RNA-sequencing based identification of crucial genes for esophageal squamous cell carcinoma

• Published in: Journal of cancer research and therapeutics Vol. 11; no. 2; pp. 420 - 425
• Main Authors: Fu, Jian-Hua, Wang, Li-Quan, Li, Tao, Ma, Guo-Jun
• Format: Journal Article
• Language: English
• Published: India Medknow Publications and Media Pvt. Ltd 01.04.2015; Medknow Publications & Media Pvt. Ltd
• Subjects: Analysis; Arachidonic Acid - genetics; Carcinoma, Squamous Cell - genetics; Cell Adhesion - genetics; Cell Differentiation - genetics; Cell Movement - genetics; Collagen; Collagen - genetics; Computational Biology - methods; Cyclin-dependent kinases; Databases, Genetic; Diagnosis; Down-Regulation - genetics; Esophageal cancer; Esophageal Neoplasms - genetics; Esophageal Squamous Cell Carcinoma; Extracellular matrix; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation, Neoplastic - genetics; Genes; Genetic aspects; Humans; Keratin; Kinases; Matrix Metalloproteinases - genetics; Medical prognosis; Metastasis; Physiological aspects; Prostate cancer; Proteins; RNA - genetics; RNA sequencing; Sequence Analysis, RNA - methods; Studies; Up-Regulation - genetics; Vascular endothelial growth factor; India
• ISSN: 0973-1482; 1998-4138
• DOI: 10.4103/0973-1482.160122

To identify key genes and pathways in the development of esophageal squamous cell carcinoma with RNA-seq data. RNA-seq data including three paired samples were downloaded from Sequence Read Archive database under accession number SRP007169 and differentially expressed genes (DEGs) were identified with package edge R of R. Functional enrichment analysis was performed to uncover their biological functions with the Database for Annotation, Visualization, and Integrated Discovery (DAVID) tools. A total of 5561 DEGs were obtained, including 1829 upregulated and 3732 downregulated. Quite a few upregulated genes were components of collagen and matrix metallopeptidases (MMPs), which are involved in cell adhesion, cell mobility and so on. Keratin, mucin and cysteine-rich secretory protein were found to be significantly downregulated. Significantly over-represented biological processes for downregulated genes were epidermis development, epidermal cell differentiation and arachidonic acid metabolism. These identified DEGs may be underlying targets for diagnosis and treatment of esophageal squamous cell carcinoma.