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

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 c

SUBMITTER: Shen Y 

PROVIDER: S-EPMC4223754 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature