Clinical Features	MRNA_CNMF		MRNA_CHIERARCHICAL		CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL		MIRSEQ_MATURE_CNMF		MIRSEQ_MATURE_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	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	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
1p gain	9 (2%)	356	NA	NA	NA	NA	0.0018832	1	0.0073827	1	0.024148	1	1	1	3.1295e-08	2.43e-05	0.0063901	1	0.11366	1	0.0060822	1	0.0031739	1	0.073347	1
1q gain	14 (4%)	351	NA	NA	NA	NA	0.00026385	0.188	0.0041267	1	0.43569	1	0.73827	1	0.00021975	0.157	0.10961	1	0.53663	1	0.11838	1	0.11036	1	0.11835	1
2p gain	6 (2%)	359	NA	NA	NA	NA	0.058533	1	0.11499	1	0.31113	1	0.43043	1	0.06101	1	0.39391	1	0.16485	1	0.26543	1	0.22274	1	0.030887	1
2q gain	5 (1%)	360	NA	NA	NA	NA	0.25582	1	0.097732	1	0.31113	1	0.43043	1	0.042971	1	0.71665	1	0.18762	1	0.40981	1	0.48025	1	0.040743	1
3p gain	8 (2%)	357	NA	NA	NA	NA	1	1	0.75293	1	0.69099	1	0.5601	1	0.00015513	0.112	0.88896	1	0.19098	1	1	1	0.64535	1	1	1
3q gain	7 (2%)	358	NA	NA	NA	NA	0.54853	1	0.27499	1	0.055985	1	0.74032	1	8.6518e-06	0.00645	0.60321	1	0.33829	1	0.49672	1	0.29512	1	0.76558	1
4p gain	8 (2%)	357	NA	NA	NA	NA	0.023294	1	0.097501	1	0.092496	1	1	1	0.12865	1	0.35696	1	0.48613	1	0.048462	1	0.07432	1	0.24627	1
4q gain	3 (1%)	362	NA	NA	NA	NA	0.18641	1	0.57496	1	0.33677	1	1	1	0.0040202	1	1	1	0.91173	1	0.019736	1	0.4382	1	1	1
5p gain	6 (2%)	359	NA	NA	NA	NA	0.015801	1	0.077489	1	0.021682	1	1	1	1.2526e-07	9.58e-05	0.047673	1	0.18762	1	0.0045781	1	0.10167	1	0.16636	1
5q gain	4 (1%)	361	NA	NA	NA	NA	0.04305	1	0.027655	1	NA	NA	NA	NA	0.024814	1	0.17172	1	0.063824	1	0.2735	1	0.099664	1	0.33579	1
6p gain	5 (1%)	360	NA	NA	NA	NA	1	1	0.15332	1	0.19674	1	1	1	0.32076	1	0.48421	1	0.49093	1	0.40981	1	0.024206	1	0.040743	1
7p gain	89 (24%)	276	0.7446	1	0.64812	1	1.1906e-28	9.56e-26	9.439e-16	7.52e-13	0.00037853	0.266	0.013099	1	7.1583e-12	5.68e-09	2.1701e-05	0.016	0.0031145	1	0.028965	1	4.0163e-05	0.0295	1.5283e-06	0.00115
7q gain	114 (31%)	251	0.7639	1	0.49526	1	7.645e-29	6.15e-26	2.5112e-14	2e-11	0.0053135	1	0.038605	1	6.3659e-08	4.9e-05	1.1027e-05	0.0082	0.011353	1	0.087775	1	0.0013233	0.9	6.2982e-05	0.046
8p gain	30 (8%)	335	NA	NA	NA	NA	0.0068247	1	0.032089	1	0.085763	1	0.63029	1	0.34862	1	0.037871	1	0.56112	1	0.065387	1	0.04617	1	0.038305	1
8q gain	37 (10%)	328	0.051852	1	0.30256	1	0.00027191	0.193	0.0035789	1	0.012919	1	0.61811	1	0.017285	1	0.0051968	1	0.36509	1	0.056782	1	0.049791	1	0.010206	1
9p gain	13 (4%)	352	NA	NA	NA	NA	0.042697	1	0.076592	1	0.29435	1	0.81972	1	0.086836	1	0.3789	1	0.28599	1	0.049314	1	0.05599	1	0.27288	1
9q gain	17 (5%)	348	NA	NA	NA	NA	0.02313	1	0.25892	1	0.25818	1	0.66107	1	0.0067856	1	0.18619	1	0.1914	1	0.0015144	1	0.0718	1	0.25985	1
10p gain	36 (10%)	329	1	1	0.087863	1	1.8594e-11	1.47e-08	1.749e-09	1.37e-06	0.023328	1	0.54644	1	4.0965e-05	0.03	0.00063763	0.443	0.31492	1	0.63718	1	0.0018654	1	0.15741	1
10q gain	5 (1%)	360	NA	NA	NA	NA	0.019865	1	0.15332	1	0.5732	1	0.66838	1	0.023186	1	0.58477	1	0.083553	1	0.061366	1	0.50751	1	0.40095	1
11p gain	25 (7%)	340	NA	NA	NA	NA	0.063609	1	0.0024378	1	0.026963	1	0.49573	1	0.014428	1	0.038804	1	0.14981	1	0.74462	1	0.025797	1	0.43668	1
11q gain	42 (12%)	323	0.61538	1	0.11658	1	0.23317	1	0.034213	1	0.083688	1	0.14103	1	0.16786	1	0.17235	1	0.37013	1	1	1	0.22878	1	1	1
12p gain	24 (7%)	341	0.75385	1	0.087863	1	0.046003	1	0.2828	1	0.26076	1	0.87476	1	0.20911	1	0.080283	1	0.10357	1	0.014122	1	0.053526	1	0.070996	1
12q gain	11 (3%)	354	NA	NA	NA	NA	0.057237	1	0.24686	1	0.17332	1	1	1	0.037163	1	0.070252	1	0.18451	1	0.062103	1	0.012349	1	0.077956	1
13q gain	4 (1%)	361	NA	NA	NA	NA	0.23443	1	0.32548	1	NA	NA	NA	NA	0.5235	1	0.66292	1	0.41398	1	0.2735	1	0.36938	1	0.33579	1
14q gain	3 (1%)	362	NA	NA	NA	NA	0.35388	1	1	1	NA	NA	NA	NA	0.88708	1	0.40561	1	0.19633	1	0.5918	1	0.00049335	0.344	0.096085	1
15q gain	6 (2%)	359	NA	NA	NA	NA	0.072947	1	0.2184	1	0.11375	1	0.46484	1	1.0317e-06	0.000782	0.047673	1	0.49093	1	0.020862	1	0.72436	1	0.040743	1
16p gain	12 (3%)	353	NA	NA	NA	NA	0.60984	1	0.72932	1	0.56065	1	0.65772	1	0.0066532	1	0.23562	1	0.13593	1	0.0093718	1	0.16809	1	0.015673	1
16q gain	13 (4%)	352	NA	NA	NA	NA	0.43418	1	0.63251	1	0.46901	1	0.73827	1	0.011535	1	0.16334	1	0.42306	1	0.0059339	1	0.20567	1	0.01337	1
17p gain	11 (3%)	354	NA	NA	NA	NA	0.28146	1	0.85262	1	0.6368	1	0.53058	1	0.000721	0.497	0.13391	1	0.067363	1	0.026228	1	0.017871	1	0.073693	1
17q gain	12 (3%)	353	NA	NA	NA	NA	0.34834	1	0.69386	1	0.6368	1	0.53058	1	0.00083233	0.572	0.11098	1	0.022706	1	0.017625	1	0.007279	1	0.036771	1
18p gain	11 (3%)	354	NA	NA	NA	NA	0.0076548	1	0.066576	1	0.022636	1	0.20533	1	1.4489e-09	1.14e-06	0.28834	1	0.67417	1	0.053671	1	0.41723	1	0.6631	1
18q gain	8 (2%)	357	NA	NA	NA	NA	0.027745	1	0.16055	1	0.08038	1	0.14214	1	3.2319e-07	0.000247	0.60321	1	0.86764	1	0.034825	1	0.29714	1	1	1
19p gain	66 (18%)	299	0.22111	1	0.83612	1	4.4002e-07	0.000335	2.6403e-09	2.06e-06	0.56691	1	0.36087	1	0.00031479	0.222	0.023242	1	0.31591	1	0.78078	1	0.18177	1	0.83837	1
19q gain	18 (5%)	347	NA	NA	NA	NA	5.6396e-08	4.35e-05	2.1774e-09	1.7e-06	0.057135	1	0.41803	1	1.1264e-06	0.000853	0.0014958	1	0.038731	1	0.25803	1	3.4021e-06	0.00255	0.018174	1
20p gain	34 (9%)	331	NA	NA	NA	NA	1.9762e-08	1.54e-05	1.2243e-09	9.65e-07	0.0010111	0.691	0.1579	1	4.3701e-06	0.00326	0.0013924	0.944	0.18052	1	0.080444	1	0.000366	0.258	0.0011838	0.806
20q gain	34 (9%)	331	NA	NA	NA	NA	4.2085e-08	3.25e-05	5.4492e-11	4.32e-08	0.00089846	0.615	0.1097	1	3.9284e-08	3.04e-05	9.6212e-05	0.0698	0.017652	1	0.019823	1	2.5556e-05	0.0188	5.8861e-05	0.043
21q gain	19 (5%)	346	NA	NA	NA	NA	0.032832	1	0.028801	1	0.10983	1	0.53086	1	0.013461	1	0.46618	1	0.54017	1	1	1	0.20633	1	0.41942	1
22q gain	12 (3%)	353	NA	NA	NA	NA	0.00056695	0.395	0.00016911	0.122	1	1	0.5601	1	0.00067384	0.466	0.00067805	0.469	0.011385	1	0.089842	1	9.9766e-05	0.0723	0.03724	1
xq gain	30 (8%)	335	NA	NA	NA	NA	0.0078198	1	3.0376e-05	0.0223	0.18166	1	0.75326	1	0.0059741	1	0.0073168	1	0.35573	1	0.51098	1	0.0032287	1	0.084145	1
1p loss	133 (36%)	232	0.028572	1	0.00017271	0.124	1.7992e-53	1.46e-50	4.24e-72	3.45e-69	0.0003111	0.22	0.142	1	1.2477e-37	1.01e-34	3.3482e-44	2.71e-41	3.3683e-10	2.66e-07	1.8371e-05	0.0136	1.4887e-10	1.18e-07	2.0629e-09	1.62e-06
1q loss	19 (5%)	346	0.34359	1	0.14393	1	0.44779	1	0.39751	1	0.5517	1	0.54013	1	0.11238	1	0.42778	1	0.23317	1	0.11845	1	0.27735	1	0.79957	1
2p loss	16 (4%)	349	NA	NA	NA	NA	0.20336	1	0.063764	1	0.33106	1	1	1	0.016011	1	0.028652	1	0.51528	1	0.00024462	0.174	0.43369	1	0.22434	1
2q loss	15 (4%)	350	NA	NA	NA	NA	0.077936	1	0.0096062	1	0.0692	1	0.62827	1	0.0083215	1	0.044486	1	0.16239	1	0.027724	1	0.26796	1	0.12419	1
3p loss	19 (5%)	346	NA	NA	NA	NA	0.2308	1	0.69291	1	0.0065168	1	0.48289	1	0.00027203	0.193	0.081301	1	0.030524	1	0.012803	1	0.075	1	0.0050968	1
3q loss	22 (6%)	343	0.17504	1	0.56068	1	0.20468	1	0.36809	1	0.25799	1	0.19137	1	0.0026503	1	0.17995	1	0.24309	1	0.072277	1	0.24123	1	0.043906	1
4p loss	54 (15%)	311	1	1	0.60733	1	1.1403e-05	0.00847	1.7982e-08	1.4e-05	0.41483	1	0.035287	1	2.2368e-08	1.74e-05	1.1587e-07	8.88e-05	0.017786	1	0.050633	1	0.00014737	0.106	0.12454	1
4q loss	70 (19%)	295	1	1	0.19622	1	0.00072745	0.501	5.7848e-07	0.00044	0.26597	1	0.066479	1	4.0971e-06	0.00306	1.0131e-06	0.000769	0.0044687	1	0.0080866	1	7.4275e-05	0.0541	0.054334	1
5p loss	28 (8%)	337	0.7446	1	0.042206	1	1.7452e-05	0.0129	0.00026841	0.191	0.84862	1	1	1	0.10526	1	0.019	1	0.096025	1	0.18952	1	0.033543	1	0.90448	1
5q loss	27 (7%)	338	0.44623	1	0.018246	1	0.00041018	0.288	0.00048944	0.342	0.021796	1	0.50804	1	2.2847e-10	1.8e-07	0.0025813	1	0.002464	1	0.0040943	1	0.0025811	1	0.11172	1
6p loss	24 (7%)	341	NA	NA	NA	NA	0.068361	1	0.070579	1	0.18595	1	0.70781	1	0.33119	1	0.41832	1	0.060426	1	0.75231	1	0.714	1	0.009055	1
6q loss	49 (13%)	316	NA	NA	NA	NA	0.00010373	0.0751	0.0027489	1	0.25362	1	0.39785	1	0.18838	1	0.037711	1	0.00062757	0.436	0.2306	1	0.52726	1	0.031064	1
8p loss	12 (3%)	353	0.61538	1	0.0013675	0.929	0.0038697	1	0.0035244	1	0.018505	1	0.62827	1	2.4855e-05	0.0183	0.043879	1	0.10138	1	0.25478	1	0.0029869	1	0.028165	1
8q loss	8 (2%)	357	NA	NA	NA	NA	0.0016724	1	0.000186	0.133	0.080624	1	0.74032	1	0.00037927	0.266	0.11969	1	0.037924	1	0.13108	1	0.0017427	1	0.016302	1
9p loss	82 (22%)	283	0.38387	1	0.26997	1	0.022522	1	0.019081	1	0.031773	1	0.066426	1	0.003709	1	0.47333	1	0.9816	1	0.53025	1	0.40828	1	0.14004	1
9q loss	34 (9%)	331	NA	NA	NA	NA	0.50285	1	0.90998	1	0.60738	1	0.50613	1	0.029684	1	0.48346	1	0.92745	1	0.57825	1	0.42044	1	0.62158	1
10p loss	57 (16%)	308	0.27077	1	0.56068	1	1.2838e-27	1.03e-24	8.2783e-39	6.7e-36	2.5375e-07	0.000194	0.0023175	1	6.3222e-26	5.06e-23	1.7889e-06	0.00134	0.0018379	1	0.013496	1	9.2303e-16	7.37e-13	1.4491e-06	0.00109
10q loss	69 (19%)	296	0.27077	1	0.56068	1	7.7413e-26	6.19e-23	3.6102e-32	2.91e-29	1.3209e-06	0.000999	0.00087376	0.599	4.3162e-25	3.45e-22	5.88e-08	4.53e-05	0.0025889	1	0.017116	1	8.7164e-13	6.93e-10	1.4628e-06	0.0011
11p loss	46 (13%)	319	1	1	0.013836	1	1.7308e-06	0.0013	2.981e-08	2.31e-05	0.012703	1	0.5899	1	1.7317e-08	1.35e-05	8.6761e-05	0.0631	0.031539	1	0.017226	1	0.0014374	0.973	0.1035	1
11q loss	17 (5%)	348	NA	NA	NA	NA	0.0021052	1	0.0020211	1	0.017879	1	1	1	2.6428e-08	2.05e-05	0.03239	1	0.52499	1	0.0025039	1	0.041186	1	0.068354	1
12p loss	18 (5%)	347	NA	NA	NA	NA	0.04841	1	0.13145	1	0.43367	1	0.35972	1	0.53513	1	0.080983	1	0.53129	1	0.25803	1	0.62294	1	0.41942	1
12q loss	35 (10%)	330	1	1	0.087863	1	9.0706e-08	6.97e-05	0.00022029	0.157	0.68633	1	0.68996	1	0.2647	1	0.0029055	1	0.2195	1	0.63718	1	0.37127	1	1	1
13q loss	85 (23%)	280	0.1801	1	0.00061812	0.43	0.11742	1	0.033715	1	0.029095	1	0.56555	1	0.036203	1	0.31587	1	0.28694	1	0.070142	1	0.040596	1	0.27398	1
14q loss	56 (15%)	309	0.46711	1	0.47324	1	0.00018926	0.136	0.0011346	0.774	0.045908	1	0.14769	1	0.00024495	0.174	0.086624	1	0.00034837	0.246	0.0021622	1	0.00011008	0.0796	0.12818	1
15q loss	34 (9%)	331	1	1	0.89231	1	0.014069	1	0.0015311	1	0.27699	1	0.047616	1	0.00078342	0.539	0.015449	1	0.13901	1	0.33792	1	0.50771	1	0.28631	1
16p loss	10 (3%)	355	NA	NA	NA	NA	0.055055	1	0.47711	1	0.86477	1	0.44682	1	0.0019582	1	0.91551	1	0.10419	1	0.029563	1	0.66915	1	0.014691	1
16q loss	16 (4%)	349	NA	NA	NA	NA	0.044475	1	0.017414	1	0.37381	1	0.21908	1	0.27644	1	0.24753	1	0.4137	1	1	1	0.47174	1	0.019365	1
17p loss	13 (4%)	352	NA	NA	NA	NA	0.098172	1	0.0612	1	0.91623	1	0.53086	1	0.00064804	0.449	0.082072	1	0.060049	1	0.0095711	1	0.020261	1	0.10221	1
17q loss	9 (2%)	356	NA	NA	NA	NA	0.19848	1	0.28218	1	0.9672	1	0.38286	1	0.21545	1	0.43751	1	0.098508	1	0.34806	1	0.085472	1	0.073347	1
18p loss	48 (13%)	317	0.32144	1	0.31568	1	0.34742	1	0.013437	1	0.57345	1	0.080072	1	0.3326	1	0.45678	1	0.7001	1	0.19177	1	0.74407	1	0.8399	1
18q loss	43 (12%)	322	0.34359	1	0.21231	1	0.051653	1	0.0031414	1	0.28483	1	0.20172	1	0.044036	1	0.12187	1	0.64142	1	0.21807	1	0.67341	1	0.88957	1
19p loss	16 (4%)	349	0.57414	1	0.17751	1	0.84836	1	0.9527	1	0.37628	1	0.18153	1	0.40951	1	0.49286	1	0.64339	1	0.47101	1	0.66425	1	0.25985	1
19q loss	148 (41%)	217	0.090788	1	0.078629	1	5.4254e-51	4.4e-48	6.4556e-59	5.25e-56	0.021609	1	0.13778	1	7.2807e-32	5.86e-29	3.4869e-38	2.82e-35	1.5712e-06	0.00118	4.6769e-05	0.0342	1.4814e-09	1.16e-06	1.063e-07	8.15e-05
20p loss	3 (1%)	362	NA	NA	NA	NA	0.35388	1	0.48309	1	0.79242	1	1	1	0.0048499	1	1	1	0.78267	1	0.5918	1	0.75753	1	1	1
21q loss	27 (7%)	338	0.61538	1	0.40684	1	0.061445	1	0.022729	1	0.46096	1	0.83387	1	0.12832	1	0.063404	1	0.082831	1	0.02567	1	0.32361	1	0.36541	1
22q loss	39 (11%)	326	0.81538	1	0.10604	1	5.4492e-08	4.21e-05	6.4203e-06	0.00479	7.5833e-05	0.0552	0.040536	1	4.9462e-07	0.000376	0.00014611	0.105	0.17703	1	0.097067	1	0.00086823	0.596	0.067151	1
xq loss	49 (13%)	316	0.83946	1	0.022012	1	0.042343	1	0.00046728	0.327	0.087429	1	0.014276	1	2.0258e-05	0.015	2.4405e-05	0.018	0.089607	1	0.34044	1	0.1126	1	0.34896	1