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

Aims: To identify key genes and pathways in the development of esophageal squamous cell carcinoma with RNA-seq data. Materials and Methods: 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. Results: 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. Conclusion: These identified DEGs may be underlying targets for diagnosis and treatment of esophageal squamous cell carcinoma.