Clinical Features	MRNA_CNMF		MRNA_CHIERARCHICAL		CN_CNMF		RPPA_CNMF		RPPA_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	Fisher's exact test_P	Fisher's exact test_Q
APC	103 (66%)	52	0.043762	1	0.028639	1	0.1013	1	0.16387	1	0.2193	1	1	1	1	1
BRAF	20 (13%)	135	5.5796e-06	0.00427	8.4332e-08	6.47e-05	8.4985e-05	0.0648	0.84394	1	0.53553	1	0.14533	1	1	1
FBXW7	29 (19%)	126	0.17593	1	0.10916	1	0.00082466	0.618	0.041909	1	0.071857	1	0.58342	1	0.65747	1
KRAS	58 (37%)	97	0.0032367	1	0.00094661	0.708	0.14993	1	0.61314	1	0.4652	1	1	1	0.61348	1
NRAS	15 (10%)	140	0.13137	1	0.40792	1	0.531	1	0.4731	1	0.53553	1	1	1	1	1
PIK3CA	26 (17%)	129	0.25208	1	0.38479	1	0.01783	1	0.017139	1	0.075075	1	1	1	0.59239	1
TP53	75 (48%)	80	0.003715	1	0.0088308	1	1.0799e-09	8.29e-07	0.89593	1	0.86249	1	0.36629	1	0.80713	1
SMAD4	18 (12%)	137	0.21227	1	0.58105	1	0.010006	1	0.79277	1	0.1262	1	1	1	1	1
FAM123B	19 (12%)	136	0.16813	1	0.033615	1	0.019023	1	0.36282	1	0.45269	1	0.49751	1	0.49751	1
TTN	69 (45%)	86	0.0059853	1	0.0080269	1	0.0010973	0.818	0.29027	1	0.92104	1	0.65532	1	0.79319	1
WBSCR17	17 (11%)	138	0.48014	1	0.3758	1	0.38775	1	0.422	1	0.35662	1	0.10888	1	0.10888	1
ACVR1B	13 (8%)	142	0.2704	1	0.45977	1	0.00744	1	0.30941	1	0.072905	1	1	1	0.38574	1
TNFRSF10C	6 (4%)	149	0.42597	1	1	1	0.081139	1	0.1334	1	0.12712	1	1	1	1	1
SMAD2	10 (6%)	145	0.027971	1	0.23317	1	0.033333	1	0.80923	1	0.56529	1	0.2827	1	1	1
MAP2K4	9 (6%)	146	0.48535	1	0.13273	1	0.051238	1	0.34056	1	0.60151	1	1	1	0.2549	1
PCBP1	4 (3%)	151	0.38468	1	0.38615	1	0.48567	1	NA	NA	NA	NA	1	1	1	1
FAT4	29 (19%)	126	0.017569	1	0.0068034	1	0.00017245	0.131	0.27105	1	0.74279	1	0.24089	1	0.021801	1
LRP1B	30 (19%)	125	0.00437	1	0.0010235	0.765	0.0011237	0.836	0.54939	1	0.86687	1	1	1	0.0078875	1
NRXN1	17 (11%)	138	0.2095	1	0.20792	1	0.013449	1	0.77289	1	1	1	1	1	0.45495	1
GRIA1	14 (9%)	141	0.22798	1	0.10344	1	0.32931	1	NA	NA	NA	NA	1	1	0.00041107	0.31
SDK1	25 (16%)	130	0.015802	1	0.001875	1	0.30989	1	0.90449	1	0.63812	1	1	1	0.57467	1
SOX9	9 (6%)	146	0.25523	1	0.43623	1	0.5849	1	0.85692	1	1	1	1	1	1	1
DMD	27 (17%)	128	0.022223	1	0.0062726	1	0.008545	1	0.55928	1	0.2216	1	1	1	0.09984	1
CNTN6	15 (10%)	140	0.12615	1	0.16225	1	0.32931	1	0.72576	1	0.67396	1	1	1	0.36117	1
GABRA5	8 (5%)	147	0.66265	1	1	1	1	1	NA	NA	NA	NA	0.19671	1	0.19671	1
OR2M4	8 (5%)	147	0.0056911	1	0.25918	1	0.077134	1	0.72576	1	0.51095	1	1	1	0.2549	1
OR6N1	8 (5%)	147	0.0020556	1	0.008217	1	0.009709	1	NA	NA	NA	NA	0.22624	1	1	1
PCDH9	16 (10%)	139	0.28019	1	0.71092	1	0.35408	1	0.87509	1	0.75677	1	1	1	0.40955	1
TXNDC3	10 (6%)	145	0.09493	1	0.28756	1	0.054831	1	0.45346	1	0.048951	1	1	1	0.2827	1
MGC26647	7 (5%)	148	0.27419	1	0.79574	1	0.88724	1	0.36742	1	0.51095	1	1	1	0.16628	1
FAM22F	8 (5%)	147	0.9181	1	0.27228	1	0.90578	1	0.87509	1	0.60151	1	1	1	1	1
ACVR2A	8 (5%)	147	0.018823	1	0.33741	1	0.098006	1	0.16608	1	0.40559	1	1	1	0.2549	1
TCF7L2	11 (7%)	144	0.11592	1	0.81475	1	0.087525	1	0.62361	1	1	1	1	1	0.2827	1
AFF2	15 (10%)	140	0.01043	1	0.029288	1	0.64821	1	0.16113	1	0.11112	1	0.40955	1	0.40955	1
CNBD1	6 (4%)	149	0.47166	1	0.77251	1	0.31246	1	NA	NA	NA	NA	1	1	0.19671	1
OTOL1	7 (5%)	148	0.38468	1	1	1	1	1	NA	NA	NA	NA	1	1	0.22624	1
KCNA4	10 (6%)	145	0.077752	1	0.089459	1	0.12251	1	0.16613	1	0.13944	1	1	1	1	1
ISL1	8 (5%)	147	0.098658	1	0.38881	1	0.75626	1	0.44465	1	1	1	1	1	0.2549	1
MGC42105	10 (6%)	145	0.0085864	1	0.10281	1	0.16218	1	0.23097	1	0.11112	1	1	1	1	1
ACOT4	3 (2%)	152	0.6764	1	0.39584	1	0.73592	1	NA	NA	NA	NA	1	1	1	1
CDH11	13 (8%)	142	0.13203	1	0.16823	1	0.25835	1	1	1	1	1	0.33582	1	1	1
ATM	21 (14%)	134	0.11603	1	0.43454	1	0.0020755	1	0.46922	1	1	1	1	1	0.07021	1
TPTE	11 (7%)	144	0.013187	1	0.28756	1	0.12922	1	1	1	1	1	1	1	0.30967	1
BTNL8	3 (2%)	152	0.34258	1	0.39584	1	0.31707	1	0.16608	1	1	1	1	1	1	1
KLHL4	12 (8%)	143	0.0085864	1	0.2024	1	0.0061785	1	0.061371	1	1	1	0.2827	1	0.2827	1
ROBO1	14 (9%)	141	0.1185	1	0.054293	1	0.086645	1	0.078682	1	0.79587	1	1	1	0.38574	1
GGT1	3 (2%)	152	NA	NA	NA	NA	0.31707	1	NA	NA	NA	NA	1	1	1	1
FLG	26 (17%)	129	0.00023212	0.176	0.0092663	1	0.00027044	0.205	0.077194	1	0.52811	1	1	1	0.60952	1
PCDHB2	13 (8%)	142	0.040402	1	0.010816	1	0.091203	1	0.77289	1	1	1	1	1	0.33582	1
POSTN	11 (7%)	144	0.2704	1	0.50081	1	0.075931	1	0.26866	1	0.40559	1	1	1	1	1
OR51V1	9 (6%)	146	0.006221	1	0.0043879	1	0.0043555	1	0.69203	1	1	1	1	1	0.2827	1
GRIK3	14 (9%)	141	0.33006	1	0.039598	1	0.47617	1	0.54939	1	0.53553	1	1	1	1	1
LRRN3	9 (6%)	146	0.018823	1	0.077171	1	0.28789	1	0.16613	1	0.13944	1	0.22624	1	1	1
PRDM9	11 (7%)	144	0.0015154	1	0.50081	1	0.12922	1	0.12662	1	0.74262	1	1	1	0.33582	1
ADAM29	9 (6%)	146	0.80904	1	0.35413	1	0.2679	1	NA	NA	NA	NA	1	1	1	1
KIAA1486	9 (6%)	146	0.81675	1	0.63101	1	0.46946	1	0.62361	1	1	1	1	1	0.2549	1
PSG8	8 (5%)	147	0.40571	1	0.51145	1	0.19659	1	NA	NA	NA	NA	0.22624	1	0.1022	1
NCKAP5	13 (8%)	142	0.16633	1	0.050544	1	0.14301	1	0.017202	1	1	1	1	1	0.36117	1
C8B	9 (6%)	146	0.19353	1	0.17354	1	0.85262	1	0.80923	1	1	1	1	1	1	1
DNAH5	28 (18%)	127	4.2602e-06	0.00326	0.001314	0.974	0.01336	1	0.30973	1	0.71994	1	0.58452	1	0.64205	1
CASP8	10 (6%)	145	0.00051772	0.39	1.2056e-05	0.00921	0.0017353	1	0.72576	1	1	1	1	1	0.2549	1
CCDC160	5 (3%)	150	0.52141	1	0.83099	1	0.50583	1	NA	NA	NA	NA	1	1	0.16628	1
DCAF4L2	9 (6%)	146	0.05674	1	0.0043879	1	0.23243	1	NA	NA	NA	NA	1	1	1	1
DKK2	5 (3%)	150	0.0064186	1	0.024538	1	0.50583	1	0.44465	1	0.60151	1	1	1	1	1
EPHA3	13 (8%)	142	0.003937	1	0.054293	1	0.25835	1	0.14317	1	0.6783	1	1	1	0.36117	1
ERBB4	14 (9%)	141	0.11164	1	0.1647	1	0.053794	1	0.91261	1	0.74262	1	1	1	0.36117	1
GUCY1A3	10 (6%)	145	0.17128	1	0.23317	1	0.22681	1	NA	NA	NA	NA	1	1	0.2827	1
IFT80	7 (5%)	148	0.15526	1	0.026986	1	0.13528	1	NA	NA	NA	NA	0.19671	1	1	1
INHBA	7 (5%)	148	0.11323	1	0.24966	1	0.31246	1	NA	NA	NA	NA	0.16628	1	0.16628	1
KLK2	3 (2%)	152	1	1	0.1981	1	0.73592	1	NA	NA	NA	NA	1	1	NA	NA
LPPR4	11 (7%)	144	0.13203	1	0.011076	1	0.28319	1	0.090753	1	0.75677	1	1	1	1	1
OR7C1	6 (4%)	149	0.0296	1	0.037862	1	0.74406	1	NA	NA	NA	NA	1	1	0.19671	1
SCN7A	12 (8%)	143	0.0011547	0.858	0.01161	1	0.16076	1	0.30837	1	0.74262	1	1	1	0.33582	1
TGFBR2	7 (5%)	148	0.029308	1	0.22961	1	0.06093	1	NA	NA	NA	NA	0.19671	1	0.19671	1
TRPS1	13 (8%)	142	0.089059	1	0.23317	1	0.00054694	0.411	NA	NA	NA	NA	1	1	0.33582	1
OR8J1	4 (3%)	151	0.084409	1	0.31933	1	0.61855	1	NA	NA	NA	NA	1	1	0.10266	1
RIMS2	12 (8%)	143	0.0080388	1	0.28194	1	0.042877	1	0.62361	1	1	1	1	1	0.33582	1
SFMBT2	12 (8%)	143	0.45048	1	0.25928	1	0.21014	1	0.85692	1	1	1	1	1	0.36117	1
IL18R1	8 (5%)	147	0.28634	1	0.25918	1	0.29391	1	0.62361	1	1	1	1	1	0.2549	1
PCDH17	14 (9%)	141	0.34684	1	0.92678	1	0.67283	1	0.62361	1	0.40559	1	1	1	0.36117	1
FLRT2	11 (7%)	144	0.67972	1	0.7887	1	0.36706	1	0.17138	1	1	1	1	1	0.2827	1
ZC3H13	17 (11%)	138	0.0014412	1	0.00026591	0.202	0.0068161	1	0.69203	1	0.44292	1	1	1	0.40955	1
PTEN	4 (3%)	151	0.017043	1	0.68799	1	0.13154	1	NA	NA	NA	NA	1	1	0.13494	1
ZFHX4	17 (11%)	138	0.51589	1	0.3758	1	0.45486	1	0.87509	1	1	1	1	1	0.045233	1
NRXN3	15 (10%)	140	0.0010942	0.816	0.038537	1	0.050618	1	1	1	0.26283	1	1	1	0.38574	1
LIFR	13 (8%)	142	0.032531	1	0.57844	1	0.35501	1	1	1	0.56529	1	1	1	0.025341	1
ZNF429	7 (5%)	148	0.090816	1	0.51145	1	0.88724	1	NA	NA	NA	NA	1	1	0.19671	1
OR2M2	6 (4%)	149	0.40571	1	1	1	0.5737	1	NA	NA	NA	NA	1	1	0.16628	1
TMEM132D	15 (10%)	140	0.00035268	0.267	0.00078112	0.587	0.027151	1	0.69203	1	1	1	1	1	1	1
SAT1	4 (3%)	151	0.0039159	1	0.071025	1	0.61855	1	0.45346	1	0.075566	1	1	1	1	1
CDH18	10 (6%)	145	0.017893	1	0.16545	1	0.047141	1	0.28487	1	0.6783	1	1	1	0.2827	1
P2RY10	6 (4%)	149	0.32821	1	0.44214	1	0.74406	1	NA	NA	NA	NA	1	1	1	1
SYT16	6 (4%)	149	0.029308	1	0.10102	1	0.059649	1	0.45346	1	0.40559	1	0.19671	1	1	1
DKK4	4 (3%)	151	0.070977	1	0.071025	1	0.18793	1	NA	NA	NA	NA	1	1	1	1
NALCN	14 (9%)	141	0.012026	1	0.091974	1	0.012928	1	0.75549	1	0.81954	1	1	1	0.36117	1
SULT1C4	3 (2%)	152	0.012416	1	0.026986	1	0.068363	1	NA	NA	NA	NA	1	1	NA	NA
UMOD	7 (5%)	148	0.11703	1	0.13595	1	0.16601	1	0.45346	1	0.56529	1	1	1	0.13494	1
CPXCR1	6 (4%)	149	0.070977	1	0.15116	1	0.5737	1	NA	NA	NA	NA	0.19671	1	0.014141	1
PDZRN4	12 (8%)	143	0.0050896	1	0.0029475	1	0.0059339	1	0.62361	1	1	1	0.30967	1	0.30967	1
USP17L2	7 (5%)	148	0.32898	1	0.33741	1	0.74406	1	1	1	0.60151	1	0.19671	1	0.19671	1
ESR1	11 (7%)	144	0.13466	1	0.073628	1	0.10536	1	0.45346	1	0.56529	1	1	1	0.2827	1
FAM5C	10 (6%)	145	0.11812	1	0.38889	1	0.047141	1	0.26866	1	0.56529	1	0.2827	1	0.2827	1
MIER3	10 (6%)	145	0.00087529	0.656	0.0080266	1	0.0030329	1	0.77289	1	1	1	1	1	0.30967	1
NLRP5	10 (6%)	145	0.025901	1	0.73205	1	0.16218	1	NA	NA	NA	NA	1	1	0.2549	1
OR6T1	6 (4%)	149	0.93425	1	0.58955	1	0.74406	1	NA	NA	NA	NA	0.16628	1	1	1
PCDH10	14 (9%)	141	0.13616	1	0.16225	1	0.23663	1	0.4673	1	1	1	1	1	0.36117	1
PCDHB5	12 (8%)	143	0.087007	1	0.28194	1	0.16076	1	0.54939	1	0.16829	1	1	1	0.30967	1
TRPC6	8 (5%)	147	0.10459	1	0.79574	1	0.3495	1	NA	NA	NA	NA	1	1	0.19671	1
RHOA	4 (3%)	151	NA	NA	NA	NA	0.61855	1	NA	NA	NA	NA	0.13494	1	1	1
SYNE1	37 (24%)	118	0.00014592	0.111	0.00047214	0.356	0.00028853	0.218	0.48999	1	0.67606	1	1	1	0.18111	1
CYTL1	4 (3%)	151	0.28741	1	0.77574	1	0.61855	1	NA	NA	NA	NA	1	1	0.13494	1
CHRM2	8 (5%)	147	0.47166	1	0.24966	1	0.13832	1	0.85692	1	1	1	0.22624	1	0.22624	1
GALNT14	9 (6%)	146	0.17726	1	0.54079	1	0.080745	1	0.033215	1	0.064191	1	1	1	0.22624	1
LRRIQ3	7 (5%)	148	0.63531	1	0.43324	1	0.4703	1	0.16608	1	0.56529	1	1	1	0.22624	1
NAALAD2	11 (7%)	144	0.026189	1	0.038073	1	0.012724	1	0.62361	1	0.40559	1	1	1	0.2827	1
PCDH11X	11 (7%)	144	0.10237	1	0.50081	1	0.12922	1	NA	NA	NA	NA	1	1	0.30967	1
TFAP2D	5 (3%)	150	0.58164	1	0.8643	1	0.50583	1	0.72576	1	0.51095	1	1	1	1	1
TNR	15 (10%)	140	0.013872	1	0.025334	1	0.0012541	0.931	0.34056	1	1	1	1	1	1	1
CNTNAP4	10 (6%)	145	0.01017	1	0.68822	1	0.02265	1	0.346	1	1	1	0.2827	1	0.03248	1
DOCK2	16 (10%)	139	0.0024534	1	0.0038836	1	0.0075402	1	0.33438	1	0.53553	1	1	1	0.43261	1