Screening and functional pathway analysis of genes associated with pediatric allergic asthma using a DNA microarray

Abstract

The present study aimed to identify differentially expressed genes (DEGs) associated with pediatric allergic asthma, and to analyze the functional pathways of the selected target genes, in order to explore the pathogenesis of the disease. The GSE18965 gene expression profile was downloaded from the Gene Expression Omnibus database and was preprocessed. This gene expression profile consisted of seven normal samples and nine samples from patients with pediatric allergic asthma. The DEGs between the normal and pediatric allergic asthma samples were screened using limma package in R, and the cut‑off value was set at false discovery rate <0.05 and log fold change >1. Following hierarchical clustering of the DEGs based on the expression profiles, the up‑ and downregulated genes underwent a functional enrichment analysis by topological approach (P<0.05), using the Database for Annotation, Visualization and Integrated Discovery. A total of 127 DEGs were identified between the normal and pediatric allergic asthma samples. The up‑ and downregulated genes were significantly enriched in the actin filament‑based process and the monosaccharide metabolic process, respectively. Seven downregulated DEGs (M6PR, TPP1, GLB1, NEU1, ACP2, LAMP1 and HGSNAT) were identified in the lysosomal pathway, with P=6.4x10(‑9). These results suggested that variation in lysosomal function, triggered by the seven downregulated genes, may lead to aberrant functioning of the T lymphocytes, resulting in asthma. Further research regarding the treatment of pediatric allergic asthma through targeting lysosomal function is required.

Figure 1

Clustering of differentially expressed genes using the hierarchical clustering method. Colors changing from blue to orange represent the differences in gene expression between the disease group and the healthy group, from downregulation to upregulation. Samples underlined red represent samples from the patients with pediatric allergic asthma. Samples displayed are all the ones in the dataset GSE18965. Each row represents a single gene; each column represents a tissue sample. AA, asthma atopic; HN, healthy non-atopic.

Figure 2

Functional enrichment of the up-and downregulated DEGs. Height of the bar represents the number of DEG enriched in the function nodes. The red line displays the negative logarithm of the P-values. White bars represent the functional enrichment of the downregulated DEGs, and black bars represent the upregulated DEGs. DEG, differentially expressed gene.

Figure 3

The lysosomal pathway is closely associated with the downregulated DEGs. Genes in green boxes represent the selected down-regulated DEGs. DEG, differentially expressed gene.