• RNA expression profils of HER2-possetive advanced gastric or gastroesophageal junction cancer and healthy gastric mucosa control FFPE samples
  • Zahra Aghababaie,1,*
    1. international azad university of Najaf abad


  • Introduction: Stomach (gastric) cancer is cancer that starts in the cells lining the stomach. The stomach is an organ on the left side of the upper abdomen that digests food. The stomach is part of the digestive tract, a series of hollow, muscular organs joined in a long, twisting tube from the mouth to the anus. Competitive endogenous RNAs (ce RNAs) theory have revealed a new mechanism of interaction between RNAs (mRNA-mi RNAs and lnc RNAs) that is used to find the involved genes. In this study we used bioinformatics analysis and signaling pathway to target appropriate gene.
  • Methods: to begin with GSE220917 has been chosen from GEO to analysed genes with significant decrease/increase in expression regulation . ATP4A was selected and by using encore and Gepia2 checked the expression – survival and correlation analysis then used KEEG and Reactome and finally mRNA can establish a ceRNA network with miRwalk and miRNA was searched in LncRNAs 3.0. for pro-pro interacton used string and for miRNA-mRNA interaction used miwalk and for lncRNA-miRNA interaction used lncbase .
  • Results: after carefule analysis of a significant gene that effective on advanced gastric cancer (GSE220917) , a total number of 2000 differentially expressed genes (DEGs)were detected . ATP4A is a decreasing gene. DEGs with adjustedp –valu <0.05 and |logFC|>2 were considered significant. In encori and GEPIA2 analysed the expression and survival and we have significant p – valu and the correlations between ATP4A (decreaseasing gene) and UBD ( increasing gene) were negative. And in keg and reactome this gene have impact on mineral obsorption and gastric acid secretion and Metallothioneins Bind Metals R-HSA – 5661231and many other pathways . After that in miRNASNP we found some SNP that the probable cause to decresead this gene. And we had negative deltaG duplex.Also p220648 was a protein that changed the Amino Acide in HOPE. Fainally ATP4A demonstrated a connection with has-miR-4787-5p in miR-walk. The picked mRNA was searched in LncBase.v.3. to make sure that the LncRNAs are correct we checked in a GeneCards .
  • Conclusion: The GSE220917 microarray dataset was used to identify difrentally expressed genes between GKN1 -GIF -PGC -ATP4A . we select this significant gene and did a variation and use some sites to check a gene survival and the rate of deaths . We choose a ATP4A that have low express and check which SNP is on it and can be effective for low express so we approached top-down .We checked the interaction and this gene have a role in STAD cancer progression .
  • Keywords: systems biology , RNA interaction , High-throughput data analyss , pathway enrichment