Figure 2 . Altered transcripts involved in immune processes
identified by GO, across all tested groups (subjects with allergy,
subjects with allergy without asthma and AD, and subjects with allergic
asthma and AD) in comparison to control group. Individual cells show
log2 fold changes (left panel), and p-values (right panel).
Functional analysis
Using GSEA, we observed 60 altered entities (including biological
processes, cell processes, biomarkers, diseases, metabolic pathways,
pathological processes, and signal processing) in participants with
allergy, 186 entities in participants with allergic asthma and AD, and
115 entities in participants with allergy without asthma and AD
(Supplementary Material 3). Enriched entities for each of these
categories are catalogued into five main clusters: immunoglobulins;
interleukins; CD molecules; mast cells; chemokines; and receptor
tyrosine kinases (Table 3). Other significant pathways related mainly to
tumor necrosis factors (TNFs) and TNF receptors (TNFRs), toll-like
receptors (TLRs), or chemokines are presented in Supplementary Material
3.
Further, applying SNEA on cell processes, we identified 484 altered cell
processes in participants with allergy, 288 cell processes in
participants with allergic asthma and AD, and 514 cell processes in
participants with allergy without asthma and AD (Supplementary Material
4). Chosen cCell processes altered in at least two of the three tested
groups with corresponding p-values are depicted in Table 4. These
processes are clustered into five main domains, namely APCs; Th cells;
Th2 cells, B cell activation and IgE production; mast cells and
eosinophils; and T cytotoxic cells. Among the processes, APC survival,
eosinophil chemotaxis, and CD8+ T-cell lymphocyte anergy have been found
significantly altered in all three tested groups (Figure 3).
Finally, applying SNEA on clinical parameters (i.e., identification of
parameters that would be impacted), we observed 297 clinical parameters
in subjects with allergy, 136 clinical parameters in participants with
allergic asthma and AD, and 304 clinical parameters in participants with
allergy without asthma and AD. The altered clinical parameters are
dominantly associated with pulmonary and skin problems, but also include
networks related to mast cells, Th cells, eosinophils, or parasite
infection (Supplementary Material 5).
Table 3 . Deregulated pathways identified in participants with
allergy, subjects with allergy without asthma and AD, and subjects with
allergic asthma and AD in comparison to control group using GSEA.