Identification of genes and long non-coding RNAs associated with the pathogenesis of gastric cancer

Gastric cancer is a lethal disease characterized by high diffusivity and mortality. To examine the mechanisms involved in gastric cancer, we analyzed the microarray of GSE41476. GSE41476 was downloaded from the Gene Expression Omnibus and included 3 primary cell culture samples from gastric cancer tissues, 3 gastric cancer cell lines and 2 normal tissue samples. Long non-coding RNAs (IncRNAs) and differentially expressed genes (DEGs) were screened by Cuffdiff software. Functions of the DEGs were predicted by functional and pathway enrichment analyses. The interaction relationships of the proteins encoded by DEGs that were obtained from the STRING database and protein-protein interaction (PPI) network were visualized using Cytoscape. Modules analysis of PPI network was performed using CFinder. Moreover, lncRNA analysis was performed. A total of 86 lneRNAs, and 1,088 up- and 1,537 downregulated transcriptions were screened. For DEGs in module A of the PPI network for upregulated genes, the enriched pathways included ECM-receptor interaction and focal adhesion, both of which involved COL and ITG genes. The COL genes interacted with the ITG genes (e.g., COL1A1-ITGA5 and COL1A2-ITGB1). For DEGs in module B of the PPI network for downregulated genes, the enriched pathways for DEGs included the T-cell receptor signaling pathway, which involved PIK3CG and PIK3R5. PIK3CG had an interaction relationship with PIK3R5. In addition, IL7 was co-expressed with TCONS-00068220. In summary, the results showed that COL and ITG genes, PIK3CG,PIK3R5,IL7 and lncRNA TCONS-00068220 may play a role in gastric cancer.