Table 4. Associations of APC mutation and MYC copy number gains with estimates of immune cell levels.

Variant	Signature	Breast	Breast (LumB)	Colon	Head and Neck	Kidney Papillary Cell	Stomach
APC mutant	MFm2			-0.75 (5)
APC mutant	Mono			-0.77 (5.2)
APC mutant	NK					5.09 (9.4)
APC mutant	NKCD8					4.81 (7.2)
MYC gain	Bcell				-0.27 (1.9)		-0.22 (1.9)
MYC gain	MFm2		0.2 (2.2)
MYC gain	Mono		0.19 (1.7)
MYC gain	TregCD8	0.1 (1.5)

Values are reported as Effect Size with associated P values in parenthesis (-log10 P). The units of effect size are change in signature score (units of standard deviation) for mutant versus wild type in the case of mutations. For copy number changes the effect size is in S.D. units per change in GISTIC2 score.