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

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.

DNA Methylation and Asthma Acquisition during Adolescence and Post-Adolescence, an Epigenome-Wide Longitudinal Study

“…Although we did not identify statistically significant biological processes after adjusting for multiple testing, biological processes involved in host immune function related to IL-7 (i.e., the interleukin-7-mediated signalling pathway, responses to interleukin-7, and cellular responses to interleukin-7) were among the top processes determined based on statistical significance. These processes, along with the genes involved, may lead to potential cellular targets for prevention, precise diagnosis, and treatment [44][45][46]. The IRS1 gene was involved in the processes related to IL-7, and its mapped CpG (cg11620807) showed a consistent association between the two cohorts.…”