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	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
1p gain	28 (11%)	216	0.009294	1	0.26523	1	0.14788	1	0.51716	1	0.081128	1	0.65624	1	0.96476	1	0.24881	1
1q gain	77 (32%)	167	7.1457e-09	4.4e-06	0.008452	1	0.36626	1	0.17243	1	0.07992	1	0.38509	1	0.19992	1	0.071675	1
2p gain	30 (12%)	214	0.0032081	1	0.30673	1	0.069563	1	0.39109	1	0.016512	1	0.030339	1	0.17319	1	0.017055	1
2q gain	28 (11%)	216	0.0024594	1	0.47482	1	0.01976	1	0.3842	1	0.0049157	1	0.0056436	1	0.022703	1	0.0057395	1
3p gain	23 (9%)	221	0.057977	1	0.067723	1	1	1	0.77075	1	0.24156	1	0.081495	1	0.47532	1	0.32495	1
3q gain	30 (12%)	214	0.15788	1	0.16407	1	0.56458	1	0.59406	1	0.17985	1	0.23223	1	0.90268	1	0.48199	1
4p gain	24 (10%)	220	0.001778	1	0.052276	1	0.97929	1	0.46856	1	0.81574	1	0.76897	1	0.77787	1	0.84797	1
4q gain	20 (8%)	224	0.0010149	0.587	0.035712	1	0.92289	1	0.9449	1	0.42655	1	0.53835	1	0.32754	1	0.88126	1
5p gain	28 (11%)	216	0.0096612	1	0.26523	1	0.75834	1	0.81906	1	0.90643	1	0.80627	1	0.13454	1	0.74811	1
5q gain	14 (6%)	230	0.021312	1	0.38881	1	0.62874	1	0.40445	1	0.3993	1	0.63396	1	0.18898	1	0.31932	1
6p gain	76 (31%)	168	2.2085e-10	1.37e-07	1.8746e-05	0.0113	0.089368	1	0.58862	1	0.26659	1	0.045788	1	0.01007	1	0.00081013	0.471
6q gain	18 (7%)	226	0.25042	1	0.056384	1	1	1	0.4979	1	0.66122	1	0.36691	1	0.76179	1	0.5572	1
7p gain	101 (41%)	143	3.047e-10	1.89e-07	0.10904	1	0.1947	1	0.29812	1	0.00048535	0.285	0.05916	1	0.83089	1	0.46126	1
7q gain	104 (43%)	140	6.5174e-12	4.05e-09	0.23604	1	0.13043	1	0.16729	1	0.00022244	0.133	0.044882	1	0.3064	1	0.10847	1
8p gain	49 (20%)	195	1.1591e-09	7.16e-07	0.011834	1	0.056231	1	0.36356	1	0.0084639	1	0.030795	1	0.70739	1	0.42515	1
8q gain	78 (32%)	166	1.6004e-09	9.87e-07	2.0133e-05	0.0121	0.60323	1	0.92449	1	0.00033537	0.199	0.0074954	1	0.55811	1	0.5814	1
9p gain	9 (4%)	235	0.76134	1	0.14419	1	0.11973	1	0.4352	1	0.39508	1	0.89388	1	0.55492	1	0.51219	1
9q gain	10 (4%)	234	0.098271	1	0.46761	1	0.23617	1	0.59993	1	0.39385	1	0.82347	1	0.55492	1	0.51219	1
11p gain	17 (7%)	227	0.0098626	1	0.90146	1	0.14706	1	0.47436	1	0.023079	1	0.047658	1	0.37076	1	0.096301	1
11q gain	15 (6%)	229	0.00031444	0.186	0.4127	1	0.30722	1	0.71982	1	0.014565	1	0.036449	1	0.36773	1	0.15393	1
12p gain	23 (9%)	221	4.4055e-07	0.000269	0.14692	1	0.88313	1	0.92836	1	0.0017199	0.991	0.20852	1	0.30561	1	0.45702	1
12q gain	11 (5%)	233	0.00069107	0.404	0.62881	1	0.84658	1	0.80659	1	0.059725	1	0.097092	1	0.56444	1	0.12402	1
13q gain	39 (16%)	205	7.0002e-06	0.00424	2.3002e-05	0.0138	0.39853	1	0.17425	1	0.0082774	1	0.014069	1	0.50247	1	0.3079	1
14q gain	16 (7%)	228	0.034793	1	0.061424	1	0.043079	1	0.2567	1	1	1	0.74844	1	0.79768	1	0.6765	1
15q gain	35 (14%)	209	1.9991e-06	0.00122	0.41977	1	0.56665	1	0.91224	1	0.50374	1	0.49192	1	1	1	0.12342	1
16p gain	16 (7%)	228	0.00055354	0.325	0.009132	1	0.45191	1	0.7244	1	0.013166	1	0.28021	1	0.59188	1	0.62276	1
16q gain	15 (6%)	229	0.015371	1	0.046195	1	0.19217	1	0.52674	1	0.02221	1	0.36403	1	0.4777	1	0.34165	1
17p gain	16 (7%)	228	0.063618	1	0.20687	1	0.71856	1	0.79003	1	0.4638	1	0.38826	1	0.21273	1	0.3981	1
17q gain	28 (11%)	216	0.021379	1	0.044147	1	0.70178	1	0.29297	1	0.29845	1	0.2084	1	0.10798	1	0.78437	1
18p gain	27 (11%)	217	0.051139	1	0.16055	1	0.90985	1	0.80089	1	0.067558	1	0.18121	1	0.093474	1	0.21122	1
18q gain	16 (7%)	228	0.034793	1	0.21921	1	0.53556	1	0.30764	1	0.27632	1	0.079526	1	0.94043	1	0.78744	1
19p gain	16 (7%)	228	0.0081165	1	0.028035	1	0.62295	1	0.20364	1	0.0050192	1	0.027242	1	0.16453	1	0.92982	1
19q gain	20 (8%)	224	0.0076074	1	0.039644	1	0.41539	1	0.6776	1	0.00068291	0.4	0.070401	1	0.65052	1	0.73484	1
20p gain	70 (29%)	174	6.076e-06	0.00369	0.0019492	1	0.34505	1	0.90363	1	0.00014894	0.0891	0.0088747	1	0.079493	1	0.26876	1
20q gain	89 (36%)	155	1.6575e-08	1.02e-05	0.0019876	1	0.44788	1	0.80222	1	0.00077071	0.449	0.058451	1	0.35103	1	0.5121	1
21q gain	29 (12%)	215	0.038424	1	0.00026081	0.155	0.18161	1	0.40155	1	0.10605	1	0.055284	1	0.53814	1	1	1
22q gain	59 (24%)	185	0.0020942	1	0.19746	1	0.80323	1	0.93285	1	0.32407	1	0.81142	1	0.60119	1	0.46918	1
Xq gain	4 (2%)	240	0.82894	1	0.8353	1	1	1	0.50711	1	0.20716	1	0.089739	1	0.53504	1	0.57653	1
1p loss	15 (6%)	229	0.060475	1	0.025611	1	0.38276	1	0.41634	1	0.014209	1	0.10122	1	0.83296	1	0.78744	1
1q loss	7 (3%)	237	0.063679	1	0.34458	1	0.5445	1	0.56303	1	0.18207	1	0.60249	1	0.61233	1	1	1
2p loss	18 (7%)	226	0.0088328	1	0.1057	1	0.30574	1	0.038365	1	0.69519	1	0.077127	1	0.0004823	0.284	0.0059174	1
2q loss	19 (8%)	225	0.022495	1	0.01715	1	0.20779	1	0.14965	1	0.34087	1	0.078433	1	0.00085164	0.494	0.027986	1
3p loss	22 (9%)	222	0.058538	1	0.076118	1	0.38163	1	0.36403	1	0.0040479	1	0.031001	1	0.87683	1	0.27023	1
3q loss	19 (8%)	225	0.073473	1	0.060552	1	0.42121	1	0.20933	1	0.10527	1	0.25218	1	0.863	1	0.21416	1
4p loss	30 (12%)	214	0.32186	1	0.1933	1	0.34168	1	0.13245	1	0.0079875	1	0.0088585	1	0.79282	1	0.1789	1
4q loss	31 (13%)	213	0.14155	1	0.066384	1	0.30806	1	0.02057	1	0.0097391	1	0.0028079	1	0.39092	1	0.045319	1
5p loss	32 (13%)	212	0.70134	1	0.26232	1	0.27238	1	0.33303	1	0.33057	1	0.14236	1	0.062426	1	0.26012	1
5q loss	46 (19%)	198	0.51477	1	0.043646	1	0.068857	1	0.55318	1	0.27254	1	0.25117	1	0.63721	1	0.66317	1
6p loss	28 (11%)	216	0.0085675	1	0.21544	1	0.4665	1	0.34726	1	0.35524	1	0.23223	1	0.33201	1	0.21323	1
6q loss	90 (37%)	154	0.0001109	0.0664	0.00070463	0.411	0.35417	1	0.45416	1	0.0041618	1	0.015958	1	0.53464	1	0.25699	1
7p loss	7 (3%)	237	0.79857	1	0.034783	1	0.6645	1	0.47064	1	0.79542	1	1	1	0.41949	1	1	1
7q loss	6 (2%)	238	0.676	1	0.091108	1	0.77926	1	0.70257	1	1	1	0.87817	1	1	1	0.83903	1
8p loss	28 (11%)	216	0.067891	1	0.11105	1	0.05702	1	0.4862	1	0.052526	1	0.20066	1	0.080375	1	0.12424	1
8q loss	5 (2%)	239	1	1	0.07052	1	0.13857	1	0.51542	1	0.326	1	0.03845	1	0.84365	1	0.79769	1
9p loss	134 (55%)	110	3.3095e-08	2.03e-05	1.9293e-05	0.0117	0.18758	1	0.13065	1	0.0029192	1	0.0029718	1	1	1	0.4069	1
9q loss	100 (41%)	144	0.0056598	1	0.00044053	0.26	0.44783	1	0.36355	1	0.23775	1	0.89541	1	0.49633	1	0.63614	1
10p loss	103 (42%)	141	2.1931e-07	0.000134	5.5327e-05	0.0333	0.4398	1	0.15768	1	1.1268e-06	0.000686	0.0008637	0.5	0.57614	1	0.16343	1
10q loss	112 (46%)	132	3.0176e-10	1.87e-07	9.7807e-05	0.0587	0.53898	1	0.19182	1	1.1062e-06	0.000675	0.00066066	0.387	0.98494	1	0.376	1
11p loss	57 (23%)	187	0.0021874	1	0.0018017	1	0.48381	1	0.26981	1	0.055087	1	0.0063412	1	0.12025	1	0.66482	1
11q loss	64 (26%)	180	0.00038169	0.226	0.024619	1	0.91636	1	0.76364	1	0.0502	1	0.0013593	0.784	0.60915	1	0.46776	1
12p loss	15 (6%)	229	0.16712	1	0.0088094	1	0.50038	1	0.81364	1	0.25943	1	0.29831	1	0.87953	1	0.7039	1
12q loss	24 (10%)	220	0.0053754	1	0.0023858	1	0.83898	1	0.8748	1	0.32909	1	0.24096	1	0.77787	1	0.84797	1
13q loss	36 (15%)	208	0.32194	1	0.45389	1	0.17234	1	0.65644	1	0.66158	1	0.97097	1	0.082695	1	0.22373	1
14q loss	54 (22%)	190	6.9208e-08	4.24e-05	0.050793	1	0.41145	1	0.27586	1	0.004304	1	0.13386	1	1	1	0.43207	1
15q loss	15 (6%)	229	0.0002698	0.161	0.08491	1	0.6509	1	0.13763	1	0.6339	1	0.61053	1	0.26696	1	0.14857	1
16p loss	22 (9%)	222	0.02156	1	0.0056679	1	0.95625	1	0.2043	1	0.19926	1	0.26929	1	0.042029	1	0.50978	1
16q loss	46 (19%)	198	0.0058317	1	0.02925	1	0.57131	1	0.37339	1	0.054456	1	0.28605	1	0.040682	1	0.096079	1
17p loss	50 (20%)	194	0.61872	1	0.17506	1	0.4931	1	0.68797	1	0.067269	1	0.9546	1	0.64569	1	0.38799	1
17q loss	22 (9%)	222	0.080492	1	0.5136	1	0.38701	1	0.47028	1	0.12273	1	0.35699	1	0.49305	1	1	1
18p loss	48 (20%)	196	0.0038535	1	0.0043616	1	0.37245	1	0.41519	1	0.00028798	0.171	0.029072	1	0.93245	1	0.88545	1
18q loss	44 (18%)	200	0.012846	1	0.018225	1	0.050228	1	0.18768	1	0.05183	1	0.22137	1	0.86327	1	0.61631	1
19p loss	19 (8%)	225	0.21033	1	0.53995	1	0.0057819	1	0.53606	1	0.14237	1	0.36666	1	0.47249	1	0.93551	1
19q loss	19 (8%)	225	0.21997	1	0.36584	1	0.65383	1	0.3467	1	0.39526	1	0.94991	1	0.70687	1	0.93551	1
20p loss	12 (5%)	232	0.5281	1	0.42244	1	0.15262	1	0.74441	1	0.7551	1	0.22203	1	0.18359	1	0.55235	1
20q loss	3 (1%)	241	0.50252	1	0.18669	1	NA	NA	NA	NA	0.50817	1	0.2135	1	1	1	1	1
21q loss	28 (11%)	216	0.26105	1	0.26523	1	0.823	1	0.63417	1	0.43571	1	0.45139	1	0.80946	1	0.30461	1
22q loss	19 (8%)	225	0.49801	1	0.20517	1	0.59089	1	0.42806	1	0.6444	1	0.42789	1	0.20791	1	0.80598	1
Xq loss	10 (4%)	234	0.27658	1	0.0032853	1	0.28298	1	0.18795	1	0.39585	1	0.081892	1	0.40427	1	0.63117	1