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Comprehensive Bioinformation Analysis of the MRNA Profile of Fascin Knockdown in Esophageal Squamous Cell Carcinoma

  • Wu, Bing-Li (Department of Biochemistry and Molecular Biology, Shantou University Medical College) ;
  • Luo, Lie-Wei (Department of Biochemistry and Molecular Biology, Guangdong Pharmaceutical University Guangzhou Higher Education Mega Center) ;
  • Li, Chun-Quan (College of Bioinformatics Science and Technology, Harbin Medical University) ;
  • Xie, Jian-Jun (Department of Biochemistry and Molecular Biology, Shantou University Medical College) ;
  • Du, Ze-Peng (Departments of Pathology, Shantou Central Hospital) ;
  • Wu, Jian-Yi (Department of Biochemistry and Molecular Biology, Shantou University Medical College) ;
  • Zhang, Pi-Xian (Department of Biochemistry and Molecular Biology, Shantou University Medical College) ;
  • Xu, Li-Yan (Institute of Oncologic Pathology, Shantou University Medical College) ;
  • Li, En-Min (Department of Biochemistry and Molecular Biology, Shantou University Medical College)
  • Published : 2013.12.31

Abstract

Background: Fascin, an actin-bundling protein forming actin bundles including filopodia and stress fibers, is overexpressed in multiple human epithelial cancers including esophageal squamous cell carcinoma (ESCC). Previously we conducted a microarray experiment to analyze fascin knockdown by RNAi in ESCC. Method: In this study, the differentially expressed genes from mRNA expression profilomg of fascin knockdown were analyzed by multiple bioinformatics methods for a comprehensive understanding of the role of fascin. Results: Gene Ontology enrichment found terms associated with cytoskeleton organization, including cell adhesion, actin filament binding and actin cytoskeleton, which might be related to fascin function. Except GO categories, the differentially expressed genes were annotated by 45 functional categories from the Functional Annotation Chart of DAVID. Subpathway analysis showed thirty-nine pathways were disturbed by the differentially expressed genes, providing more detailed information than traditional pathway enrichment analysis. Two subpathways derivated from regulation of the actin cytoskeleton were shown. Promoter analysis results indicated distinguishing sequence patterns and transcription factors in response to the co-expression of downregulated or upregulated differentially expressed genes. MNB1A, c-ETS, GATA2 and Prrx2 potentially regulate the transcription of the downregulated gene set, while Arnt-Ahr, ZNF42, Ubx and TCF11-MafG might co-regulate the upregulated genes. Conclusions: This multiple bioinformatic analysis helps provide a comprehensive understanding of the roles of fascin after its knockdown in ESCC.

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