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	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	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	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	Chi-square test_P	Chi-square test_Q
1p gain	0 (0%)	158	NA	NA	NA	NA	0.7078	1	0.47526	1	0.61573	1	0.10804	1	0.64296	1	0.11363	1	0.14978	1	0.74803	1	NA	NA	NA	NA
1q gain	0 (0%)	135	0.67102	1	1	1	0.033243	1	0.2328	1	0.1693	1	0.40239	1	0.30722	1	0.035757	1	0.42954	1	0.76098	1	0.037451	1	0.22571	1
2p gain	0 (0%)	142	0.10768	1	0.35923	1	0.15693	1	0.93028	1	0.6788	1	0.70858	1	0.12466	1	0.10713	1	0.55319	1	0.34623	1	0.60286	1	0.041884	1
2q gain	0 (0%)	141	0.014129	1	0.093054	1	0.70065	1	0.74011	1	0.28795	1	0.88061	1	0.017022	1	0.0084949	1	0.10802	1	0.72622	1	0.064199	1	0.0010269	0.837
3p gain	0 (0%)	145	0.83204	1	1	1	0.025198	1	0.48017	1	0.10942	1	0.7752	1	0.53483	1	0.73469	1	0.34403	1	0.013752	1	0.5985	1	0.46751	1
3q gain	0 (0%)	139	1	1	0.89386	1	0.0083154	1	1	1	0.42814	1	0.32257	1	0.75883	1	0.75385	1	0.51783	1	0.041012	1	0.42126	1	0.34636	1
4p gain	0 (0%)	158	NA	NA	NA	NA	0.3914	1	0.47526	1	0.46275	1	0.58714	1	NA	NA	NA	NA	0.36628	1	0.50094	1	0.60581	1	0.35407	1
4q gain	0 (0%)	159	NA	NA	NA	NA	0.28558	1	NA	NA	0.47602	1	0.51514	1	NA	NA	NA	NA	0.7797	1	0.51232	1	NA	NA	NA	NA
5p gain	0 (0%)	142	0.75938	1	0.91093	1	0.072042	1	0.078281	1	0.32624	1	0.86977	1	0.0037236	1	0.017857	1	0.33128	1	0.68016	1	0.026035	1	0.24632	1
5q gain	0 (0%)	150	0.36983	1	0.31392	1	0.056034	1	0.041401	1	0.066026	1	0.27065	1	0.097694	1	0.20819	1	0.39709	1	0.44731	1	0.092342	1	0.076657	1
6p gain	0 (0%)	135	0.39298	1	0.024769	1	3.0322e-05	0.0249	0.015783	1	0.35328	1	0.14454	1	0.51885	1	0.88786	1	0.74817	1	0.6941	1	0.50865	1	0.89993	1
6q gain	0 (0%)	135	0.39298	1	0.024769	1	7.7444e-05	0.0635	0.1688	1	0.35328	1	0.14454	1	1	1	0.31783	1	0.8615	1	0.6941	1	0.7661	1	0.64721	1
7p gain	0 (0%)	72	0.001251	1	0.0016815	1	1.2799e-06	0.00105	0.011429	1	0.5628	1	0.92247	1	0.10439	1	0.079279	1	0.15074	1	0.030206	1	0.02062	1	0.10532	1
7q gain	0 (0%)	83	0.0028413	1	0.0044075	1	6.4701e-07	0.000534	0.090769	1	0.29295	1	0.74169	1	0.11601	1	0.16086	1	0.65099	1	0.35359	1	0.1623	1	0.42827	1
8p gain	0 (0%)	135	0.47527	1	0.42106	1	0.0077538	1	0.70356	1	0.35776	1	0.054398	1	0.023603	1	0.14784	1	0.94036	1	0.49871	1	0.22904	1	0.52017	1
8q gain	0 (0%)	90	0.0069239	1	0.079268	1	3.133e-08	2.59e-05	0.28748	1	0.32593	1	0.4967	1	0.12872	1	0.19172	1	0.48799	1	0.28791	1	0.54734	1	0.58984	1
9p gain	0 (0%)	127	0.030379	1	0.1912	1	0.48174	1	0.08243	1	0.89381	1	0.17786	1	0.11278	1	0.025895	1	0.15273	1	0.71245	1	0.20702	1	0.2204	1
9q gain	0 (0%)	136	0.036827	1	0.19516	1	0.13481	1	0.54084	1	0.80291	1	0.21018	1	0.49622	1	0.11571	1	0.30562	1	0.46537	1	0.22837	1	0.38649	1
10p gain	0 (0%)	154	1	1	0.43638	1	0.24476	1	0.47526	1	0.72729	1	0.55766	1	NA	NA	NA	NA	0.39067	1	0.8702	1	NA	NA	NA	NA
10q gain	0 (0%)	158	NA	NA	NA	NA	0.4435	1	NA	NA	1	1	0.9271	1	NA	NA	NA	NA	0.6308	1	0.7882	1	NA	NA	NA	NA
11p gain	0 (0%)	141	0.04983	1	0.064598	1	0.081297	1	0.20932	1	0.43614	1	0.71978	1	0.12106	1	0.15897	1	0.46379	1	0.1498	1	0.0048015	1	0.046486	1
11q gain	0 (0%)	145	0.12746	1	0.079902	1	0.0013112	1	0.011775	1	0.78383	1	0.41956	1	0.062285	1	0.068538	1	0.93565	1	0.79649	1	0.22919	1	0.72126	1
12p gain	0 (0%)	134	0.81464	1	0.75324	1	0.020147	1	0.74011	1	0.3894	1	0.059794	1	1	1	0.79475	1	0.29727	1	0.16384	1	0.26036	1	0.41903	1
12q gain	0 (0%)	143	1	1	0.60226	1	0.31984	1	0.44858	1	0.45063	1	0.077811	1	1	1	0.82168	1	0.34235	1	0.48477	1	0.048227	1	0.14416	1
13q gain	0 (0%)	60	0.18633	1	0.56757	1	1.2791e-07	0.000106	0.21057	1	0.97271	1	0.5515	1	0.48956	1	0.8722	1	0.031611	1	0.108	1	0.0070507	1	0.038349	1
14q gain	0 (0%)	158	NA	NA	NA	NA	0.7078	1	0.67782	1	0.46275	1	0.49448	1	0.51987	1	0.61462	1	0.11123	1	0.18991	1	NA	NA	NA	NA
16p gain	0 (0%)	133	0.20831	1	0.76568	1	0.010133	1	0.6732	1	0.78442	1	0.681	1	0.25056	1	0.52549	1	0.44894	1	0.332	1	0.063026	1	0.3693	1
16q gain	0 (0%)	132	0.24333	1	1	1	0.00011437	0.0937	0.81034	1	0.73343	1	0.7546	1	0.079542	1	0.23964	1	0.039697	1	0.096416	1	0.02447	1	0.24253	1
17p gain	0 (0%)	159	NA	NA	NA	NA	0.1107	1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
17q gain	0 (0%)	144	0.23872	1	0.30959	1	0.039743	1	0.90418	1	0.57027	1	0.82522	1	0.057571	1	0.021509	1	0.40869	1	0.3104	1	0.18334	1	0.17722	1
18p gain	0 (0%)	155	0.51712	1	1	1	0.11764	1	0.36292	1	1	1	0.79157	1	0.51987	1	0.61462	1	0.75669	1	1	1	0.8595	1	0.70199	1
18q gain	0 (0%)	158	NA	NA	NA	NA	0.7078	1	0.18112	1	1	1	0.79235	1	0.51987	1	0.61462	1	0.73544	1	0.50094	1	0.8595	1	0.70199	1
19p gain	0 (0%)	142	0.0044793	1	0.056493	1	0.0052367	1	0.75949	1	0.79853	1	0.60852	1	0.72434	1	0.89386	1	0.35735	1	0.23202	1	0.66008	1	0.17212	1
19q gain	0 (0%)	139	0.012193	1	0.11777	1	0.0056817	1	0.55776	1	0.25784	1	0.18075	1	1	1	0.90447	1	0.40701	1	0.78836	1	0.77985	1	0.75593	1
20p gain	0 (0%)	67	0.33294	1	0.2165	1	0.14675	1	0.64091	1	0.071532	1	0.66234	1	0.88084	1	0.70908	1	0.57709	1	0.18954	1	0.63591	1	0.18182	1
20q gain	0 (0%)	30	0.025262	1	0.44562	1	0.00026508	0.217	0.325	1	0.2768	1	0.5512	1	0.41778	1	0.92913	1	0.79121	1	0.465	1	0.79623	1	0.81357	1
21q gain	0 (0%)	155	0.76906	1	0.010688	1	0.46683	1	0.81727	1	0.72815	1	0.6103	1	0.31948	1	1	1	0.30663	1	1	1	0.39811	1	0.407	1
22q gain	0 (0%)	157	0.29668	1	0.24045	1	0.56273	1	NA	NA	0.31829	1	0.065396	1	NA	NA	NA	NA	0.6308	1	0.7882	1	NA	NA	NA	NA
Xq gain	0 (0%)	155	1	1	0.81966	1	0.59091	1	1	1	0.76234	1	0.70061	1	1	1	0.61462	1	0.74396	1	0.8702	1	0.8595	1	0.48257	1
1p loss	0 (0%)	141	0.74494	1	0.14013	1	0.023885	1	0.42644	1	0.47446	1	0.15447	1	0.36285	1	0.79475	1	0.38743	1	0.46324	1	0.73055	1	0.058723	1
1q loss	0 (0%)	155	0.83204	1	0.5419	1	0.53643	1	0.6123	1	0.57014	1	0.75237	1	0.19982	1	1	1	0.5198	1	0.8702	1	0.60581	1	0.35407	1
2p loss	0 (0%)	157	0.51093	1	0.27969	1	0.41334	1	NA	NA	0.68197	1	0.12026	1	NA	NA	NA	NA	0.096523	1	0.074073	1	NA	NA	NA	NA
3p loss	0 (0%)	154	1	1	0.20833	1	0.48585	1	0.45682	1	0.80667	1	0.7068	1	0.83382	1	1	1	0.75425	1	0.77528	1	0.67546	1	0.64855	1
3q loss	0 (0%)	158	NA	NA	NA	NA	0.46336	1	NA	NA	1	1	0.29306	1	NA	NA	NA	NA	0.41347	1	1	1	NA	NA	NA	NA
4p loss	0 (0%)	123	0.60987	1	0.43109	1	0.0019968	1	0.78095	1	0.6332	1	0.46752	1	0.049788	1	0.14279	1	0.78348	1	1	1	0.81019	1	0.84943	1
4q loss	0 (0%)	116	0.8447	1	0.31504	1	0.00085574	0.698	0.3985	1	0.42395	1	0.491	1	0.13339	1	0.534	1	0.88508	1	0.81794	1	0.8132	1	0.54137	1
5p loss	0 (0%)	151	0.18343	1	0.22897	1	0.74525	1	0.27445	1	0.9027	1	0.71244	1	0.31558	1	0.085709	1	0.43828	1	0.12678	1	0.33623	1	0.32699	1
5q loss	0 (0%)	139	0.02383	1	0.016902	1	0.20374	1	0.16715	1	0.64258	1	0.81244	1	0.92576	1	0.67765	1	0.7735	1	0.15984	1	0.59058	1	0.60452	1
6p loss	0 (0%)	154	0.31607	1	0.81966	1	0.57174	1	0.013025	1	0.09715	1	0.70467	1	0.68484	1	1	1	0.75669	1	0.8702	1	0.68777	1	0.52758	1
6q loss	0 (0%)	148	0.74494	1	0.30959	1	0.26916	1	0.36677	1	0.31048	1	0.84253	1	0.51577	1	0.52286	1	0.18574	1	0.13476	1	0.43737	1	0.31393	1
8p loss	0 (0%)	106	0.45662	1	0.70182	1	0.025841	1	0.60942	1	0.51133	1	0.60305	1	0.5365	1	0.57893	1	0.71576	1	0.10188	1	0.25078	1	0.043834	1
8q loss	0 (0%)	159	NA	NA	NA	NA	0.48599	1	NA	NA	0.78507	1	0.9271	1	NA	NA	NA	NA	0.52659	1	1	1	NA	NA	NA	NA
9p loss	0 (0%)	150	0.86646	1	0.8654	1	0.10082	1	0.41257	1	0.78383	1	0.59283	1	0.31558	1	0.73051	1	0.96481	1	1	1	0.88697	1	0.97838	1
9q loss	0 (0%)	151	0.54396	1	0.88783	1	0.26545	1	1	1	0.61444	1	0.69385	1	0.45849	1	1	1	0.64533	1	0.31657	1	1	1	0.77852	1
10p loss	0 (0%)	145	0.042872	1	0.042848	1	0.35303	1	0.55776	1	0.035097	1	0.11804	1	0.83815	1	0.57997	1	0.91033	1	1	1	0.40085	1	0.72108	1
10q loss	0 (0%)	141	0.13231	1	0.34613	1	0.069234	1	0.49373	1	0.081421	1	0.28243	1	0.47274	1	0.42867	1	0.97004	1	0.89448	1	0.32098	1	0.38261	1
11p loss	0 (0%)	143	0.11627	1	0.44132	1	0.030298	1	0.090958	1	0.15789	1	0.072435	1	0.91431	1	1	1	0.85595	1	0.66092	1	0.45377	1	0.20976	1
11q loss	0 (0%)	139	0.11627	1	0.44132	1	0.022142	1	0.11786	1	0.30391	1	0.12628	1	0.33031	1	0.39744	1	0.10086	1	0.22141	1	0.1528	1	0.092929	1
12p loss	0 (0%)	150	0.72868	1	0.84047	1	0.33055	1	0.0087556	1	0.40478	1	0.063848	1	0.7318	1	0.61976	1	0.8706	1	0.53527	1	0.44042	1	0.72586	1
12q loss	0 (0%)	154	1	1	0.60148	1	0.54141	1	0.36677	1	0.36838	1	0.54054	1	0.68484	1	0.55525	1	0.48255	1	0.56962	1	0.69525	1	0.89022	1
13q loss	0 (0%)	157	NA	NA	NA	NA	0.091987	1	0.11069	1	0.13275	1	0.60805	1	1	1	1	1	0.34494	1	0.84283	1	0.33397	1	0.39021	1
14q loss	0 (0%)	111	0.61983	1	0.30461	1	0.00040574	0.331	1	1	0.54531	1	0.17592	1	0.67151	1	0.7285	1	0.9648	1	0.37125	1	0.2627	1	0.71266	1
15q loss	0 (0%)	104	0.61808	1	0.040574	1	0.0022859	1	0.64475	1	0.15628	1	0.15265	1	0.62281	1	0.87616	1	0.56643	1	0.71444	1	0.66534	1	0.065659	1
16p loss	0 (0%)	156	0.29668	1	0.24045	1	0.22498	1	0.47526	1	0.87757	1	0.50543	1	1	1	0.17991	1	0.56834	1	1	1	0.8595	1	0.70199	1
16q loss	0 (0%)	152	0.038053	1	0.15528	1	0.005393	1	0.51639	1	0.80667	1	0.50055	1	0.51577	1	0.11214	1	0.61167	1	0.60346	1	1	1	0.65151	1
17p loss	0 (0%)	73	0.86612	1	0.905	1	0.25213	1	0.80561	1	0.7628	1	0.45764	1	1	1	0.64134	1	0.61504	1	0.89322	1	0.31933	1	0.29949	1
17q loss	0 (0%)	147	0.3602	1	0.43638	1	0.30293	1	0.4428	1	0.61384	1	0.55484	1	0.83815	1	0.44029	1	0.33629	1	0.73555	1	0.40085	1	0.25267	1
18p loss	0 (0%)	48	0.041264	1	0.41113	1	1.1699e-05	0.00962	0.24871	1	0.37617	1	0.69093	1	0.10961	1	0.17268	1	0.5823	1	0.40608	1	0.0072594	1	0.054728	1
18q loss	0 (0%)	36	0.028428	1	0.11219	1	9.1647e-07	0.000755	0.18221	1	0.44785	1	0.70808	1	0.34477	1	0.50645	1	0.61255	1	0.66794	1	0.0014734	1	0.023339	1
19p loss	0 (0%)	155	NA	NA	NA	NA	0.26545	1	0.4274	1	0.36838	1	0.42391	1	0.023857	1	0.2929	1	0.1426	1	0.14073	1	0.14443	1	0.72586	1
19q loss	0 (0%)	155	NA	NA	NA	NA	0.49446	1	0.10047	1	0.57067	1	0.56803	1	0.023857	1	0.2929	1	0.70089	1	0.35052	1	0.74274	1	0.45458	1
20p loss	0 (0%)	144	1	1	0.91697	1	0.16195	1	0.64477	1	0.31942	1	0.77681	1	0.31948	1	0.67191	1	0.030547	1	0.091641	1	0.018338	1	0.1935	1
21q loss	0 (0%)	119	0.93581	1	0.81458	1	0.25011	1	0.80659	1	0.32782	1	0.62503	1	1	1	0.63991	1	0.098961	1	0.6627	1	0.70097	1	0.10754	1
22q loss	0 (0%)	120	0.83316	1	0.32357	1	0.50033	1	0.16601	1	0.45508	1	0.45691	1	0.47511	1	0.72287	1	0.11911	1	0.78782	1	0.86084	1	0.43559	1
Xq loss	0 (0%)	156	0.76906	1	0.60148	1	0.28273	1	0.47526	1	0.85476	1	0.73886	1	0.51987	1	0.34812	1	0.84267	1	0.84283	1	0.8595	1	0.47406	1