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European Journal of Medical Research

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Open Access 01-12-2014 | Research

RETRACTED ARTICLE: Ranking candidate genes of esophageal squamous cell carcinomas based on differentially expressed genes and the topological properties of the co-expression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

Authors: Yuzhou Shen, Jicheng Tantai, Heng Zhao

Published in: European Journal of Medical Research | Issue 1/2014

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 (Cri_n 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.

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Title: RETRACTED ARTICLE: Ranking candidate genes of esophageal squamous cell carcinomas based on differentially expressed genes and the topological properties of the co-expression network
Authors: Yuzhou Shen
Jicheng Tantai
Heng Zhao
Publication date: 01-12-2014
Publisher: BioMed Central
Published in: European Journal of Medical Research / Issue 1/2014
Electronic ISSN: 2047-783X
DOI: https://doi.org/10.1186/s40001-014-0052-x

Keynote webinar | Spotlight on medication adherence

Springer Medicine

RETRACTED ARTICLE: Ranking candidate genes of esophageal squamous cell carcinomas based on differentially expressed genes and the topological properties of the co-expression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

Abstract

Background

Methods

Results

Conclusion

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Abstract

Background

Methods

Results

Conclusion

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