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Characterization of differentially expressed genes involved in pathways associated with gastric cancer

ABSTRACT: To explore the patterns of gene expression in gastric cancer, a total of 32 paired gastric cancer and noncancerous tissues from patients were collected for gene expression microarray analyses. Limma methods were applied to analyze the data, and genes were considered to be significantly differentially expressed if the False Discovery Rate (FDR) values < 0.01, P-value < 0.01 and the fold change >2. Subsequently, Gene Ontology (GO) analysis was used to analyze the main functions of the differentially expressed genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found pathways significantly associated with the differential genes. Gene-Act network and Co-Expression networks were built respectively based on the relationships among the genes, proteins and compounds in the database. There were 2371 differential mRNAs and 350 differential lncRNAs in our microarray data. The GO categories, pathway analyses and the Gene-Act network showed a consistent result that up-regulated genes were involved in tumorigenesis, migration, angiogenesis and microenvironment formation, while down-regulated genes were involved in metabolism. The results of this study provide some novel findings on genes, pathways and the co-expression network in gastric cancer which will be useful to guide further investigation and target therapy for this disease.

ORGANISM(S): Homo sapiens

PROVIDER: GSE65801 | GEO | 2015/02/11

SECONDARY ACCESSION(S): PRJNA275101

REPOSITORIES: GEO

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Project description:Purpose: We compared the levels of miRNA specific for DEGs in isograft corneas with those in normal corneas, as well as the levels of miRNA specific for DEGs in allograft corneas with those in isograft corneas, to gain a better understanding of molecular variables that affect corneal graft rejection pathways. Methods: Illumina Hiseq 2500 deep sequencing was used to screen for differentially expressed genes (DEGs) in matched pairs of isograft corneas and normal corneas, allograft corneas and isograft corneas. Potential target genes among the DEGs were predicted using target prediction software (TargetScan, Miranda, miRDB, and CLIP), and the overlay portion was analyzed using the Gene Ontology (GO) database and the Kyoto Encyclopedia of Genes and Genomes (KEGG). An analysis of the interactions between DEG proteins (PPI analysis) and a MetaCore software analysis. Results: Our results showed that 22 miRNAs were significantly upregulated and 4 were significantly downregulated in the isograft group when compared with the control group (P < 0.01), while 17 miRNAs were significantly upregulated and 3 were significantly downregulated in the allograft group when compared with the isograft group (P < 0.01). Among the miRNAs with altered expression levels, miR-155-5p, miR-142-3p, miR-142-5p, and miR-223-3p displayed simultaneous changes in the above two comparisons. Potential target genes among the DEGs were predicted using target prediction software, and the overlay portion was analyzed using the Gene Ontology (GO) database and the Kyoto Encyclopedia of Genes and Genomes (KEGG). GO and KEGG analyses showed that the DEGs were mainly involved in metabolic pathways, cytokine secretion, and tumor immunity functions. An analysis of the interactions between DEG proteins (PPI analysis) and a MetaCore software analysis of 4 key DEGs revealed that the genes regulated by miR-155-5p played important roles in the miRNA-mRNA regulatory network. Furthermore, the MetaCore analysis identified C/EBP beta, p53, and sp1 as key transcription factors in that network. Conclusions: Our study identified transplanted corneas-specific miRNA in matched pairs of isograft corneas and normal corneas, allograft corneas and isograft corneas. Furthermore, bioinformatics analysis of the key miRNA regulatory network revealed the molecular mechanisms, which suggests miRNAs may as new molecular targets for treating corneal injuries and corneal transplant rejection

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Characterization of differentially expressed genes involved in pathways associated with gastric cancer

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