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	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	88 (18%)	402	0.087709	1	0.10824	1	0.32557	1	0.44536	1	0.48201	1	0.30494	1	0.74544	1	0.031186	1	0.78902	1	0.44805	1	1	1	0.87987	1
1q gain	199 (41%)	291	0.6706	1	0.70352	1	0.00018228	0.156	5.6595e-05	0.0497	0.57053	1	0.29028	1	0.0062032	1	0.00012908	0.111	0.019427	1	0.0010851	0.878	0.064621	1	0.25355	1
2p gain	218 (44%)	272	0.078138	1	0.043303	1	1.0916e-11	1.03e-08	4.2839e-06	0.00386	0.40303	1	0.48362	1	1.2719e-06	0.00116	3.2205e-05	0.0285	0.0011291	0.911	0.0021543	1	0.00060919	0.503	0.0018007	1
2q gain	136 (28%)	354	0.3498	1	0.35868	1	5.738e-05	0.0504	0.031281	1	0.4413	1	0.4874	1	0.0027791	1	0.0062324	1	0.10107	1	0.082874	1	0.0051255	1	0.10856	1
3p gain	107 (22%)	383	0.97247	1	0.31804	1	0.15149	1	0.037419	1	0.83378	1	0.24257	1	0.1749	1	0.14421	1	0.77563	1	0.62595	1	0.67366	1	0.69132	1
3q gain	307 (63%)	183	0.58822	1	0.33595	1	0.0023949	1	0.30854	1	1	1	0.25993	1	0.22882	1	0.030824	1	0.10971	1	0.11847	1	0.9779	1	0.25467	1
4p gain	30 (6%)	460	0.32569	1	0.23834	1	2.5514e-05	0.0226	0.14614	1	0.27702	1	0.14784	1	0.02076	1	0.020253	1	0.25468	1	0.22146	1	0.20517	1	0.037139	1
4q gain	22 (4%)	468	0.58543	1	0.60843	1	0.0057023	1	0.11177	1	0.67792	1	0.13403	1	0.76302	1	0.70622	1	0.75487	1	0.51254	1	0.43343	1	0.55786	1
5p gain	304 (62%)	186	0.74873	1	0.85952	1	0.00082192	0.672	0.79454	1	0.38193	1	0.57669	1	0.35396	1	0.73202	1	0.934	1	0.066385	1	0.33864	1	0.13808	1
5q gain	93 (19%)	397	0.1198	1	0.16752	1	0.033493	1	0.1839	1	0.47506	1	0.11543	1	0.17598	1	0.20092	1	0.040211	1	0.11817	1	0.16822	1	0.67788	1
6p gain	106 (22%)	384	0.05493	1	0.26237	1	0.0014841	1	0.93417	1	0.92139	1	0.27107	1	0.0075918	1	0.0096602	1	0.74887	1	0.46173	1	0.73779	1	0.78871	1
6q gain	91 (19%)	399	0.069783	1	0.21589	1	0.00063929	0.527	0.50376	1	0.92295	1	0.93774	1	0.020791	1	0.0031832	1	0.6473	1	0.54214	1	0.97136	1	0.67267	1
7p gain	234 (48%)	256	0.036403	1	0.035434	1	1.9739e-05	0.0175	0.00015811	0.136	0.66386	1	0.87141	1	0.00011865	0.103	6.0107e-07	0.000552	0.0046404	1	0.0049462	1	0.003482	1	0.034487	1
7q gain	214 (44%)	276	0.0013764	1	0.0039184	1	2.6448e-11	2.5e-08	3.2179e-07	0.000297	0.9699	1	0.30174	1	4.3954e-09	4.11e-06	7.3833e-10	6.92e-07	0.00077723	0.637	0.00012769	0.11	0.0045394	1	0.0010846	0.878
8p gain	123 (25%)	367	0.59119	1	0.57051	1	0.2268	1	0.10001	1	0.5591	1	0.83276	1	0.091999	1	0.017959	1	0.50497	1	0.87569	1	1	1	0.30222	1
8q gain	247 (50%)	243	0.04905	1	0.076374	1	0.041313	1	0.0074207	1	0.2218	1	0.95859	1	0.013021	1	0.035411	1	0.02691	1	0.12372	1	0.21881	1	0.26779	1
9p gain	60 (12%)	430	0.092414	1	0.21147	1	0.0001082	0.0939	9.6695e-05	0.084	0.18629	1	0.026186	1	7.2126e-06	0.00648	9.8643e-07	0.000903	0.083915	1	0.19995	1	0.0070852	1	0.057894	1
9q gain	91 (19%)	399	0.015722	1	0.03231	1	2.8944e-12	2.75e-09	2.567e-10	2.42e-07	0.05836	1	0.013267	1	4.9406e-14	4.71e-11	6.4764e-16	6.19e-13	4.3396e-05	0.0382	0.0011781	0.948	0.0013464	1	0.0010783	0.875
10p gain	76 (16%)	414	0.32331	1	0.77521	1	0.067619	1	0.16191	1	0.063014	1	0.057095	1	0.12576	1	0.48481	1	0.026549	1	0.00054642	0.455	0.48394	1	0.6568	1
10q gain	43 (9%)	447	0.11314	1	0.24787	1	0.082051	1	0.58778	1	0.027274	1	0.18374	1	0.13102	1	0.12648	1	0.28588	1	0.17625	1	0.58834	1	0.85416	1
11p gain	72 (15%)	418	0.68047	1	1	1	0.042663	1	0.21972	1	0.34148	1	0.0029698	1	0.76786	1	0.90886	1	0.010862	1	0.40741	1	0.11712	1	0.87337	1
11q gain	89 (18%)	401	0.018913	1	0.11484	1	0.0006337	0.523	0.4192	1	0.39949	1	0.0025567	1	0.18967	1	0.027045	1	0.056758	1	0.50802	1	0.14609	1	0.66654	1
12p gain	224 (46%)	266	0.018694	1	0.090648	1	5.2529e-10	4.94e-07	0.0014735	1	0.2218	1	0.63026	1	6.6173e-05	0.0578	0.0041537	1	0.023514	1	0.058042	1	0.073733	1	0.14825	1
12q gain	151 (31%)	339	0.023738	1	0.32496	1	9.2348e-07	0.000846	0.002136	1	0.50681	1	0.59775	1	0.0051667	1	0.001109	0.896	0.28563	1	0.044038	1	0.00043004	0.36	0.084884	1
13q gain	39 (8%)	451	0.70112	1	0.45466	1	0.45945	1	0.85687	1	0.43032	1	0.81525	1	0.52746	1	0.84573	1	0.22938	1	0.78113	1	0.42999	1	0.13492	1
14q gain	124 (25%)	366	0.14335	1	0.26373	1	0.22721	1	0.11196	1	0.24846	1	0.12034	1	0.053269	1	0.015557	1	0.0024375	1	0.035301	1	0.20244	1	1	1
15q gain	104 (21%)	386	0.82515	1	0.5509	1	0.0020439	1	0.0018166	1	0.22519	1	0.77926	1	0.00065118	0.535	0.00026351	0.223	0.012298	1	0.0015057	1	0.024347	1	0.0057659	1
16p gain	86 (18%)	404	0.35505	1	0.044924	1	0.042908	1	0.50159	1	0.60537	1	0.87854	1	0.65783	1	0.13795	1	0.049463	1	0.49306	1	0.0016466	1	0.2929	1
16q gain	85 (17%)	405	0.92086	1	0.37664	1	0.018099	1	0.33216	1	0.69433	1	0.46258	1	0.14736	1	0.097696	1	0.15148	1	0.88487	1	0.095277	1	0.17599	1
17p gain	65 (13%)	425	0.0045871	1	0.070678	1	1.7027e-07	0.000158	0.00084188	0.686	0.81167	1	0.26845	1	0.00012775	0.11	4.9633e-05	0.0437	0.020252	1	0.0031431	1	0.0042713	1	0.023382	1
17q gain	156 (32%)	334	0.00092232	0.751	2.8863e-05	0.0255	1.5065e-15	1.44e-12	5.7643e-10	5.41e-07	0.23429	1	0.54576	1	1.9856e-09	1.86e-06	3.705e-10	3.49e-07	3.4965e-05	0.0308	0.0023617	1	2.3773e-07	0.00022	5.0917e-06	0.00459
18p gain	147 (30%)	343	0.0084337	1	0.0030956	1	5.0536e-09	4.72e-06	2.9989e-06	0.00272	0.47843	1	0.22124	1	0.00082829	0.676	0.0021241	1	0.0021121	1	0.023994	1	0.002434	1	0.0015671	1
18q gain	105 (21%)	385	0.0088356	1	0.023625	1	3.9647e-07	0.000365	0.0019506	1	0.40545	1	0.24873	1	0.00042156	0.353	1.6319e-05	0.0145	0.048664	1	0.0053415	1	0.083669	1	0.024488	1
19p gain	109 (22%)	381	0.03696	1	0.13599	1	7.2454e-09	6.75e-06	0.00025254	0.215	0.018326	1	0.03907	1	0.0018976	1	0.00032177	0.271	0.022297	1	0.0014318	1	0.036322	1	0.08927	1
19q gain	155 (32%)	335	0.11339	1	0.21403	1	0.00011485	0.0993	0.0097819	1	0.22511	1	0.10184	1	0.05954	1	0.0040842	1	0.59208	1	0.31893	1	0.077393	1	0.55266	1
20p gain	254 (52%)	236	0.019765	1	0.15118	1	4.9286e-07	0.000453	0.00059647	0.494	0.87501	1	0.20074	1	0.10349	1	0.0090758	1	0.066037	1	0.91889	1	0.40376	1	0.65858	1
20q gain	243 (50%)	247	0.6532	1	0.48019	1	0.00013098	0.112	0.14651	1	0.46707	1	0.49609	1	0.44096	1	0.26606	1	0.058864	1	0.0055749	1	0.45927	1	1	1
21q gain	56 (11%)	434	0.88804	1	0.8292	1	0.74341	1	0.064908	1	0.36488	1	0.90128	1	0.58318	1	0.90871	1	0.2161	1	0.57714	1	0.29909	1	1	1
22q gain	218 (44%)	272	0.0077664	1	0.039354	1	0.0048816	1	0.038483	1	0.94621	1	0.046696	1	0.003834	1	0.01491	1	0.072233	1	0.215	1	0.086485	1	0.50421	1
xq gain	77 (16%)	413	0.35885	1	0.73148	1	5.7757e-05	0.0507	0.0053263	1	0.69596	1	0.38932	1	0.0076887	1	0.0253	1	0.0016664	1	0.16541	1	0.020991	1	0.068926	1
1p loss	147 (30%)	343	1.5617e-05	0.0139	1.8431e-06	0.00168	1.1661e-20	1.12e-17	2.1604e-10	2.04e-07	0.88222	1	0.085989	1	1.5588e-12	1.48e-09	2.6629e-13	2.54e-10	0.00019276	0.165	6.5532e-05	0.0573	0.010278	1	0.00035028	0.295
1q loss	57 (12%)	433	0.5544	1	0.40057	1	0.00044397	0.371	0.084125	1	1	1	0.58398	1	0.027842	1	0.022776	1	0.29957	1	0.24267	1	0.67261	1	0.014125	1
2p loss	21 (4%)	469	0.046208	1	0.11086	1	0.034438	1	0.15058	1	0.14019	1	0.11316	1	0.62216	1	0.035059	1	0.0040513	1	0.66312	1	0.028267	1	0.014494	1
2q loss	41 (8%)	449	0.4933	1	0.66369	1	0.096757	1	0.33739	1	0.8811	1	0.39275	1	0.29367	1	0.0030213	1	0.00034391	0.29	0.77406	1	0.00779	1	0.008554	1
3p loss	303 (62%)	187	0.60598	1	0.67987	1	0.12642	1	0.0010195	0.828	0.93569	1	0.40692	1	0.32066	1	0.19997	1	0.079257	1	0.20964	1	0.052821	1	0.040342	1
3q loss	71 (14%)	419	0.92564	1	0.49762	1	0.47243	1	0.65128	1	0.47146	1	0.72687	1	0.89307	1	0.91588	1	0.92397	1	0.45948	1	0.048862	1	0.052417	1
4p loss	307 (63%)	183	0.00079507	0.651	0.0055078	1	6.5125e-13	6.2e-10	8.2337e-08	7.63e-05	0.20712	1	0.1219	1	1.7375e-06	0.00158	3.0759e-06	0.00279	0.00012115	0.104	0.46025	1	0.0001135	0.0983	1.2301e-05	0.011
4q loss	290 (59%)	200	0.0012325	0.991	0.0040918	1	5.1804e-11	4.9e-08	3.2819e-05	0.029	0.25489	1	0.33843	1	2.8831e-06	0.00262	4.1278e-06	0.00373	0.0072406	1	0.054787	1	0.0084685	1	0.0015674	1
5p loss	76 (16%)	414	0.63796	1	0.30689	1	0.06522	1	0.0016134	1	0.46339	1	0.076365	1	0.26965	1	0.63751	1	0.18663	1	0.81449	1	0.34705	1	0.0083602	1
5q loss	284 (58%)	206	0.16589	1	0.14309	1	0.0013372	1	0.006657	1	0.10923	1	0.068656	1	0.0088135	1	0.0049013	1	0.0093514	1	0.0066784	1	0.15558	1	0.033419	1
6p loss	109 (22%)	381	0.036464	1	0.010311	1	0.00025359	0.215	9.4123e-05	0.0819	0.14498	1	0.14521	1	7.1128e-06	0.0064	5.5776e-07	0.000513	0.29505	1	0.15984	1	0.0051987	1	0.023903	1
6q loss	109 (22%)	381	0.0052435	1	0.0053886	1	0.0014598	1	0.0009629	0.783	0.55599	1	0.38507	1	0.0013816	1	0.0012656	1	0.1215	1	0.25379	1	0.14521	1	0.044806	1
7p loss	58 (12%)	432	0.55041	1	0.46931	1	0.0007139	0.586	0.27229	1	0.66336	1	0.12999	1	0.22624	1	0.04847	1	0.41636	1	0.17119	1	0.8251	1	0.48798	1
7q loss	51 (10%)	439	0.16197	1	0.017534	1	0.030802	1	0.21078	1	0.92975	1	0.087006	1	0.00011257	0.0976	8.785e-05	0.0766	0.05308	1	0.17443	1	0.82044	1	0.37062	1
8p loss	237 (48%)	253	0.90132	1	0.9554	1	0.071268	1	0.0020866	1	0.13244	1	0.22156	1	0.165	1	0.020167	1	0.041505	1	0.90713	1	0.37034	1	0.18352	1
8q loss	49 (10%)	441	0.34767	1	0.17776	1	0.2638	1	0.0031718	1	0.042098	1	0.61582	1	0.21302	1	0.071852	1	0.43451	1	0.075011	1	0.80165	1	0.29785	1
9p loss	304 (62%)	186	0.0074323	1	0.0022683	1	1.2253e-05	0.011	0.019013	1	0.20197	1	0.058424	1	6.3138e-07	0.000579	0.00030036	0.254	0.051283	1	0.0082828	1	0.16546	1	0.49341	1
9q loss	239 (49%)	251	1.1387e-05	0.0102	7.3657e-06	0.00661	1.1925e-17	1.14e-14	1.7521e-09	1.64e-06	0.16704	1	0.017819	1	5.613e-20	5.38e-17	5.032e-18	4.82e-15	2.3189e-08	2.16e-05	3.769e-10	3.55e-07	0.00064653	0.532	0.0028486	1
10p loss	210 (43%)	280	0.20356	1	0.28903	1	3.7857e-06	0.00342	2.7366e-08	2.54e-05	0.46702	1	0.28426	1	1.3475e-06	0.00123	4.701e-08	4.36e-05	6.4731e-05	0.0567	1.3655e-05	0.0122	0.00058575	0.486	0.013353	1
10q loss	223 (46%)	267	0.0013258	1	0.00082416	0.673	1.6059e-06	0.00146	3.6658e-07	0.000338	0.095336	1	0.092692	1	6.6722e-09	6.22e-06	7.1555e-10	6.71e-07	0.00017075	0.146	8.3405e-06	0.00748	0.00054817	0.456	0.02597	1
11p loss	168 (34%)	322	0.24806	1	0.081403	1	0.0028079	1	0.003742	1	0.12962	1	0.00040981	0.343	0.16941	1	0.093778	1	0.38493	1	0.1436	1	0.1119	1	0.10149	1
11q loss	139 (28%)	351	0.98292	1	0.93345	1	0.0022955	1	0.0014367	1	0.5412	1	0.73167	1	0.28014	1	0.15737	1	0.018121	1	0.95178	1	0.21528	1	0.069303	1
12p loss	38 (8%)	452	0.023509	1	0.036595	1	0.30318	1	0.87389	1	0.098728	1	0.82583	1	0.9615	1	0.20575	1	0.1373	1	0.037772	1	0.5826	1	0.16085	1
12q loss	48 (10%)	442	0.36789	1	0.32038	1	0.96332	1	0.69347	1	0.026675	1	0.48501	1	0.78761	1	0.40113	1	0.18228	1	0.0098679	1	0.52575	1	0.72386	1
13q loss	305 (62%)	185	0.61374	1	0.75756	1	0.01645	1	0.053199	1	0.70066	1	0.57311	1	0.20268	1	0.087992	1	0.31178	1	0.13181	1	0.0015049	1	0.0088862	1
14q loss	165 (34%)	325	7.2226e-05	0.0631	0.040791	1	0.059784	1	0.11279	1	0.052356	1	0.18499	1	3.9195e-10	3.69e-07	2.6411e-12	2.51e-09	1.6697e-07	0.000155	3.767e-06	0.00341	0.010307	1	0.014407	1
15q loss	137 (28%)	353	0.71957	1	0.24213	1	0.2491	1	0.052264	1	0.32508	1	0.0025834	1	0.071399	1	0.010234	1	0.048248	1	0.15328	1	0.011339	1	0.90067	1
16p loss	155 (32%)	335	0.90026	1	0.82889	1	0.001165	0.939	0.12091	1	0.12563	1	0.47936	1	0.43677	1	0.40593	1	0.091391	1	0.30619	1	0.091527	1	0.23947	1
16q loss	177 (36%)	313	0.76192	1	0.63128	1	0.0051	1	0.16188	1	0.13007	1	0.8161	1	0.045517	1	0.025969	1	0.012733	1	0.031226	1	0.003702	1	0.021713	1
17p loss	285 (58%)	205	0.0051012	1	0.30974	1	0.0013672	1	0.010819	1	0.43814	1	0.0077013	1	0.00031018	0.262	0.0057141	1	0.028188	1	0.0089987	1	0.69615	1	0.91116	1
17q loss	90 (18%)	400	0.0055526	1	0.0099452	1	0.00051139	0.427	0.00011989	0.103	0.33489	1	0.64422	1	2.1654e-05	0.0192	1.0534e-05	0.00944	0.17435	1	0.038634	1	0.052062	1	0.0006018	0.498
18p loss	139 (28%)	351	0.84736	1	0.60039	1	0.018732	1	0.084063	1	0.61543	1	0.93255	1	0.17584	1	0.065397	1	0.38722	1	0.017981	1	0.0080434	1	0.53813	1
18q loss	182 (37%)	308	0.17541	1	0.10912	1	0.079459	1	0.32269	1	0.64125	1	0.76742	1	0.4243	1	0.0069279	1	0.20478	1	0.038064	1	0.059221	1	0.82008	1
19p loss	164 (33%)	326	0.052113	1	0.0027155	1	1.36e-05	0.0121	0.57304	1	0.83224	1	0.42397	1	0.1255	1	0.020334	1	0.032491	1	0.00023645	0.201	0.75199	1	0.90645	1
19q loss	110 (22%)	380	0.60158	1	0.17078	1	0.0099865	1	0.048234	1	0.34498	1	0.92211	1	0.62982	1	0.8306	1	0.28101	1	0.14279	1	0.60476	1	0.2943	1
20p loss	41 (8%)	449	0.14263	1	0.43831	1	0.0028007	1	0.0076831	1	0.11368	1	0.22436	1	0.19516	1	0.16046	1	0.051432	1	0.7171	1	0.21317	1	0.40349	1
20q loss	46 (9%)	444	0.057961	1	0.18197	1	0.0064233	1	0.050819	1	0.24645	1	0.29986	1	0.0003607	0.303	0.00024316	0.207	0.12797	1	0.58674	1	0.17246	1	0.54914	1
21q loss	260 (53%)	230	0.88964	1	0.58714	1	1.5528e-06	0.00142	0.036355	1	0.49515	1	0.50432	1	0.094776	1	0.0058146	1	0.002008	1	0.040073	1	0.19062	1	0.015037	1
22q loss	95 (19%)	395	0.0094388	1	0.097161	1	0.10913	1	0.040154	1	0.24034	1	0.01937	1	0.00027311	0.231	0.00054301	0.452	0.29921	1	0.046952	1	0.673	1	0.77714	1
xq loss	110 (22%)	380	0.20644	1	0.23791	1	0.00027915	0.236	0.0005727	0.475	0.777	1	0.6574	1	0.027086	1	0.039698	1	0.00037122	0.311	0.10792	1	8.8369e-05	0.077	0.0001971	0.168