Table 5. Alignments of Sample Groups with clinical features within cancer types.

For each cancer type, the representative values (features) of selected subtypes of each Sample Group are reported.

cancer type	sample group	subtype	subtype	subtype	subtype	subtype	subtype	subtype
ACC		C1A/C1B	mRNA	methylation	SCNA	COC
	1	C1B	steroid-low	CIMP-low	chromosomal	COC1
	2	C1B		CIMP-med	chromosomal	COC1
	3	C1A	steroid-high	CIMP-med	chromosomal	COC2
	4	C1A	proliferation	CIMP-high	noisy	COC3
BLCA		mRNA
	1	2
	2	1
	3	1
	4	1
	5	2
	6	3
	7
BRCA		ER	PR	HER2	PAM50
	1	+	+	-	luminal A
	2	+	+	-	luminal A
	3	-	-	-	basal-like
	4	mixed	mixed	+	HER2-enriched
	5	+	+	-	luminal A,B
	6	+	+	-	luminal A,B
CESC		Dx	SCNA	icluster	paradigm
	1	adenocarcinoma	low	C3	C2
	2	adenocarcinoma	low	C3	C2
	3	adenocarcinoma	low	C3	C2
	4	squamous	high	C2	C1
	5	squamous	high	C2	C3
	6	squamous	high	C2	C4
	7	squamous	high	C2
	8	squamous	mixed	C2	C1
COAD		MSI	MLH1-silencing	mRNA	hypermutated	CIMP	CMS
	1	MSI-L	0	MSI/CIMP	mixed	CIMP.Neg	CMS4
	2	MSI-H	1	MSI/CIMP		1 CIMP.High	CMS1
	3						CMS3
	4	mixed	0	invasive		0 CIMP.Neg	CMS3
	5	MSS	0	invasive		0 CIMP.Neg	mixed
	6	MSS	0	CIN		0 CIMP.Neg	CMS2
	7	MSS	0	CIN		0 CIMP.Neg	CMS2
	8	MSS	0	mixed		0 CIMP.Neg	CMS4
	9	MSS	0	mixed		0 CIMP.Neg	mixed
ESCA		histology	ESCC subtype	methylation	SCNA	mRNA	mir
	1	ESCC	C1,C2	C2	C3	C2,C3	C3
	2	ESCC	C1	C2	C3	C3	C2
	3	ESCC	C1	C2	C3	C3	C3
	4	EAC		C1	C1,C2	C1	C1
	5	EAC		C1	C1,C2	C1	C1
	6	EAC		C1	C1,C2	C1	C1
	7	EAC		C1	C1,C2	C1	C1
GBM		CIMP	mRNA
	1
	2	G-CIMP	G-CIMP
	3	G-CIMP	G-CIMP
	4	non-G-CIMP	proneural
	5	non-G-CIMP	proneural
	6	non-G-CIMP	proneural
	7	G-CIMP	G-CIMP
	8	non-G-CIMP	proneural,neural
	9	non-G-CIMP	mixed
	10	non-G-CIMP	classical
	11	non-G-CIMP	classical
	12	non-G-CIMP	classical
	13	non-G-CIMP	mesenchymal
	14	non-G-CIMP	mesenchymal
	15	non-G-CIMP	mesenchymal
HNSC		mRNA	paradigm
	1	basal	C4
	2	basal,mesenchy.	C4
	3	mesenchymal	C1
	4	basal	C4
	5
	6	mesenchy.,atypical	C1, C5
	7	mixed	mixed
	8	classical	C2, C5
	9	atypical,mesenchy.	C5
cancer type	sample group	subtype	subtype	subtype	subtype	subtype	subtype	subtype
KIRC		mRNA
	1	C1
	2
	3	C1
	4	C1
	5	C4, C1
	6	C2
	7	C2, C4
	8	C3
KIRP		mRNA	RPPA	COC
	1	C2	C3	C2
	2	C2	C3	C2
	3	C2	mixed	C2
	4	C2	mixed	C2
	5	C1	C2	C1
	6	C1	C2	C1
	7	C1	mixed	C1
	8	mixed	C3	C1
LAML		mRNA
	1	mixed
	2	mixed
	3	C5
	4	C5
	5	mixed
	6	C4
	7	C6, C3
	8	C6
	9	C3
	10	mixed
LGG		IDH	mRNA	methylation	mir	SCNA	oncosign	COCcluster
	1	IDHwt	R2	M4	mixed	C2	P3	coc2
	2	IDHwt		M4	mi2	C2		coc2
	3	IDHmut-noncodel	R1	M5	mi2	C1	P1	coc1
	4	IDHmut-noncodel	R1	M3, M5	mi2	C1	P2	coc1
	5	IDHmut-noncodel	R1	M3, M5	mi2	C1	P2	coc1
	6	IDHmut-codel	R3	M2, M3	mi2	C3	P2	coc3
	7	IDHmut-both	R4	M3, M5	mi2	C3, C1	P4	coc3, coc1
	8	mixed	R4	mixed	mi1	C3, C1	P4	coc3, coc1
LIHC		mRNA	paradigm	icluster
	1	mixed	mixed	mixed
	2	mixed	C1, C4	mixed
	3	C3, C4	mixed	C2, C3
	4	C5	C1, C4	C2, C3
	5	C4	C2	C3
	6	mixed	C4, C2	C1, C2
	7	C1	C3	C1
	8	C1	C2, C3	C1, C3
	9	C1	C2, C3	C1, C3
LUAD		icluster
	1	C5, C6
	2	C5
	3	C1, C4
	4	C3
	5	C3, C6
	6	C3, C6
	7	C2
LUSC		subtype
	1
	2	secretory
	3	basal, secretory
	4	basal, primitive
	5	classical
	6	classical
PAAD		mRNA2	mRNA3	methylation1
	1
	2	C2	C3	lowpurity
	3	mixed	C2, C3	lowpurity
	4	C2	C3	lowpurity
	5	C1	C1, C3	C2
	6	mixed	C1	C1, C2
	7	C1, C2	C3	C2
	8	C1	C3	C1
PCPG		mRNA	methylation
	1	cortical admixture	low-methylated
	2	pseudohypoxia	intermediate
	3	pseudohypoxia	intermediate
	4	pseudohypoxia	hyper-methylated
	5	mixed	mixed
	6	kinase signaling	low-methylated
	7	kinase signaling	low-methylated
cancer type	sample group	subtype	subtype	subtype	subtype	subtype	subtype	subtype
PRAD		icluster	mRNA
	1	mixed	mixed
	2	C3	C3
	3	C3	C3
	4	C3	C3
	5	C1	C1
	6
	7	C1, C2	C1, C2
READ		CMS
	1	CMS4
	2	mixed
	3	CMS2
	4	CMS2, CMS3
	5	mixed
SARC		histology	methylation	mRNA	mir	RPPA	paradigm	icluster
	1	ULMS, STLMS	M3, M5	C3	C1	C1	C3	C1
	2	STLMS, ULMS	M3	C3	C1	C1	C3	C1
	3	ULMS, SS	M5, M2	C3, C2	C1, C2	mixed	C2	C1, C2
	4	mixed	M1	C2, C1	C2	C5, C4	C2, C4	C4, C2, C3
	5	DDLPS	M1	C1	C2	C3, C4, C5	C4	C3
	6	UPS, MFS	M4	C1	C2	C2	C5	C5
	7	UPS, MFS	M1, M4	C1	C2	C2, C3	C1	C5, C3
THCA		histology	mRNA	mir	methylation	RPPA-number
	1	follicular	C1	C4	follicular,CpG	C4, C1
	2	classical	C1, C5	C5, C4	class. 2,follicular	mixed
	3	follicular	C1, C5	C4	class. 2,follicular	C1
	4	classical	C5, C2	mixed	class. 2,follicular	mixed
	5	classical, tall	C4	C2	classical 2	C4
	6	classical	C3	C3	classical 2	C3, C4
	7	classical	C5	mixed	classical 2	mixed
	8	classical	C4	C2	classical 1,2	C2
UCEC		icluster	mRNA	histology
	1	notassigned(NA)	mixex	endometrioid
	2	NA,CN low	C2	endometrioid
	3	mixed	C1	serous
	4	mixed	C2, C3	endometrioid
	5	mixed	C3	endometrioid
	6	CN high	C1	serous
	7	NA	C1, C2	endometrioid
	8	MSI,NA	C2	endometrioid
	9	POLE,NA	C1	endometrioid
UCS		methylation
	1	mixed
	2	C1, C3
	3	C1
	4	C2
UVM		SCNA	methylation	lncRNA	mRNA	paradigm
	1	C1	C1	C1, C2	C1, C2	C1, C2
	2	C2	C2	C2, C1	C2, C1	C2, C1
	3	C3	C4	C3	C3	C3
	4	C4	C4	C4	C4	C4