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Table 3 SKAT p-values for top 5 functional pathway- mutation associations, by mutation type

From: Gastrointestinal stromal tumors: a case-only analysis of single nucleotide polymorphisms and somatic mutations

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