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.