title: Gene expression profiles analysis identifies key genes for acute lung injury in patients with sepsis.
abstract: BACKGROUND
  To identify critical genes and biological pathways in acute lung injury (ALI), a comparative analysis of gene expression profiles of patients with ALI + sepsis compared with patients with sepsis alone were performed with bioinformatic tools.
  
  
  METHODS
  GSE10474 was downloaded from Gene Expression Omnibus, including a collective of 13 whole blood samples with ALI + sepsis and 21 whole blood samples with sepsis alone. After pre-treatment with robust multichip averaging (RMA) method, differential analysis was conducted using simpleaffy package based upon t-test and fold change. Hierarchical clustering was also performed using function hclust from package stats. Beisides, functional enrichment analysis was conducted using iGepros. Moreover, the gene regulatory network was constructed with information from Kyoto Encyclopedia of Genes and Genomes (KEGG) and then visualized by Cytoscape.
  
  
  RESULTS
  A total of 128 differentially expressed genes (DEGs) were identified, including 47 up- and 81 down-regulated genes. The significantly enriched functions included negative regulation of cell proliferation, regulation of response to stimulus and cellular component morphogenesis. A total of 27 DEGs were significantly enriched in 16 KEGG pathways, such as protein digestion and absorption, fatty acid metabolism, amoebiasis, etc. Furthermore, the regulatory network of these 27 DEGs was constructed, which involved several key genes, including protein tyrosine kinase 2 (PTK2), v-src avian sarcoma (SRC) and Caveolin 2 (CAV2).
  
  
  CONCLUSIONS
  PTK2, SRC and CAV2 may be potential markers for diagnosis and treatment of ALI.
  The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5865162912987143.
authors.affiliation: Department of Thoracic surgery, Putuo Hospital,Shanghai University of Traditional Chinese Medicine, No. 164 Lan Xi Road, Shanghai, 200062, China. 13321990498@189.cn.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Guo
authors.affiliation: Department of Thoracic surgery, Putuo Hospital,Shanghai University of Traditional Chinese Medicine, No. 164 Lan Xi Road, Shanghai, 200062, China. zhaochch@sina.com.
authors.forename: Chuncheng
authors.initials: C
authors.lastname: Zhao
authors.affiliation: Department of Thoracic surgery, Putuo Hospital,Shanghai University of Traditional Chinese Medicine, No. 164 Lan Xi Road, Shanghai, 200062, China. pzxxwk@163.com.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wang