title: Identification of crucial genes in ventilator associated pneumonia through protein-protein interaction network.
abstract: OBJECTIVE
  Ventilator-associated pneumonia (VAP) is still an important cause of morbidity and mortality in patients receiving mechanical ventilation. This research aimed to investigate the genes related to VAP and potential diagnosis targets.
  
  
  METHODS
  Gene expression profiles data of GSE30385 were downloaded from Gene Expression Omnibus, which included 10 samples of patients with VAP and 10 samples of patients without VAP. The differentially expressed genes (DEGs) between two types of patients were identified by limma package and the functions and pathways of DEGs were predicted by Gene Ontology and KEGG pathway enrichment analyses. Next, the protein-protein interaction (PPI) pairs of all genes in the samples were obtained from STRING database. Then we searched genes related to VAP in NCBI, and constructed a PPI network of these genes. Subsequently, the overlapped genes between genes in the PPI network and DEGs were searched, followed by expression patterns analysis. Furthermore, genes in PPI network were subjected to function and pathway enrichment analysis, and transcription factors were screened on the basis of TRANSFAC database.
  
  
  RESULTS
  A total of 69 DEGs were screened between two types of patient samples, and 7 genes related to VAP were obtained. The overlapped genes (e.g. LTF, MAPK14) were enriched in MAPK cascade and immune system-related processes. In addition, MAPK14 was enriched in MAPK signaling pathway.
  
  
  CONCLUSIONS
  The VAP-related genes (MAPK14 and LTF) might be the crucial genes in the pathogenesis of VAP, and be served as potential diagnostic targets.
authors.affiliation: 1Department of Infection Management, Jinling Hospital, Medical School of Nanjing University , Nanjing , China.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Xu
authors.forename: Bo
authors.initials: B
authors.lastname: Yuan
authors.forename: Zhaorong
authors.initials: Z
authors.lastname: Shi
authors.forename: Quan
authors.initials: Q
authors.lastname: Liang
authors.forename: Huimin
authors.initials: H
authors.lastname: Huang
authors.forename: Xiangyi
authors.initials: X
authors.lastname: Yin
authors.forename: Xiaoyue
authors.initials: X
authors.lastname: Sheng
authors.forename: Niuyan
authors.initials: N
authors.lastname: Nie
authors.forename: Hongmei
authors.initials: H
authors.lastname: Fang
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D053717:Pneumonia, Ventilator-Associated / Q000235:genetics*; D060066:Protein Interaction Maps / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
keywords: diagnosis; differentially expressed genes; protein–protein interaction network; ventilator-associated pneumonia