Bioinformatics analysis of gene expression profiles of esophageal squamous cell carcinoma

The objective of this study is to explore the potential target genes in the pathogenesis of esophageal squamous cell carcinoma (ESCC). The mRNA expression profile data of GSE17351 were downloaded from the Gene Expression Omnibus database, including five paired ESCC and normal tissue samples from five ESCC patients. The differentially expressed genes (DEGs) between ESCC and normal samples were identified using the limma package. The identified DEGs were then performed clustering analysis and functional enrichment analysis. Additionally, gene-miRNA network, gene-transcription factor network, and protein-protein interaction (PPI) network for the DEGs were constructed, and then significant modules were selected from the constructed PPI network. Furthermore, esophageal carcinoma RNAseq data including 185 esophageal carcinoma and 13 normal samples were downloaded from The Cancer Genome Atlas database to confirm our results. A total of 409 up- and 341 downregulated DEGs were identified. The DEGs were separated into two clusters and were mainly enriched in cell cycle function. CHEK1, CCNA2, COL11A1, and MME were hub nodes in the PPI network. Besides, total seven modules were selected in the PPI network. Genes in the most significant module were upregulated and were enriched in cell cycle. The Cancer Genome Atlas data validation identified 370 DEGs, all of which were differentially expressed in the GSE17351 dataset. Besides, the expression change direction was consistent with the DEGs in GSE17351. Cell cycle may play a role in ESCC development. The genes such as CHEK1, CCNA2, COL11A1, and MME may be served as target genes in ESCC treatment.