		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	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	0 (0%)	416	NA	NA	NA	NA	0.28763	1	0.69775	1	0.17792	1	0.38396	1	0.76751	1	0.2439	1	0.59751	1	0.73342	1	1	1	1	1
1q gain	0 (0%)	378	0.040536	1	0.53602	1	0.068244	1	0.19906	1	0.28159	1	0.048087	1	0.2243	1	0.29141	1	0.69748	1	0.71034	1	0.14959	1	0.44377	1
2p gain	0 (0%)	386	0.124	1	0.074608	1	0.017312	1	0.0092079	1	0.027828	1	0.39257	1	0.0022673	1	0.080023	1	0.23447	1	0.48791	1	0.10736	1	0.0079929	1
2q gain	0 (0%)	388	0.073705	1	0.050976	1	0.0065166	1	0.0016508	1	0.046379	1	0.45047	1	0.0291	1	0.14102	1	0.27504	1	0.40969	1	0.11295	1	0.12104	1
3p gain	0 (0%)	407	0.29804	1	0.42991	1	0.15845	1	0.38775	1	0.36361	1	0.72105	1	0.84424	1	1	1	0.86007	1	0.71392	1	0.75554	1	0.6213	1
3q gain	0 (0%)	397	0.37494	1	0.16405	1	0.0047223	1	0.23384	1	0.53594	1	0.75209	1	0.1315	1	0.62922	1	0.43585	1	0.74622	1	0.90669	1	0.26524	1
4p gain	0 (0%)	424	NA	NA	NA	NA	0.24353	1	0.18519	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
4q gain	0 (0%)	422	NA	NA	NA	NA	0.25126	1	0.78972	1	NA	NA	NA	NA	NA	NA	NA	NA	0.52699	1	0.54257	1	NA	NA	NA	NA
5p gain	0 (0%)	387	0.21767	1	0.098835	1	0.0020345	1	0.11981	1	0.66219	1	0.97123	1	0.42788	1	0.75957	1	0.57529	1	0.63666	1	0.074765	1	0.88243	1
5q gain	0 (0%)	405	0.54511	1	0.63094	1	0.055489	1	0.18979	1	0.53291	1	0.29256	1	0.68626	1	0.25016	1	1	1	0.73751	1	0.26109	1	0.73285	1
6p gain	0 (0%)	374	0.58873	1	0.013558	1	0.00061307	0.467	0.37295	1	0.56827	1	0.44268	1	0.24983	1	0.1063	1	0.41432	1	0.5155	1	0.45432	1	0.89697	1
6q gain	0 (0%)	380	0.34847	1	0.027446	1	0.0043711	1	0.22816	1	0.48409	1	0.43338	1	0.46619	1	0.74348	1	0.35909	1	0.58999	1	0.11529	1	0.54927	1
7p gain	0 (0%)	221	0.00304	1	0.0022344	1	1.0053e-14	8.48e-12	6.7399e-05	0.0534	0.0059037	1	0.039715	1	1.2495e-06	0.00102	7.3702e-06	0.00596	0.65392	1	0.15045	1	5.9525e-05	0.0473	0.39411	1
7q gain	0 (0%)	247	0.014468	1	0.012963	1	2.4973e-09	2.07e-06	0.0047286	1	0.10508	1	0.071977	1	0.0001282	0.101	8.9079e-05	0.0704	0.83256	1	0.24161	1	0.00056332	0.433	0.81078	1
8p gain	0 (0%)	342	0.69139	1	0.35662	1	8.0329e-13	6.72e-10	0.051921	1	0.066874	1	0.16116	1	0.44604	1	0.060011	1	0.63034	1	0.19257	1	0.43573	1	0.85063	1
8q gain	0 (0%)	260	0.72973	1	0.69124	1	1.3151e-19	1.13e-16	0.00024258	0.19	0.55377	1	0.039861	1	0.035339	1	0.033076	1	0.15116	1	0.63075	1	0.012924	1	0.45183	1
9p gain	0 (0%)	379	0.0064524	1	0.19232	1	0.15206	1	0.29066	1	0.067883	1	0.17919	1	0.52042	1	0.83468	1	0.73066	1	0.43563	1	0.8879	1	0.6139	1
9q gain	0 (0%)	387	0.011043	1	0.07296	1	0.26963	1	0.093569	1	0.019498	1	0.033971	1	0.29385	1	0.58893	1	0.040153	1	0.036918	1	0.7566	1	0.038002	1
10p gain	0 (0%)	408	0.69067	1	0.51996	1	0.15194	1	0.023004	1	0.18433	1	0.7266	1	0.69468	1	0.43262	1	0.4482	1	0.51533	1	0.0028962	1	0.74938	1
10q gain	0 (0%)	416	NA	NA	NA	NA	0.28763	1	0.013855	1	0.37729	1	0.4977	1	0.83178	1	0.36224	1	0.16677	1	0.21673	1	0.097272	1	0.76431	1
11p gain	0 (0%)	407	0.13759	1	0.0013887	1	6.9297e-05	0.0549	0.00017117	0.135	0.54774	1	0.80443	1	0.6818	1	0.36745	1	0.94704	1	0.76733	1	0.31718	1	0.24629	1
11q gain	0 (0%)	403	0.021447	1	0.0027657	1	4.5012e-06	0.00365	0.00029607	0.231	0.33374	1	0.80795	1	0.16638	1	0.034677	1	0.65879	1	0.18047	1	0.033554	1	0.2468	1
12p gain	0 (0%)	361	0.26725	1	0.38249	1	0.00054363	0.418	0.0050527	1	0.85042	1	0.8128	1	0.66521	1	0.65947	1	0.049946	1	0.1353	1	0.033203	1	0.24758	1
12q gain	0 (0%)	366	0.34121	1	0.54177	1	0.0004513	0.348	0.00076658	0.583	0.77922	1	0.66875	1	0.67847	1	0.81614	1	0.0060567	1	0.11505	1	0.035953	1	0.24293	1
13q gain	0 (0%)	210	1.0588e-05	0.00854	1.6648e-05	0.0134	2.2007e-29	1.89e-26	6.3672e-05	0.0506	0.0088414	1	0.0051019	1	1.4917e-05	0.012	2.2443e-07	0.000184	0.1947	1	0.21198	1	1.4804e-07	0.000122	0.81307	1
14q gain	0 (0%)	411	0.482	1	0.44276	1	0.13974	1	0.20339	1	0.28461	1	0.30896	1	0.064561	1	0.0097796	1	1	1	0.65875	1	1	1	0.65004	1
15q gain	0 (0%)	422	NA	NA	NA	NA	0.10909	1	0.68497	1	0.058038	1	0.033319	1	0.65987	1	0.69436	1	0.48486	1	0.44038	1	0.3941	1	0.30231	1
16p gain	0 (0%)	360	0.0074852	1	0.00080364	0.611	9.2454e-15	7.81e-12	0.11786	1	0.72438	1	0.032865	1	0.038299	1	0.030102	1	0.080523	1	0.018276	1	0.085023	1	0.95593	1
16q gain	0 (0%)	361	0.0060209	1	0.0011609	0.873	1.4109e-15	1.2e-12	0.12979	1	0.84714	1	0.019909	1	0.038299	1	0.030102	1	0.16394	1	0.014938	1	0.0087357	1	0.67595	1
17p gain	0 (0%)	417	NA	NA	NA	NA	1	1	0.81248	1	0.60292	1	0.18188	1	0.071771	1	0.13113	1	0.56793	1	0.59512	1	0.62887	1	1	1
17q gain	0 (0%)	381	0.029211	1	0.049528	1	0.0027024	1	0.0051126	1	0.90953	1	0.22627	1	0.0031678	1	0.0096072	1	0.037882	1	0.85425	1	0.12442	1	0.2208	1
18p gain	0 (0%)	412	0.1437	1	0.63479	1	0.0014538	1	0.011894	1	0.72142	1	0.96788	1	0.21637	1	0.26204	1	0.1298	1	0.15475	1	0.80511	1	0.65975	1
18q gain	0 (0%)	418	NA	NA	NA	NA	0.011733	1	0.019047	1	0.50152	1	0.15769	1	0.070847	1	0.14738	1	0.28456	1	0.15764	1	0.44951	1	0.62727	1
19p gain	0 (0%)	391	0.056278	1	0.20791	1	0.020928	1	0.03541	1	0.17716	1	0.078152	1	0.21315	1	0.39553	1	0.69933	1	0.75829	1	0.25699	1	0.13177	1
19q gain	0 (0%)	383	0.047596	1	0.053692	1	0.17649	1	0.10248	1	0.055465	1	0.012945	1	0.11441	1	0.23391	1	0.90359	1	0.75057	1	0.66406	1	0.35602	1
20p gain	0 (0%)	233	0.0017044	1	8.7011e-07	0.000712	6.8921e-17	5.89e-14	0.0028737	1	0.011195	1	0.037085	1	6.2459e-07	0.000512	2.2929e-08	1.89e-05	0.2097	1	0.0024497	1	7.965e-05	0.063	0.88064	1
20q gain	0 (0%)	153	1.1373e-12	9.5e-10	4.9702e-15	4.21e-12	1.2233e-44	1.05e-41	2.0071e-11	1.67e-08	3.0946e-05	0.0248	1.5779e-06	0.00128	2.5825e-14	2.17e-11	1.3891e-16	1.19e-13	0.47779	1	0.00035297	0.273	1.566e-12	1.31e-09	0.057047	1
21q gain	0 (0%)	414	0.16982	1	0.19519	1	0.43364	1	0.20339	1	0.30604	1	0.27487	1	0.58731	1	0.90875	1	0.84807	1	0.7936	1	1	1	0.85338	1
Xq gain	0 (0%)	415	0.065925	1	0.77725	1	0.0039366	1	0.20339	1	0.1315	1	0.42563	1	0.63693	1	1	1	0.56793	1	0.3418	1	0.18268	1	0.85338	1
1p loss	0 (0%)	376	0.0028289	1	0.00097194	0.735	3.5534e-05	0.0284	0.004922	1	0.45789	1	0.69838	1	0.15194	1	0.33325	1	0.49777	1	0.074717	1	0.26919	1	0.019884	1
1q loss	0 (0%)	409	0.35571	1	0.13462	1	0.13457	1	0.29495	1	0.37327	1	0.79115	1	0.14775	1	0.40316	1	0.88952	1	0.80232	1	0.43422	1	0.32743	1
2p loss	0 (0%)	422	0.89774	1	0.31456	1	0.065022	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	0.39139	1	0.28782	1	NA	NA	NA	NA
2q loss	0 (0%)	421	1	1	0.15598	1	0.31581	1	NA	NA	0.20425	1	0.24525	1	NA	NA	NA	NA	0.18083	1	0.21627	1	NA	NA	NA	NA
3p loss	0 (0%)	397	0.413	1	0.18694	1	0.00047887	0.369	0.33047	1	0.31159	1	1	1	0.26035	1	0.15034	1	0.4134	1	0.64907	1	0.12265	1	0.40185	1
3q loss	0 (0%)	413	0.74475	1	0.63094	1	0.27787	1	1	1	0.016306	1	0.18667	1	0.15229	1	0.63518	1	0.85882	1	1	1	0.51308	1	0.17527	1
4p loss	0 (0%)	339	0.0027141	1	0.019893	1	1.2546e-13	1.05e-10	0.0025488	1	0.31695	1	0.70846	1	0.00030615	0.238	0.00059045	0.452	0.13003	1	0.38193	1	0.014501	1	0.080021	1
4q loss	0 (0%)	354	0.0036142	1	0.010724	1	3.5642e-11	2.96e-08	0.001402	1	0.1178	1	0.42703	1	0.00039233	0.303	0.0029328	1	0.0053306	1	0.029675	1	0.038807	1	0.079153	1
5p loss	0 (0%)	403	0.40597	1	0.11759	1	0.0011168	0.841	0.082729	1	0.48671	1	0.74469	1	0.062284	1	0.037791	1	0.832	1	0.91573	1	0.15621	1	0.40185	1
5q loss	0 (0%)	388	0.05989	1	0.0075721	1	1.7879e-05	0.0144	0.20132	1	0.0077932	1	0.24187	1	0.0016257	1	0.010294	1	0.65865	1	0.53658	1	0.02868	1	0.47482	1
6p loss	0 (0%)	415	0.45647	1	0.24739	1	0.068393	1	1	1	0.40295	1	0.94247	1	0.64186	1	0.16721	1	0.65206	1	0.26219	1	1	1	0.30231	1
6q loss	0 (0%)	406	0.91546	1	0.78906	1	0.15735	1	0.83716	1	0.52784	1	0.87128	1	0.94394	1	0.39437	1	0.61438	1	0.60215	1	0.69432	1	0.78723	1
8p loss	0 (0%)	330	0.00033214	0.257	0.0005809	0.446	2.3198e-16	1.98e-13	0.0003133	0.243	0.061709	1	0.075269	1	0.020324	1	0.00088561	0.671	0.18953	1	0.031871	1	0.0001134	0.0894	0.27516	1
8q loss	0 (0%)	417	0.27385	1	0.38628	1	0.012081	1	0.57739	1	0.074997	1	0.33065	1	1	1	1	1	0.063367	1	0.37061	1	1	1	0.68912	1
9p loss	0 (0%)	400	0.80979	1	0.12326	1	0.00025415	0.198	0.057788	1	0.16348	1	0.33017	1	0.053544	1	0.045125	1	0.33979	1	0.90188	1	0.10504	1	0.045415	1
9q loss	0 (0%)	401	0.30814	1	0.13882	1	3.5789e-05	0.0286	0.00059347	0.453	0.23511	1	0.33017	1	0.0036083	1	0.0077546	1	0.093483	1	0.27876	1	0.0066926	1	0.07878	1
10p loss	0 (0%)	402	0.69986	1	0.67266	1	0.031432	1	0.81332	1	0.22615	1	0.96162	1	0.46061	1	0.11684	1	0.27065	1	0.32857	1	0.72184	1	1	1
10q loss	0 (0%)	401	0.59691	1	0.71065	1	0.0047593	1	0.66084	1	0.14312	1	1	1	0.23999	1	0.01944	1	0.67461	1	0.92069	1	0.39187	1	0.56432	1
11p loss	0 (0%)	405	0.44508	1	0.067986	1	0.0002537	0.198	0.00022575	0.177	0.4167	1	0.31686	1	0.0044125	1	0.0048641	1	0.046304	1	0.27424	1	0.0040894	1	0.036943	1
11q loss	0 (0%)	399	0.28782	1	0.038614	1	9.0064e-05	0.0711	1.3369e-06	0.00109	0.57969	1	0.59998	1	0.17629	1	0.037791	1	0.084203	1	0.5338	1	0.22064	1	0.56432	1
12p loss	0 (0%)	406	0.079183	1	0.12326	1	1.7279e-05	0.0139	0.22261	1	0.41852	1	0.92193	1	0.1296	1	0.0097672	1	0.42988	1	0.22843	1	0.28805	1	0.2054	1
12q loss	0 (0%)	407	0.2078	1	0.13882	1	5.7852e-06	0.00468	0.093821	1	0.82947	1	0.87951	1	0.01489	1	0.061692	1	0.35956	1	0.14457	1	0.075174	1	0.2054	1
13q loss	0 (0%)	420	NA	NA	NA	NA	0.31178	1	0.26512	1	0.014449	1	0.093067	1	0.21142	1	0.62389	1	0.55388	1	0.3087	1	0.3941	1	0.046415	1
14q loss	0 (0%)	331	3.1842e-08	2.62e-05	2.1385e-06	0.00174	1.433e-20	1.23e-17	4.0132e-06	0.00326	0.0010597	0.799	0.026613	1	1.9449e-05	0.0156	3.6265e-05	0.0289	0.26756	1	0.0059612	1	0.00059324	0.453	0.047757	1
15q loss	0 (0%)	326	0.010775	1	0.0027528	1	5.434e-18	4.65e-15	0.0045301	1	0.046704	1	0.3927	1	0.0017166	1	2.145e-05	0.0172	0.27925	1	0.0097363	1	0.0040981	1	0.46332	1
16p loss	0 (0%)	417	0.27385	1	0.5545	1	0.9004	1	0.015896	1	0.92726	1	0.90449	1	0.84957	1	0.53069	1	1	1	0.72691	1	1	1	0.49858	1
16q loss	0 (0%)	419	0.51949	1	1	1	0.5853	1	0.18519	1	0.25405	1	0.49319	1	NA	NA	NA	NA	0.18083	1	0.21627	1	NA	NA	NA	NA
17p loss	0 (0%)	255	3.7718e-05	0.03	5.3729e-06	0.00435	8.6959e-22	7.47e-19	4.7778e-08	3.93e-05	0.062301	1	0.055165	1	1.5886e-07	0.00013	2.1082e-08	1.74e-05	0.36709	1	0.15154	1	5.0755e-09	4.2e-06	0.014093	1
17q loss	0 (0%)	390	0.091774	1	0.22668	1	0.00017446	0.137	0.078988	1	0.53068	1	0.42811	1	0.0024728	1	0.024547	1	0.78271	1	0.45623	1	0.022897	1	0.07878	1
18p loss	0 (0%)	208	3.9306e-13	3.29e-10	3.8289e-10	3.17e-07	2.2233e-47	1.92e-44	8.4584e-15	7.16e-12	0.00027462	0.214	0.00038057	0.294	4.4688e-15	3.79e-12	1.3841e-14	1.17e-11	0.64821	1	0.023319	1	3.9209e-14	3.3e-11	0.00089228	0.675
18q loss	0 (0%)	193	3.4196e-13	2.87e-10	8.7941e-11	7.3e-08	1.1017e-44	9.5e-42	6.41e-16	5.46e-13	0.0036804	1	0.0013775	1	7.1581e-15	6.06e-12	9.0846e-16	7.73e-13	0.31599	1	0.028328	1	2.5017e-12	2.08e-09	0.045481	1
19p loss	0 (0%)	411	1	1	0.3199	1	0.03103	1	0.028939	1	0.55089	1	0.18296	1	0.00082222	0.624	0.02439	1	0.47065	1	0.59793	1	0.35793	1	0.036943	1
19q loss	0 (0%)	414	0.92438	1	0.3813	1	0.13263	1	0.13096	1	0.86446	1	0.36307	1	0.0099902	1	0.03406	1	0.48992	1	0.60047	1	0.13466	1	0.063764	1
20p loss	0 (0%)	390	0.050821	1	0.054425	1	0.0012996	0.975	0.083762	1	0.75768	1	0.32744	1	0.47182	1	0.047619	1	0.78923	1	0.56802	1	0.32219	1	0.23636	1
20q loss	0 (0%)	424	NA	NA	NA	NA	0.16426	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
21q loss	0 (0%)	351	0.014096	1	0.0022745	1	1.4356e-06	0.00117	0.59127	1	0.39327	1	0.57198	1	0.030115	1	0.071898	1	0.056569	1	0.40265	1	0.21734	1	0.13654	1
22q loss	0 (0%)	340	0.00032035	0.249	0.0005809	0.446	7.0639e-13	5.91e-10	0.034264	1	0.20645	1	0.13829	1	0.00098291	0.742	0.0012372	0.929	0.28878	1	0.11301	1	0.011056	1	0.26711	1
Xq loss	0 (0%)	422	NA	NA	NA	NA	0.81994	1	1	1	0.15882	1	0.82096	1	NA	NA	NA	NA	0.71597	1	0.52526	1	0.64095	1	1	1
