		Molecular subtypes	MRNA_CNMF		MRNA_CHIERARCHICAL		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	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	15 (3%)	560	0.40379	1	0.11161	1	0.93194	1	0.49686	1	0.22398	1	0.021338	1	0.86431	1	0.82875	1	0.11131	1	0.91089	1
1q gain	80 (14%)	495	0.50855	1	0.9267	1	0.015823	1	0.92569	1	0.13658	1	0.47695	1	0.0034264	1	0.68127	1	0.072884	1	0.97845	1
2p gain	60 (10%)	515	0.014923	1	0.0023214	1	0.0081555	1	0.00025563	0.174	0.28728	1	0.41413	1	0.00063229	0.424	0.0055327	1	0.2161	1	0.020869	1
2q gain	59 (10%)	516	0.0039614	1	0.0026158	1	0.0010069	0.672	5.8199e-06	0.00409	0.55043	1	0.49702	1	0.002176	1	0.0023277	1	0.25079	1	0.050357	1
3p gain	36 (6%)	539	0.13149	1	0.48961	1	0.00018128	0.124	0.25722	1	0.082715	1	0.48833	1	0.51365	1	0.48369	1	0.20792	1	0.36632	1
3q gain	53 (9%)	522	0.23939	1	0.13772	1	2.4908e-06	0.00176	0.035341	1	0.027661	1	0.39769	1	0.69028	1	0.26875	1	0.11128	1	0.54357	1
4p gain	6 (1%)	569	NA	NA	NA	NA	0.062196	1	0.22614	1	0.17038	1	0.080969	1	NA	NA	NA	NA	0.13662	1	0.052496	1
4q gain	7 (1%)	568	0.70318	1	0.32105	1	0.24967	1	0.787	1	0.56819	1	0.73216	1	0.43522	1	0.7455	1	0.38271	1	0.80878	1
5p gain	60 (10%)	515	0.1166	1	0.68118	1	0.0015014	0.992	0.17846	1	0.17225	1	0.94858	1	0.061132	1	0.054405	1	0.7844	1	0.35435	1
5q gain	33 (6%)	542	0.45561	1	0.61736	1	0.0035603	1	0.35577	1	0.66143	1	0.63879	1	0.43179	1	0.46292	1	0.81846	1	0.48285	1
6p gain	77 (13%)	498	0.23811	1	0.0038625	1	1.5453e-06	0.00109	0.40135	1	0.36062	1	0.53227	1	0.03791	1	0.17817	1	0.84813	1	0.39161	1
6q gain	71 (12%)	504	0.3841	1	0.04477	1	7.4722e-07	0.000532	0.15877	1	0.27477	1	0.17031	1	0.06571	1	0.40924	1	0.74931	1	0.25108	1
7p gain	290 (50%)	285	0.00029113	0.197	0.0082373	1	1.8943e-21	1.42e-18	7.2886e-07	0.00052	0.030273	1	0.0041616	1	5.7235e-07	0.000409	5.1771e-07	0.000371	0.070344	1	0.030432	1
7q gain	255 (44%)	320	0.00040574	0.273	0.039255	1	6.9527e-16	5.16e-13	8.6118e-06	0.00603	0.31448	1	0.022715	1	7.4939e-07	0.000533	8.39e-06	0.00588	0.24522	1	0.15535	1
8p gain	108 (19%)	467	0.89962	1	0.65317	1	1.0033e-08	7.29e-06	0.43331	1	0.12137	1	0.078438	1	0.70795	1	0.69234	1	0.49022	1	0.89065	1
8q gain	235 (41%)	340	0.053147	1	0.58855	1	1.0571e-33	8e-31	0.0094198	1	0.044454	1	0.40774	1	0.01124	1	0.071859	1	0.45899	1	0.63306	1
9p gain	79 (14%)	496	0.49142	1	0.90688	1	0.17843	1	0.79019	1	0.40713	1	0.44565	1	0.043512	1	0.05195	1	0.78008	1	0.78126	1
9q gain	64 (11%)	511	0.47006	1	0.85659	1	0.214	1	0.43338	1	0.18653	1	0.22648	1	0.096484	1	0.067707	1	0.4082	1	0.73861	1
10p gain	28 (5%)	547	0.080429	1	1	1	0.009811	1	0.012541	1	0.88682	1	0.83514	1	0.44915	1	0.6739	1	0.6164	1	0.49637	1
10q gain	13 (2%)	562	0.68886	1	0.59527	1	0.19283	1	0.043666	1	0.72072	1	0.21014	1	1	1	0.79532	1	0.69363	1	0.90189	1
11p gain	39 (7%)	536	0.06836	1	0.66349	1	1.7136e-05	0.0119	0.00021429	0.146	0.81461	1	0.93018	1	0.0097121	1	0.059332	1	0.24559	1	0.88201	1
11q gain	39 (7%)	536	0.10493	1	0.045848	1	1.3278e-06	0.000941	0.00091055	0.608	0.50555	1	0.33191	1	0.00048721	0.328	0.0068436	1	0.55893	1	0.40622	1
12p gain	93 (16%)	482	0.3536	1	0.87209	1	0.25584	1	0.017053	1	0.55594	1	0.14248	1	0.053622	1	0.06651	1	0.21996	1	0.11247	1
12q gain	78 (14%)	497	0.233	1	0.80126	1	0.098608	1	0.0019341	1	0.89257	1	0.14534	1	0.14551	1	0.15691	1	0.22169	1	0.16642	1
13q gain	314 (55%)	261	1.3056e-07	9.44e-05	2.6706e-05	0.0186	1.6222e-37	1.23e-34	1.7064e-08	1.24e-05	0.011966	1	0.12547	1	5.4793e-08	3.97e-05	3.7457e-10	2.73e-07	0.010037	1	0.44955	1
14q gain	19 (3%)	556	0.49275	1	0.48023	1	0.030087	1	0.70858	1	0.35152	1	0.27726	1	0.16915	1	0.069902	1	1	1	0.37109	1
15q gain	7 (1%)	568	NA	NA	NA	NA	0.51457	1	0.88163	1	0.024671	1	0.060576	1	NA	NA	NA	NA	0.86981	1	0.37371	1
16p gain	96 (17%)	479	0.10937	1	0.09264	1	1.2625e-16	9.39e-14	0.010804	1	0.42568	1	0.02825	1	0.03518	1	0.0063358	1	0.57733	1	0.34666	1
16q gain	96 (17%)	479	0.049245	1	0.071183	1	3.0211e-18	2.25e-15	0.0039079	1	0.19047	1	0.015545	1	0.01025	1	0.0053383	1	0.46459	1	0.27723	1
17p gain	13 (2%)	562	0.77944	1	0.0078853	1	1	1	0.84961	1	0.37254	1	0.67272	1	0.30844	1	0.47995	1	0.69363	1	0.90189	1
17q gain	67 (12%)	508	0.050374	1	0.04235	1	0.00026856	0.182	0.0014284	0.946	0.2781	1	0.076049	1	0.0001175	0.0805	0.0021178	1	0.078543	1	0.35388	1
18p gain	21 (4%)	554	0.18989	1	0.013971	1	0.00061013	0.409	0.0095456	1	0.36482	1	0.71333	1	0.031133	1	0.0081684	1	0.56836	1	0.39747	1
18q gain	12 (2%)	563	NA	NA	NA	NA	0.17246	1	0.0072864	1	0.26926	1	0.31397	1	NA	NA	NA	NA	0.10546	1	0.13438	1
19p gain	52 (9%)	523	0.17831	1	0.2994	1	5.843e-05	0.0402	0.023588	1	0.065616	1	0.077059	1	0.021726	1	0.12222	1	0.71797	1	0.74542	1
19q gain	61 (11%)	514	0.013287	1	0.017832	1	0.012239	1	0.071518	1	0.0080504	1	0.036565	1	0.0034005	1	0.00026229	0.178	0.83213	1	0.49525	1
20p gain	288 (50%)	287	5.9034e-05	0.0406	5.8857e-08	4.26e-05	4.248e-22	3.2e-19	7.6737e-05	0.0526	0.030338	1	0.092448	1	1.222e-05	0.00853	4.0842e-10	2.97e-07	0.62537	1	0.47156	1
20q gain	403 (70%)	172	6.9517e-19	5.19e-16	2.9349e-16	2.18e-13	2.2246e-46	1.69e-43	9.0386e-13	6.64e-10	0.0010995	0.732	0.0011261	0.749	2.4236e-20	1.82e-17	5.5161e-24	4.16e-21	0.46311	1	0.10066	1
21q gain	19 (3%)	556	0.43486	1	0.40075	1	0.0026802	1	0.70858	1	0.21405	1	0.21885	1	0.26556	1	1	1	0.68566	1	0.14321	1
22q gain	7 (1%)	568	0.68886	1	0.0078853	1	0.23406	1	0.46578	1	0.90794	1	0.49331	1	0.13995	1	0.47995	1	0.45861	1	0.59561	1
Xq gain	17 (3%)	558	0.14489	1	0.64382	1	0.016685	1	0.33848	1	0.1409	1	0.34423	1	0.75925	1	0.86915	1	0.48172	1	0.70461	1
1p loss	68 (12%)	507	0.057568	1	0.0028037	1	7.5476e-06	0.0053	3.8428e-05	0.0265	0.78421	1	0.68655	1	0.064324	1	0.051439	1	0.19261	1	0.62049	1
1q loss	25 (4%)	550	0.40436	1	0.011513	1	0.082264	1	0.031495	1	0.64964	1	0.82476	1	0.14783	1	0.33215	1	0.42483	1	0.72532	1
2p loss	10 (2%)	565	1	1	0.48497	1	0.073513	1	NA	NA	0.003485	1	0.77992	1	0.23187	1	0.018607	1	0.015125	1	0.013286	1
2q loss	8 (1%)	567	0.74121	1	0.45558	1	0.54823	1	NA	NA	0.079184	1	0.37432	1	0.19756	1	0.012658	1	0.058427	1	0.045527	1
3p loss	35 (6%)	540	0.93797	1	0.45115	1	0.83112	1	0.83463	1	0.92667	1	0.9171	1	0.37574	1	0.89025	1	0.10485	1	0.72944	1
3q loss	17 (3%)	558	0.61793	1	0.73598	1	0.75688	1	0.015667	1	0.1344	1	0.44011	1	0.77345	1	0.63231	1	0.73957	1	0.7721	1
4p loss	122 (21%)	453	0.059837	1	0.11702	1	5.4975e-11	4.02e-08	0.0035973	1	0.35044	1	0.75914	1	0.12284	1	0.068242	1	0.045027	1	0.76936	1
4q loss	113 (20%)	462	0.075165	1	0.13597	1	3.1754e-12	2.33e-09	0.0016838	1	0.39156	1	0.54777	1	0.23847	1	0.045606	1	0.012191	1	0.56362	1
5p loss	34 (6%)	541	0.26054	1	0.29696	1	0.00054432	0.366	0.034068	1	0.30584	1	0.50549	1	0.78678	1	0.88042	1	0.96862	1	0.82879	1
5q loss	60 (10%)	515	0.014457	1	0.027363	1	5.5316e-07	0.000396	0.081603	1	0.43095	1	0.87835	1	0.063737	1	0.19653	1	0.96346	1	0.57856	1
6p loss	18 (3%)	557	0.11	1	0.096247	1	0.026043	1	0.2767	1	0.476	1	0.85529	1	0.072336	1	0.149	1	0.60161	1	0.92285	1
6q loss	33 (6%)	542	0.45201	1	0.43263	1	0.09827	1	1	1	0.092797	1	0.66783	1	0.24713	1	0.4567	1	0.26225	1	0.29769	1
7q loss	3 (1%)	572	NA	NA	NA	NA	0.21176	1	NA	NA	0.81833	1	1	1	NA	NA	NA	NA	0.76387	1	1	1
8p loss	145 (25%)	430	0.014973	1	0.0063117	1	1.1426e-18	8.52e-16	0.00037323	0.252	0.074422	1	0.18411	1	4.2326e-05	0.0292	0.0028634	1	0.51503	1	0.73021	1
8q loss	12 (2%)	563	0.60231	1	0.74106	1	0.082808	1	0.58001	1	0.020699	1	0.59992	1	0.22102	1	0.22645	1	0.15853	1	0.27077	1
9p loss	39 (7%)	536	0.57149	1	0.18219	1	2.8967e-05	0.0201	0.0015809	1	0.18837	1	0.20084	1	0.31696	1	0.37747	1	0.12745	1	1	1
9q loss	37 (6%)	538	0.051767	1	0.016107	1	1.9547e-06	0.00138	3.4176e-05	0.0236	0.3571	1	0.29431	1	0.031424	1	0.0062802	1	0.049149	1	0.81952	1
10p loss	40 (7%)	535	0.88427	1	0.52136	1	0.00086224	0.577	0.41929	1	0.082083	1	0.62077	1	0.95393	1	0.26231	1	0.13213	1	0.59051	1
10q loss	46 (8%)	529	0.76192	1	0.31077	1	1.4367e-06	0.00102	0.15314	1	0.023912	1	0.99055	1	0.9684	1	0.28567	1	0.71404	1	0.81051	1
11p loss	40 (7%)	535	0.74503	1	0.94823	1	0.0097676	1	0.70583	1	0.17945	1	0.27693	1	0.080784	1	0.38999	1	0.11333	1	0.35936	1
11q loss	51 (9%)	524	0.97536	1	0.95223	1	0.0016581	1	0.23178	1	0.84064	1	0.2502	1	0.25268	1	0.17791	1	0.12883	1	0.83548	1
12p loss	33 (6%)	542	0.11645	1	0.18844	1	5.424e-07	0.000388	0.25849	1	0.70692	1	0.66426	1	0.56781	1	0.077255	1	0.54148	1	0.22186	1
12q loss	28 (5%)	547	0.1355	1	0.047551	1	1.1071e-06	0.000786	0.52201	1	0.91844	1	0.86567	1	0.20779	1	0.041592	1	0.6164	1	0.6809	1
13q loss	12 (2%)	563	0.29429	1	0.11456	1	0.049459	1	0.22645	1	0.42534	1	0.093235	1	0.28039	1	0.23184	1	0.7263	1	0.40273	1
14q loss	143 (25%)	432	3.4103e-06	0.0024	2.029e-07	0.000146	1.1184e-31	8.46e-29	1.9699e-07	0.000142	2.8208e-05	0.0196	0.0061784	1	1.0866e-05	0.0076	3.0922e-07	0.000222	0.11445	1	0.70906	1
15q loss	156 (27%)	419	0.0072292	1	0.0047672	1	2.0874e-24	1.58e-21	0.015774	1	0.021763	1	0.98712	1	0.35727	1	0.0013665	0.906	0.3675	1	0.24605	1
16p loss	15 (3%)	560	0.2543	1	0.34884	1	0.09948	1	0.22645	1	0.56989	1	0.64645	1	0.44085	1	0.65232	1	1	1	0.91089	1
16q loss	17 (3%)	558	0.013213	1	0.19425	1	0.0022089	1	0.49228	1	0.52636	1	0.75763	1	0.73887	1	0.83118	1	0.13425	1	0.25684	1
17p loss	252 (44%)	323	0.00015906	0.109	0.0012407	0.824	5.4882e-22	4.13e-19	2.4395e-07	0.000176	0.18403	1	0.53849	1	0.0034427	1	0.00018787	0.128	0.027	1	0.49718	1
17q loss	45 (8%)	530	0.77587	1	0.44092	1	0.0023038	1	0.85708	1	0.9226	1	0.96968	1	0.25327	1	0.12058	1	0.11572	1	0.63456	1
18p loss	324 (56%)	251	2.4529e-15	1.82e-12	2.18e-12	1.6e-09	4.2634e-47	3.24e-44	4.3282e-19	3.24e-16	0.013937	1	0.0074165	1	6.9762e-14	5.16e-11	7.3041e-14	5.39e-11	0.065035	1	0.7872	1
18q loss	352 (61%)	223	4.0764e-13	3e-10	5.3218e-12	3.9e-09	6.8004e-51	5.18e-48	8.0336e-21	6.03e-18	0.028641	1	0.079562	1	9.1925e-11	6.71e-08	5.5051e-14	4.07e-11	0.0093757	1	0.37782	1
19p loss	20 (3%)	555	0.4888	1	0.60371	1	1.4622e-05	0.0102	0.024428	1	0.75557	1	0.72431	1	0.68974	1	0.52508	1	0.23499	1	0.37109	1
19q loss	18 (3%)	557	0.4888	1	0.60371	1	0.00023546	0.16	0.096499	1	0.56989	1	0.64645	1	0.68974	1	0.52508	1	0.42424	1	0.097617	1
20p loss	47 (8%)	528	0.18145	1	0.22804	1	4.5625e-07	0.000328	0.039019	1	0.20554	1	0.5838	1	0.035329	1	0.17745	1	0.55412	1	0.48621	1
21q loss	114 (20%)	461	0.047073	1	0.22252	1	3.6397e-05	0.0252	0.055504	1	0.33189	1	0.5314	1	0.61435	1	0.28666	1	0.11838	1	0.3424	1
22q loss	122 (21%)	453	0.056679	1	0.0048373	1	7.7977e-14	5.75e-11	0.35208	1	0.19378	1	0.46368	1	0.33507	1	0.019564	1	0.066218	1	0.10019	1
Xq loss	11 (2%)	564	0.76407	1	0.84019	1	0.33904	1	0.44599	1	0.014792	1	0.40186	1	0.40978	1	1	1	0.51495	1	0.65187	1
