title: Comprehensive analysis of gene-expression profile in chronic obstructive pulmonary disease.
abstract: OBJECTIVE
  To investigate the gene-expression profile of chronic obstructive pulmonary disease (COPD) patients and explore the possible therapeutic targets.
  
  
  METHODS
  The microarray raw dataset GSE29133, including three COPD samples and three normal samples, was obtained from Gene Expression Omnibus. After data preprocessing with the Affy package, Student's t-test was employed to identify the differentially expressed genes (DEGs). The up- and downregulated DEGs were then pooled for gene-ontology and pathway-enrichment analyses using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The upstream regulatory elements of these DEGs were also explored by using Whole-Genome rVISTA. Furthermore, we constructed a protein-protein interaction (PPI) network for DEGs. The surfactant protein D (SP-D) serum level and HLA-A gene frequency in COPD patients and healthy controls were also measured by enzyme-linked immunosorbent assay (ELISA) and real-time polymerase chain reaction, respectively.
  
  
  RESULTS
  A total of 39 up- and 15 downregulated DEGs were screened. Most of the upregulated genes were involved in the immune response process, while the downregulated genes were involved in the steroid metabolic process. Moreover, we also found that HLA-A has the highest degree in the PPI network. The SP-D serum level and HLA-A gene frequency in COPD patients were significantly higher than those in healthy controls (13.62±2.09 ng/mL vs 10.28±2.86 ng/mL; 62.5% vs 12.5%; P<0.05).
  
  
  CONCLUSIONS
  Our results may help further the understanding of the mechanisms of COPD. The identified DEGs, especially HLA-A, may serve as diagnosis markers for COPD.
authors.affiliation: Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, People's Republic of China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wei
authors.affiliation: Medical College of Soochow University, Suzhou, People's Republic of China.
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.affiliation: Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, People's Republic of China.
authors.forename: Yechang
authors.initials: Y
authors.lastname: Qian
authors.affiliation: Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, People's Republic of China.
authors.forename: Guoyi
authors.initials: G
authors.lastname: Huang
authors.affiliation: Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Ma
authors.affiliation: Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, People's Republic of China.
authors.forename: Fangying
authors.initials: F
authors.lastname: Liu
authors.affiliation: Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, People's Republic of China.
authors.forename: Yanhua
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, People's Republic of China.
authors.forename: Zhongfu
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, People's Republic of China.
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.affiliation: Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, People's Republic of China.
authors.forename: Shanfang
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Department of Respiratory Disease, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, People's Republic of China.
authors.forename: Yafang
authors.initials: Y
authors.lastname: Chen
mesh_terms: D000368:Aged; D016022:Case-Control Studies; D019295:Computational Biology; D030541:Databases, Genetic; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D005787:Gene Frequency; D053263:Gene Regulatory Networks; D020022:Genetic Predisposition to Disease; D015234:HLA-A Antigens / Q000235:genetics; D006801:Humans; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D029424:Pulmonary Disease, Chronic Obstructive / Q000097:blood / Q000235:genetics* / Q000276:immunology; D037663:Pulmonary Surfactant-Associated Protein D / Q000097:blood; D015398:Signal Transduction
chemical_list: D015234:HLA-A Antigens; D037663:Pulmonary Surfactant-Associated Protein D
keywords: chronic obstructive pulmonary disease; differentially expressed genes; gene-ontology analysis; protein–protein interaction