Table 5.

Processes associated with the pairwise test stratifications.

#	Test Stratification	Subgroup (n)	Process	p
1	PIR Not resistant/resistant	BDX008– (57)	Wound healing	0.048
		ICB Resistant (76)	Innate immune response	0.012
			Wound healing	0.013
		VeriStrat Good (78)	Innate immune response	0.011
			Wound healing	0.014
2	ICB sensitive/resistant	BDX008+ (43)	Complement	0.026 *
			Type 1 immune response	0.049 *
		PIR Not Resistant (70)	Complement	<0.001
			Acute inflammatory response	<0.001
			Acute phase reaction	0.001
			Immune tolerance/suppression	0.007
			IFN γ signaling/response	0.011
3	BDX008 +/−	ICB Resistant (76)	Acute phase reaction	<0.001
			Innate immune response	0.031
			Acute inflammatory response	0.031
			Type 17 immune response	0.032
			IFN γ signaling/response	0.049
		PIR Not Resistant (70)	Acute phase reaction	<0.001
			IFN γ signaling/response	0.001
			Acute inflammatory response	0.003
			Immune tolerance/suppression	0.013
			Type 17 immune response	0.013
			Complement	0.020
4	VeriStrat (VSG/VSP)	PIR Not Resistant (70)	Immune tolerance/suppression	<0.001 *
			Acute phase reaction	0.001 *
			Type 17 immune response	0.007 *
			Complement	0.008 *

* p-values calculated using the protein set enrichment analysis (PSEA) method with the standard enrichment score (ES) definition in Subramanian et al. [5] rather than the ES defined averaged over 25 splits of the dataset defined in Roder et al. [59].