Molecular subtypes	CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL	
	nCNV (%)	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	Fisher's exact test_P	Fisher's exact test_Q
1p gain	32 (11%)	256	0.33817	1	0.47718	1	0.5875	1	0.66893	1	0.75425	1	0.58219	1	0.58379	1	0.33242	1
1q gain	89 (31%)	199	0.00066596	0.384	0.15945	1	0.82488	1	0.82324	1	0.007862	1	0.89405	1	0.17662	1	0.017187	1
2p gain	31 (11%)	257	0.0035621	1	0.15804	1	0.34536	1	0.46895	1	0.013527	1	0.080396	1	0.10958	1	0.0055003	1
2q gain	28 (10%)	260	0.0016715	0.936	0.43631	1	0.18139	1	0.050319	1	0.012472	1	0.034411	1	0.0263	1	0.00078891	0.453
3p gain	25 (9%)	263	0.057929	1	0.25504	1	0.94025	1	1	1	0.052575	1	0.18597	1	0.89207	1	1	1
3q gain	32 (11%)	256	0.12217	1	0.36616	1	0.56212	1	1	1	0.056716	1	0.29824	1	0.80845	1	0.6948	1
4p gain	27 (9%)	261	0.010432	1	0.018554	1	0.69106	1	0.2108	1	0.45776	1	0.49554	1	1	1	0.83366	1
4q gain	21 (7%)	267	0.044656	1	0.021381	1	0.9217	1	0.78567	1	0.53459	1	0.88052	1	0.77395	1	0.48474	1
5p gain	35 (12%)	253	0.00030369	0.177	0.099781	1	1	1	0.81374	1	0.60628	1	0.58079	1	0.38116	1	0.70684	1
5q gain	15 (5%)	273	0.0020077	1	0.30551	1	1	1	0.89132	1	0.3889	1	0.4718	1	0.61166	1	0.2635	1
6p gain	89 (31%)	199	2.6783e-06	0.00162	1.1409e-06	0.000694	0.22248	1	0.5257	1	0.015793	1	0.13383	1	0.0011031	0.629	9.9568e-05	0.0585
6q gain	22 (8%)	266	0.16125	1	0.19759	1	0.72329	1	0.77154	1	0.58515	1	0.58591	1	0.4644	1	0.3381	1
7p gain	119 (41%)	169	3.7439e-12	2.31e-09	0.081406	1	0.038338	1	0.020605	1	0.0011611	0.661	0.0039452	1	0.52251	1	0.21159	1
7q gain	120 (42%)	168	5.8182e-11	3.59e-08	0.20728	1	0.020703	1	0.025451	1	6.7511e-05	0.04	0.0016887	0.944	0.20781	1	0.047237	1
8p gain	55 (19%)	233	0.00034296	0.199	0.015999	1	0.075866	1	0.18392	1	0.0061566	1	0.0013851	0.781	0.4169	1	0.2754	1
8q gain	92 (32%)	196	5.1189e-09	3.15e-06	1.2322e-05	0.00741	0.472	1	0.48273	1	8.3765e-05	0.0494	0.00263	1	0.51364	1	0.79264	1
9p gain	9 (3%)	279	0.71917	1	0.14378	1	0.14217	1	0.48825	1	0.22924	1	0.49655	1	0.76218	1	0.73255	1
9q gain	11 (4%)	277	0.18108	1	0.33213	1	0.14217	1	0.48825	1	0.72099	1	1	1	0.92204	1	0.50981	1
11p gain	19 (7%)	269	0.0054276	1	1	1	0.13959	1	0.019926	1	0.021346	1	0.010744	1	0.64361	1	0.043648	1
11q gain	16 (6%)	272	0.0019058	1	0.49251	1	0.28639	1	0.10547	1	0.016059	1	0.030162	1	0.6659	1	0.097481	1
12p gain	23 (8%)	265	0.00047448	0.274	0.32797	1	0.53621	1	0.32414	1	0.00093757	0.535	0.02717	1	0.38252	1	0.023315	1
12q gain	11 (4%)	277	0.061423	1	1	1	1	1	0.66701	1	0.025248	1	0.31046	1	0.53597	1	0.022624	1
13q gain	45 (16%)	243	5.6001e-10	3.45e-07	1.6018e-05	0.00958	0.4294	1	0.87628	1	0.0019765	1	0.16952	1	0.37438	1	0.73505	1
14q gain	16 (6%)	272	0.015427	1	0.058592	1	0.1659	1	0.72166	1	0.18503	1	1	1	0.8989	1	1	1
15q gain	37 (13%)	251	0.0098856	1	0.44813	1	0.94407	1	0.59187	1	0.0073144	1	0.43601	1	0.86872	1	0.13159	1
16p gain	17 (6%)	271	0.025161	1	0.026733	1	0.56162	1	0.6923	1	0.017071	1	0.10627	1	0.1028	1	0.44424	1
16q gain	16 (6%)	272	0.019146	1	0.078886	1	0.21654	1	0.24673	1	0.035048	1	0.15786	1	0.29094	1	0.12019	1
17p gain	17 (6%)	271	0.14968	1	0.21489	1	0.46396	1	0.42985	1	0.16366	1	0.69864	1	0.14537	1	0.44424	1
17q gain	30 (10%)	258	0.019533	1	0.069819	1	0.037355	1	0.011284	1	0.10275	1	0.50671	1	0.20013	1	0.31241	1
18p gain	33 (11%)	255	0.1035	1	0.1804	1	0.5875	1	0.63981	1	0.3544	1	0.48875	1	0.88955	1	0.70272	1
18q gain	23 (8%)	265	0.17593	1	0.064033	1	1	1	0.93176	1	0.26765	1	0.045187	1	0.40131	1	0.36393	1
19p gain	18 (6%)	270	0.097715	1	0.064298	1	0.11927	1	0.20348	1	0.0086679	1	0.0011919	0.677	0.55144	1	0.80486	1
19q gain	22 (8%)	266	0.0063898	1	0.023147	1	0.37323	1	0.67722	1	0.00025265	0.148	0.0013538	0.768	0.92116	1	0.651	1
20p gain	79 (27%)	209	2.6864e-05	0.016	0.0054319	1	0.3982	1	0.79026	1	6.1523e-05	0.0365	0.0042248	1	0.049556	1	0.028187	1
20q gain	100 (35%)	188	3.2332e-07	0.000197	0.0093582	1	0.24467	1	0.39803	1	0.00085488	0.489	0.014604	1	0.32066	1	0.094497	1
21q gain	31 (11%)	257	0.0027355	1	0.00034103	0.198	0.85514	1	0.71962	1	0.0061466	1	0.042675	1	0.15242	1	0.5513	1
22q gain	64 (22%)	224	7.7137e-06	0.00465	0.52488	1	0.82817	1	0.77579	1	0.15384	1	0.53754	1	0.54121	1	0.45933	1
Xq gain	6 (2%)	282	1	1	0.2934	1	0.69248	1	0.35539	1	0.13672	1	0.0081486	1	0.17875	1	0.08672	1
1p loss	20 (7%)	268	0.029614	1	0.00014222	0.0835	0.57423	1	0.49317	1	0.005338	1	0.11653	1	0.55786	1	0.63301	1
1q loss	9 (3%)	279	0.015052	1	0.14378	1	0.11863	1	0.81897	1	0.10167	1	0.48092	1	1	1	1	1
2p loss	24 (8%)	264	0.00032173	0.187	0.11895	1	0.082774	1	0.0080393	1	0.09988	1	0.31889	1	1.5647e-05	0.00937	0.0015477	0.87
2q loss	24 (8%)	264	0.0015178	0.855	0.017659	1	0.082774	1	0.011547	1	0.010942	1	0.31889	1	8.6652e-05	0.051	0.0075934	1
3p loss	24 (8%)	264	0.2712	1	0.13937	1	0.048612	1	0.23925	1	0.006707	1	0.0008414	0.482	0.96304	1	0.38718	1
3q loss	21 (7%)	267	0.1486	1	0.086714	1	0.048612	1	0.26906	1	0.11325	1	0.090058	1	0.71054	1	1	1
4p loss	35 (12%)	253	0.070832	1	0.11477	1	0.80922	1	0.28136	1	0.047695	1	0.11473	1	0.60869	1	0.57644	1
4q loss	38 (13%)	250	0.0015879	0.891	0.012637	1	0.95694	1	0.18737	1	0.055784	1	0.093169	1	0.31296	1	0.2782	1
5p loss	34 (12%)	254	0.014361	1	0.097335	1	0.048875	1	0.10005	1	0.35244	1	0.21851	1	0.5779	1	0.44552	1
5q loss	52 (18%)	236	1.0109e-05	0.00609	0.0051879	1	0.080036	1	0.37178	1	0.5981	1	0.59904	1	0.69855	1	1	1
6p loss	25 (9%)	263	0.023889	1	0.6229	1	0.28879	1	0.7462	1	0.14439	1	0.076	1	0.17875	1	0.1333	1
6q loss	100 (35%)	188	1.1993e-12	7.44e-10	0.040014	1	0.84762	1	0.22712	1	0.0092215	1	0.019952	1	0.41721	1	0.1569	1
7p loss	7 (2%)	281	0.46589	1	0.034427	1	0.26968	1	0.30546	1	0.16588	1	0.80355	1	0.62794	1	0.71451	1
7q loss	6 (2%)	282	0.67111	1	0.089954	1	0.2527	1	0.32861	1	0.69632	1	0.88323	1	1	1	1	1
8p loss	36 (12%)	252	0.4267	1	0.1591	1	0.61958	1	0.90905	1	0.34667	1	0.4195	1	0.11954	1	0.024816	1
8q loss	9 (3%)	279	0.20131	1	0.18057	1	0.65938	1	1	1	0.24912	1	0.013575	1	0.42977	1	0.49091	1
9p loss	159 (55%)	129	1.6096e-12	9.96e-10	4.4917e-07	0.000274	0.022662	1	0.95862	1	0.00023067	0.135	7.0949e-05	0.0419	0.49898	1	0.21728	1
9q loss	115 (40%)	173	0.00015354	0.09	0.0013539	0.768	0.35016	1	0.6261	1	0.17538	1	0.091142	1	0.4992	1	0.31752	1
10p loss	120 (42%)	168	4.9622e-13	3.08e-10	2.8228e-05	0.0168	0.97821	1	0.085259	1	2.3232e-07	0.000142	2.1262e-06	0.00129	0.39035	1	0.26373	1
10q loss	135 (47%)	153	2.1754e-13	1.35e-10	5.7658e-06	0.00349	0.62587	1	0.15126	1	6.8284e-08	4.18e-05	1.4716e-05	0.00883	0.73912	1	0.62274	1
11p loss	63 (22%)	225	5.0951e-08	3.12e-05	0.0051738	1	0.63214	1	0.56068	1	0.086539	1	0.54128	1	0.14349	1	0.55403	1
11q loss	72 (25%)	216	6.122e-06	0.0037	0.0049989	1	0.65271	1	1	1	0.19142	1	0.68747	1	0.78694	1	0.88806	1
12p loss	21 (7%)	267	0.15668	1	0.00078696	0.453	0.87318	1	0.20348	1	0.44829	1	0.090058	1	0.76432	1	0.81474	1
12q loss	31 (11%)	257	0.13208	1	5.402e-05	0.0321	1	1	0.53312	1	0.064267	1	0.02784	1	0.77936	1	0.42867	1
13q loss	40 (14%)	248	0.00052228	0.301	0.31589	1	0.8501	1	0.33898	1	0.93143	1	0.22578	1	0.46619	1	0.86035	1
14q loss	61 (21%)	227	1.79e-08	1.1e-05	0.015954	1	0.91254	1	0.73136	1	0.0017785	0.991	0.0052133	1	0.61221	1	0.76423	1
15q loss	17 (6%)	271	0.01054	1	0.042735	1	0.11571	1	0.22129	1	0.82705	1	0.11852	1	0.43437	1	0.60852	1
16p loss	24 (8%)	264	0.0083042	1	0.0013647	0.771	0.11927	1	0.76096	1	0.10551	1	0.86009	1	0.10681	1	0.043059	1
16q loss	57 (20%)	231	0.0017092	0.954	0.0024656	1	1	1	0.57323	1	0.0059977	1	0.7703	1	0.033494	1	0.028186	1
17p loss	56 (19%)	232	0.03614	1	0.24496	1	0.69181	1	0.48832	1	0.17324	1	0.87839	1	0.25089	1	0.35009	1
17q loss	27 (9%)	261	0.077518	1	0.33165	1	0.61419	1	0.76096	1	0.16856	1	0.37018	1	1	1	1	1
18p loss	54 (19%)	234	0.0088629	1	0.0060906	1	0.47538	1	0.80813	1	0.0003976	0.23	3.5906e-05	0.0214	0.31575	1	1	1
18q loss	49 (17%)	239	0.024731	1	0.025926	1	0.13826	1	0.20521	1	0.02232	1	0.004435	1	0.76161	1	1	1
19p loss	22 (8%)	266	0.016056	1	0.4584	1	0.27741	1	0.76096	1	0.04992	1	0.029673	1	0.19979	1	0.651	1
19q loss	22 (8%)	266	0.0018752	1	0.4584	1	0.82362	1	0.67722	1	0.34344	1	0.095325	1	0.49335	1	0.36393	1
20p loss	14 (5%)	274	0.82803	1	0.53927	1	0.36918	1	1	1	0.43628	1	0.25127	1	0.24714	1	1	1
20q loss	3 (1%)	285	0.21892	1	0.18616	1	NA	NA	NA	NA	0.48903	1	0.19115	1	0.79097	1	1	1
21q loss	33 (11%)	255	0.36685	1	0.47492	1	0.48262	1	0.84187	1	0.82411	1	0.53926	1	0.19387	1	0.56939	1
22q loss	24 (8%)	264	0.014656	1	0.042042	1	0.21358	1	0.87763	1	0.75781	1	0.21385	1	0.46713	1	0.26906	1
Xq loss	9 (3%)	279	0.35341	1	0.008844	1	0.41787	1	0.32759	1	0.32245	1	0.48092	1	0.062216	1	1	1