Identification of Key Genes Related to the Prognosis of Esophageal Squamous Cell Carcinoma Based on Chip Re-Annotation

• Main Authors: Meiqi Wang, Dan Liu, Yunchuanxiang Huang, Ziyi Jiang, Feng Wu, Yu Cen, Lan Ma
• Format: Article
• Language: English
• Published: MDPI AG 2021-04-01
• Series: Applied Sciences
• Subjects: esophageal squamous cell carcinoma; chip re-annotation; DEGs; bioinformatics analyses; prognostic biomarkers
• Online Access: https://www.mdpi.com/2076-3417/11/7/3229

Esophageal cancer (EC) is one of the deadliest cancers worldwide. However, reliable biomarkers for early diagnosis, or those for the prognosis of therapy, remain unfulfilled goals for its subtype esophageal squamous cell carcinoma (ESCC). The purpose of this study was to identify reliable biomarkers for the diagnosis and prognosis of ESCC by gene chip re-annotation technique and downstream bioinformatics analysis. In our research, the GSE53624 dataset was downloaded from the GEO database. Then, we reannotated the gene expression probe and obtained the gene expression matrix. Differential expressed genes (DEGs) were found by R packages and they were subjected to Gene Ontology enrichment analysis and protein–protein interaction (PPI) network construction. As a result, a total of 28,885 mRNA probes were reannotated, among which 210 down-regulated and 80 up-regulated DEGs were screened out. By combining these genes set in clinical prognosis information and Western blot analysis, we found four genes with diagnostic and prognostic significance, including MMP134SPP1, MMP10, and COL1A1. Furthermore, markers of infiltrating immune cells exhibited different DEG-related immune infiltration patterns.