title: A 15-gene signature for prediction of colon cancer recurrence and prognosis based on SVM.
abstract: OBJECTIVE
  To screen the gene signature for distinguishing patients with high risks from those with low-risks for colon cancer recurrence and predicting their prognosis.
  
  
  METHODS
  Five microarray datasets of colon cancer samples were collected from Gene Expression Omnibus database and one was obtained from The Cancer Genome Atlas (TCGA). After preprocessing, data in GSE17537 were analyzed using the Linear Models for Microarray data (LIMMA) method to identify the differentially expressed genes (DEGs). The DEGs further underwent PPI network-based neighborhood scoring and support vector machine (SVM) analyses to screen the feature genes associated with recurrence and prognosis, which were then validated by four datasets GSE38832, GSE17538, GSE28814 and TCGA using SVM and Cox regression analyses.
  
  
  RESULTS
  A total of 1207 genes were identified as DEGs between recurrence and no-recurrence samples, including 726 downregulated and 481 upregulated genes. Using SVM analysis and five gene expression profile data confirmation, a 15-gene signature (HES5, ZNF417, GLRA2, OR8D2, HOXA7, FABP6, MUSK, HTR6, GRIP2, KLRK1, VEGFA, AKAP12, RHEB, NCRNA00152 and PMEPA1) were identified as a predictor of recurrence risk and prognosis for colon cancer patients.
  
  
  CONCLUSIONS
  Our identified 15-gene signature may be useful to classify colon cancer patients with different prognosis and some genes in this signature may represent new therapeutic targets.
authors.affiliation: Department of Oncology, People's Hospital of Pudong District, Shanghai University of Medicine & Health Sciences, ShangHai 201299, China.
authors.forename: Guangru
authors.initials: G
authors.lastname: Xu
authors.affiliation: Department of Oncology, People's Hospital of Pudong District, Shanghai University of Medicine & Health Sciences, ShangHai 201299, China.
authors.forename: Minghui
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Department of Oncology, People's Hospital of Pudong District, Shanghai University of Medicine & Health Sciences, ShangHai 201299, China.
authors.forename: Hongxing
authors.initials: H
authors.lastname: Zhu
authors.affiliation: Department of Oncology, People's Hospital of Pudong District, Shanghai University of Medicine & Health Sciences, ShangHai 201299, China. Electronic address: wuwuuwgdg@aliyun.com.
authors.forename: Jinhua
authors.initials: J
authors.lastname: Xu
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics* / Q000378:metabolism; D003110:Colonic Neoplasms / Q000175:diagnosis* / Q000235:genetics / Q000401:mortality / Q000473:pathology; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D009363:Neoplasm Proteins / Q000235:genetics* / Q000378:metabolism; D009364:Neoplasm Recurrence, Local / Q000175:diagnosis* / Q000235:genetics / Q000401:mortality / Q000473:pathology; D011379:Prognosis; D025941:Protein Interaction Mapping; D012372:ROC Curve; D060388:Support Vector Machine; D016019:Survival Analysis; D059467:Transcriptome
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins
keywords: Colon cancer; Prognosis; Recurrence; Support vector machine