Molecular subtypes	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	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
1p gain	12 (11%)	100	0.26239	1	0.0010594	0.583	0.30724	1	0.72647	1	0.14332	1	0.11448	1	0.18174	1	0.093465	1
1q gain	33 (29%)	79	0.017878	1	0.18912	1	0.54669	1	0.77982	1	0.010659	1	0.038461	1	0.22347	1	0.24802	1
2p gain	10 (9%)	102	0.42426	1	0.91013	1	0.15603	1	0.57111	1	0.40811	1	0.65709	1	0.82026	1	0.55373	1
2q gain	9 (8%)	103	0.71903	1	0.92876	1	0.15603	1	0.57111	1	0.62139	1	0.38328	1	0.89941	1	0.41002	1
3p gain	7 (6%)	105	0.0090734	1	0.024282	1	0.58942	1	0.48234	1	0.25607	1	0.33301	1	1	1	1	1
3q gain	8 (7%)	104	0.019821	1	0.15775	1	0.36222	1	0.18775	1	0.066532	1	0.017676	1	1	1	0.86435	1
4p gain	10 (9%)	102	0.2149	1	0.0091894	1	0.70463	1	0.44494	1	0.63607	1	0.64081	1	0.024618	1	0.50039	1
4q gain	10 (9%)	102	0.003349	1	0.02896	1	0.5516	1	0.48255	1	0.40811	1	0.74532	1	0.024618	1	0.50039	1
5p gain	12 (11%)	100	0.03136	1	0.564	1	0.70327	1	0.89381	1	0.24619	1	0.18953	1	0.19693	1	0.57373	1
5q gain	5 (4%)	107	0.1274	1	0.099437	1	0.12657	1	0.56072	1	0.36455	1	0.42893	1	0.628	1	1	1
6p gain	35 (31%)	77	0.0018169	0.992	0.025382	1	0.3994	1	0.8135	1	0.49883	1	0.4043	1	0.56242	1	0.047709	1
6q gain	8 (7%)	104	0.59372	1	0.73418	1	0.75012	1	0.93691	1	0.21459	1	0.74293	1	0.3176	1	0.61026	1
7p gain	44 (39%)	68	0.00022821	0.128	0.021681	1	0.96818	1	0.46507	1	0.025946	1	0.3496	1	0.21174	1	0.13021	1
7q gain	44 (39%)	68	0.00028555	0.16	0.0010291	0.567	0.8729	1	0.30254	1	0.031806	1	0.091472	1	0.074688	1	0.084609	1
8p gain	18 (16%)	94	1.9679e-05	0.0111	0.0028407	1	0.41601	1	0.29746	1	0.0061128	1	0.1082	1	0.63504	1	0.23594	1
8q gain	31 (28%)	81	1.4925e-05	0.00849	1.6644e-05	0.00944	0.49937	1	0.64984	1	0.00059911	0.334	0.024688	1	0.85634	1	0.22595	1
9q gain	4 (4%)	108	0.69549	1	0.90857	1	0.20265	1	0.37181	1	0.060498	1	0.0122	1	0.057441	1	0.38676	1
11p gain	8 (7%)	104	0.5222	1	0.085393	1	0.45888	1	0.60777	1	0.090379	1	0.068869	1	0.28337	1	0.0008291	0.46
11q gain	5 (4%)	107	0.26406	1	0.17438	1	0.12216	1	0.63128	1	0.086226	1	0.40404	1	0.83982	1	0.017063	1
12p gain	10 (9%)	102	0.0097015	1	0.025062	1	0.64777	1	1	1	0.039681	1	0.17106	1	0.076366	1	0.22577	1
12q gain	4 (4%)	108	0.15157	1	0.034088	1	NA	NA	NA	NA	0.67418	1	0.088094	1	0.028222	1	0.029943	1
13q gain	15 (13%)	97	0.0050491	1	0.074777	1	0.25552	1	0.63606	1	0.1117	1	0.90974	1	0.93564	1	0.62075	1
14q gain	9 (8%)	103	0.16243	1	0.35326	1	0.25015	1	0.35046	1	0.18296	1	0.049962	1	0.9068	1	0.22883	1
15q gain	16 (14%)	96	0.0035385	1	0.60218	1	0.11627	1	0.27629	1	0.94102	1	0.34728	1	0.45353	1	0.2043	1
16p gain	6 (5%)	106	0.028584	1	0.0094411	1	0.63457	1	1	1	0.19247	1	0.020754	1	0.20568	1	0.50308	1
16q gain	6 (5%)	106	0.070316	1	0.062026	1	0.85655	1	0.28526	1	0.38284	1	0.23628	1	0.015318	1	0.061306	1
17p gain	8 (7%)	104	0.49046	1	0.36931	1	0.38909	1	0.03033	1	0.40729	1	0.79282	1	0.45471	1	0.86435	1
17q gain	15 (13%)	97	0.041414	1	0.12522	1	0.8044	1	0.4701	1	0.43362	1	0.79341	1	0.04144	1	0.68234	1
18p gain	14 (12%)	98	0.07924	1	0.020308	1	0.97654	1	0.72314	1	0.20371	1	0.40663	1	0.012544	1	0.23176	1
18q gain	6 (5%)	106	0.17916	1	0.072134	1	0.51249	1	0.93691	1	0.23689	1	0.1471	1	0.74676	1	1	1
19p gain	8 (7%)	104	0.27336	1	0.03854	1	0.49952	1	0.42936	1	0.012785	1	0.0052472	1	0.50752	1	0.15346	1
19q gain	9 (8%)	103	0.01745	1	0.0037031	1	0.88616	1	0.84256	1	0.0042955	1	0.001336	0.732	0.48894	1	0.067869	1
20p gain	31 (28%)	81	1.0994e-05	0.00627	0.00033951	0.189	0.57915	1	0.95296	1	0.0039191	1	0.025302	1	0.21848	1	0.80161	1
20q gain	39 (35%)	73	2.2369e-05	0.0126	0.00069051	0.384	0.81335	1	0.61378	1	0.0052879	1	0.061205	1	0.12696	1	0.60354	1
21q gain	11 (10%)	101	0.59605	1	0.04408	1	0.31077	1	0.57111	1	0.47693	1	0.45243	1	0.66003	1	1	1
22q gain	24 (21%)	88	0.19122	1	0.36396	1	0.34754	1	0.401	1	0.73358	1	0.091354	1	0.75507	1	0.81676	1
1p loss	8 (7%)	104	0.053969	1	0.14722	1	0.64777	1	0.51367	1	0.27234	1	0.21736	1	1	1	0.28491	1
2p loss	12 (11%)	100	0.16794	1	0.14818	1	0.50566	1	0.18417	1	0.24619	1	0.75851	1	0.02493	1	0.041351	1
2q loss	11 (10%)	101	0.020325	1	0.19202	1	0.67327	1	0.68018	1	0.3997	1	0.71893	1	0.063142	1	0.059473	1
3p loss	5 (4%)	107	0.0018315	0.998	0.15956	1	0.43596	1	0.72948	1	0.20927	1	0.061042	1	0.35211	1	0.76497	1
3q loss	8 (7%)	104	0.010729	1	0.43216	1	0.1423	1	0.27909	1	0.18759	1	0.23152	1	0.40558	1	0.61026	1
4p loss	9 (8%)	103	0.49394	1	0.040461	1	0.58745	1	0.44494	1	0.10116	1	0.16921	1	0.13133	1	0.1273	1
4q loss	10 (9%)	102	0.54026	1	0.50274	1	0.61181	1	0.62696	1	0.63607	1	0.37657	1	0.14238	1	0.43521	1
5p loss	14 (12%)	98	0.35959	1	0.001117	0.613	0.29102	1	0.63606	1	0.15053	1	0.014664	1	0.12299	1	0.35899	1
5q loss	24 (21%)	88	0.21747	1	0.15449	1	0.45496	1	0.66433	1	0.41086	1	0.066165	1	0.3458	1	0.76828	1
6p loss	9 (8%)	103	0.3957	1	0.76605	1	0.10032	1	0.92607	1	1	1	0.96422	1	0.23465	1	0.054704	1
6q loss	40 (36%)	72	4.7917e-05	0.027	0.01657	1	0.21739	1	0.65232	1	0.035862	1	0.073027	1	0.059306	1	0.12995	1
8p loss	14 (12%)	98	0.58348	1	0.072651	1	0.65259	1	0.51713	1	0.38647	1	0.28458	1	0.013737	1	0.016336	1
8q loss	3 (3%)	109	1	1	0.065611	1	0.12216	1	1	1	0.61966	1	0.70478	1	0.16339	1	0.68712	1
9p loss	57 (51%)	55	1.5466e-05	0.00878	0.0009047	0.5	0.61435	1	0.85476	1	0.0023688	1	0.16696	1	0.030607	1	0.24173	1
9q loss	42 (38%)	70	0.021561	1	0.018602	1	0.65575	1	0.39696	1	0.029519	1	0.35333	1	0.014303	1	0.24324	1
10p loss	45 (40%)	67	0.013921	1	0.025361	1	0.094459	1	0.051718	1	0.00096462	0.532	0.0054827	1	0.0017923	0.98	0.11316	1
10q loss	49 (44%)	63	0.016826	1	0.01027	1	0.24188	1	0.11505	1	0.00027241	0.153	0.0019932	1	0.02191	1	0.16268	1
11p loss	26 (23%)	86	0.00087894	0.487	0.0091037	1	0.40101	1	0.38636	1	0.027955	1	0.1989	1	0.1368	1	0.32952	1
11q loss	30 (27%)	82	0.00013694	0.077	0.0027582	1	0.32682	1	0.57602	1	0.011081	1	0.0070857	1	0.13111	1	0.13441	1
12p loss	5 (4%)	107	0.48015	1	0.76014	1	0.20346	1	0.51828	1	0.7392	1	0.8134	1	0.43806	1	0.60608	1
12q loss	8 (7%)	104	0.17168	1	0.10404	1	0.95925	1	0.81016	1	0.81497	1	0.69572	1	0.17153	1	0.33897	1
13q loss	17 (15%)	95	0.0036985	1	0.60517	1	0.53971	1	0.77074	1	0.79572	1	0.87809	1	0.049052	1	0.26694	1
14q loss	25 (22%)	87	0.0048687	1	0.05279	1	0.1434	1	0.56901	1	0.22074	1	0.087939	1	0.39729	1	0.58715	1
15q loss	7 (6%)	105	0.084293	1	0.070844	1	0.99942	1	1	1	0.25607	1	0.94738	1	0.6924	1	0.7026	1
16p loss	8 (7%)	104	0.44663	1	0.43216	1	0.10113	1	0.56072	1	0.27234	1	0.81878	1	0.005412	1	0.61026	1
16q loss	16 (14%)	96	0.62003	1	0.24619	1	0.1085	1	0.196	1	0.073612	1	0.26073	1	0.013439	1	0.14506	1
17p loss	28 (25%)	84	0.32507	1	0.00012953	0.0729	0.38084	1	0.74615	1	0.062212	1	0.027929	1	0.12733	1	0.20933	1
17q loss	13 (12%)	99	0.39938	1	0.4733	1	0.75382	1	0.72647	1	0.19921	1	0.49596	1	1	1	0.50901	1
18p loss	18 (16%)	94	0.28939	1	0.0037116	1	0.50068	1	0.50599	1	0.0043675	1	0.017993	1	0.037152	1	0.6585	1
18q loss	18 (16%)	94	0.36989	1	0.0025543	1	0.85476	1	0.088445	1	0.04054	1	0.034113	1	0.089197	1	0.92345	1
19p loss	12 (11%)	100	0.70822	1	0.7557	1	0.4811	1	0.73593	1	0.28909	1	0.016148	1	0.019366	1	0.33736	1
19q loss	12 (11%)	100	0.084855	1	0.60851	1	0.47107	1	0.79506	1	0.14332	1	0.049939	1	0.18174	1	0.44773	1
20p loss	3 (3%)	109	0.45664	1	0.59898	1	NA	NA	NA	NA	0.24825	1	0.297	1	0.16339	1	0.68712	1
21q loss	15 (13%)	97	0.5483	1	0.14889	1	0.75689	1	0.57891	1	0.56903	1	0.90974	1	0.0028768	1	0.62075	1
22q loss	7 (6%)	105	0.1785	1	0.69715	1	0.49448	1	1	1	0.25607	1	0.77001	1	0.14899	1	0.84813	1
Xq loss	3 (3%)	109	0.23571	1	0.38891	1	NA	NA	NA	NA	0.78606	1	0.4861	1	0.60592	1	0.68712	1