		Clinical Features	MRNA_CNMF		MRNA_CHIERARCHICAL		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	Fisher's exact test_P	Fisher's exact test_Q	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	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
DSPP	26 (3%)	746	0.94555	1	0.41992	1	0.56725	1	0.97457	1	0.098697	1	0.38708	1	0.59294	1	0.41694	1	0.095993	1	0.5539	1
PIK3R1	21 (3%)	751	0.16772	1	0.43697	1	0.78678	1	0.57242	1	0.53782	1	0.29702	1	0.40284	1	0.9234	1	0.5913	1	0.84896	1
AKT1	19 (2%)	753	0.050739	1	0.92649	1	0.0032893	1	0.00011243	0.0819	0.16241	1	0.34532	1	2.9898e-05	0.0219	0.38446	1	0.022568	1	0.022528	1
AOAH	19 (2%)	753	NA	NA	NA	NA	0.59091	1	0.72237	1	NA	NA	NA	NA	0.44243	1	0.53831	1	0.022568	1	0.84896	1
DCP1B	5 (1%)	767	NA	NA	NA	NA	0.34998	1	0.0064834	1	NA	NA	NA	NA	0.71385	1	0.62346	1	0.38371	1	0.12153	1
GATA3	81 (10%)	691	0.0013815	0.984	0.00011625	0.0845	0.004254	1	0.014608	1	0.0011529	0.822	0.00040708	0.294	1.1415e-06	0.000846	1.0631e-07	7.94e-05	2.2963e-05	0.0169	3.3384e-07	0.000249
MAP3K4	18 (2%)	754	0.10561	1	0.84894	1	0.76286	1	0.28732	1	0.073322	1	0.68963	1	0.38102	1	0.42276	1	0.51797	1	0.059533	1
MEF2A	14 (2%)	758	NA	NA	NA	NA	0.60661	1	0.39935	1	NA	NA	NA	NA	0.70106	1	0.68373	1	0.13386	1	0.73446	1
NCOA3	29 (4%)	743	0.61458	1	0.78888	1	0.92486	1	0.5366	1	1	1	1	1	0.50494	1	0.80375	1	0.81377	1	0.19239	1
NCOR2	29 (4%)	743	0.6932	1	1	1	0.07219	1	0.63052	1	0.83853	1	0.68963	1	0.99677	1	0.60765	1	0.73425	1	0.27586	1
NR1H2	18 (2%)	754	0.37516	1	0.57978	1	0.77064	1	0.070118	1	0.063975	1	0.11594	1	0.075937	1	0.013839	1	0.31277	1	0.083174	1
PIK3CA	261 (34%)	511	1.3977e-14	1.06e-11	4.1035e-10	3.08e-07	1.2371e-12	9.33e-10	9.273e-11	6.97e-08	1.6388e-05	0.0121	1.0648e-06	0.00079	4.2336e-29	3.22e-26	1.0987e-12	8.3e-10	7.2218e-07	0.000537	4.8365e-11	3.64e-08
RBMX	13 (2%)	759	NA	NA	NA	NA	0.001919	1	0.078909	1	NA	NA	NA	NA	0.30573	1	0.21376	1	0.47178	1	0.15421	1
TP53	257 (33%)	515	3.2919e-36	2.51e-33	1.1205e-32	8.53e-30	7.8526e-46	6e-43	5.7958e-21	4.39e-18	1.8749e-27	1.42e-24	1.102e-23	8.35e-21	5.6778e-52	4.35e-49	2.6022e-49	1.99e-46	8.1396e-38	6.21e-35	8.2286e-47	6.29e-44
TPRX1	7 (1%)	765	NA	NA	NA	NA	0.31538	1	0.51084	1	NA	NA	NA	NA	0.98933	1	1	1	1	1	0.40802	1
ZNF384	14 (2%)	758	NA	NA	NA	NA	0.45596	1	0.47801	1	NA	NA	NA	NA	0.59073	1	1	1	0.8158	1	0.36151	1
RUNX1	25 (3%)	747	0.00628	1	0.081763	1	7.8943e-07	0.000587	0.014004	1	1	1	0.25194	1	0.13336	1	0.13068	1	0.066966	1	0.039161	1
PTEN	29 (4%)	743	0.27293	1	0.44538	1	0.23196	1	0.43146	1	0.88203	1	0.2657	1	0.73063	1	0.80375	1	0.26485	1	0.61747	1
TBX3	18 (2%)	754	0.84712	1	0.38465	1	0.48075	1	0.16071	1	0.15974	1	0.55094	1	0.48982	1	0.38446	1	0.80533	1	0.84608	1
CBFB	16 (2%)	756	0.16955	1	0.73909	1	0.03216	1	0.0042514	1	0.34961	1	0.56866	1	0.014899	1	0.085086	1	0.14318	1	0.05803	1
MAP2K4	32 (4%)	740	0.070433	1	0.0047509	1	0.042665	1	0.012346	1	0.0023792	1	0.034428	1	0.0064934	1	0.00047465	0.341	0.000298	0.215	0.00061358	0.439
CDH1	55 (7%)	717	1.4496e-06	0.00107	6.0625e-05	0.0443	7.0882e-08	5.32e-05	0.0033971	1	0.00025549	0.185	0.00057945	0.415	3.3687e-05	0.0247	9.2417e-08	6.92e-05	0.00087288	0.624	0.00013691	0.0994
MAP3K1	57 (7%)	715	1.2107e-07	9.03e-05	4.9323e-05	0.0361	6.6048e-05	0.0481	0.027992	1	0.00020416	0.148	1.9896e-06	0.00147	1.0057e-07	7.52e-05	3.2819e-05	0.0241	7.8743e-06	0.0058	4.4639e-06	0.00329
FOXA1	15 (2%)	757	0.74202	1	0.097034	1	0.34299	1	0.039511	1	1	1	0.5168	1	0.4227	1	0.3339	1	0.68261	1	0.30233	1
MLL3	56 (7%)	716	0.23261	1	0.94813	1	0.5048	1	0.90195	1	0.74035	1	0.93484	1	0.59062	1	0.94985	1	0.098451	1	0.19069	1
ATN1	17 (2%)	755	0.31448	1	0.12457	1	0.048478	1	0.87369	1	0.16884	1	0.29141	1	0.05451	1	0.52014	1	0.84374	1	1	1
SF3B1	14 (2%)	758	0.75873	1	0.20458	1	0.39644	1	0.27646	1	0.25347	1	0.004986	1	0.41885	1	0.42229	1	0.087541	1	0.73446	1
CCDC144NL	8 (1%)	764	NA	NA	NA	NA	0.00040511	0.292	0.32541	1	NA	NA	NA	NA	0.63881	1	0.090866	1	0.33041	1	0.67672	1
MUC12	44 (6%)	728	0.26646	1	0.038037	1	0.52513	1	0.13242	1	0.36378	1	0.49852	1	0.71834	1	0.041341	1	0.17461	1	0.56345	1
KRTAP4-7	7 (1%)	765	NA	NA	NA	NA	0.20786	1	0.59948	1	NA	NA	NA	NA	0.88342	1	0.58153	1	0.3736	1	1	1
ZFP36L1	10 (1%)	762	0.85586	1	0.61645	1	0.00041179	0.296	0.39563	1	0.025798	1	0.39178	1	0.91842	1	0.30123	1	0.42861	1	0.37225	1
NCOR1	31 (4%)	741	0.42166	1	0.50495	1	0.3893	1	0.3095	1	0.72317	1	0.72615	1	0.63419	1	0.46737	1	0.30701	1	0.53522	1
KRAS	6 (1%)	766	0.57656	1	1	1	0.5507	1	0.18412	1	0.33082	1	1	1	0.4761	1	1	1	0.46983	1	0.57824	1
PHLDA1	9 (1%)	763	0.35241	1	0.31546	1	0.33768	1	0.70192	1	1	1	0.28034	1	0.85088	1	1	1	0.58459	1	1	1
VEZF1	8 (1%)	764	NA	NA	NA	NA	0.65336	1	0.53708	1	NA	NA	NA	NA	0.24329	1	0.79889	1	1	1	0.56156	1
ERBB2	12 (2%)	760	0.30816	1	0.89336	1	0.00056776	0.408	0.0078504	1	0.45096	1	0.77302	1	0.0023508	1	0.43689	1	0.47899	1	0.1826	1
CTCF	18 (2%)	754	0.023947	1	0.28931	1	0.013178	1	0.013724	1	0.068249	1	0.36929	1	0.00093087	0.665	0.16306	1	0.055077	1	0.034207	1
KRTAP9-9	6 (1%)	766	NA	NA	NA	NA	0.26156	1	0.17686	1	NA	NA	NA	NA	0.068324	1	1	1	0.20992	1	0.1845	1
BCL6B	8 (1%)	764	NA	NA	NA	NA	0.13526	1	0.695	1	NA	NA	NA	NA	0.27271	1	0.62522	1	0.8896	1	0.56156	1
CTU2	5 (1%)	767	NA	NA	NA	NA	0.24161	1	0.57709	1	NA	NA	NA	NA	0.74938	1	0.73215	1	0.84669	1	0.72465	1
RB1	14 (2%)	758	0.51341	1	0.093023	1	0.17881	1	0.32702	1	0.48293	1	0.76154	1	0.41203	1	0.26233	1	0.2019	1	0.25038	1
HIST1H3B	7 (1%)	765	0.37926	1	1	1	0.53866	1	0.74996	1	1	1	0.82708	1	0.2688	1	0.387	1	0.77583	1	1	1
AQP7	8 (1%)	764	0.62604	1	0.13795	1	0.35122	1	0.64055	1	NA	NA	NA	NA	0.73161	1	0.73686	1	0.68363	1	0.51094	1
MYB	11 (1%)	761	0.7585	1	1	1	0.10438	1	0.40723	1	1	1	0.68963	1	0.18983	1	0.54859	1	0.70492	1	1	1
E2F4	4 (1%)	768	NA	NA	NA	NA	0.93436	1	NA	NA	NA	NA	NA	NA	0.85157	1	0.36857	1	1	1	1	1
MUC20	10 (1%)	762	NA	NA	NA	NA	0.074772	1	0.10329	1	NA	NA	NA	NA	0.054189	1	0.16047	1	0.228	1	0.028121	1
AKD1	19 (2%)	753	0.771	1	0.44885	1	0.058601	1	0.36771	1	0.46668	1	0.24234	1	0.34098	1	0.076124	1	0.25307	1	0.84896	1
CDKN1B	7 (1%)	765	0.31625	1	0.20282	1	0.0033076	1	0.024653	1	0.33082	1	0.39197	1	0.12158	1	0.23661	1	0.078332	1	0.23302	1
KRTAP4-5	4 (1%)	768	NA	NA	NA	NA	0.47337	1	0.2244	1	NA	NA	NA	NA	0.82403	1	0.34593	1	0.81652	1	1	1
RPGR	14 (2%)	758	0.59688	1	0.29945	1	0.92325	1	0.70556	1	0.74488	1	0.60567	1	0.5237	1	0.26974	1	0.4325	1	0.21132	1
CASP8	10 (1%)	762	0.32406	1	0.33204	1	0.91749	1	0.50497	1	0.40246	1	1	1	0.50568	1	0.84037	1	0.5115	1	0.16026	1
HLA-A	4 (1%)	768	0.80623	1	0.27503	1	0.26601	1	NA	NA	1	1	0.82708	1	0.0032376	1	1	1	0.64494	1	0.44762	1
FGFR2	7 (1%)	765	0.59112	1	0.37016	1	0.85982	1	0.37401	1	1	1	0.82708	1	0.20036	1	0.62522	1	0.23831	1	0.071828	1
TBL1XR1	9 (1%)	763	0.091668	1	0.26872	1	0.03404	1	NA	NA	0.45536	1	0.56866	1	0.075601	1	0.21166	1	0.15288	1	0.26562	1
PRRX1	6 (1%)	766	0.55153	1	0.60565	1	0.46842	1	0.12248	1	0.83853	1	0.39197	1	0.36192	1	0.14811	1	0.25379	1	0.1845	1
ZNF69	5 (1%)	767	0.61279	1	1	1	0.25486	1	0.75024	1	NA	NA	NA	NA	0.35768	1	0.73215	1	0.84669	1	0.72465	1
GNRH2	3 (0%)	769	NA	NA	NA	NA	0.26036	1	NA	NA	NA	NA	NA	NA	0.41123	1	1	1	0.099498	1	0.20935	1
HLA-DRB1	8 (1%)	764	0.52427	1	0.44356	1	0.22304	1	0.20909	1	NA	NA	NA	NA	0.4074	1	1	1	0.048762	1	0.82592	1
DENND4B	8 (1%)	764	NA	NA	NA	NA	0.18796	1	0.051526	1	NA	NA	NA	NA	0.3988	1	0.20437	1	0.21846	1	0.1871	1
CCDC66	9 (1%)	763	0.38866	1	0.33204	1	0.87628	1	0.67304	1	NA	NA	NA	NA	0.053416	1	0.19189	1	0.061018	1	0.49467	1
AFF2	15 (2%)	757	0.6873	1	0.050289	1	0.18818	1	0.22852	1	0.062251	1	0.015033	1	0.50079	1	0.33378	1	0.24682	1	0.24078	1
HNF1A	9 (1%)	763	NA	NA	NA	NA	0.068544	1	0.60319	1	NA	NA	NA	NA	0.21171	1	0.1236	1	0.53215	1	0.26562	1
RAI1	7 (1%)	765	NA	NA	NA	NA	0.22511	1	0.91195	1	1	1	0.78219	1	0.72103	1	0.87783	1	0.73956	1	0.76955	1
GPS2	6 (1%)	766	0.0075946	1	0.102	1	0.14704	1	0.3499	1	1	1	1	1	0.54017	1	0.24637	1	0.8627	1	0.57824	1
PCMTD1	3 (0%)	769	NA	NA	NA	NA	0.4952	1	0.65714	1	NA	NA	NA	NA	0.58373	1	0.79157	1	0.74297	1	0.20935	1
SLC25A5	3 (0%)	769	NA	NA	NA	NA	0.25487	1	0.69327	1	NA	NA	NA	NA	NA	NA	NA	NA	0.28632	1	0.32128	1
STXBP2	9 (1%)	763	NA	NA	NA	NA	0.79264	1	0.69167	1	NA	NA	NA	NA	0.67602	1	0.63615	1	0.90118	1	1	1
FAM21A	7 (1%)	765	0.47498	1	0.22469	1	0.050405	1	0.11502	1	0.11142	1	0.49725	1	0.29188	1	0.12249	1	0.32467	1	0.13414	1
ZNF587	9 (1%)	763	0.057583	1	0.7208	1	0.25599	1	0.191	1	0.63038	1	1	1	0.0074817	1	0.027162	1	0.12107	1	0.074691	1
POLR2J3	3 (0%)	769	NA	NA	NA	NA	0.70106	1	0.69327	1	NA	NA	NA	NA	0.92938	1	0.11278	1	0.28632	1	0.32128	1
AXL	6 (1%)	766	NA	NA	NA	NA	0.25539	1	0.41265	1	NA	NA	NA	NA	0.50246	1	0.031637	1	1	1	0.2622	1
MUC21	6 (1%)	766	0.37704	1	0.80553	1	0.14704	1	0.0090754	1	NA	NA	NA	NA	0.77826	1	0.44777	1	0.8627	1	0.46103	1
MED23	13 (2%)	759	0.0090186	1	0.020134	1	0.2639	1	0.21953	1	0.12058	1	0.19073	1	0.15445	1	0.027096	1	0.10895	1	0.091365	1
KRT38	4 (1%)	768	0.59112	1	0.68975	1	0.2508	1	0.74752	1	0.40246	1	0.63316	1	0.65521	1	1	1	1	1	1	1
HS6ST1	5 (1%)	767	NA	NA	NA	NA	0.013019	1	0.68318	1	NA	NA	NA	NA	0.83811	1	0.62346	1	0.11095	1	0.72465	1
RALY	6 (1%)	766	NA	NA	NA	NA	0.64692	1	0.76041	1	NA	NA	NA	NA	0.090255	1	0.67279	1	0.14224	1	0.76955	1
UBC	8 (1%)	764	0.28596	1	0.78888	1	0.014356	1	0.33937	1	0.55623	1	0.82708	1	0.63338	1	1	1	0.8896	1	0.82592	1
TLR4	11 (1%)	761	0.36355	1	0.32571	1	0.76253	1	0.98793	1	0.27965	1	0.33213	1	0.98358	1	0.39348	1	0.70492	1	1	1
ODF1	5 (1%)	767	NA	NA	NA	NA	0.93436	1	0.68318	1	NA	NA	NA	NA	0.40893	1	0.29527	1	1	1	1	1
PABPC3	8 (1%)	764	0.16192	1	0.80553	1	0.71084	1	0.82433	1	NA	NA	NA	NA	0.5223	1	0.81627	1	1	1	0.4549	1
KCNT2	11 (1%)	761	0.33186	1	0.37117	1	0.12858	1	0.5434	1	0.52369	1	1	1	0.14774	1	0.28657	1	0.45016	1	0.35046	1
NEK5	9 (1%)	763	0.80692	1	0.33183	1	0.77466	1	0.72042	1	0.74255	1	1	1	0.91427	1	0.91078	1	0.90118	1	0.39901	1
ASPHD1	3 (0%)	769	NA	NA	NA	NA	0.70106	1	0.88737	1	NA	NA	NA	NA	0.84544	1	0.79157	1	1	1	0.20935	1
FAM47B	7 (1%)	765	0.61979	1	0.31546	1	0.75638	1	0.57289	1	0.52174	1	1	1	0.77704	1	0.70931	1	0.32467	1	0.81259	1
PCDH19	14 (2%)	758	0.22018	1	0.91851	1	0.79035	1	0.7849	1	1	1	0.91721	1	0.37939	1	0.62109	1	0.71164	1	0.81559	1
ZIC3	4 (1%)	768	NA	NA	NA	NA	0.83021	1	0.52004	1	NA	NA	NA	NA	0.61267	1	0.56995	1	0.29432	1	1	1
FAM21C	6 (1%)	766	0.47498	1	0.014457	1	0.026815	1	0.0064834	1	NA	NA	NA	NA	0.098958	1	0.0033257	1	0.0045468	1	0.065403	1
VSTM2B	3 (0%)	769	NA	NA	NA	NA	0.96993	1	NA	NA	NA	NA	NA	NA	0.94539	1	1	1	1	1	0.66032	1
SELPLG	7 (1%)	765	NA	NA	NA	NA	0.26645	1	0.14045	1	NA	NA	NA	NA	0.044479	1	0.20536	1	0.68363	1	0.23302	1
SLC30A10	5 (1%)	767	0.68036	1	0.80553	1	0.55507	1	0.66532	1	0.40246	1	0.37879	1	0.9484	1	0.53753	1	1	1	0.54214	1
RGS7	8 (1%)	764	0.57839	1	0.23957	1	0.089001	1	0.4392	1	0.74255	1	0.62468	1	0.67473	1	0.38776	1	0.33041	1	0.0084383	1
