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.