		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	30 (7%)	397	0.80979	1	0.6576	1	0.026562	1	1	1	0.012554	1	0.085835	1	0.70078	1	0.042613	1	0.66923	1	0.6113	1	0.7789	1	1	1
1q gain	75 (18%)	352	0.52759	1	0.68588	1	0.0019352	1	0.20562	1	0.24286	1	0.029786	1	0.43902	1	0.03363	1	0.92505	1	0.95713	1	0.034187	1	0.76521	1
2p gain	74 (17%)	353	0.074272	1	0.035959	1	0.00037341	0.294	0.019539	1	0.11231	1	0.40351	1	0.007583	1	0.015475	1	0.39593	1	0.062272	1	0.28185	1	0.0034718	1
2q gain	70 (16%)	357	0.074272	1	0.035959	1	0.00020938	0.167	0.023294	1	0.28899	1	0.51786	1	0.030607	1	0.053457	1	0.49339	1	0.11076	1	0.47093	1	0.167	1
3p gain	42 (10%)	385	0.13733	1	0.13714	1	2.0621e-05	0.0173	0.36985	1	0.15078	1	0.041684	1	0.035523	1	0.22558	1	0.67828	1	0.33281	1	0.59493	1	0.21832	1
3q gain	61 (14%)	366	0.096621	1	0.0040264	1	7.8958e-08	6.9e-05	0.076689	1	0.096321	1	0.052149	1	8.1952e-05	0.0669	0.012194	1	0.65849	1	0.28026	1	0.15411	1	0.49736	1
4p gain	9 (2%)	418	NA	NA	NA	NA	0.016367	1	0.38021	1	0.31576	1	0.70831	1	0.37451	1	0.17746	1	0.60974	1	0.88734	1	0.50543	1	1	1
4q gain	15 (4%)	412	0.12729	1	0.3199	1	0.0073873	1	1	1	0.0067975	1	0.74547	1	0.23575	1	0.23679	1	0.14268	1	0.096558	1	0.3941	1	1	1
5p gain	63 (15%)	364	0.35704	1	0.15349	1	0.034911	1	0.44648	1	0.51756	1	0.9639	1	0.66698	1	0.00622	1	0.84996	1	0.3189	1	0.20984	1	0.55772	1
5q gain	39 (9%)	388	0.78376	1	0.68292	1	0.019139	1	0.49155	1	0.39224	1	0.45286	1	0.52982	1	0.065461	1	0.5463	1	0.44379	1	0.7998	1	1	1
6p gain	79 (19%)	348	0.072134	1	2.0499e-05	0.0173	4.3913e-10	3.91e-07	0.068673	1	0.64613	1	0.59617	1	0.0025582	1	0.00057541	0.448	0.58419	1	0.29551	1	0.0019478	1	0.2198	1
6q gain	72 (17%)	355	0.18973	1	0.0011453	0.862	7.7808e-08	6.81e-05	0.2536	1	0.95035	1	0.2417	1	0.023399	1	0.018941	1	0.51578	1	0.4593	1	0.00018821	0.151	0.16693	1
7p gain	233 (55%)	194	0.0062031	1	0.0010711	0.809	4.5578e-15	4.16e-12	0.00063478	0.489	0.00027878	0.221	0.0098189	1	9.4942e-09	8.35e-06	1.0141e-08	8.91e-06	0.53604	1	0.0095884	1	9.1385e-06	0.00774	0.94622	1
7q gain	211 (49%)	216	0.0040723	1	0.003122	1	6.8818e-10	6.12e-07	0.015038	1	0.0059737	1	0.0098751	1	4.344e-07	0.000377	1.4704e-07	0.000128	0.47803	1	0.0053079	1	2.9485e-05	0.0246	0.86833	1
8p gain	123 (29%)	304	0.96317	1	0.4815	1	0.0024882	1	0.84453	1	0.51399	1	0.16129	1	0.024222	1	0.10144	1	0.59653	1	0.31904	1	0.92558	1	0.3853	1
8q gain	212 (50%)	215	0.87178	1	0.14272	1	4.7108e-18	4.32e-15	0.0097878	1	0.12741	1	0.043741	1	0.0013298	0.997	0.0015602	1	0.72366	1	0.79036	1	0.024451	1	0.054287	1
9p gain	74 (17%)	353	0.19755	1	0.061108	1	0.0036064	1	0.70526	1	0.001851	1	0.58421	1	0.36958	1	0.38092	1	0.85898	1	0.97936	1	0.076174	1	0.80834	1
9q gain	65 (15%)	362	0.1707	1	0.022137	1	0.036674	1	0.64171	1	0.0004025	0.316	0.59832	1	0.51784	1	0.85826	1	0.41064	1	0.46053	1	0.30851	1	0.82161	1
10p gain	32 (7%)	395	0.59691	1	0.8884	1	0.035071	1	0.50136	1	0.024107	1	0.049878	1	0.26369	1	0.065337	1	0.40228	1	0.18219	1	0.0093291	1	0.51061	1
10q gain	18 (4%)	409	0.16982	1	0.82865	1	0.27889	1	0.105	1	0.36322	1	0.79393	1	1	1	0.69849	1	0.74727	1	0.37975	1	0.037088	1	0.32433	1
11p gain	50 (12%)	377	0.00074376	0.569	0.00028292	0.224	1.0818e-10	9.69e-08	0.00012536	0.102	0.076177	1	0.091774	1	7.777e-05	0.0637	0.0014556	1	0.88975	1	0.026281	1	0.012843	1	0.13538	1
11q gain	48 (11%)	379	0.00020437	0.163	9.2074e-05	0.0748	1.387e-11	1.25e-08	0.00092399	0.701	0.030638	1	0.24239	1	2.4226e-06	0.00208	0.00038026	0.299	0.64375	1	0.0080185	1	0.0065929	1	0.15904	1
12p gain	87 (20%)	340	0.17946	1	0.33864	1	0.04165	1	0.025568	1	0.71716	1	0.92096	1	0.53128	1	0.88465	1	0.27432	1	0.35554	1	0.45607	1	0.67317	1
12q gain	80 (19%)	347	0.19795	1	0.42244	1	0.013074	1	0.0082957	1	0.54466	1	0.75964	1	0.21019	1	0.42004	1	0.11234	1	0.24142	1	0.25343	1	0.44442	1
13q gain	245 (57%)	182	6.2648e-05	0.0514	2.7378e-05	0.0229	2.7982e-31	2.6e-28	0.0017521	1	0.031254	1	0.052336	1	1.6317e-09	1.44e-06	2.8245e-09	2.5e-06	0.42588	1	0.094442	1	5.2592e-06	0.00448	0.55549	1
14q gain	34 (8%)	393	0.3404	1	0.29877	1	0.25419	1	0.63028	1	0.41671	1	0.39002	1	0.28567	1	0.34766	1	0.66188	1	0.85399	1	0.295	1	0.74504	1
15q gain	11 (3%)	416	1	1	0.31456	1	0.36738	1	0.20275	1	0.080765	1	0.16718	1	0.86374	1	0.86029	1	0.92307	1	0.61883	1	0.67487	1	0.55468	1
16p gain	102 (24%)	325	4.4702e-05	0.0368	3.7046e-05	0.0307	1.4186e-20	1.31e-17	0.098211	1	0.16035	1	0.27739	1	7.7787e-05	0.0637	8.5983e-06	0.00731	0.5576	1	0.0015195	1	0.011617	1	0.87814	1
16q gain	99 (23%)	328	3.1249e-05	0.0261	6.0574e-05	0.0498	1.0671e-19	9.83e-17	0.19389	1	0.22755	1	0.2867	1	8.1845e-05	0.0669	2.4268e-05	0.0204	0.71847	1	0.00070928	0.545	0.0032947	1	0.61578	1
17p gain	25 (6%)	402	0.84075	1	0.18934	1	0.25582	1	0.50898	1	0.2135	1	0.61628	1	0.13375	1	0.11853	1	0.4977	1	0.35018	1	0.93942	1	0.77869	1
17q gain	75 (18%)	352	0.12221	1	0.094481	1	1.8963e-07	0.000165	0.0010144	0.769	0.3448	1	0.057522	1	6.6076e-07	0.000573	0.00036703	0.289	0.022894	1	0.47285	1	0.15173	1	0.32369	1
18p gain	22 (5%)	405	0.091833	1	0.46284	1	8.6021e-06	0.00731	0.00050109	0.392	0.82899	1	0.6358	1	0.020199	1	0.0050516	1	0.18142	1	0.049489	1	0.26789	1	0.43022	1
18q gain	14 (3%)	413	0.1437	1	0.63479	1	0.0016039	1	0.0029128	1	0.59656	1	0.19399	1	0.0039025	1	0.059055	1	0.41483	1	0.12145	1	0.1454	1	0.48541	1
19p gain	67 (16%)	360	0.14845	1	0.073181	1	3.9875e-05	0.0329	0.068077	1	0.25905	1	0.21143	1	0.0077433	1	0.017036	1	0.077909	1	0.0076362	1	0.0050995	1	0.32416	1
19q gain	76 (18%)	351	0.087031	1	0.012907	1	0.0051744	1	0.35829	1	0.041477	1	0.086439	1	0.035246	1	0.016913	1	0.18129	1	0.0078987	1	0.022284	1	0.14974	1
20p gain	229 (54%)	198	0.0012161	0.915	1.0061e-06	0.000868	4.129e-13	3.75e-10	0.00073968	0.567	0.041265	1	0.15311	1	2.2169e-08	1.94e-05	2.3461e-06	0.00202	0.64579	1	0.011543	1	0.00070373	0.541	0.81645	1
20q gain	302 (71%)	125	3.636e-10	3.25e-07	4.4104e-11	3.96e-08	2.2939e-36	2.13e-33	2.0614e-12	1.86e-09	9.418e-05	0.0764	0.00018864	0.151	2.3478e-23	2.17e-20	1.6401e-18	1.51e-15	0.89823	1	8.2292e-05	0.0671	1.1072e-12	1e-09	0.26175	1
21q gain	21 (5%)	406	0.035655	1	0.27469	1	0.026279	1	0.89352	1	0.73056	1	1	1	0.57523	1	0.34028	1	0.22224	1	0.22904	1	0.3698	1	1	1
22q gain	10 (2%)	417	1	1	1	1	0.12906	1	0.38021	1	0.63669	1	1	1	0.2667	1	0.15926	1	1	1	0.83945	1	0.85792	1	0.12522	1
xq gain	68 (16%)	359	0.035082	1	0.29714	1	0.0028656	1	0.16903	1	0.25569	1	0.1628	1	0.44054	1	0.15323	1	0.27769	1	0.76242	1	0.21967	1	0.41923	1
1p loss	91 (21%)	336	0.027515	1	0.059696	1	6.8913e-11	6.18e-08	0.00092171	0.701	0.57684	1	0.54683	1	9.1535e-05	0.0744	8.9419e-06	0.00758	0.7774	1	0.003912	1	0.0042894	1	0.0067383	1
1q loss	52 (12%)	375	0.2731	1	0.54392	1	3.6034e-05	0.03	0.060943	1	0.43931	1	0.22673	1	0.0046263	1	0.0024394	1	0.65163	1	0.010923	1	0.0065362	1	0.106	1
2p loss	6 (1%)	421	0.89774	1	0.31456	1	0.033855	1	NA	NA	0.70306	1	1	1	0.17283	1	0.34069	1	0.63943	1	0.43036	1	NA	NA	NA	NA
2q loss	7 (2%)	420	1	1	0.15598	1	0.185	1	NA	NA	0.30984	1	0.46454	1	0.064362	1	0.20067	1	0.38933	1	0.32825	1	NA	NA	NA	NA
3p loss	50 (12%)	377	0.7802	1	0.36383	1	0.0039866	1	0.13602	1	0.60518	1	0.56646	1	0.044292	1	0.048033	1	0.6091	1	0.50306	1	0.00060374	0.467	0.47484	1
3q loss	31 (7%)	396	0.82499	1	1	1	0.029028	1	0.55784	1	0.39633	1	0.49239	1	0.72171	1	0.38654	1	0.24662	1	0.9081	1	0.012411	1	0.35225	1
4p loss	127 (30%)	300	8.4542e-05	0.0688	0.0074671	1	2.365e-14	2.15e-11	0.00045801	0.359	0.10455	1	0.096616	1	4.0195e-06	0.00343	1.6054e-06	0.00138	0.45203	1	0.057519	1	2.7298e-05	0.0229	0.53096	1
4q loss	115 (27%)	312	0.00016271	0.131	0.0064741	1	2.0618e-14	1.88e-11	9.4627e-06	0.00801	0.10445	1	0.19434	1	0.0003405	0.269	3.4014e-06	0.00291	0.21914	1	0.022857	1	4.4047e-05	0.0363	0.24614	1
5p loss	54 (13%)	373	0.63591	1	0.86461	1	0.00015536	0.125	0.0083871	1	0.3292	1	0.55796	1	0.030329	1	0.011525	1	0.72916	1	0.53673	1	0.094723	1	0.93444	1
5q loss	74 (17%)	353	0.30633	1	0.18044	1	6.7673e-07	0.000586	0.0066613	1	0.0089425	1	0.0072873	1	3.7062e-05	0.0307	3.4615e-06	0.00296	0.97922	1	0.4593	1	0.0022012	1	1	1
6p loss	33 (8%)	394	1	1	1	1	0.59467	1	0.51491	1	0.18595	1	0.57624	1	0.96054	1	0.68529	1	0.61308	1	0.11381	1	0.033121	1	0.21401	1
6q loss	44 (10%)	383	0.82195	1	0.81084	1	0.96119	1	0.36705	1	0.20186	1	0.20165	1	0.77207	1	0.73348	1	0.58051	1	0.16833	1	0.28649	1	0.4441	1
7q loss	3 (1%)	424	NA	NA	NA	NA	0.11832	1	0.615	1	NA	NA	NA	NA	0.42229	1	0.61854	1	0.56127	1	0.59972	1	NA	NA	NA	NA
8p loss	133 (31%)	294	0.023502	1	0.0016996	1	3.206e-16	2.93e-13	3.6338e-05	0.0302	0.010537	1	0.0010883	0.821	3.5029e-07	0.000304	4.3333e-06	0.00369	0.5603	1	0.10861	1	2.8521e-06	0.00244	0.47407	1
8q loss	23 (5%)	404	0.80979	1	0.6576	1	0.0038285	1	0.33957	1	0.27401	1	0.10795	1	0.90339	1	0.14055	1	0.5093	1	0.076816	1	0.14916	1	0.49035	1
9p loss	49 (11%)	378	0.57125	1	0.013623	1	3.9782e-05	0.0329	0.0024693	1	0.88566	1	0.34046	1	0.00073984	0.567	0.00054262	0.424	0.36921	1	0.12602	1	0.00082995	0.632	0.24695	1
9q loss	49 (11%)	378	0.11811	1	0.060601	1	3.9782e-05	0.0329	0.00024513	0.195	0.96705	1	0.35639	1	0.00028423	0.225	0.00054262	0.424	0.43779	1	0.0086883	1	1.3169e-05	0.0111	0.35196	1
10p loss	64 (15%)	363	0.020994	1	0.033981	1	2.9439e-08	2.58e-05	0.0038794	1	0.013592	1	0.124	1	9.7805e-06	0.00826	0.000196	0.157	0.48686	1	0.0060618	1	0.001341	1	0.55035	1
10q loss	68 (16%)	359	0.02472	1	0.017668	1	2.5007e-10	2.24e-07	0.00057458	0.448	0.012108	1	0.063813	1	3.6553e-06	0.00312	3.26e-05	0.0272	0.61035	1	0.050816	1	0.00014808	0.12	0.84245	1
11p loss	49 (11%)	378	0.22558	1	0.041045	1	0.0023201	1	0.021611	1	0.72298	1	0.69292	1	0.21139	1	0.022664	1	0.82366	1	0.70267	1	0.00023854	0.19	0.80755	1
11q loss	59 (14%)	368	0.04223	1	0.0020698	1	0.00031219	0.247	0.001286	0.966	0.60141	1	0.87104	1	0.12377	1	0.017997	1	0.85143	1	0.38293	1	0.00021871	0.175	0.58342	1
12p loss	44 (10%)	383	0.061639	1	0.011297	1	1.6582e-10	1.48e-07	0.042046	1	0.40144	1	0.60017	1	0.00024624	0.196	0.0027774	1	0.86715	1	0.21068	1	0.0028921	1	0.66421	1
12q loss	47 (11%)	380	0.10982	1	0.010531	1	3.7574e-09	3.31e-06	0.013644	1	0.51298	1	0.68619	1	2.9391e-05	0.0246	0.00069231	0.533	0.94371	1	0.10495	1	0.00059558	0.462	0.18923	1
13q loss	12 (3%)	415	0.87394	1	0.19429	1	0.15658	1	0.040553	1	0.001601	1	0.008184	1	0.76444	1	0.21624	1	0.59751	1	0.071649	1	0.07925	1	0.15011	1
14q loss	128 (30%)	299	7.3259e-07	0.000634	1.6461e-06	0.00142	1.9304e-28	1.79e-25	7.3269e-07	0.000634	0.0017995	1	0.045247	1	1.7742e-11	1.6e-08	3.8196e-10	3.41e-07	0.25253	1	7.0019e-05	0.0574	2.2407e-05	0.0188	0.084721	1
15q loss	145 (34%)	282	0.0017216	1	0.0020458	1	8.8286e-21	8.15e-18	0.00060014	0.465	0.012251	1	0.03246	1	2.8509e-09	2.52e-06	1.5741e-08	1.38e-05	0.85247	1	0.0001381	0.112	4.5835e-05	0.0377	0.42877	1
16p loss	27 (6%)	400	0.40597	1	0.71065	1	1	1	0.42884	1	0.39227	1	0.33501	1	0.067337	1	0.13574	1	0.50856	1	0.25221	1	0.2481	1	0.39213	1
16q loss	25 (6%)	402	0.40597	1	0.71065	1	0.59502	1	0.59112	1	0.13654	1	0.25112	1	0.28023	1	0.43422	1	0.40419	1	0.62562	1	0.19556	1	0.78103	1
17p loss	222 (52%)	205	2.0969e-07	0.000183	1.0695e-06	0.000922	4.8624e-29	4.51e-26	1.2834e-09	1.14e-06	0.019678	1	0.00092282	0.701	2.7946e-12	2.52e-09	4.5585e-13	4.13e-10	0.79079	1	0.10008	1	9.3916e-10	8.34e-07	0.11687	1
17q loss	61 (14%)	366	0.11319	1	0.68588	1	0.00058772	0.457	0.013836	1	0.57436	1	0.47572	1	0.058881	1	0.017916	1	0.56933	1	0.25084	1	0.0032512	1	0.030092	1
18p loss	237 (56%)	190	1.4606e-12	1.32e-09	7.6271e-10	6.78e-07	1.0469e-44	9.76e-42	8.2259e-18	7.53e-15	0.00075088	0.574	0.00060703	0.469	4.677e-24	4.33e-21	6.1473e-18	5.64e-15	1	1	0.0064521	1	7.557e-15	6.88e-12	0.0093992	1
18q loss	252 (59%)	175	6.3991e-12	5.77e-09	9.6007e-10	8.52e-07	1.1223e-42	1.04e-39	2.9462e-15	2.69e-12	0.0041836	1	0.00081399	0.621	1.2341e-25	1.14e-22	7.589e-18	6.95e-15	0.70069	1	0.010111	1	2.2623e-13	2.05e-10	0.082179	1
19p loss	38 (9%)	389	1	1	0.16701	1	0.027993	1	0.3771	1	0.60608	1	0.25972	1	0.090236	1	0.0053177	1	0.041343	1	0.49904	1	0.46829	1	0.04611	1
19q loss	32 (7%)	395	0.83826	1	0.2968	1	0.06015	1	0.53063	1	0.18047	1	0.11948	1	0.26053	1	0.023527	1	0.33848	1	0.72302	1	0.36899	1	0.12859	1
20p loss	43 (10%)	384	0.19429	1	0.13714	1	0.0010509	0.794	0.20455	1	0.86312	1	0.4709	1	0.069627	1	0.12952	1	0.87855	1	0.14673	1	0.12411	1	0.086273	1
20q loss	6 (1%)	421	NA	NA	NA	NA	1	1	0.82201	1	0.032052	1	1	1	0.87533	1	0.76899	1	1	1	1	1	0.19834	1	0.31943	1
21q loss	117 (27%)	310	0.009922	1	0.0075797	1	5.0974e-09	4.49e-06	0.060574	1	0.22921	1	0.18586	1	0.0044825	1	0.00062107	0.479	0.4651	1	0.29778	1	0.0018001	1	0.46209	1
22q loss	138 (32%)	289	0.00041772	0.327	0.00019004	0.152	1.6611e-18	1.53e-15	0.0003207	0.253	0.17036	1	0.63997	1	2.6584e-07	0.000231	0.00017317	0.139	0.1361	1	0.0010438	0.79	1.0405e-05	0.00878	0.29058	1
xq loss	46 (11%)	381	0.029763	1	0.19962	1	0.01049	1	0.24701	1	0.08566	1	0.20454	1	0.16775	1	0.3248	1	0.078532	1	0.52108	1	0.049774	1	0.20004	1
