		Molecular subtypes	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	Chi-square test_P	Chi-square 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	0 (0%)	499	NA	NA	NA	NA	0.10534	1	NA	NA	0.43887	1	0.035855	1	0.84555	1	0.85029	1	0.4573	1	1	1	NA	NA	NA	NA
1q gain	0 (0%)	472	0.61119	1	0.6172	1	2.0852e-08	1.57e-05	0.60988	1	0.43377	1	0.19022	1	0.0097169	1	0.15038	1	0.013372	1	0.18921	1	0.32173	1	0.38652	1
2p gain	0 (0%)	455	0.56067	1	0.40029	1	1.959e-05	0.0135	0.57885	1	0.046154	1	0.78296	1	0.14408	1	0.078453	1	0.2281	1	0.16042	1	0.23185	1	0.60482	1
2q gain	0 (0%)	454	0.56067	1	0.40029	1	0.00040618	0.263	0.47882	1	0.052756	1	0.86158	1	0.051935	1	0.049818	1	0.14587	1	0.16042	1	0.4974	1	0.39708	1
3p gain	0 (0%)	497	NA	NA	NA	NA	0.20369	1	1	1	0.10217	1	0.0032938	1	0.29418	1	0.16078	1	0.011355	1	0.052832	1	0.33546	1	0.46969	1
3q gain	0 (0%)	475	0.024921	1	0.028901	1	4.3826e-07	0.000324	0.05251	1	0.007183	1	0.00010715	0.0718	0.00070456	0.447	0.0052174	1	0.00012609	0.0839	0.0041593	1	0.0012407	0.759	0.21034	1
4p gain	0 (0%)	496	NA	NA	NA	NA	0.12082	1	0.61532	1	0.42832	1	0.080261	1	0.025659	1	0.37796	1	0.00050042	0.321	0.040706	1	NA	NA	NA	NA
4q gain	0 (0%)	496	NA	NA	NA	NA	0.48562	1	0.7899	1	0.87831	1	0.33815	1	0.011216	1	0.5092	1	0.0039355	1	0.14678	1	NA	NA	NA	NA
5p gain	0 (0%)	361	0.59284	1	0.51614	1	0.00027296	0.179	0.1957	1	0.081729	1	0.054605	1	0.045779	1	0.0084423	1	0.036235	1	0.0059502	1	0.11794	1	0.029555	1
5q gain	0 (0%)	345	0.10537	1	0.068922	1	0.003077	1	0.18584	1	0.1584	1	0.17451	1	0.038112	1	0.0051214	1	0.11594	1	0.0014103	0.857	0.35741	1	0.041343	1
6p gain	0 (0%)	498	NA	NA	NA	NA	0.87575	1	0.68265	1	0.8188	1	0.87678	1	0.21454	1	0.44902	1	0.34197	1	0.38929	1	NA	NA	NA	NA
6q gain	0 (0%)	499	NA	NA	NA	NA	0.5357	1	0.61532	1	0.57144	1	0.62591	1	0.44232	1	0.57135	1	0.73725	1	0.43074	1	NA	NA	NA	NA
7p gain	0 (0%)	376	0.87675	1	1	1	1.7465e-09	1.33e-06	0.040031	1	0.00026802	0.176	0.0056517	1	0.067954	1	0.082377	1	0.025081	1	0.70261	1	0.017149	1	0.28227	1
7q gain	0 (0%)	374	0.87675	1	1	1	1.8359e-09	1.4e-06	0.029729	1	0.00011777	0.0787	0.00071795	0.455	0.058061	1	0.13146	1	0.012911	1	0.48104	1	0.0051758	1	0.099412	1
8p gain	0 (0%)	488	NA	NA	NA	NA	1.7356e-05	0.012	0.063494	1	0.086779	1	0.14595	1	0.00097842	0.607	0.00068297	0.434	0.0030191	1	0.11654	1	0.0029628	1	0.046711	1
8q gain	0 (0%)	468	0.053628	1	0.062305	1	5.9402e-11	4.57e-08	0.0006132	0.391	0.010176	1	0.044916	1	1.1473e-07	8.55e-05	4.879e-05	0.033	6.766e-06	0.00478	0.018229	1	2.1202e-06	0.00154	0.00012389	0.0825
9p gain	0 (0%)	496	NA	NA	NA	NA	0.38505	1	0.7899	1	0.17017	1	0.17028	1	0.10317	1	0.05713	1	0.90224	1	0.030618	1	0.054885	1	0.57731	1
9q gain	0 (0%)	496	NA	NA	NA	NA	0.068012	1	0.45562	1	0.10371	1	0.33815	1	0.52284	1	0.63567	1	0.60179	1	0.17809	1	0.16274	1	0.81683	1
10p gain	0 (0%)	498	NA	NA	NA	NA	0.44552	1	1	1	0.98053	1	1	1	0.267	1	0.31138	1	0.76999	1	0.38929	1	1	1	1	1
10q gain	0 (0%)	500	NA	NA	NA	NA	0.16408	1	1	1	0.71582	1	0.61472	1	0.68786	1	0.50758	1	0.83162	1	0.36659	1	NA	NA	NA	NA
11p gain	0 (0%)	487	0.76851	1	0.78254	1	0.01691	1	0.65908	1	0.43744	1	0.3949	1	0.49103	1	0.26531	1	0.94985	1	0.40973	1	0.25941	1	0.63365	1
11q gain	0 (0%)	489	0.76851	1	0.78254	1	0.047116	1	0.57168	1	0.54134	1	0.48032	1	0.58591	1	0.50493	1	0.94611	1	0.35537	1	0.53778	1	1	1
12p gain	0 (0%)	424	0.19401	1	0.20097	1	1.3502e-08	1.02e-05	0.0027348	1	5.6676e-07	0.000417	0.013931	1	1.1022e-05	0.00772	1.8938e-05	0.0131	6.9492e-06	0.0049	0.71233	1	3.3632e-06	0.00242	0.00095756	0.596
12q gain	0 (0%)	423	0.19401	1	0.20097	1	6.4238e-09	4.86e-06	0.0027348	1	1.4633e-07	0.000109	0.010396	1	6.0642e-06	0.00429	9.2165e-06	0.00648	3.2112e-06	0.00231	0.6206	1	1.1517e-06	0.000841	0.00033266	0.217
13q gain	0 (0%)	490	NA	NA	NA	NA	0.83245	1	0.05452	1	0.46728	1	0.77086	1	0.068473	1	0.63576	1	0.61422	1	0.91356	1	0.90197	1	0.73097	1
14q gain	0 (0%)	499	NA	NA	NA	NA	0.061006	1	0.61532	1	0.86889	1	0.059647	1	0.0035445	1	0.047744	1	0.065944	1	0.0053427	1	NA	NA	NA	NA
15q gain	0 (0%)	490	NA	NA	NA	NA	0.065196	1	0.57749	1	0.64372	1	0.23718	1	0.11643	1	0.37881	1	0.83526	1	0.50332	1	0.45877	1	0.61995	1
16p gain	0 (0%)	436	0.10023	1	0.30233	1	0.10532	1	0.64214	1	0.01148	1	0.066314	1	0.63473	1	0.11281	1	0.15601	1	0.5981	1	0.065724	1	0.1697	1
16q gain	0 (0%)	443	0.07055	1	0.17446	1	0.1007	1	0.8918	1	0.044287	1	0.12194	1	0.69647	1	0.33614	1	0.22959	1	0.90341	1	0.054236	1	0.3529	1
17p gain	0 (0%)	488	0.0052247	1	0.0066496	1	0.0040542	1	0.42452	1	0.32105	1	0.033572	1	0.19135	1	0.032663	1	0.72594	1	0.048765	1	0.33546	1	0.10899	1
17q gain	0 (0%)	482	0.0082659	1	0.01062	1	0.0091949	1	0.16197	1	0.55304	1	0.054698	1	0.25322	1	0.0094887	1	0.41669	1	0.022547	1	0.059614	1	0.079278	1
18p gain	0 (0%)	486	0.076398	1	0.043624	1	0.4357	1	0.15609	1	0.31926	1	0.14269	1	0.097694	1	0.40967	1	0.90877	1	0.74438	1	0.41672	1	0.26411	1
18q gain	0 (0%)	486	0.076398	1	0.043624	1	0.4357	1	0.15609	1	0.31926	1	0.14269	1	0.097694	1	0.40967	1	0.90877	1	0.74438	1	0.41672	1	0.26411	1
19p gain	0 (0%)	479	0.18897	1	0.20731	1	1.4682e-05	0.0102	0.2878	1	0.044845	1	0.39709	1	0.042771	1	0.011532	1	0.042287	1	0.065961	1	0.016469	1	0.30891	1
19q gain	0 (0%)	476	0.053628	1	0.062305	1	1.5317e-06	0.00112	0.20712	1	0.055965	1	0.15391	1	0.018535	1	0.004142	1	0.013987	1	0.06605	1	0.0075821	1	0.18413	1
20p gain	0 (0%)	437	0.10193	1	0.14864	1	1.9289e-14	1.51e-11	0.0019806	1	0.00045333	0.292	0.00097912	0.607	3.5945e-06	0.00258	5.2899e-06	0.00377	2.5415e-06	0.00184	0.034351	1	2.9768e-08	2.23e-05	4.5863e-05	0.0311
20q gain	0 (0%)	435	0.075297	1	0.10636	1	1.3743e-15	1.08e-12	0.0019806	1	3.5385e-05	0.0242	0.00085487	0.537	3.298e-07	0.000244	1.4673e-06	0.00107	1.8346e-07	0.000136	0.034979	1	2.6028e-09	1.98e-06	5.3076e-06	0.00378
21q gain	0 (0%)	469	0.82033	1	0.81824	1	0.00075731	0.478	0.094609	1	0.036798	1	0.83574	1	0.070901	1	0.080022	1	0.29502	1	0.81064	1	0.041993	1	0.0038873	1
22q gain	0 (0%)	479	0.58042	1	0.043624	1	0.0024291	1	0.047539	1	0.45167	1	0.21702	1	0.82643	1	0.84565	1	0.9646	1	0.84436	1	0.45328	1	0.86197	1
Xq gain	0 (0%)	495	NA	NA	NA	NA	0.47221	1	0.85097	1	0.12587	1	0.33815	1	0.065059	1	0.15314	1	0.19823	1	0.16306	1	1	1	0.73051	1
1p loss	0 (0%)	472	0.00083595	0.527	5.3764e-05	0.0363	2.7723e-05	0.019	0.47485	1	5.0549e-08	3.79e-05	0.00043538	0.281	0.012254	1	4.6432e-06	0.00332	0.018745	1	1.007e-10	7.71e-08	0.62339	1	0.028332	1
1q loss	0 (0%)	484	0.010729	1	0.013331	1	6.8492e-07	0.000502	1	1	0.00086281	0.541	0.0011155	0.685	1.8963e-05	0.0131	3.1744e-06	0.00229	0.084079	1	4.2165e-10	3.22e-07	0.2243	1	0.0073224	1
2p loss	0 (0%)	494	0.00024867	0.163	0.00038936	0.253	6.1255e-07	0.00045	0.47032	1	1.3686e-05	0.00955	0.00018904	0.125	4.7244e-07	0.000349	1.8734e-08	1.41e-05	0.00059758	0.382	1.2533e-12	9.75e-10	1	1	0.018426	1
2q loss	0 (0%)	493	0.00024867	0.163	0.00038936	0.253	2.3783e-06	0.00172	1	1	0.00012943	0.0859	4.4152e-05	0.03	8.96e-08	6.68e-05	7.9136e-08	5.92e-05	0.00019855	0.131	4.8112e-12	3.72e-09	1	1	0.018426	1
3p loss	0 (0%)	193	0.010564	1	0.0092852	1	9.3488e-35	7.36e-32	5.4918e-06	0.0039	0.00010498	0.0705	1.5412e-05	0.0107	2.0885e-11	1.61e-08	7.0891e-10	5.41e-07	4.2268e-05	0.0288	1.4882e-14	1.17e-11	0.02087	1	3.6438e-05	0.0249
3q loss	0 (0%)	430	0.70139	1	0.69962	1	2.7189e-06	0.00196	0.19436	1	0.095454	1	0.0066057	1	0.51828	1	0.80379	1	0.82187	1	0.0074706	1	0.16242	1	0.2213	1
4p loss	0 (0%)	469	0.28864	1	0.29792	1	0.0035363	1	0.13245	1	0.81614	1	0.94781	1	0.088816	1	0.36552	1	0.5131	1	0.74876	1	0.43594	1	0.49854	1
4q loss	0 (0%)	476	1	1	1	1	2.6588e-05	0.0183	0.11182	1	0.25143	1	0.31278	1	0.063101	1	0.05733	1	0.96875	1	0.37116	1	0.22656	1	0.19597	1
6p loss	0 (0%)	445	0.013899	1	0.0040792	1	7.1338e-11	5.47e-08	0.002772	1	0.00012166	0.0811	7.0349e-06	0.00495	0.00072213	0.457	0.0010519	0.648	2.8747e-09	2.18e-06	0.00039442	0.256	0.0009729	0.604	0.00015462	0.103
6q loss	0 (0%)	419	0.039296	1	0.020472	1	2.4575e-09	1.87e-06	0.13348	1	0.0013994	0.852	0.0010327	0.637	0.20388	1	0.47751	1	1.4245e-05	0.00993	0.0022635	1	0.031157	1	0.0011758	0.721
8p loss	0 (0%)	405	0.77713	1	0.78375	1	0.0033881	1	0.65428	1	0.73834	1	0.6558	1	0.1413	1	0.56142	1	0.15752	1	0.42257	1	0.44634	1	0.52131	1
8q loss	0 (0%)	464	0.49011	1	0.59084	1	0.93369	1	0.15121	1	0.4757	1	0.69952	1	0.18804	1	0.055243	1	0.91022	1	0.27208	1	0.50064	1	0.25826	1
9p loss	0 (0%)	415	0.37846	1	0.12379	1	6.5705e-33	5.16e-30	2.9698e-12	2.3e-09	0.0046325	1	0.0072553	1	1.3893e-11	1.07e-08	2.7121e-12	2.1e-09	8.7344e-09	6.59e-06	0.20099	1	9.0333e-07	0.000661	1.1676e-05	0.00816
9q loss	0 (0%)	410	0.37846	1	0.12379	1	2.791e-34	2.19e-31	2.7811e-13	2.17e-10	0.00099938	0.618	0.010359	1	1.315e-12	1.02e-09	3.9392e-14	3.08e-11	3.8216e-10	2.92e-07	0.17316	1	9.4471e-07	0.000691	3.2769e-05	0.0224
10p loss	0 (0%)	472	0.026008	1	0.030636	1	3.8818e-06	0.00278	0.15729	1	0.19525	1	0.036955	1	0.012254	1	0.019724	1	0.15453	1	0.00046991	0.302	0.18956	1	0.050436	1
10q loss	0 (0%)	456	0.097195	1	0.12088	1	0.0010719	0.659	0.014975	1	0.22014	1	0.012532	1	0.094952	1	0.12585	1	0.31235	1	0.014631	1	0.50609	1	0.015136	1
11p loss	0 (0%)	499	NA	NA	NA	NA	0.031326	1	0.61532	1	0.15609	1	0.035855	1	0.35902	1	0.46204	1	0.54528	1	0.087946	1	NA	NA	NA	NA
11q loss	0 (0%)	497	NA	NA	NA	NA	0.0053392	1	0.82663	1	0.053318	1	0.21517	1	0.37721	1	0.31138	1	0.3494	1	0.029845	1	0.33546	1	0.10899	1
13q loss	0 (0%)	473	0.025253	1	0.038105	1	5.9738e-06	0.00424	0.088845	1	0.001372	0.838	0.0013857	0.845	0.0024962	1	0.00045951	0.296	0.00083783	0.527	0.00028462	0.186	0.034323	1	0.0014876	0.901
14q loss	0 (0%)	342	0.0017916	1	0.0019678	1	7.3524e-13	5.73e-10	6.2474e-05	0.0422	6.6084e-12	5.11e-09	2.0759e-07	0.000154	6.9702e-11	5.35e-08	2.8039e-07	0.000208	4.3263e-06	0.0031	0.50712	1	0.031573	1	0.013038	1
15q loss	0 (0%)	492	0.58042	1	0.58612	1	0.0046092	1	0.45562	1	0.45072	1	0.70387	1	0.073285	1	0.13618	1	0.23177	1	1	1	0.059614	1	0.079278	1
16q loss	0 (0%)	498	NA	NA	NA	NA	0.24437	1	0.34511	1	0.16723	1	0.45624	1	1	1	0.29246	1	0.83162	1	0.26215	1	0.8262	1	0.034821	1
17p loss	0 (0%)	478	0.00011676	0.0781	0.00019745	0.13	6.4411e-07	0.000473	0.60806	1	2.9244e-05	0.02	5.1787e-06	0.0037	1.9025e-06	0.00138	1.5033e-08	1.13e-05	4.9039e-07	0.000361	8.5376e-09	6.45e-06	0.079633	1	0.0064971	1
17q loss	0 (0%)	492	0.00066805	0.426	0.00089279	0.558	6.8422e-06	0.00483	0.47032	1	1.4598e-05	0.0102	1.0235e-05	0.00717	1.9121e-06	0.00139	7.9136e-08	5.92e-05	8.9765e-05	0.0604	4.0474e-11	3.12e-08	1	1	0.018426	1
18p loss	0 (0%)	458	0.19401	1	0.48625	1	4.4062e-05	0.03	0.027756	1	0.018255	1	0.0047251	1	6.0578e-06	0.00429	0.00019604	0.129	0.00036016	0.234	0.0026242	1	0.0007355	0.465	0.00019449	0.129
18q loss	0 (0%)	456	0.2588	1	0.30233	1	6.3021e-05	0.0425	0.046802	1	0.055096	1	0.012751	1	2.8663e-05	0.0197	0.00057363	0.367	0.00094833	0.591	0.0054578	1	0.0005163	0.331	0.00092275	0.576
19p loss	0 (0%)	500	NA	NA	NA	NA	0.12572	1	0.34511	1	0.2794	1	0.035855	1	0.34103	1	0.37884	1	0.83162	1	0.26215	1	NA	NA	NA	NA
20p loss	0 (0%)	498	NA	NA	NA	NA	0.20915	1	1	1	0.017173	1	0.87678	1	0.267	1	0.74728	1	0.072132	1	0.23201	1	NA	NA	NA	NA
21q loss	0 (0%)	470	0.014517	1	0.023819	1	0.00010597	0.0711	0.15109	1	0.0050057	1	0.039896	1	0.0019241	1	1.7176e-05	0.0119	0.2401	1	9.5148e-06	0.00668	0.58709	1	0.11574	1
22q loss	0 (0%)	492	NA	NA	NA	NA	0.0014252	0.865	0.011237	1	0.046179	1	0.39292	1	0.00088773	0.556	0.019143	1	0.36314	1	0.53066	1	0.61244	1	0.11347	1
Xq loss	0 (0%)	494	0.25555	1	0.27216	1	0.71708	1	0.62589	1	0.31024	1	0.2869	1	0.067592	1	0.0076322	1	0.030752	1	0.04285	1	NA	NA	NA	NA
