Table 3 SKAT p-values for top 5 functional pathway- mutation associations, by mutation type
KIT exon 11 codon 557–558 deletion | Pathway | Negative regulation of cell proliferation | Intracellular signal transduction | Protein tyrosine kinase phosphatase activity | Humoral immune response | Cytokine mediated signaling pathway |
p-value | 0.09 | 0.10 | 0.11 | 0.13 | 0.13 | |
KIT exon 11 other (non-codon 557–8) deletion | Pathway | Response to stress | Negative regulation of apoptosis | Protein tyrosine kinase activity | Response to Hypoxia | T cell receptor signaling pathway |
p-value | 0.02 | 0.03 | 0.04 | 0.06 | 0.08 | |
KIT exon 11 insertion | Pathway | Positive regulation of immune response | Cytochrome P450 | Humoral immune response | Signal transduction | Signal transducer activity |
p-value | 0.10 | 0.11 | 0.17 | 0.17 | 0.20 | |
KIT exon 11 point mutation | Pathway | T cell receptor signaling pathway | Immune response | Positive regulation of cell proliferation | Intracellular signal transduction | Phase I/II metabolizing |
p-value | 0.06 | 0.18 | 0.19 | 0.20 | 0.20 | |
Other KIT mutation | Pathway | AHR/dioxin response | G-protein coupled receptor signaling pathway | Protein phosphorylation | Negative regulation of immune response | Cytochrome P450 |
p-value | 0.01 | 0.06 | 0.08 | 0.08 | 0.09 | |
PDGFRA mutation | Pathway | Defense Response | Negative regulation of immune response | Protein phosphorylation | Positive regulation of immune response | AHR/dioxin response |
p-value | 0.005 | 0.01 | 0.02 | 0.03 | 0.03 | |
Wild type | Pathway | Humoral immune response | Defense response to bacteria | Transmembrane receptor protein tyrosine phosphatase activity | Cytokine receptor activity | Response to oxidative stress |
p-value | 0.02 | 0.11 | 0.13 | 0.14 | 0.14 |