title: Revealing the underlying mechanism of ischemia reperfusion injury using bioinformatics approach.
abstract: OBJECTIVE
  To reveal the potential pathogenesis of ischemia/reperfusion (I/R) injury.
  
  
  METHODS
  GSE9943 were downloaded from Genome Expression Omnibus database, including I/R and control samples for both Brown Norway (BN) and Sprague Dawley (SD) rats (3 rats/each group). Then differentially expressed genes (DEGs) were identified by limma package. miRNA-target gene network pairs were predicted using WebGestalt, and protein-protein interactions (PPI) were identified based on STRING database, followed by the networks construction using Cytoscape. Next, ClusterONE was used for modules screening. Furthermore, functional analyses were performed to common DEGs and genes.
  
  
  RESULTS
  Totally, 23 common DEGs of BR and SD rats were screened, enriched in functions, such as regulation of cellular protein metabolic process, response to wounding, proteinaceous extracellular matrix, and Enzyme inhibitor activity. MIR-29A, MIR-29B and MIR-29C were discovered both in up- and down-regulated miRNA-target gene networks. Genes in the PPI network were significantly disturbed in p53 signaling, complement and coagulation cascades pathway. Four modules were found significantly disturbed cytochrome P450, Serine/threonine protein kinase, calcium binding and Transient receptor potential channel protein domains.
  
  
  CONCLUSIONS
  During I/R injury, many genes mutated, interrupting several biological functions, pathways and protein domains. MIR-29C and TRPC6 were suggested to be potential novel targets for this disease. © 2014 S. Karger AG, Basel.
authors.affiliation: Department of kidney, Southwest hospital of Third Military Medical University, Chongqing City, 400038, China.
authors.forename: Bingbing
authors.initials: B
authors.lastname: Shen
authors.forename: Shan
authors.initials: S
authors.lastname: Zhou
authors.forename: Yue
authors.initials: Y
authors.lastname: He
authors.forename: Hongwen
authors.initials: H
authors.lastname: Zhao
authors.forename: Mei
authors.initials: M
authors.lastname: Mei
authors.forename: Xiongfei
authors.initials: X
authors.lastname: Wu
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D015870:Gene Expression / Q000235:genetics / Q000502:physiology; D053263:Gene Regulatory Networks / Q000235:genetics / Q000502:physiology; D035683:MicroRNAs / Q000096:biosynthesis / Q000235:genetics; D051381:Rats; D011914:Rats, Inbred BN; D017207:Rats, Sprague-Dawley; D015427:Reperfusion Injury / Q000235:genetics / Q000473:pathology*; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology; D050052:TRPC Cation Channels / Q000096:biosynthesis / Q000235:genetics
chemical_list: C526366:MIRN29 microRNA, rat; D035683:MicroRNAs; D050052:TRPC Cation Channels; C492145:Trpc6 protein, rat