. 2013 Oct 26;3:12. doi: 10.1186/2045-3329-3-12

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
KIT exon 11 codon 557–558 deletion	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
KIT exon 11 other (non-codon 557–8) deletion	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
KIT exon 11 insertion	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
KIT exon 11 point mutation	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
Other KIT mutation	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
PDGFRA mutation	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
Wild type	p-value	0.02	0.11	0.13	0.14	0.14