DNA microarray-based screening of differentially expressed genes related to acute lung injury and functional analysis
Chen, Y.; Shi, J.-X.; Pan, X.-F.; Feng, J.; Zhao, H.
European Review for Medical and Pharmacological Sciences 17(8): 1044-1050
2013
ISSN/ISBN: 1128-3602 PMID: 23661517 Document Number: 671401
The purpose of this study was to identify differentially expressed genes (DEGs) related to acute lung injury (ALI) induced by sepsis with DNA microarray. Gene expression profile GSE10474 was downloaded from Gene Expression Omnibus (GEO) database which includes 34 samples, among which 13 patients with ALI + sepsis and 21 patients with sepsis alone. The DEGs were identified between ALI + sepsis and sepsis alone samples using R, which were further analyzed using bioinformatics methods. Firstly, HitPredict was used to search protein-protein interactions of the DEGs. Secondly, WebGestalt was adopted for functional enrichment analysis of genes in the interaction networks. Finally, DNA methylation was analyzed to explain the differential expression. A total of 12 genes were identified as DEGs by comparing chip data from ALI + sepsis samples and those from sepsis alone samples, among which occludin (OCLN) and major histocompatibility complex, class II, DQ beta 1 (HLA-DQB1) had 21 and 6 interactors, respectively. Functional enrichment analysis revealed several significantly over-represented terms: cellular component organization, macromolecular organization and biosynthesis, and response to stimulus. In addition, methylation was found in the promoters of OCLN and HLA-DQB1. We screened DEGs in septic ALI samples, and several interesting genes were obtained, especially OCLN and HLA-DQB1. They may be developed into marker genes for diagnosis or treatment of ALI.