Clinical Features	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
1p gain	8 (9%)	79	0.15577	0.606	0.76571	0.952	0.10684	0.559	0.076449	0.482	1	1	0.76259	0.952	0.92018	1	0.78753	0.964	0.54038	0.872	0.45854	0.83
1q gain	20 (23%)	67	0.078389	0.482	0.23286	0.667	0.9454	1	0.89548	0.989	0.03873	0.383	0.14205	0.589	0.2038	0.643	0.10608	0.559	0.42343	0.808	0.30695	0.738
2p gain	4 (5%)	83	0.0184	0.26	0.6482	0.927	0.37736	0.771	0.74873	0.949	0.61921	0.916	0.75773	0.949	0.46811	0.831	0.14409	0.589	0.58321	0.898	0.1567	0.607
2q gain	6 (7%)	81	0.29093	0.727	0.41057	0.795	0.86939	0.986	0.2868	0.726	0.48328	0.844	0.57674	0.897	0.25706	0.696	0.65974	0.932	0.16147	0.611	0.056249	0.435
3p gain	17 (20%)	70	0.15344	0.604	1	1	0.36659	0.768	0.40851	0.795	0.77546	0.957	0.53411	0.87	0.59796	0.91	0.88239	0.986	0.77928	0.957	0.42567	0.808
3q gain	19 (22%)	68	0.068059	0.476	0.96215	1	0.62477	0.92	0.43508	0.814	0.77112	0.957	0.3148	0.738	0.64974	0.927	0.46669	0.831	0.61968	0.916	0.32294	0.743
5p gain	24 (28%)	63	0.21601	0.648	0.214	0.648	0.80608	0.964	0.93629	1	0.68942	0.937	0.80404	0.964	0.19326	0.643	0.43367	0.814	0.51488	0.864	0.6788	0.934
5q gain	14 (16%)	73	0.066979	0.473	0.66336	0.933	0.70432	0.937	0.99147	1	0.69949	0.937	0.85414	0.984	0.21797	0.648	0.50651	0.857	0.20093	0.643	0.84262	0.977
6p gain	7 (8%)	80	0.37681	0.771	0.18322	0.634	1	1	0.12464	0.583	0.31645	0.74	0.34283	0.747	0.64628	0.927	0.96542	1	0.8811	0.986	0.81325	0.965
6q gain	4 (5%)	83	0.23841	0.668	0.64991	0.927	1	1	0.74611	0.949	0.83707	0.976	0.61592	0.916	0.90595	0.998	0.93558	1	0.37593	0.771	1	1
7p gain	25 (29%)	62	0.49726	0.849	0.37043	0.769	0.03162	0.348	0.26463	0.7	0.17268	0.627	0.051579	0.429	0.17599	0.63	0.04233	0.392	0.17325	0.627	0.052209	0.429
7q gain	22 (25%)	65	0.7087	0.937	0.5312	0.87	0.0099299	0.234	0.11391	0.559	0.26947	0.701	0.02195	0.286	0.32476	0.743	0.18109	0.633	0.32364	0.743	0.24524	0.677
8p gain	12 (14%)	75	0.71818	0.937	0.44031	0.814	0.01905	0.264	0.22832	0.664	0.75778	0.949	0.87639	0.986	0.28064	0.716	0.03837	0.383	0.32949	0.744	0.31109	0.738
8q gain	14 (16%)	73	0.95719	1	0.077669	0.482	0.084179	0.497	0.72439	0.938	0.7933	0.964	0.86887	0.986	0.60618	0.915	0.58305	0.898	0.47665	0.838	0.50223	0.853
9q gain	3 (3%)	84	0.17144	0.627	0.03194	0.348	NA	NA	NA	NA	0.19933	0.643	0.28748	0.726	0.36395	0.768	0.11232	0.559	1	1	0.89352	0.988
10p gain	3 (3%)	84	0.47757	0.838	0.67624	0.933	NA	NA	NA	NA	0.32497	0.743	0.92765	1	0.87724	0.986	0.26523	0.7	1	1	0.59699	0.91
10q gain	3 (3%)	84	0.47863	0.838	0.67213	0.933	NA	NA	NA	NA	0.32747	0.744	0.92744	1	0.87656	0.986	0.26304	0.7	1	1	0.5967	0.91
11p gain	12 (14%)	75	0.03102	0.348	0.34511	0.747	0.15952	0.611	0.82111	0.969	0.33014	0.744	0.053209	0.429	0.2883	0.726	0.58435	0.898	0.6722	0.933	0.66451	0.933
11q gain	12 (14%)	75	0.17681	0.63	0.073089	0.478	0.40952	0.795	0.9563	1	0.18228	0.634	0.02382	0.296	0.31069	0.738	0.54664	0.873	0.21188	0.648	0.53368	0.87
12p gain	18 (21%)	69	0.01279	0.234	0.48706	0.844	0.55221	0.877	0.14236	0.589	0.85486	0.984	0.79865	0.964	0.72251	0.937	0.92296	1	0.94273	1	0.93182	1
12q gain	18 (21%)	69	0.01238	0.234	0.48454	0.844	0.55206	0.877	0.14124	0.589	0.85674	0.984	0.80111	0.964	0.7221	0.937	0.92188	1	0.94152	1	0.93114	1
13q gain	5 (6%)	82	0.39064	0.786	0.092579	0.52	1	1	0.88337	0.986	0.02343	0.296	0.02221	0.286	0.19412	0.643	0.4318	0.814	1	1	0.1804	0.633
15q gain	10 (11%)	77	0.26897	0.701	0.0053599	0.177	1	1	0.04311	0.392	0.01642	0.257	0.10984	0.559	0.0072199	0.204	0.01311	0.234	0.47583	0.838	0.20079	0.643
16p gain	16 (18%)	71	0.25114	0.688	0.061009	0.448	0.21981	0.648	0.75506	0.949	0.089789	0.515	0.10464	0.558	0.57977	0.898	0.33338	0.745	0.36415	0.768	0.33184	0.744
16q gain	16 (18%)	71	0.1521	0.604	0.19729	0.643	0.070939	0.478	0.87609	0.986	0.04652	0.394	0.072399	0.478	0.38403	0.779	0.66027	0.932	0.82308	0.97	0.62997	0.924
17p gain	8 (9%)	79	0.25419	0.691	0.66916	0.933	0.03582	0.376	0.01101	0.234	0.31445	0.738	0.67147	0.933	0.71025	0.937	0.075559	0.482	0.89061	0.988	0.30921	0.738
17q gain	17 (20%)	70	0.22966	0.664	0.31162	0.738	0.01731	0.26	0.11397	0.559	0.01777	0.26	0.11492	0.559	0.42399	0.808	0.86718	0.986	0.82977	0.974	0.57194	0.897
18p gain	8 (9%)	79	0.15571	0.606	0.193	0.643	0.61281	0.916	0.8282	0.974	0.1128	0.559	0.14373	0.589	0.02139	0.286	0.13671	0.589	0.88052	0.986	0.22953	0.664
18q gain	4 (5%)	83	0.46888	0.831	0.31166	0.738	0.23729	0.667	0.2805	0.716	0.36555	0.768	0.6388	0.927	0.053579	0.429	0.083739	0.497	0.79029	0.964	0.063269	0.451
19p gain	14 (16%)	73	0.01078	0.234	0.01113	0.234	0.81049	0.964	0.57794	0.897	0.1411	0.589	0.22826	0.664	0.22052	0.648	0.17423	0.627	1	1	0.21265	0.648
19q gain	11 (13%)	76	0.28126	0.716	0.26913	0.701	0.15093	0.604	0.52125	0.869	0.67665	0.933	0.39879	0.792	0.070849	0.478	0.86326	0.986	0.68771	0.937	0.93171	1
20p gain	8 (9%)	79	0.26275	0.7	0.35154	0.753	0.67971	0.934	0.495	0.849	0.27348	0.708	0.80574	0.964	0.88056	0.986	0.44108	0.814	0.72115	0.937	0.59998	0.911
20q gain	11 (13%)	76	0.096079	0.528	0.93151	1	1	1	0.72207	0.937	0.75312	0.949	1	1	0.4175	0.805	0.93294	1	0.3305	0.744	0.72104	0.937
21q gain	6 (7%)	81	0.26279	0.7	0.0072199	0.204	1	1	0.60488	0.915	0.2049	0.643	0.13005	0.589	0.00197	0.0834	0.34239	0.747	0.080159	0.484	0.16615	0.62
xp gain	7 (8%)	80	0.54401	0.872	0.20687	0.643	0.298	0.735	0.44319	0.814	0.72852	0.938	0.69557	0.937	0.64351	0.927	0.96605	1	0.68655	0.937	1	1
xq gain	6 (7%)	81	0.6844	0.937	0.23576	0.667	0.29427	0.731	0.68768	0.937	0.65168	0.927	0.53307	0.87	0.53696	0.87	0.83989	0.976	1	1	0.93359	1
1p loss	9 (10%)	78	0.01086	0.234	0.46507	0.831	0.69205	0.937	0.54522	0.872	0.31799	0.741	0.64288	0.927	0.8408	0.976	0.3887	0.786	1	1	0.7738	0.957
2p loss	6 (7%)	81	0.060919	0.448	0.00309	0.111	0.69297	0.937	0.11638	0.559	0.20668	0.643	0.24079	0.669	0.057759	0.442	0.58471	0.898	1	1	0.18089	0.633
2q loss	5 (6%)	82	0.086949	0.509	0.04607	0.394	1	1	0.24438	0.677	0.35488	0.758	0.612	0.916	0.19663	0.643	0.46984	0.831	0.80629	0.964	0.8337	0.974
3p loss	8 (9%)	79	0.14168	0.589	0.69707	0.937	0.63183	0.925	0.53753	0.87	0.17138	0.627	0.11421	0.559	0.02965	0.345	0.71208	0.937	0.13447	0.589	0.13094	0.589
3q loss	7 (8%)	80	0.4895	0.845	0.37985	0.773	0.62945	0.924	0.21415	0.648	0.21598	0.648	0.26952	0.701	0.052669	0.429	0.71994	0.937	0.34204	0.747	0.16196	0.611
4p loss	33 (38%)	54	9.9999e-06	0.0024	0.063239	0.451	0.57838	0.897	0.61797	0.916	0.14035	0.589	0.01477	0.247	0.071099	0.478	0.38999	0.786	0.44745	0.817	0.3991	0.792
4q loss	34 (39%)	53	9.9999e-06	0.0024	0.01363	0.234	0.41851	0.805	0.51639	0.865	0.00192	0.0834	0.00023	0.0166	0.01005	0.234	0.14253	0.589	0.48786	0.844	0.02764	0.332
5p loss	4 (5%)	83	0.76541	0.952	0.93751	1	0.24067	0.669	0.53733	0.87	0.52492	0.87	0.72552	0.938	0.90652	0.998	0.93573	1	1	1	0.20247	0.643
5q loss	9 (10%)	78	0.15044	0.604	0.7469	0.949	0.19022	0.643	0.2117	0.648	0.50026	0.852	0.093359	0.52	0.25447	0.691	0.66795	0.933	0.89027	0.988	0.80765	0.964
6p loss	8 (9%)	79	0.40443	0.795	0.15892	0.611	0.23669	0.667	0.79138	0.964	0.43748	0.814	0.6106	0.916	0.11772	0.559	0.21964	0.648	0.88955	0.988	0.15299	0.604
6q loss	29 (33%)	58	4e-05	0.00576	0.46343	0.831	0.97093	1	0.65544	0.931	0.37323	0.771	0.69036	0.937	0.17246	0.627	0.52107	0.869	0.11262	0.559	0.21869	0.648
8p loss	13 (15%)	74	0.75472	0.949	0.090139	0.515	0.85929	0.985	0.93466	1	0.553	0.877	0.73673	0.944	0.14338	0.589	0.75198	0.949	0.73632	0.944	0.75743	0.949
8q loss	4 (5%)	83	0.42641	0.808	0.81611	0.966	0.23513	0.667	0.27687	0.714	0.44221	0.814	0.51261	0.862	0.04353	0.392	0.1181	0.559	0.3751	0.771	0.43947	0.814
9p loss	28 (32%)	59	0.00253	0.0959	0.062259	0.451	0.093879	0.52	0.11094	0.559	0.04404	0.392	0.04171	0.392	0.10414	0.558	0.49212	0.848	0.95695	1	0.19603	0.643
9q loss	22 (25%)	65	0.089829	0.515	0.30124	0.738	0.03914	0.383	0.2508	0.688	0.30021	0.738	0.34258	0.747	0.059299	0.448	0.53418	0.87	0.29096	0.727	0.49355	0.848
10p loss	25 (29%)	62	0.00212	0.0848	0.1315	0.589	0.51078	0.861	0.80683	0.964	0.068929	0.477	0.080709	0.484	0.01316	0.234	0.23553	0.667	0.45794	0.83	0.19837	0.643
10q loss	19 (22%)	68	0.19328	0.643	0.32382	0.743	0.21106	0.648	0.92215	1	0.48574	0.844	0.30547	0.738	0.1159	0.559	0.72188	0.937	0.94234	1	0.85653	0.984
11p loss	4 (5%)	83	0.39425	0.79	0.45052	0.819	0.23651	0.667	0.20558	0.643	0.36784	0.768	0.34343	0.747	1	1	0.39602	0.79	0.80578	0.964	0.83161	0.974
11q loss	5 (6%)	82	1	1	0.16195	0.611	0.03607	0.376	0.34557	0.747	0.0074199	0.204	0.0062299	0.195	0.34676	0.747	0.35885	0.762	0.80494	0.964	0.832	0.974
12p loss	4 (5%)	83	0.12739	0.589	0.8115	0.964	0.33813	0.747	0.1786	0.633	0.44226	0.814	0.39517	0.79	0.5966	0.91	0.81796	0.967	1	1	0.8916	0.988
13q loss	33 (38%)	54	0.01816	0.26	0.52829	0.87	0.53489	0.87	0.11001	0.559	0.32965	0.744	0.64707	0.927	0.55955	0.885	0.18801	0.643	0.01338	0.234	0.34006	0.747
14q loss	35 (40%)	52	9.9999e-06	0.0024	0.00018	0.0144	0.30937	0.738	0.42803	0.809	5.9999e-05	0.0072	2e-05	0.0036	0.02994	0.345	0.00057999	0.0321	0.13641	0.589	0.00082999	0.0427
15q loss	11 (13%)	76	0.66401	0.933	0.84016	0.976	0.57405	0.897	0.49778	0.849	0.34089	0.747	0.37813	0.771	0.20409	0.643	0.30596	0.738	0.72985	0.938	0.54175	0.872
16p loss	8 (9%)	79	0.0116	0.234	0.70755	0.937	0.46223	0.831	0.63382	0.925	0.43832	0.814	0.1948	0.643	0.44744	0.817	0.32189	0.743	0.89034	0.988	0.95923	1
16q loss	11 (13%)	76	0.04239	0.392	0.95164	1	0.4097	0.795	0.86445	0.986	0.20723	0.643	0.31325	0.738	0.46783	0.831	0.14386	0.589	1	1	0.5727	0.897
17p loss	23 (26%)	64	0.80685	0.964	0.097369	0.528	0.75789	0.949	0.0302	0.345	0.67332	0.933	0.50682	0.857	0.14024	0.589	0.1395	0.589	0.055789	0.435	0.19149	0.643
17q loss	7 (8%)	80	0.61739	0.916	0.14766	0.597	0.33762	0.747	0.078149	0.482	0.64654	0.927	0.63479	0.925	0.69905	0.937	0.53131	0.87	0.41088	0.795	0.35652	0.759
18p loss	9 (10%)	78	0.00051999	0.0312	0.70778	0.937	0.36722	0.768	0.54378	0.872	0.70154	0.937	0.57317	0.897	0.78913	0.964	0.75553	0.949	0.65991	0.932	0.57382	0.897
18q loss	14 (16%)	73	0.01581	0.256	0.74746	0.949	0.80863	0.964	0.40512	0.795	0.72721	0.938	0.85184	0.984	0.46463	0.831	0.092499	0.52	0.56131	0.886	0.16527	0.62
19p loss	4 (5%)	83	0.76491	0.952	0.264	0.7	1	1	0.097449	0.528	0.61723	0.916	0.44805	0.817	0.70421	0.937	0.34832	0.749	0.14743	0.597	0.62421	0.92
19q loss	7 (8%)	80	1	1	0.61716	0.916	0.69494	0.937	0.02171	0.286	1	1	0.8814	0.986	0.86982	0.986	0.78954	0.964	0.28149	0.716	0.70194	0.937
20p loss	14 (16%)	73	0.077909	0.482	0.076109	0.482	0.67624	0.933	0.7743	0.957	0.13381	0.589	0.53623	0.87	0.84631	0.98	0.7219	0.937	0.36905	0.768	0.11948	0.562
21q loss	11 (13%)	76	0.31192	0.738	0.60183	0.912	0.65045	0.927	0.77873	0.957	0.26102	0.7	0.072819	0.478	0.19281	0.643	0.29359	0.731	0.7759	0.957	0.86396	0.986
22q loss	67 (77%)	20	0.1126	0.559	0.0085399	0.22	0.16792	0.623	0.97235	1	0.01707	0.26	0.0054199	0.177	0.01601	0.256	0.64556	0.927	0.29577	0.732	0.42214	0.808
xp loss	27 (31%)	60	0.00091999	0.0442	8.9999e-05	0.0081	0.01287	0.234	0.13337	0.589	0.03465	0.372	0.055889	0.435	0.060549	0.448	0.41914	0.805	0.04612	0.394	0.04406	0.392
xq loss	28 (32%)	59	3e-04	0.0196	6.9999e-05	0.0072	0.0076599	0.204	0.40321	0.795	0.04615	0.394	0.02628	0.321	0.079939	0.484	0.40991	0.795	0.03907	0.383	0.03935	0.383