Project description: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. 32 gastric cancer tissues and 32 paired noncancerous tissues were collected for this microarray analysis.
Project description: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.
Project description:This is a commercially available Affymetrix chip from 16 pairs of gastric cancer and corresponding adjacent normal tissues, used for screening differentially expressed genes associated with gastric cancer.
Project description:PHF8, an important epigenetic regulator of cell cycle progression, rRNA synthesis and chromatin organization, is often overexpressed in different types of cancer including gastric cancer. Notably, elevated expression of PHF8 is associated with a poor clinical outcome in patients with gastric cancer. A global transcriptomic analysis between control and PHF8-knockdown MKN28 cells reveals differentially expressed genes involved in cell mortility and cell migration, suggesting PHF8 acts as an important regulator of cell migration related genes.
