Systematic identification of key functional modules and genes in esophageal cancer

• Main Authors: Rui Wu, Hao Zhuang, Yu-Kun Mei, Jin-Yu Sun, Tao Dong, Li-Li Zhao, Zhi-Ning Fan, Li Liu
• Format: Article
• Language: English
• Published: BMC 2021-02-01
• Series: Cancer Cell International
• Subjects: Esophageal cancer; Integrated transcriptomic analysis; Weighted gene co-expression network analysis; Bioinformatics; CCNB1
• Online Access: https://doi.org/10.1186/s12935-021-01826-x

Abstract Background Esophageal cancer is associated with high incidence and mortality worldwide. Differential expression genes (DEGs) and weighted gene co-expression network analysis (WGCNA) are important methods to screen the core genes as bioinformatics methods. Methods The DEGs and WGCNA were combined to screen the hub genes, and pathway enrichment analyses were performed on the hub module in the WGCNA. The CCNB1 was identified as the hub gene based on the intersection between DEGs and the greenyellow module in WGCNA. Expression levels and prognostic values of CCNB1 were verified in UALCAN, GEPIA2, HCMDB, Kaplan–Meier plotter, and TIMER databases. Results We identified 1,044 DEGs from dataset GSE20347, 1,904 from GSE29001, and 2,722 from GSE111044, and 32 modules were revealed by WGCNA. The greenyellow module was identified as the hub module in the WGCNA. CCNB1 gene was identified as the hub gene, which was upregulated in tumour tissues. Moreover, esophageal cancer patients with higher expression of CCNB1 showed a worse prognosis. However, CCNB1 ‘might not play an important role in immune cell infiltration. Conclusions Based on DEGs and key modules related to esophageal cancer, CCNB1 was identified as the hub gene, which offered novel insights into the development and treatment of esophageal cancer.