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. 2018 Sep;16(3):1613-1620.
doi: 10.3892/etm.2018.6366. Epub 2018 Jun 28.

Microarray data analysis to identify differentially expressed genes and biological pathways associated with asthma

Shanshan Qi  1 , Guanghui Liu  2 , Xiang Dong  2 , Nan Huang  2 , Wenjing Li  2 , Hao Chen  2
Affiliations

Microarray data analysis to identify differentially expressed genes and biological pathways associated with asthma

Shanshan Qi et al. Exp Ther Med. 2018 Sep.

Abstract

The present study aimed to identify differentially expressed genes (DEGs) and biological processes (BPs) associated with asthma. DEGs between allergic asthma and healthy controls were screened from GSE15823. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction network was constructed, followed by module mining and functional analysis. Additionally, GSE41649 was downloaded to validate the reliability of the results. In GSE41649, DEGs were identified and compared with key DEGs identified in GSE15823. A total of 43 upregulated and 275 downregulated DEGs were obtained from GSE15823. Upregulated DEGs, such as nitric oxide synthase 2 (NOS2), were enriched in BPs related to oxidation reduction. Downregulated DEGs, such as chemokine (C-C motif) ligand 19 (CCL21) and Cys-X-Cys ligand (CXCL9), were enriched in immune response-related BPs. Protein tyrosine phosphatase receptor type C (PTPRC), CCL21, and CXCL9 were identified as hub genes. The DEGs in module 1 were significantly involved in the chemokine signaling pathway (P<0.05). The expression of the key genes obtained in GSE15823 demonstrated the same variation directions in the two datasets. The immune response, oxidants and nitric oxide metabolic pathways may have important roles in the progression of asthma. DEGs of PTPRC, CCL21, CXCL9 and NOS2 may be the potential targets for asthma diagnosis and treatment.

Keywords: asthma; biological process; differentially expressed genes; protein-protein interaction network.

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Figures

Figure 1.
Figure 1.
Box plots of the normalization of expression data. Data (A) prior to and (B) following normalization. Log intensity, gene expression values.
Figure 2.
Figure 2.
Protein-protein interaction network of DEGs. Red node represents upregulated DEGs; green node represents downregulated DEGs; the different shade of color represents the significance of the difference, with deeper color indicating a more significant difference. DEGs, differentially expressed genes.
Figure 3.
Figure 3.
Modules in the protein-protein interaction network. There are (A) 9 nodes in module 1, (B) 6 nodes in module 2 and (C) 6 nodes in module 3.
See this image and copyright information in PMC

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