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	0.18312	1	0.00074638	0.537	0.078598	1	0.36179	1	0.00042781	0.309	2.5388e-06	0.00185	4.5308e-06	0.0033	0.083695	1
CDKN2A	65 (21%)	241	0.0033673	1	0.0030617	1	0.39488	1	0.45884	1	0.20091	1	0.20586	1	0.48428	1	0.12417	1
HRAS	10 (3%)	296	6.9316e-05	0.0503	0.061224	1	0.42365	1	0.69044	1	0.003386	1	0.0010975	0.787	0.14226	1	1	1
NFE2L2	17 (6%)	289	0.68816	1	0.0002966	0.215	0.82126	1	0.82839	1	1	1	0.46393	1	0.49212	1	0.14569	1
PIK3CA	64 (21%)	242	0.048649	1	0.055398	1	0.37244	1	0.85599	1	0.11863	1	0.39808	1	0.099342	1	0.60595	1
TP53	214 (70%)	92	7.1718e-11	5.25e-08	3.1376e-18	2.3e-15	1	1	0.60784	1	0.011311	1	0.001427	1	0.1325	1	0.0014783	1
CASP8	27 (9%)	279	0.0010205	0.733	7.2174e-06	0.00524	1	1	0.77797	1	2.999e-07	0.000219	5.2752e-07	0.000385	0.019862	1	0.40376	1
FAT1	72 (24%)	234	0.32533	1	0.22666	1	0.30053	1	0.48684	1	0.15214	1	0.2878	1	0.29365	1	0.17216	1
JUB	18 (6%)	288	0.16051	1	0.079858	1	0.40721	1	0.080556	1	0.30529	1	0.22128	1	0.32549	1	1	1
MLL2	56 (18%)	250	0.0028631	1	0.047117	1	0.17392	1	0.31098	1	0.05323	1	0.0079522	1	0.12217	1	0.0037318	1
FBXW7	15 (5%)	291	0.77704	1	0.13419	1	0.052716	1	0.47828	1	0.88141	1	0.63644	1	1	1	1	1
NSD1	33 (11%)	273	0.36067	1	3.0433e-23	2.23e-20	0.16769	1	0.22445	1	0.00041073	0.297	6.406e-06	0.00466	0.021185	1	0.03411	1
BAGE2	11 (4%)	295	0.52238	1	0.099878	1	0.573	1	0.21029	1	0.25251	1	0.2914	1	0.33897	1	0.13931	1
POTEC	15 (5%)	291	0.16717	1	0.036389	1	0.6386	1	0.90713	1	0.16984	1	0.25422	1	0.59978	1	0.16876	1
ZNF750	13 (4%)	293	0.89749	1	0.15861	1	0.32507	1	0.24832	1	0.11882	1	0.12797	1	0.87981	1	1	1
EP300	25 (8%)	281	0.43347	1	0.15087	1	0.93892	1	0.30184	1	0.0095454	1	0.0046706	1	0.24864	1	0.85551	1
POM121L12	14 (5%)	292	0.19547	1	0.30441	1	0.10474	1	0.10909	1	0.65763	1	0.65691	1	0.48072	1	0.20731	1
RHOA	4 (1%)	302	0.11404	1	0.54046	1	0.2312	1	0.42419	1	0.24544	1	0.14075	1	0.23703	1	0.39517	1
B2M	7 (2%)	299	0.54747	1	0.061816	1	NA	NA	NA	NA	0.51513	1	0.51674	1	0.57133	1	0.76671	1
RAC1	9 (3%)	297	0.83024	1	0.58476	1	1	1	0.37859	1	0.19472	1	0.1923	1	0.32391	1	0.49735	1
ZNF804B	21 (7%)	285	0.48247	1	0.48729	1	0.93939	1	0.91505	1	0.81207	1	0.74561	1	0.95949	1	0.75892	1
KCNT2	17 (6%)	289	0.14765	1	0.23504	1	0.72685	1	0.47828	1	0.049998	1	0.12118	1	0.05791	1	0.011662	1
RASA1	14 (5%)	292	0.30613	1	0.23951	1	0.48535	1	0.78591	1	0.35652	1	0.27144	1	0.27207	1	0.042474	1
PRIM2	9 (3%)	297	0.21437	1	0.30452	1	1	1	0.50005	1	0.40008	1	0.39492	1	0.53044	1	0.49735	1
CDH10	23 (8%)	283	0.17052	1	0.5313	1	0.59322	1	0.55753	1	0.074284	1	0.26547	1	0.24228	1	0.48306	1
CNTNAP5	15 (5%)	291	0.065465	1	0.11464	1	0.37006	1	1	1	0.010107	1	0.03537	1	0.016385	1	0.16876	1
POTEG	10 (3%)	296	0.095902	1	0.086947	1	0.028507	1	0.74073	1	0.15961	1	0.1427	1	0.79027	1	0.43603	1
ZNF99	22 (7%)	284	0.68692	1	0.12635	1	0.23255	1	0.43593	1	0.034327	1	0.011617	1	0.01305	1	0.0033196	1
OR2T12	11 (4%)	295	0.10583	1	0.12035	1	0.88406	1	0.69044	1	0.55168	1	0.50157	1	0.64002	1	0.6796	1
REG1A	8 (3%)	298	0.37534	1	0.10221	1	1	1	0.33935	1	0.057985	1	0.0013135	0.94	0.076546	1	0.051465	1
PABPC5	9 (3%)	297	0.69804	1	0.40719	1	0.84278	1	0.60177	1	0.088988	1	0.23749	1	0.32391	1	0.80998	1
IL32	4 (1%)	302	0.07807	1	0.0017661	1	NA	NA	NA	NA	0.56087	1	1	1	0.47389	1	1	1
PRAMEF11	10 (3%)	296	0.42101	1	0.43786	1	1	1	0.87408	1	0.66869	1	0.60635	1	0.85323	1	1	1
EPHA2	14 (5%)	292	0.2958	1	0.0025554	1	0.6386	1	1	1	0.49923	1	0.57024	1	0.34793	1	0.18551	1
FCRL4	13 (4%)	293	0.078432	1	0.017864	1	0.52487	1	1	1	0.40452	1	0.10557	1	0.28115	1	0.72405	1
LCP1	12 (4%)	294	0.1333	1	0.00085124	0.612	0.55545	1	0.035921	1	0.87253	1	0.75835	1	1	1	0.24415	1
LRFN5	13 (4%)	293	0.017516	1	0.070039	1	0.52143	1	0.85464	1	0.27909	1	0.076526	1	0.03317	1	0.38661	1
MAPK1	4 (1%)	302	0.78668	1	0.92435	1	0.84162	1	1	1	0.69142	1	0.68627	1	0.82489	1	1	1
PEG3	23 (8%)	283	0.1015	1	0.022004	1	0.37102	1	0.089156	1	0.021699	1	0.053035	1	0.12389	1	0.29584	1
PRSS1	8 (3%)	298	0.78827	1	0.47771	1	0.84162	1	1	1	1	1	0.89031	1	1	1	1	1
DOK6	8 (3%)	298	0.23529	1	0.58219	1	0.44671	1	1	1	1	1	1	1	0.60524	1	0.78635	1
GABRB3	11 (4%)	295	0.55945	1	0.014716	1	0.46877	1	1	1	0.25251	1	0.19188	1	0.33897	1	0.6796	1
STEAP4	10 (3%)	296	0.18742	1	0.63586	1	0.65304	1	0.63327	1	0.081342	1	0.099651	1	0.068652	1	1	1
ASXL3	21 (7%)	285	0.71205	1	0.6317	1	0.40932	1	0.33115	1	0.95964	1	0.71364	1	1	1	0.35944	1
NTM	7 (2%)	299	0.9478	1	0.2397	1	0.12773	1	0.02259	1	0.18181	1	0.08768	1	0.14083	1	0.40543	1
FAM155A	11 (4%)	295	0.25296	1	0.058504	1	0.33234	1	0.077004	1	0.23251	1	0.17452	1	0.14616	1	0.27668	1
HLA-A	9 (3%)	297	0.58575	1	0.33457	1	0.43951	1	1	1	0.072015	1	0.03106	1	0.29552	1	0.3857	1
KRTAP1-5	3 (1%)	303	0.83806	1	0.80674	1	NA	NA	NA	NA	0.78043	1	0.63019	1	0.052484	1	1	1
CTCF	11 (4%)	295	0.38621	1	0.40129	1	0.12127	1	0.61741	1	0.63562	1	0.6318	1	0.92855	1	1	1
BRWD3	16 (5%)	290	0.89121	1	0.53205	1	0.20508	1	1	1	0.25635	1	0.13614	1	0.31579	1	0.045577	1
CNPY3	3 (1%)	303	0.33566	1	0.48043	1	NA	NA	NA	NA	0.50041	1	0.49872	1	0.37988	1	0.61044	1
FAM101A	4 (1%)	302	0.47688	1	0.37439	1	NA	NA	NA	NA	0.69142	1	1	1	0.82489	1	0.69198	1
HLA-B	9 (3%)	297	0.25273	1	0.095674	1	0.087718	1	0.69044	1	0.0034112	1	0.0042541	1	0.070764	1	0.1602	1
PSG8	9 (3%)	297	0.16486	1	0.61808	1	0.70258	1	0.571	1	0.48293	1	0.48354	1	0.91768	1	0.3857	1
OR56A1	8 (3%)	298	0.3702	1	0.015766	1	0.75062	1	0.81233	1	0.35726	1	0.35167	1	0.20148	1	0.28695	1
OR2M2	8 (3%)	298	0.0067458	1	0.12587	1	NA	NA	NA	NA	0.18139	1	0.011835	1	0.49779	1	0.094577	1
OR4M2	8 (3%)	298	0.79941	1	0.87958	1	0.33953	1	0.37859	1	0.64281	1	0.63923	1	0.40316	1	0.60254	1
CPXCR1	7 (2%)	299	0.62196	1	0.53599	1	0.20626	1	0.19159	1	0.34511	1	0.49754	1	0.72342	1	0.13149	1
EYA1	10 (3%)	296	0.10477	1	0.63586	1	0.19076	1	0.83091	1	0.027385	1	0.026268	1	0.91908	1	0.18664	1
LINGO2	10 (3%)	296	0.26777	1	0.81951	1	0.0035853	1	1	1	0.014981	1	0.014411	1	0.089367	1	0.1167	1
SEMA5A	19 (6%)	287	0.00073601	0.531	0.0031799	1	1	1	1	1	0.0066098	1	0.023377	1	0.37879	1	0.063516	1
TGFBR2	10 (3%)	296	0.35267	1	0.20104	1	0.9031	1	1	1	0.3133	1	0.78514	1	0.66629	1	1	1
PLSCR1	5 (2%)	301	0.0056959	1	0.23001	1	0.80202	1	1	1	0.52389	1	0.52618	1	0.73734	1	0.49419	1
LIN28B	6 (2%)	300	0.40937	1	0.9375	1	0.80202	1	1	1	0.73749	1	0.73858	1	0.51418	1	0.51518	1
AGTR1	8 (3%)	298	0.61608	1	0.40061	1	0.16905	1	0.10575	1	0.18139	1	0.19975	1	0.076546	1	0.60254	1
C6	12 (4%)	294	0.73428	1	0.59106	1	0.15722	1	1	1	0.076231	1	0.22204	1	0.53407	1	0.5823	1
MS4A14	9 (3%)	297	0.39686	1	0.41799	1	0.058438	1	1	1	0.40008	1	0.48354	1	0.26782	1	0.49735	1
HIST1H4E	5 (2%)	301	0.73198	1	0.7312	1	0.15599	1	0.74073	1	0.86583	1	0.38575	1	0.19273	1	0.22398	1
LBP	7 (2%)	299	0.75979	1	0.83672	1	NA	NA	NA	NA	0.77455	1	0.77062	1	1	1	0.56505	1
RGS17	5 (2%)	301	0.60336	1	0.81016	1	NA	NA	NA	NA	0.1573	1	0.15513	1	0.19273	1	0.22398	1
LILRB1	12 (4%)	294	0.30206	1	0.16556	1	0.65304	1	0.81233	1	0.86125	1	0.92866	1	0.75419	1	0.42299	1
MAGEL2	12 (4%)	294	0.20931	1	0.005664	1	0.46877	1	0.35219	1	0.53756	1	0.34126	1	0.65921	1	0.5823	1
OR8D4	6 (2%)	300	0.99215	1	0.11929	1	0.51018	1	0.42046	1	0.38709	1	1	1	0.44449	1	0.7475	1
HIST1H1B	7 (2%)	299	0.42857	1	0.35579	1	0.44671	1	0.81233	1	0.80235	1	0.71677	1	0.72342	1	0.13149	1
C3ORF59	8 (3%)	298	0.14203	1	0.47552	1	0.16905	1	0.006873	1	1	1	1	1	0.81975	1	1	1
C8ORF34	7 (2%)	299	0.84688	1	0.089198	1	0.17687	1	0.42046	1	0.80235	1	1	1	0.42908	1	0.56505	1
OR8J1	9 (3%)	297	0.22373	1	0.31895	1	0.12773	1	0.02259	1	0.2447	1	0.26514	1	0.26782	1	0.20672	1
RAB32	3 (1%)	303	0.45336	1	0.82511	1	0.61326	1	0.10575	1	0.11415	1	0.11555	1	0.49245	1	0.34248	1
TMEM195	8 (3%)	298	0.71292	1	0.44781	1	0.53082	1	0.571	1	0.82063	1	0.90483	1	1	1	1	1
PCDH11X	21 (7%)	285	0.76354	1	0.71046	1	0.40086	1	0.057201	1	0.34612	1	0.37747	1	0.88182	1	0.75892	1
SLITRK4	12 (4%)	294	0.46833	1	0.17829	1	0.58737	1	0.59594	1	0.092015	1	0.089615	1	0.27302	1	0.20026	1
FRG2B	6 (2%)	300	0.76015	1	0.69185	1	1	1	0.6636	1	0.29107	1	0.28901	1	0.094292	1	0.7475	1
OR2L13	7 (2%)	299	0.45223	1	0.10127	1	0.84278	1	1	1	0.34511	1	0.49754	1	0.72342	1	0.13149	1
CUL3	10 (3%)	296	0.42307	1	0.12422	1	0.9031	1	0.51771	1	0.40329	1	0.85167	1	0.85323	1	0.52027	1
FOSL2	7 (2%)	299	0.17833	1	0.61146	1	0.84278	1	1	1	0.34511	1	0.71677	1	0.086909	1	0.56505	1
GPR158	12 (4%)	294	0.63539	1	0.13094	1	0.46877	1	0.85464	1	0.53756	1	0.5313	1	0.75419	1	0.5823	1
PTPRT	19 (6%)	287	0.20243	1	0.092527	1	1	1	0.74918	1	0.099629	1	0.69254	1	0.5005	1	0.19874	1
POTEH	7 (2%)	299	0.21122	1	0.54991	1	0.10186	1	0.60177	1	0.12311	1	0.10312	1	0.64663	1	0.76671	1
OR5D13	7 (2%)	299	0.59121	1	0.15964	1	0.68517	1	1	1	1	1	1	1	1	1	0.76671	1
PRB1	7 (2%)	299	0.55381	1	0.17704	1	0.61326	1	0.6636	1	0.88966	1	0.63923	1	0.14083	1	0.18606	1
NEUROD6	7 (2%)	299	0.66756	1	0.86226	1	NA	NA	NA	NA	0.50177	1	0.56324	1	1	1	1	1
DPP10	16 (5%)	290	0.16058	1	0.11984	1	0.78329	1	0.21029	1	0.16984	1	0.057442	1	0.015381	1	0.045577	1
DPPA4	7 (2%)	299	0.010845	1	0.0035004	1	0.57524	1	0.11946	1	0.12311	1	0.04607	1	0.72342	1	0.76671	1
EPDR1	6 (2%)	300	0.58415	1	0.79866	1	0.27746	1	0.60177	1	0.32685	1	0.67497	1	0.7737	1	0.7475	1