Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Meta-Analysis
. 2014 Oct 29;19(1):52.
doi: 10.1186/s40001-014-0052-x.

Ranking candidate genes of esophageal squamous cell carcinomas based on differentially expressed genes and the topological properties of the co-expression network

Yuzhou Shen, Jicheng Tantai, Heng Zhao
Meta-Analysis

Ranking candidate genes of esophageal squamous cell carcinomas based on differentially expressed genes and the topological properties of the co-expression network

Yuzhou Shen et al. Eur J Med Res. .

Retraction in

Abstract

Background: The aim of this study was to identify the candidate genes of esophageal squamous cell carcinoma (ESCC).

Methods: Gene expression profiling of 17 ESCC samples and 17 adjacent normal samples, GSE20347, was downloaded from Gene Expression Omnibus database. The raw data were preprocessed, and the differentially expressed genes (DEGs) between ESCC and normal samples were identified by using SAM software (false discovery rate <0.001). Then, the co-expression network of DEGs was constructed based on Pearson's correlation test (r-value ≥0.8). Furthermore, the topological properties of the co-expression network were analyzed through NetworkAnalyzer (default settings) of Cytoscape. The expression fold changes of DEGs and topological properties were utilized to identify the candidate genes of ESCC (Crin score >4), which were further analyzed based on DAVID functional enrichment analysis (P-value <0.05).

Results: A total of 1,063 DEGs were identified, including 490 up-regulated and 573 down-regulated DEGs. Then, the co-expression network of DEGs was constructed, containing 999 nodes and 46,323 edges. Based on the expression fold changes of DEGs and the topological properties of the co-expression network, DEGs were ranked, and the top 24 genes were candidate genes of ESCC, such as CRISP3, EREG, CXCR2, and CRNN. Furthermore, the 24 genes were significantly enriched in bio-functions regarding cell differentiation, glucan biosynthetic process and immune response.

Conclusion: The present study suggested that CRISP3, EREG, CXCR2, and CRNN might be causative genes of ESCC, and play vital roles in the development of ESCC. However, further experimental studies are needed to confirm our results.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Bidirectional hierarchical clustering analysis of differentially expressed genes. The green to red gradation represented the changes of expression value from down-regulation to up-regulation.
See this image and copyright information in PMC

References

    1. Lam AKY. Molecular biology of esophageal squamous cell carcinoma. Crit Rev Oncol Hematol. 2000;33:71–90. doi: 10.1016/S1040-8428(99)00054-2. - DOI - PubMed
    1. Hu N, Clifford R, Yang H, Wang C, Goldstein A, Ding T, Taylor P, Lee M. Genome wide analysis of DNA copy number neutral loss of heterozygosity (CNNLOH) and its relation to gene expression in esophageal squamous cell carcinoma. BMC Genomics. 2010;11:576. doi: 10.1186/1471-2164-11-576. - DOI - PMC - PubMed
    1. Wieder HA, Brücher BL, Zimmermann F, Becker K, Lordick F, Beer A, Schwaiger M, Fink U, Siewert JR, Stein HJ. Time course of tumor metabolic activity during chemoradiotherapy of esophageal squamous cell carcinoma and response to treatment. J Clin Oncol. 2004;22:900–908. doi: 10.1200/JCO.2004.07.122. - DOI - PubMed
    1. Brücher BL, Weber W, Bauer M, Fink U, Avril N, Stein HJ, Werner M, Zimmerman F, Siewert JR, Schwaiger M. Neoadjuvant therapy of esophageal squamous cell carcinoma: response evaluation by positron emission tomography. Ann Surg. 2001;233:300. doi: 10.1097/00000658-200103000-00002. - DOI - PMC - PubMed
    1. Stahl M, Stuschke M, Lehmann N, Meyer H-J, Walz MK, Seeber S, Klump B, Budach W, Teichmann R, Schmitt M. Chemoradiation with and without surgery in patients with locally advanced squamous cell carcinoma of the esophagus. J Clin Oncol. 2005;23:2310–2317. doi: 10.1200/JCO.2005.00.034. - DOI - PubMed

MeSH terms