• J Buon · Nov 2018

    Biological information analysis of differentially expressed genes in oral squamous cell carcinoma tissues in GEO database.

    • Yitong Wang, Hongyi Fan, and Liwei Zheng.
    • College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, P.R.China.
    • J Buon. 2018 Nov 1; 23 (6): 1662-1670.

    PurposeThis study aimed to detect the differentially expressed genes between oral squamous cell carcinoma (OSCC) tissues and adjacent normal tissues, and perform pathway analysis and protein-protein interaction (PPI) analysis on differentially expressed genes (DEGs).MethodsGene Expression Omnibus (GEO) database related to human tumors was selected from the National Center for Biotechnology Information (NCBI), and GSE31056 and GSE3524, two microarrays containing OSCC gene expression data, were extracted from it. Analysis of differentially expressed genes in the two microarrays was performed using "R" software, and the volcanic map was drawn. Then, Venn diagram was used to integrate the differentially expressed genes screened out by the two microarrays, and PPI [Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG)] analysis of DEGs after integration was performed using Cytoscape, DAVID, STRING and KOBAS. A total of 207 differentially expressed genes were screened out by the two microarrays. 103 proteins encoded by differentially expressed genes screened out by STRING software had interaction. The expression network of differentially expressed genes was constructed, and some proteins, closely related to other proteins such as STAT1, were screened out by Cytoscape software.ResultsGO analysis and KEGG analysis found that the differentially expressed genes were mainly enriched in "extracellular region", "extracellular region part" and "membrane-bound vesicle", and mainly involved in biological processes such as "Amoebiasis", "Glycerolipid metabolism" and "Arachidonic acid metabolism". In this study, 207 differentially expressed genes were successfully screened out from the two OSCC microarrays. PPI, GO and KEGG pathways of 103 interacting proteins were successfully constructed. Key genes were screened out, annotation and pathway analysis of which were performed.ConclusionThis study was helpful to further study the relationship between OSCC gene directions.

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