Clinical Features	CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL	
	nMutated (%)	nWild-Type	Chi-square test_P	Chi-square test_Q	Chi-square test_P	Chi-square 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
NOTCH1	57 (19%)	249	0.488	1	0.00074638	0.536	0.018664	1	0.27863	1	0.00042781	0.308	2.5388e-06	0.00185	7.7268e-05	0.056	0.57201	1
CDKN2A	65 (21%)	241	0.045098	1	0.0030617	1	0.034863	1	0.58275	1	0.20091	1	0.20586	1	0.35352	1	0.11529	1
HRAS	10 (3%)	296	1.3339e-05	0.00968	0.061224	1	0.16801	1	0.5987	1	0.003386	1	0.0010975	0.785	0.10872	1	0.50396	1
NFE2L2	17 (6%)	289	0.90925	1	0.0002966	0.215	0.12543	1	0.76487	1	1	1	0.46393	1	0.22251	1	0.11007	1
PIK3CA	64 (21%)	242	0.012321	1	0.055398	1	0.094762	1	0.92753	1	0.11863	1	0.39808	1	0.023442	1	0.15187	1
TP53	214 (70%)	92	1.8429e-16	1.35e-13	3.1376e-18	2.3e-15	0.11042	1	0.77572	1	0.011311	1	0.001427	1	0.042613	1	0.000589	0.424
CASP8	27 (9%)	279	0.00032614	0.236	7.2174e-06	0.00525	0.69899	1	0.73884	1	2.999e-07	0.000219	5.2752e-07	0.000385	0.32875	1	0.28613	1
FAT1	72 (24%)	234	0.30766	1	0.22666	1	0.79449	1	0.48676	1	0.15214	1	0.2878	1	0.8202	1	0.25204	1
JUB	18 (6%)	288	0.2635	1	0.079858	1	0.064612	1	0.081604	1	0.30529	1	0.22128	1	0.37988	1	1	1
MLL2	56 (18%)	250	0.11813	1	0.047117	1	0.68729	1	0.5209	1	0.05323	1	0.0079522	1	0.070698	1	0.0065137	1
FBXW7	15 (5%)	291	0.21031	1	0.13419	1	0.091967	1	0.30302	1	0.88141	1	0.63644	1	0.94533	1	0.86757	1
NSD1	33 (11%)	273	0.37677	1	3.0433e-23	2.23e-20	0.24387	1	0.73048	1	0.00041073	0.297	6.406e-06	0.00466	0.013268	1	0.033875	1
BAGE2	11 (4%)	295	0.27864	1	0.099878	1	0.41437	1	0.085722	1	0.25251	1	0.2914	1	0.17838	1	0.10107	1
POTEC	15 (5%)	291	0.07188	1	0.036389	1	0.8467	1	1	1	0.16984	1	0.25422	1	0.53479	1	0.21009	1
ZNF750	13 (4%)	293	0.72102	1	0.15861	1	0.94567	1	0.35321	1	0.11882	1	0.12797	1	0.63201	1	1	1
EP300	25 (8%)	281	0.034544	1	0.15087	1	0.76939	1	0.26447	1	0.0095454	1	0.0046706	1	0.33792	1	0.52586	1
POM121L12	14 (5%)	292	0.057769	1	0.30441	1	0.11616	1	0.15118	1	0.65763	1	0.65691	1	0.47993	1	0.45371	1
RHOA	4 (1%)	302	0.082572	1	0.54046	1	0.37867	1	0.44449	1	0.24544	1	0.14075	1	0.23982	1	0.2544	1
B2M	7 (2%)	299	0.76697	1	0.061816	1	NA	NA	NA	NA	0.51513	1	0.51674	1	0.14103	1	0.76683	1
RAC1	9 (3%)	297	0.37417	1	0.58476	1	1	1	0.51895	1	0.19472	1	0.1923	1	0.26838	1	0.30055	1
ZNF804B	21 (7%)	285	0.82524	1	0.48729	1	0.62634	1	0.51362	1	0.81207	1	0.74561	1	0.91979	1	0.90447	1
KCNT2	17 (6%)	289	0.19749	1	0.23504	1	0.70191	1	0.56227	1	0.049998	1	0.12118	1	0.051958	1	0.038821	1
RASA1	14 (5%)	292	0.061668	1	0.23951	1	1	1	0.40235	1	0.35652	1	0.27144	1	0.31299	1	0.030125	1
PRIM2	9 (3%)	297	0.080712	1	0.30452	1	0.82183	1	0.40376	1	0.40008	1	0.39492	1	0.26838	1	0.30055	1
CDH10	23 (8%)	283	0.32605	1	0.5313	1	0.32875	1	0.69459	1	0.074284	1	0.26547	1	0.20703	1	0.69352	1
CNTNAP5	15 (5%)	291	0.044911	1	0.11464	1	0.55292	1	1	1	0.010107	1	0.03537	1	0.01008	1	0.30047	1
POTEG	10 (3%)	296	0.0014828	1	0.086947	1	0.22852	1	0.75361	1	0.15961	1	0.1427	1	0.72814	1	0.50396	1
ZNF99	22 (7%)	284	0.2294	1	0.12635	1	0.32221	1	0.40235	1	0.034327	1	0.011617	1	0.0060636	1	0.006534	1
OR2T12	11 (4%)	295	0.023574	1	0.12035	1	0.51167	1	0.5987	1	0.55168	1	0.50157	1	0.59287	1	0.67164	1
REG1A	8 (3%)	298	0.16831	1	0.10221	1	0.49632	1	0.36016	1	0.057985	1	0.0013135	0.938	0.056864	1	0.061716	1
PABPC5	9 (3%)	297	0.20683	1	0.40719	1	0.69228	1	0.77857	1	0.088988	1	0.23749	1	0.26838	1	1	1
IL32	4 (1%)	302	0.11613	1	0.0017661	1	NA	NA	NA	NA	0.56087	1	1	1	0.56332	1	0.67991	1
PRAMEF11	10 (3%)	296	0.093171	1	0.43786	1	0.96337	1	0.77741	1	0.66869	1	0.60635	1	0.55085	1	1	1
EPHA2	14 (5%)	292	0.01271	1	0.0025554	1	0.81071	1	0.90612	1	0.49923	1	0.57024	1	0.77361	1	0.071019	1
FCRL4	13 (4%)	293	0.11999	1	0.017864	1	0.78846	1	1	1	0.40452	1	0.10557	1	0.46039	1	0.84708	1
LCP1	12 (4%)	294	0.46342	1	0.00085124	0.61	0.66661	1	0.04358	1	0.87253	1	0.75835	1	0.4979	1	0.84244	1
LRFN5	13 (4%)	293	0.0010447	0.748	0.070039	1	0.7661	1	0.8654	1	0.27909	1	0.076526	1	0.019557	1	0.42381	1
MAPK1	4 (1%)	302	0.72508	1	0.92435	1	0.56865	1	1	1	0.69142	1	0.68627	1	0.69099	1	0.13226	1
PEG3	23 (8%)	283	0.17193	1	0.022004	1	0.082694	1	0.10264	1	0.021699	1	0.053035	1	0.25337	1	0.24099	1
PRSS1	8 (3%)	298	0.01404	1	0.47771	1	0.05885	1	1	1	1	1	0.89031	1	0.82011	1	0.20473	1
DOK6	8 (3%)	298	0.37509	1	0.58219	1	0.70542	1	1	1	1	1	1	1	0.66637	1	1	1
GABRB3	11 (4%)	295	0.22152	1	0.014716	1	0.14801	1	0.54076	1	0.25251	1	0.19188	1	0.59287	1	0.67164	1
STEAP4	10 (3%)	296	0.17392	1	0.63586	1	0.17512	1	0.65586	1	0.081342	1	0.099651	1	0.089308	1	1	1
ASXL3	21 (7%)	285	0.61806	1	0.6317	1	0.22479	1	0.35562	1	0.95964	1	0.71364	1	0.50058	1	0.38288	1
NTM	7 (2%)	299	0.23807	1	0.2397	1	0.094882	1	0.023833	1	0.18181	1	0.08768	1	0.10394	1	0.089299	1
FAM155A	11 (4%)	295	0.15095	1	0.058504	1	0.010639	1	0.069434	1	0.23251	1	0.17452	1	0.11929	1	0.066659	1
HLA-A	9 (3%)	297	0.52845	1	0.33457	1	1	1	1	1	0.072015	1	0.03106	1	0.63296	1	0.6125	1
KRTAP1-5	3 (1%)	303	0.82581	1	0.80674	1	NA	NA	NA	NA	0.78043	1	0.63019	1	0.024495	1	1	1
CTCF	11 (4%)	295	0.55064	1	0.40129	1	0.39328	1	0.54076	1	0.63562	1	0.6318	1	0.8604	1	0.3656	1
BRWD3	16 (5%)	290	0.88007	1	0.53205	1	0.53716	1	1	1	0.25635	1	0.13614	1	0.5836	1	0.23406	1
CNPY3	3 (1%)	303	0.59793	1	0.48043	1	NA	NA	NA	NA	0.50041	1	0.49872	1	0.4951	1	0.59855	1
FAM101A	4 (1%)	302	0.58072	1	0.37439	1	NA	NA	NA	NA	0.69142	1	1	1	0.070687	1	1	1
HLA-B	9 (3%)	297	0.19357	1	0.095674	1	0.95199	1	0.5987	1	0.0034112	1	0.0042541	1	0.36069	1	0.30055	1
PSG8	9 (3%)	297	0.22082	1	0.61808	1	1	1	0.70994	1	0.48293	1	0.48354	1	0.91776	1	0.36174	1
OR56A1	8 (3%)	298	0.55831	1	0.015766	1	0.89435	1	0.82166	1	0.35726	1	0.35167	1	0.20057	1	0.34129	1
OR2M2	8 (3%)	298	0.0050049	1	0.12587	1	NA	NA	NA	NA	0.18139	1	0.011835	1	0.6049	1	0.11561	1
OR4M2	8 (3%)	298	0.37331	1	0.87958	1	0.74607	1	0.51895	1	0.64281	1	0.63923	1	0.6049	1	0.77641	1
CPXCR1	7 (2%)	299	0.76697	1	0.53599	1	0.20206	1	0.20931	1	0.34511	1	0.49754	1	0.49984	1	0.3992	1
EYA1	10 (3%)	296	0.21492	1	0.63586	1	0.79013	1	0.84343	1	0.027385	1	0.026268	1	0.72814	1	0.21483	1
LINGO2	10 (3%)	296	0.31606	1	0.81951	1	0.28388	1	1	1	0.014981	1	0.014411	1	0.17243	1	0.13833	1
SEMA5A	19 (6%)	287	0.00073685	0.53	0.0031799	1	0.93559	1	1	1	0.0066098	1	0.023377	1	0.29907	1	0.035076	1
TGFBR2	10 (3%)	296	0.4597	1	0.20104	1	0.46896	1	1	1	0.3133	1	0.78514	1	0.79049	1	1	1
PLSCR1	5 (2%)	301	0.14124	1	0.23001	1	1	1	1	1	0.52389	1	0.52618	1	0.15468	1	0.46252	1
LIN28B	6 (2%)	300	0.63383	1	0.9375	1	0.51348	1	1	1	0.73749	1	0.73858	1	0.51453	1	0.13922	1
AGTR1	8 (3%)	298	0.3983	1	0.40061	1	0.17308	1	0.10825	1	0.18139	1	0.19975	1	0.056864	1	0.77641	1
C6	12 (4%)	294	0.58018	1	0.59106	1	0.061955	1	1	1	0.076231	1	0.22204	1	0.53487	1	1	1
MS4A14	9 (3%)	297	0.23776	1	0.41799	1	0.58815	1	1	1	0.40008	1	0.48354	1	0.48609	1	1	1
HIST1H4E	5 (2%)	301	0.65806	1	0.7312	1	0.25523	1	0.75361	1	0.86583	1	0.38575	1	0.33258	1	0.27829	1
LBP	7 (2%)	299	0.42606	1	0.83672	1	NA	NA	NA	NA	0.77455	1	0.77062	1	1	1	1	1
RGS17	5 (2%)	301	0.70581	1	0.81016	1	NA	NA	NA	NA	0.1573	1	0.15513	1	0.15468	1	0.27829	1
LILRB1	12 (4%)	294	0.26868	1	0.16556	1	0.41899	1	0.82166	1	0.86125	1	0.92866	1	0.70435	1	0.46223	1
MAGEL2	12 (4%)	294	0.22844	1	0.005664	1	0.16968	1	0.44601	1	0.53756	1	0.34126	1	0.39667	1	0.573	1
OR8D4	6 (2%)	300	0.90164	1	0.11929	1	0.89435	1	0.438	1	0.38709	1	1	1	0.38552	1	0.73172	1
HIST1H1B	7 (2%)	299	0.62728	1	0.35579	1	0.70542	1	0.82166	1	0.80235	1	0.71677	1	0.18253	1	0.12535	1
C3ORF59	8 (3%)	298	0.45865	1	0.47552	1	0.17308	1	0.008625	1	1	1	1	1	0.90831	1	1	1
C8ORF34	7 (2%)	299	0.93095	1	0.089198	1	0.41899	1	0.061658	1	0.80235	1	1	1	0.34476	1	1	1
OR8J1	9 (3%)	297	0.1611	1	0.31895	1	0.034635	1	0.023833	1	0.2447	1	0.26514	1	0.29596	1	0.6125	1
RAB32	3 (1%)	303	0.079345	1	0.82511	1	0.8562	1	0.67201	1	0.11415	1	0.11555	1	0.38102	1	0.35015	1
TMEM195	8 (3%)	298	0.50818	1	0.44781	1	0.79013	1	0.70994	1	0.82063	1	0.90483	1	0.82011	1	1	1
PCDH11X	21 (7%)	285	0.42189	1	0.71046	1	0.69735	1	0.024771	1	0.34612	1	0.37747	1	0.78049	1	0.90447	1
SLITRK4	12 (4%)	294	0.14724	1	0.17829	1	0.46508	1	0.61334	1	0.092015	1	0.089615	1	0.19366	1	0.28295	1
FRG2B	6 (2%)	300	0.77267	1	0.69185	1	0.3245	1	0.67201	1	0.29107	1	0.28901	1	0.29093	1	0.73172	1
OR2L13	7 (2%)	299	0.23851	1	0.10127	1	0.0082072	1	1	1	0.34511	1	0.49754	1	0.49984	1	0.0043187	1
CUL3	10 (3%)	296	0.046335	1	0.12422	1	0.73733	1	0.6364	1	0.40329	1	0.85167	1	0.55085	1	0.40291	1
FOSL2	7 (2%)	299	0.39453	1	0.61146	1	0.64405	1	1	1	0.34511	1	0.71677	1	0.34476	1	0.28102	1
GPR158	12 (4%)	294	0.45424	1	0.13094	1	1	1	0.8654	1	0.53756	1	0.5313	1	0.93405	1	0.573	1
PTPRT	19 (6%)	287	0.7428	1	0.092527	1	0.57616	1	0.75208	1	0.099629	1	0.69254	1	0.47743	1	0.5007	1
POTEH	7 (2%)	299	0.89243	1	0.54991	1	0.15218	1	0.15533	1	0.12311	1	0.10312	1	0.57025	1	0.76683	1
OR5D13	7 (2%)	299	0.75632	1	0.15964	1	1	1	1	1	1	1	1	1	1	1	0.76683	1
PRB1	7 (2%)	299	0.49966	1	0.17704	1	0.75664	1	0.67201	1	0.88966	1	0.63923	1	0.10394	1	1	1
NEUROD6	7 (2%)	299	0.89243	1	0.86226	1	NA	NA	NA	NA	0.50177	1	0.56324	1	1	1	1	1
DPP10	16 (5%)	290	0.061299	1	0.11984	1	0.1154	1	0.26044	1	0.16984	1	0.057442	1	0.0128	1	0.073082	1
DPPA4	7 (2%)	299	0.062472	1	0.0035004	1	0.44232	1	0.084534	1	0.12311	1	0.04607	1	0.49984	1	0.76683	1
EPDR1	6 (2%)	300	0.77267	1	0.79866	1	0.56135	1	0.77857	1	0.32685	1	0.67497	1	0.88087	1	1	1