title: Comparative analysis of gene expression profiles of gastric cardia adenocarcinoma and gastric non-cardia adenocarcinoma.
abstract: In the present study, gene expression profiles were analyzed to identify the molecular mechanisms underlying gastric cardia adenocarcinoma (GCA) and gastric non-cardia adenocarcinoma (GNCA). A gene expression dataset (accession number GSE29272) was downloaded from Gene Expression Omnibus, and consisted of 62 GCA samples and 62 normal controls, as well as 72 GNCA samples and 72 normal controls. The two groups of differentially-expressed genes (DEGs) were compared to obtain common and unique DEGs. A differential analysis was performed using the Linear Models for Microarray Data package in R. Functional enrichment analysis was conducted for the DEGs using the Database for Annotation, Visualization and Integrated Discovery. Protein-protein interaction (PPI) networks were constructed for the DEGs with information from the Search Tool for the Retrieval of Interacting Genes. Subnetworks were extracted from the whole network with Cytoscape. Compared with the control, 284 and 268 genes were differentially-expressed in GCA and GNCA, respectively, of which 194 DEGs were common between GCA and GNCA. Common DEGs [e.g., claudin (CLDN)7, CLDN4 and CLDN3] were associated with cell adhesion and digestion. GCA-unique DEGs [e.g., MAD1 mitotic arrest deficient like 1, cyclin (CCN)B1, CCNB2 and CCNE1] were associated with the cell cycle and the regulation of cell proliferation, while GNCA-unique DEGs (e.g., GATA binding protein 6 and hyaluronoglucosaminidase 1) were implicated in cell death. A PPI network with 141 nodes and 446 edges were obtained, from which two subnetworks were extracted. Genes [e.g., fibronectin 1, collagen type I α2 chain (COL1A2) and COL1A1] from the two subnetworks were implicated in extracellular matrix organization. These common DEGs could advance our understanding of the etiology of gastric cancer, while the unique DEGs in GCA and GNCA could better define the properties of specific cancers and provide potential biomarkers for diagnosis, prognosis or therapy.
authors.affiliation: Department of Gastrointestinal Surgery, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Bin
authors.initials: B
authors.lastname: Song
authors.affiliation: Second Department of Internal Medicine, The Tumor Hospital of Jilin, Changchun, Jilin 130012, P.R. China.
authors.forename: Juan
authors.initials: J
authors.lastname: Du
authors.affiliation: Department of Gastrointestinal Surgery, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Neng
authors.initials: N
authors.lastname: Deng
authors.affiliation: Second Department of Internal Medicine, The Tumor Hospital of Jilin, Changchun, Jilin 130012, P.R. China.
authors.forename: Ji-Chen
authors.initials: JC
authors.lastname: Ren
authors.affiliation: Department of Gastrointestinal Surgery, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Zhen-Bo
authors.initials: ZB
authors.lastname: Shu
keywords: differentially-expressed genes; functional enrichment analysis; gastric cardia adenocarcinoma; gastric non-cardia adenocarcinoma; gene expression data; protein-protein interaction network