Clinical Features	CN_CNMF		METHLYATION_CNMF		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL	
	nMutated (%)	nWild-Type	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q
CBWD1	14 (12%)	102	0.00011458	0.0289	0.077278	1	0.45655	1	0.2133	1	0.056096	1	0.19269	1
KRAS	14 (12%)	102	0.10745	1	0.41121	1	1	1	0.29937	1	0.27051	1	0.70557	1
PGM5	16 (14%)	100	6.8886e-06	0.00178	0.0034406	0.843	0.28058	1	0.15697	1	0.26155	1	0.16208	1
RPL22	9 (8%)	107	0.023415	1	NA	NA	0.41206	1	0.072949	1	0.28209	1	0.28014	1
TP53	52 (45%)	64	5.7151e-05	0.0146	0.020315	1	1	1	0.23575	1	0.0052595	1	3.6861e-05	0.00947
TRIM48	10 (9%)	106	0.013732	1	0.20624	1	1	1	1	1	0.10343	1	0.17309	1
XPOT	6 (5%)	110	0.013593	1	NA	NA	0.34487	1	1	1	0.3273	1	0.05395	1
PIK3CA	24 (21%)	92	0.00060395	0.15	1.5868e-06	0.000411	0.41206	1	0.83965	1	0.085715	1	0.00070402	0.174
ACVR2A	13 (11%)	103	0.0001451	0.0363	0.023751	1	0.69808	1	0.42391	1	0.024598	1	0.056258	1
RHOA	7 (6%)	109	0.14578	1	0.85092	1	0.48837	1	NA	NA	0.38296	1	0.68343	1
ARID1A	22 (19%)	94	7.735e-05	0.0196	0.014484	1	0.48761	1	0.27387	1	0.0056233	1	0.00046694	0.116
OR8H3	10 (9%)	106	0.61058	1	0.090685	1	0.10777	1	0.10096	1	0.87283	1	0.20522	1
EDNRB	12 (10%)	104	0.32965	1	0.54506	1	0.41206	1	0.83965	1	0.40533	1	0.16187	1
ZNF804B	18 (16%)	98	0.20228	1	0.056841	1	0.28058	1	0.88507	1	0.17749	1	0.20867	1
IRF2	8 (7%)	108	6.3777e-05	0.0162	0.049705	1	1	1	0.2785	1	0.19691	1	0.27844	1
IAPP	4 (3%)	112	0.38471	1	NA	NA	1	1	NA	NA	0.1311	1	0.56874	1
PCDH15	22 (19%)	94	0.76556	1	0.9159	1	0.72051	1	0.88507	1	0.71017	1	0.95158	1
SPRYD5	8 (7%)	108	0.16633	1	0.049976	1	1	1	0.64265	1	0.3069	1	0.80541	1
TUSC3	9 (8%)	107	0.23672	1	0.54697	1	0.48837	1	NA	NA	1	1	0.8145	1
FGF22	3 (3%)	113	0.035398	1	NA	NA	1	1	NA	NA	1	1	0.32355	1
HLA-B	9 (8%)	107	0.049105	1	0.0037719	0.92	0.60692	1	1	1	0.86895	1	0.66598	1
PTH2	3 (3%)	113	1	1	0.12453	1	NA	NA	NA	NA	0.1433	1	0.80041	1
C17ORF63	3 (3%)	113	0.75942	1	NA	NA	1	1	NA	NA	1	1	1	1
SMAD4	7 (6%)	109	0.4055	1	0.7406	1	1	1	0.74475	1	0.84967	1	1	1
POTEG	6 (5%)	110	0.18317	1	0.55603	1	1	1	1	1	0.66176	1	0.36007	1
RNF43	13 (11%)	103	5.9012e-05	0.015	0.02889	1	0.69808	1	0.73203	1	0.18386	1	0.050682	1
WBSCR17	12 (10%)	104	0.052933	1	0.0074342	1	0.60692	1	0.64265	1	0.24122	1	0.45073	1
PHF2	12 (10%)	104	0.00013036	0.0327	0.023751	1	0.66403	1	0.04721	1	0.041416	1	0.027156	1
TPTE	14 (12%)	102	0.86764	1	0.89505	1	0.41206	1	0.83965	1	0.21223	1	0.49765	1
CDH1	11 (9%)	105	0.11153	1	0.53119	1	0.60692	1	0.74475	1	0.081163	1	0.093552	1
CPS1	13 (11%)	103	0.44722	1	0.29581	1	1	1	0.86349	1	0.90179	1	0.13221	1
INO80E	5 (4%)	111	0.25014	1	NA	NA	0.60692	1	0.2785	1	0.34792	1	1	1
ELF3	5 (4%)	111	0.048352	1	0.2274	1	1	1	NA	NA	0.62229	1	0.077033	1
PARK2	9 (8%)	107	0.075539	1	0.038802	1	1	1	0.45024	1	0.86895	1	0.28014	1
LARP4B	5 (4%)	111	0.013181	1	0.20624	1	1	1	NA	NA	0.62229	1	0.077033	1
OR6K3	6 (5%)	110	0.075617	1	0.47222	1	1	1	0.38741	1	0.52184	1	0.86807	1
TM7SF4	7 (6%)	109	0.14578	1	0.29581	1	0.48837	1	NA	NA	0.84967	1	0.26715	1
UPF3A	6 (5%)	110	0.21986	1	0.20624	1	0.60692	1	0.74475	1	0.52184	1	0.22195	1
C7ORF63	5 (4%)	111	0.013181	1	NA	NA	1	1	1	1	0.62229	1	0.50728	1
KDM4B	10 (9%)	106	0.0051225	1	0.049976	1	0.34487	1	0.45024	1	0.87283	1	0.62693	1
KIAA0748	7 (6%)	109	0.34357	1	0.50703	1	1	1	NA	NA	0.25612	1	0.5987	1
OR8B4	3 (3%)	113	0.40746	1	0.0089393	1	NA	NA	NA	NA	1	1	0.60445	1
POM121L12	7 (6%)	109	0.00078734	0.194	0.25282	1	1	1	0.74475	1	0.84967	1	0.30873	1
RASA1	9 (8%)	107	0.06543	1	0.3555	1	0.66403	1	0.72994	1	0.17482	1	0.4951	1
SLITRK6	10 (9%)	106	0.55294	1	0.93438	1	0.10777	1	0.74475	1	0.17397	1	0.83495	1
TP53TG5	4 (3%)	112	0.12042	1	NA	NA	1	1	NA	NA	1	1	0.80754	1
LHCGR	7 (6%)	109	0.76025	1	0.8152	1	0.48837	1	NA	NA	0.70897	1	0.26715	1