysis\" paragraph 2", "quote": "Kaplan–Meier survival analysis was utilized to explore the association of hub gene expression with HNSCC patient survival using log‐rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In the present study, we downloaded methylation microarray dataset (GSE87053) and gene expression microarray dataset (GSE23558) conducted on HNSCC samples from Gene Expression omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). 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