title: Prediction of feature genes in trauma patients with the TNF rs1800629 A allele using support vector machine.
abstract: BACKGROUND
  Tumor necrosis factor (TNF)-α variant is closely linked to sepsis syndrome and mortality after severe trauma. We aimed to identify feature genes associated with the TNF rs1800629 A allele in trauma patients and help to direct them toward alternative successful treatment.
  
  
  METHODS
  In this study, we used 58 sets of gene expression data from Gene Expression Omnibus to predict the feature genes associated with the TNF rs1800629 A allele in trauma patients. We applied support vector machine (SVM) classifier model for classification prediction combining with leave-one-out cross validation method. Functional annotation of feature genes was carried out to study the biological function using database for annotation, visualization, and integrated discovery (DAVID).
  
  
  RESULTS
  A total of 133 feature genes were screened out and was well differentiated in the training set (14 patients with variant, 15 with wild type). Moreover, SVM classifier peaked in predictive accuracy with 100% correct rate in training set and 86.2% in testing set. Interestingly, functional annotation showed that feature genes, such as HMOX1 (heme oxygenase (decycling) 1) and RPS7 (ribosomal protein S7) were mainly enriched in terms of cell proliferation and ribosome.
  
  
  CONCLUSIONS
  HMOX1 and RPS7 may be key feature genes associated with the TNF rs1800629 A allele and may play a crucial role in the inflammatory response in trauma patients. Moreover, the cell proliferation and ribosome pathway may contribute to the progression of severe trauma.
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China.
authors.forename: Guoting
authors.initials: G
authors.lastname: Chen
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Han
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China.
authors.forename: Guofeng
authors.initials: G
authors.lastname: Li
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China.
authors.forename: Guang
authors.initials: G
authors.lastname: Li
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China.
authors.forename: Yangzhou
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wu
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China.
authors.forename: Yanxi
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China.
authors.forename: Guixin
authors.initials: G
authors.lastname: Sun
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China.
authors.forename: Zengchun
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Emergency Surgery, East Hospital, Tongji University School of Medicine, No. 150, Jimo Road, Shanghai 200120, China. Electronic address: qinchuan_li@163.com.
authors.forename: Qinchuan
authors.initials: Q
authors.lastname: Li
mesh_terms: D000483:Alleles; D020869:Gene Expression Profiling / Q000379:methods*; D051547:Heme Oxygenase-1 / Q000235:genetics; D006801:Humans; D012269:Ribosomal Proteins / Q000235:genetics; D060388:Support Vector Machine; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics*; D014947:Wounds and Injuries / Q000235:genetics* / Q000378:metabolism
chemical_list: D012269:Ribosomal Proteins; C439524:TNF protein, human; D014409:Tumor Necrosis Factor-alpha; C496541:HMOX1 protein, human; D051547:Heme Oxygenase-1
keywords: Classification; Feature gene; Severe trauma; Support vector machine; Tumor necrosis factor-α rs1800629 A allele