title: A Gibbs sampling method to determine biomarkers for asthma.
abstract: OBJECTIVE
  To identify potential biomarkers and to uncover the mechanisms underlying asthma based on Gibbs sampling.
  
  
  METHODS
  The molecular functions (MFs) with genes greater than 5 were determined using AnnotationMFGO of BAGS package, and the obtained MFs were then transformed to Markov chain (MC). Gibbs sampling was conducted to obtain a new MC. Meanwhile, the average probabilities of MFs were computed via MC Monte Carlo (MCMC) algorithm, followed by identification of differentially expressed MFs based on the probabilities of MF more than 0.6. Moreover, the differentially expressed genes (DEGs) and their correlated genes were screened and merged, called as co-expressed genes. Pathways enrichment analysis was implemented for the co-expressed genes.
  
  
  RESULTS
  Based on the gene set more than 5, overall 396 MFs were determined. After Gibbs sampling, 5 differentially expressed MF were acquired according to alfa.pi>0.6. Moreover, the genes in these 5 differentially expressed MF were merged, and 110 DEGs were identified. Subsequently, 338 co-expressed genes were gained. Based on the P value<0.01, the co-expressed genes were significantly enriched in 6 pathways. Among these, ubiquitin mediated proteolysis contained the maximum numbers of 35 co-expressed genes, and cell cycle were enriched by the second largest number of 11 co-expressed genes, respectively.
  
  
  CONCLUSIONS
  The identified pathways such as ubiquitin mediated proteolysis and cell cycle might play important roles in the development of asthma and may be useful for developing the credible therapeutic approaches for diagnosis and treatment of asthma in future.
authors.affiliation: Department of Emergency, Xiamen Hospital of Traditional Chinese Medicine, Xiamen 361009, Fujian, PR China.
authors.forename: Zhi-Jian
authors.initials: ZJ
authors.lastname: Huang
authors.affiliation: Department of Medicine, Shandong Medical College, Jinan, 250002, Shandong, PR China.
authors.forename: Qin-Hai
authors.initials: QH
authors.lastname: Shen
authors.affiliation: Department of Spine (Second), Traditional Chinese Medical Hospital of Xinjiang Uygur Autonomous Region, Urumqi, 830000, Xinjiang, PR China.
authors.forename: Yan-Sheng
authors.initials: YS
authors.lastname: Wu
authors.affiliation: Nuclear Medicine Department, Qilu Hospital of Shandong University, NO. 107 Wenhua West Road, Jinan, 250012, Shandong PR China. Electronic address: huangyaliHE@163.com.
authors.forename: Ya-Li
authors.initials: YL
authors.lastname: Huang
mesh_terms: D001249:Asthma / Q000235:genetics*; D002453:Cell Cycle / Q000235:genetics; D020869:Gene Expression Profiling; D005819:Genetic Markers; D053858:Metabolic Networks and Pathways / Q000235:genetics; D009010:Monte Carlo Method; D059748:Proteolysis
chemical_list: D005819:Genetic Markers
keywords: Asthma; Gibbs sampling; Markov chain; Molecular function; Pathway enrichment analysis