Identification of potential core genes in esophageal carcinoma using bioinformatics analysis

Jul 7, 2021Medicine

Finding key genes linked to esophageal cancer using computer analysis

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Abstract

A total of 707 differently expressed genes were identified in esophageal squamous cell carcinoma (ESCC) tissues compared to normal tissue.

Of the , 385 were upregulated and 322 downregulated.
Six were highlighted: cyclin B1, cyclin dependent kinase 1, aurora kinase A, ubiquitin conjugating enzyme E2C, cyclin A2, and cell division cycle 20.
All six hub genes were found to be highly expressed in ESCC tissues.
Only cyclin B1 and cell division cycle 20 were associated with the stage of ESCC.
No association was found between the expression of the hub genes and survival time of patients.

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BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is a common human malignancy worldwide. The tumorigenesis mechanism in ESCC is unclear.

MATERIALS AND METHODS: To explore potential therapeutic targets for ESCC, we analyzed 3 microarray datasets (GSE20347, GSE38129, and GSE67269) derived from the gene expression omnibus (GEO) database. Then, the GEO2R tool was used to screen out differently expressed genes () between ESCC and normal tissue. Gene ontology function and kyoto encyclopedia of genes and genomes pathway enrichment analysis were performed using the database for annotation, visualization and integrated discovery to identify the pathways and functional annotation of DEGs. Protein-protein interaction of these DEGs was analyzed based on the search tool for the retrieval of interacting genes database and visualized by Cytoscape software. In addition, we used encyclopedia of RNA interactomes (ENCORI), gene expression profiling interactive analysis (GEPIA), and the human protein atlas to confirm the expression of in ESCC. Finally, GEPIA was used to evaluate the prognostic value of hub genes expression in ESCC patients and we estimated the associations between hub genes expression and immune cell populations (B Cell, CD8+ T Cell, CD4+ T Cell, Macrophage, Neutrophil, and Dendritic Cell) in esophageal carcinoma (ESCA) using tumor immune estimation resource (TIMER).

RESULTS: In this study, 707 DEGs (including 385 upregulated genes and 322 downregulated genes) and 6 hub genes (cyclin B1 [CCNB1], cyclin dependent kinase 1 [CDK1], aurora kinase A [AURKA], ubiquitin conjugating enzyme E2C [UBE2C], cyclin A2 [CCNA2], and cell division cycle 20 [CDC20]) were identified. All of the 6 hub genes were highly expressed in ESCC tissues. Among of them, only CCNB1 and CDC20 were associated with stage of ESCC and all of them were not associated with survival time of patients.

CONCLUSION: DEGs and hub genes were confirmed in our study, providing a thorough, scientific and comprehensive research goals for the pathogenesis of ESCC.

Key numbers

707

Total Identified

Including 385 upregulated and 322 downregulated genes.

Identified

linked to tumor progression in ESCC.

15% to 25%

Five-Year Survival Rate

Survival rate for patients with esophageal squamous cell carcinoma.

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Identification of potential core genes in esophageal carcinoma using bioinformatics analysis

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