Pathway and network analysis
Ingenuity pathway analysis (IPA, Redwood City, CA, USA) was used to understand the functional characteristics of DEGs of AERD.16 IPA canonical pathway analysis was performed with DEGs to identify biological pathways that significantly affect mRNA expression in AERD. The gene symbols of probe, which significantly up-regulated or down-regulated in AERD (log (FC) ≥ |1| and P value < 0.05) compared to ATA were selected as significantly differentiated genes and used for IPA analysis. The significance of the association between the data set and the canonical pathways was measured as the number of molecules in each pathway that meets cutoff criteria (false discovery rate (FDR)-adjusted Pvalues < 0.05).
Network analysis was performed using asthma-related DEGs to understand and predict interactions among these genes. The biological functions that were significantly associated with the genes in the core networks were identified by functional analysis based on the Ingenuity’s knowledge base. As our study is focused on asthma population, asthma-related terms were selected and used in further analysis. We determined asthma-related terms such as refractory asthma, severe asthma, uncontrolled asthma, eosinophilia of lung, pulmonary eosinophilia, T helper 2 (Th2)-mediated asthma, and aspirin-induced asthma. The DEGs were mapped onto the networks to explore the dynamic changes during the asthma process.