Correlation between copy number variation genes and molecular subtypes

Bladder Urothelial Carcinoma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1MW2F9S

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 63 peak regions and 8 molecular subtypes across 150 patients, 43 significant findings detected with Q value < 0.25.

Amp Peak 1(1p34.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 3(1q23.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(3p25.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 7(4q13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(5p15.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(6p22.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 12(7p11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(8p11.23) cnvs correlated to 'CN_CNMF'.
Amp Peak 14(8p11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(10p15.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 22(17q11.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 24(19q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 25(19q13.43) cnvs correlated to 'CN_CNMF'.
Del Peak 4(2q34) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q37.1) cnvs correlated to 'CN_CNMF'.
Del Peak 6(3p21.31) cnvs correlated to 'CN_CNMF'.
Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 14(6q21) cnvs correlated to 'CN_CNMF'.
Del Peak 15(6q27) cnvs correlated to 'CN_CNMF'.
Del Peak 16(8p23.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 17(8p21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 19(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 22(11p15.5) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 23(11q25) cnvs correlated to 'CN_CNMF'.
Del Peak 24(13q14.2) cnvs correlated to 'CN_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.
Del Peak 26(14q32.31) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Del Peak 27(15q13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 29(16q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 30(17p12) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 63 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 43 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 4(3p25 2)	72 (48%)	78	3.36e-05 (0.0163)	0.00161 (0.72)	0.278 (1.00)	0.237 (1.00)	0.000848 (0.388)	0.000371 (0.174)	0.00289 (1.00)	0.000422 (0.197)
Del Peak 24(13q14 2)	58 (39%)	92	0.000135 (0.0642)	0.986 (1.00)	0.000229 (0.108)	0.000117 (0.0559)	0.0928 (1.00)	0.235 (1.00)	0.973 (1.00)	0.13 (1.00)
Amp Peak 1(1p34 2)	45 (30%)	105	0.0002 (0.0943)	4.09e-05 (0.0199)	0.894 (1.00)	1 (1.00)	0.0147 (1.00)	0.52 (1.00)	0.46 (1.00)	0.0512 (1.00)
Amp Peak 2(1q21 3)	76 (51%)	74	6.85e-06 (0.00337)	0.0004 (0.187)	0.0118 (1.00)	0.00635 (1.00)	0.00374 (1.00)	0.365 (1.00)	0.27 (1.00)	0.00206 (0.906)
Amp Peak 17(10p15 1)	61 (41%)	89	6.73e-09 (3.38e-06)	5.25e-06 (0.00259)	0.893 (1.00)	0.725 (1.00)	0.221 (1.00)	0.0583 (1.00)	0.468 (1.00)	0.132 (1.00)
Amp Peak 22(17q11 2)	68 (45%)	82	4.62e-08 (2.31e-05)	0.00122 (0.548)	0.76 (1.00)	0.673 (1.00)	0.000134 (0.0639)	0.00318 (1.00)	0.0155 (1.00)	0.133 (1.00)
Del Peak 7(3p14 2)	48 (32%)	102	0.000507 (0.234)	0.56 (1.00)	0.0759 (1.00)	0.0158 (1.00)	0.000425 (0.198)	0.00753 (1.00)	0.132 (1.00)	0.645 (1.00)
Del Peak 16(8p23 3)	80 (53%)	70	2.1e-08 (1.06e-05)	5.24e-05 (0.0253)	0.145 (1.00)	0.325 (1.00)	0.169 (1.00)	0.969 (1.00)	0.0945 (1.00)	0.018 (1.00)
Del Peak 17(8p21 1)	84 (56%)	66	1.53e-09 (7.71e-07)	5.2e-05 (0.0251)	0.145 (1.00)	0.325 (1.00)	0.713 (1.00)	0.498 (1.00)	0.0309 (1.00)	0.0516 (1.00)
Del Peak 22(11p15 5)	73 (49%)	77	5.12e-06 (0.00254)	0.038 (1.00)	0.195 (1.00)	0.727 (1.00)	0.125 (1.00)	0.000152 (0.0722)	0.0113 (1.00)	0.00888 (1.00)
Del Peak 26(14q32 31)	41 (27%)	109	5.95e-05 (0.0286)	0.0272 (1.00)	0.805 (1.00)	0.922 (1.00)	0.218 (1.00)	0.247 (1.00)	0.000136 (0.0645)	0.00104 (0.473)
Amp Peak 3(1q23 3)	82 (55%)	68	2.59e-05 (0.0127)	0.0124 (1.00)	0.925 (1.00)	0.681 (1.00)	0.0634 (1.00)	0.719 (1.00)	0.00104 (0.471)	0.00119 (0.534)
Amp Peak 7(4q13 3)	23 (15%)	127	8.45e-05 (0.0406)	0.16 (1.00)	0.517 (1.00)	1 (1.00)	0.571 (1.00)	0.4 (1.00)	0.378 (1.00)	0.682 (1.00)
Amp Peak 8(5p15 1)	69 (46%)	81	4.5e-05 (0.0218)	0.202 (1.00)	0.014 (1.00)	0.332 (1.00)	0.094 (1.00)	0.458 (1.00)	0.143 (1.00)	0.255 (1.00)
Amp Peak 9(6p22 3)	61 (41%)	89	0.000183 (0.0865)	0.00236 (1.00)	0.834 (1.00)	0.761 (1.00)	0.56 (1.00)	0.581 (1.00)	0.241 (1.00)	0.323 (1.00)
Amp Peak 12(7p11 2)	78 (52%)	72	4.49e-07 (0.000224)	0.002 (0.883)	0.481 (1.00)	0.186 (1.00)	0.825 (1.00)	0.678 (1.00)	0.622 (1.00)	0.89 (1.00)
Amp Peak 13(8p11 23)	48 (32%)	102	0.000492 (0.228)	0.0488 (1.00)	0.0732 (1.00)	0.0229 (1.00)	0.423 (1.00)	0.271 (1.00)	0.0786 (1.00)	0.105 (1.00)
Amp Peak 14(8p11 21)	48 (32%)	102	1.62e-05 (0.00794)	0.0146 (1.00)	0.596 (1.00)	0.528 (1.00)	0.268 (1.00)	0.448 (1.00)	0.27 (1.00)	0.136 (1.00)
Amp Peak 24(19q12)	65 (43%)	85	6.35e-06 (0.00313)	0.00271 (1.00)	0.37 (1.00)	0.681 (1.00)	0.456 (1.00)	0.438 (1.00)	0.29 (1.00)	0.211 (1.00)
Amp Peak 25(19q13 43)	63 (42%)	87	9.08e-05 (0.0435)	0.0258 (1.00)	0.778 (1.00)	0.772 (1.00)	0.0812 (1.00)	0.819 (1.00)	0.137 (1.00)	0.0957 (1.00)
Del Peak 4(2q34)	60 (40%)	90	3.53e-06 (0.00175)	0.137 (1.00)	0.309 (1.00)	0.32 (1.00)	0.152 (1.00)	0.111 (1.00)	0.0904 (1.00)	0.0586 (1.00)
Del Peak 5(2q37 1)	73 (49%)	77	3.3e-05 (0.0161)	0.0128 (1.00)	0.908 (1.00)	0.936 (1.00)	0.0659 (1.00)	0.0184 (1.00)	0.0402 (1.00)	0.0314 (1.00)
Del Peak 6(3p21 31)	47 (31%)	103	0.000394 (0.185)	0.12 (1.00)	0.00649 (1.00)	0.0681 (1.00)	0.000558 (0.257)	0.0203 (1.00)	0.0789 (1.00)	0.165 (1.00)
Del Peak 14(6q21)	63 (42%)	87	7.29e-07 (0.000363)	0.0129 (1.00)	0.0799 (1.00)	0.123 (1.00)	0.314 (1.00)	0.0153 (1.00)	0.412 (1.00)	0.117 (1.00)
Del Peak 15(6q27)	62 (41%)	88	2.04e-06 (0.00102)	0.00235 (1.00)	0.156 (1.00)	0.163 (1.00)	0.221 (1.00)	0.00625 (1.00)	0.229 (1.00)	0.168 (1.00)
Del Peak 19(9p21 3)	86 (57%)	64	0.000482 (0.224)	0.566 (1.00)	0.0718 (1.00)	0.575 (1.00)	0.251 (1.00)	0.128 (1.00)	0.15 (1.00)	0.207 (1.00)
Del Peak 23(11q25)	47 (31%)	103	4.26e-05 (0.0207)	0.337 (1.00)	0.378 (1.00)	0.454 (1.00)	0.2 (1.00)	0.549 (1.00)	0.143 (1.00)	0.294 (1.00)
Del Peak 27(15q13 1)	54 (36%)	96	0.000301 (0.141)	0.00312 (1.00)	0.0829 (1.00)	0.332 (1.00)	0.58 (1.00)	0.78 (1.00)	0.135 (1.00)	0.113 (1.00)
Del Peak 29(16q23 1)	38 (25%)	112	1.99e-05 (0.00975)	0.0434 (1.00)	0.232 (1.00)	0.52 (1.00)	0.611 (1.00)	0.96 (1.00)	0.0932 (1.00)	0.084 (1.00)
Del Peak 30(17p12)	77 (51%)	73	2.91e-08 (1.46e-05)	0.0175 (1.00)	0.556 (1.00)	0.169 (1.00)	0.0218 (1.00)	0.0245 (1.00)	0.347 (1.00)	0.363 (1.00)
Amp Peak 5(3q26 32)	84 (56%)	66	0.0044 (1.00)	0.664 (1.00)	0.161 (1.00)	0.206 (1.00)	0.601 (1.00)	0.875 (1.00)	0.535 (1.00)	0.525 (1.00)
Amp Peak 6(4p16 3)	31 (21%)	119	0.0176 (1.00)	0.172 (1.00)	0.162 (1.00)	0.137 (1.00)	0.103 (1.00)	0.118 (1.00)	0.0531 (1.00)	0.566 (1.00)
Amp Peak 10(6q12)	25 (17%)	125	0.00601 (1.00)	0.627 (1.00)	1 (1.00)	0.842 (1.00)	1 (1.00)	0.667 (1.00)	0.173 (1.00)	1 (1.00)
Amp Peak 11(6q21)	18 (12%)	132	0.245 (1.00)	0.0512 (1.00)	0.621 (1.00)	0.45 (1.00)	0.198 (1.00)	0.155 (1.00)	0.735 (1.00)	0.767 (1.00)
Amp Peak 15(8q22 3)	92 (61%)	58	0.00409 (1.00)	0.00206 (0.905)	0.168 (1.00)	0.42 (1.00)	0.108 (1.00)	0.437 (1.00)	0.0381 (1.00)	0.273 (1.00)
Amp Peak 16(8q24 21)	88 (59%)	62	0.00138 (0.616)	0.022 (1.00)	0.226 (1.00)	0.623 (1.00)	0.125 (1.00)	0.196 (1.00)	0.0749 (1.00)	0.207 (1.00)
Amp Peak 18(11q13 3)	59 (39%)	91	0.00169 (0.752)	0.237 (1.00)	0.554 (1.00)	0.648 (1.00)	0.222 (1.00)	0.319 (1.00)	0.0176 (1.00)	0.887 (1.00)
Amp Peak 19(12q15)	48 (32%)	102	0.0509 (1.00)	0.107 (1.00)	0.76 (1.00)	0.717 (1.00)	0.0082 (1.00)	0.00219 (0.961)	0.0275 (1.00)	0.131 (1.00)
Amp Peak 20(13q22 1)	49 (33%)	101	0.58 (1.00)	0.659 (1.00)	0.641 (1.00)	0.0912 (1.00)	0.886 (1.00)	0.898 (1.00)	0.446 (1.00)	0.425 (1.00)
Amp Peak 21(16p12 1)	39 (26%)	111	0.0104 (1.00)	0.112 (1.00)	0.0783 (1.00)	0.152 (1.00)	0.9 (1.00)	0.846 (1.00)	0.271 (1.00)	0.329 (1.00)
Amp Peak 23(17q12)	63 (42%)	87	0.0019 (0.842)	0.153 (1.00)	0.939 (1.00)	0.673 (1.00)	0.0505 (1.00)	0.26 (1.00)	0.00783 (1.00)	0.000821 (0.376)
Amp Peak 26(20q11 21)	104 (69%)	46	0.0007 (0.321)	0.428 (1.00)	0.342 (1.00)	0.523 (1.00)	0.204 (1.00)	0.226 (1.00)	0.352 (1.00)	0.0938 (1.00)
Amp Peak 27(22q11 23)	35 (23%)	115	0.00131 (0.586)	0.383 (1.00)	0.837 (1.00)	0.172 (1.00)	0.146 (1.00)	0.232 (1.00)	0.34 (1.00)	0.323 (1.00)
Del Peak 1(1p36 11)	27 (18%)	123	0.967 (1.00)	0.00499 (1.00)	0.0699 (1.00)	0.0826 (1.00)	0.216 (1.00)	0.181 (1.00)	0.842 (1.00)	0.881 (1.00)
Del Peak 2(1q32 1)	28 (19%)	122	0.0723 (1.00)	0.115 (1.00)	0.738 (1.00)	0.229 (1.00)	0.282 (1.00)	0.111 (1.00)	0.702 (1.00)	0.558 (1.00)
Del Peak 3(2q22 1)	43 (29%)	107	0.00317 (1.00)	0.295 (1.00)	0.315 (1.00)	0.315 (1.00)	0.577 (1.00)	0.102 (1.00)	0.376 (1.00)	0.631 (1.00)
Del Peak 8(3p12 3)	41 (27%)	109	0.0127 (1.00)	0.455 (1.00)	0.0189 (1.00)	0.0181 (1.00)	0.00164 (0.732)	0.0523 (1.00)	0.221 (1.00)	0.496 (1.00)
Del Peak 9(4q22 1)	59 (39%)	91	0.539 (1.00)	0.628 (1.00)	0.358 (1.00)	0.68 (1.00)	0.296 (1.00)	0.149 (1.00)	0.742 (1.00)	0.852 (1.00)
Del Peak 10(4q34 2)	65 (43%)	85	0.0654 (1.00)	0.374 (1.00)	0.422 (1.00)	0.151 (1.00)	0.527 (1.00)	0.0333 (1.00)	0.242 (1.00)	0.455 (1.00)
Del Peak 11(5q11 2)	75 (50%)	75	0.00105 (0.475)	0.0511 (1.00)	0.814 (1.00)	0.487 (1.00)	0.739 (1.00)	0.0906 (1.00)	0.195 (1.00)	0.0291 (1.00)
Del Peak 12(5q35 1)	72 (48%)	78	0.0228 (1.00)	0.0061 (1.00)	0.567 (1.00)	0.815 (1.00)	0.61 (1.00)	0.214 (1.00)	0.0507 (1.00)	0.123 (1.00)
Del Peak 13(6p25 3)	40 (27%)	110	0.0207 (1.00)	0.269 (1.00)	0.135 (1.00)	0.491 (1.00)	0.512 (1.00)	0.824 (1.00)	0.602 (1.00)	1 (1.00)
Del Peak 18(9p23)	65 (43%)	85	0.00199 (0.879)	0.874 (1.00)	0.274 (1.00)	0.275 (1.00)	0.46 (1.00)	0.0633 (1.00)	0.501 (1.00)	0.109 (1.00)
Del Peak 20(10p12 1)	29 (19%)	121	0.91 (1.00)	0.769 (1.00)	0.455 (1.00)	0.737 (1.00)	0.0686 (1.00)	0.0293 (1.00)	0.194 (1.00)	1 (1.00)
Del Peak 21(10q23 31)	60 (40%)	90	0.0105 (1.00)	0.0025 (1.00)	0.228 (1.00)	0.748 (1.00)	0.277 (1.00)	0.0457 (1.00)	0.366 (1.00)	0.508 (1.00)
Del Peak 25(14q12)	43 (29%)	107	0.000894 (0.407)	0.000941 (0.428)	0.805 (1.00)	0.663 (1.00)	0.142 (1.00)	0.0342 (1.00)	0.0171 (1.00)	0.000665 (0.306)
Del Peak 28(16p13 3)	54 (36%)	96	0.00332 (1.00)	0.00652 (1.00)	0.191 (1.00)	0.614 (1.00)	1 (1.00)	0.499 (1.00)	0.798 (1.00)	0.779 (1.00)
Del Peak 31(18q23)	63 (42%)	87	0.00377 (1.00)	0.485 (1.00)	0.979 (1.00)	0.822 (1.00)	0.846 (1.00)	0.37 (1.00)	0.132 (1.00)	0.249 (1.00)
Del Peak 32(19p13 3)	60 (40%)	90	0.0227 (1.00)	0.0266 (1.00)	1 (1.00)	0.715 (1.00)	0.944 (1.00)	0.0831 (1.00)	0.548 (1.00)	0.159 (1.00)
Del Peak 33(22q13 32)	60 (40%)	90	0.00112 (0.503)	0.26 (1.00)	0.128 (1.00)	0.00283 (1.00)	0.106 (1.00)	0.115 (1.00)	0.502 (1.00)	0.129 (1.00)
Del Peak 34(Xp11 3)	39 (26%)	111	0.2 (1.00)	0.00294 (1.00)	0.775 (1.00)	0.578 (1.00)	0.0767 (1.00)	0.236 (1.00)	0.631 (1.00)	0.439 (1.00)
Del Peak 35(Xq21 33)	35 (23%)	115	0.334 (1.00)	0.0789 (1.00)	0.173 (1.00)	0.471 (1.00)	0.00919 (1.00)	0.735 (1.00)	0.0536 (1.00)	0.433 (1.00)
Del Peak 36(Xq22 3)	32 (21%)	118	0.136 (1.00)	0.0173 (1.00)	0.149 (1.00)	1 (1.00)	0.0174 (1.00)	0.796 (1.00)	0.127 (1.00)	0.606 (1.00)

'Amp Peak 1(1p34.2) mutation analysis' versus 'CN_CNMF'

P value = 2e-04 (Chi-square test), Q value = 0.094

Table S1. Gene #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 1(1P34.2) MUTATED	2	11	14	3	6	9
AMP PEAK 1(1P34.2) WILD-TYPE	12	42	10	26	7	8

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 1(1p34.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.09e-05 (Fisher's exact test), Q value = 0.02

Table S2. Gene #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	50	39	25
AMP PEAK 1(1P34.2) MUTATED	20	17	3	5
AMP PEAK 1(1P34.2) WILD-TYPE	16	33	36	20

Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 2(1q21.3) mutation analysis' versus 'CN_CNMF'

P value = 6.85e-06 (Chi-square test), Q value = 0.0034

Table S3. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 2(1Q21.3) MUTATED	9	18	20	7	9	13
AMP PEAK 2(1Q21.3) WILD-TYPE	5	35	4	22	4	4

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 2(1q21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.19

Table S4. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	50	39	25
AMP PEAK 2(1Q21.3) MUTATED	29	20	15	12
AMP PEAK 2(1Q21.3) WILD-TYPE	7	30	24	13

Figure S4. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 3(1q23.3) mutation analysis' versus 'CN_CNMF'

P value = 2.59e-05 (Chi-square test), Q value = 0.013

Table S5. Gene #3: 'Amp Peak 3(1q23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 3(1Q23.3) MUTATED	9	22	21	8	8	14
AMP PEAK 3(1Q23.3) WILD-TYPE	5	31	3	21	5	3

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(1q23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 4(3p25.2) mutation analysis' versus 'CN_CNMF'

P value = 3.36e-05 (Chi-square test), Q value = 0.016

Table S6. Gene #4: 'Amp Peak 4(3p25.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 4(3P25.2) MUTATED	11	15	15	11	5	15
AMP PEAK 4(3P25.2) WILD-TYPE	3	38	9	18	8	2

Figure S6. Get High-res Image Gene #4: 'Amp Peak 4(3p25.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 4(3p25.2) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000371 (Fisher's exact test), Q value = 0.17

Table S7. Gene #4: 'Amp Peak 4(3p25.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	18	64
AMP PEAK 4(3P25.2) MUTATED	10	9	42
AMP PEAK 4(3P25.2) WILD-TYPE	29	9	22

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(3p25.2) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 4(3p25.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000422 (Fisher's exact test), Q value = 0.2

Table S8. Gene #4: 'Amp Peak 4(3p25.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	96	18
AMP PEAK 4(3P25.2) MUTATED	18	42	8
AMP PEAK 4(3P25.2) WILD-TYPE	2	54	10

Figure S8. Get High-res Image Gene #4: 'Amp Peak 4(3p25.2) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 7(4q13.3) mutation analysis' versus 'CN_CNMF'

P value = 8.45e-05 (Chi-square test), Q value = 0.041

Table S9. Gene #7: 'Amp Peak 7(4q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 7(4Q13.3) MUTATED	0	2	11	4	2	4
AMP PEAK 7(4Q13.3) WILD-TYPE	14	51	13	25	11	13

Figure S9. Get High-res Image Gene #7: 'Amp Peak 7(4q13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 8(5p15.1) mutation analysis' versus 'CN_CNMF'

P value = 4.5e-05 (Chi-square test), Q value = 0.022

Table S10. Gene #8: 'Amp Peak 8(5p15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 8(5P15.1) MUTATED	10	13	18	11	10	7
AMP PEAK 8(5P15.1) WILD-TYPE	4	40	6	18	3	10

Figure S10. Get High-res Image Gene #8: 'Amp Peak 8(5p15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 9(6p22.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000183 (Chi-square test), Q value = 0.087

Table S11. Gene #9: 'Amp Peak 9(6p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 9(6P22.3) MUTATED	8	13	16	7	10	7
AMP PEAK 9(6P22.3) WILD-TYPE	6	40	8	22	3	10

Figure S11. Get High-res Image Gene #9: 'Amp Peak 9(6p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 12(7p11.2) mutation analysis' versus 'CN_CNMF'

P value = 4.49e-07 (Chi-square test), Q value = 0.00022

Table S12. Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 12(7P11.2) MUTATED	10	12	19	13	10	14
AMP PEAK 12(7P11.2) WILD-TYPE	4	41	5	16	3	3

Figure S12. Get High-res Image Gene #12: 'Amp Peak 12(7p11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 13(8p11.23) mutation analysis' versus 'CN_CNMF'

P value = 0.000492 (Chi-square test), Q value = 0.23

Table S13. Gene #13: 'Amp Peak 13(8p11.23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 13(8P11.23) MUTATED	4	5	12	15	5	7
AMP PEAK 13(8P11.23) WILD-TYPE	10	48	12	14	8	10

Figure S13. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 14(8p11.21) mutation analysis' versus 'CN_CNMF'

P value = 1.62e-05 (Chi-square test), Q value = 0.0079

Table S14. Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 14(8P11.21) MUTATED	9	4	7	16	6	6
AMP PEAK 14(8P11.21) WILD-TYPE	5	49	17	13	7	11

Figure S14. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 17(10p15.1) mutation analysis' versus 'CN_CNMF'

P value = 6.73e-09 (Chi-square test), Q value = 3.4e-06

Table S15. Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 17(10P15.1) MUTATED	9	6	14	8	10	14
AMP PEAK 17(10P15.1) WILD-TYPE	5	47	10	21	3	3

Figure S15. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 17(10p15.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.25e-06 (Fisher's exact test), Q value = 0.0026

Table S16. Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	50	39	25
AMP PEAK 17(10P15.1) MUTATED	28	15	12	6
AMP PEAK 17(10P15.1) WILD-TYPE	8	35	27	19

Figure S16. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 22(17q11.2) mutation analysis' versus 'CN_CNMF'

P value = 4.62e-08 (Chi-square test), Q value = 2.3e-05

Table S17. Gene #22: 'Amp Peak 22(17q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 22(17Q11.2) MUTATED	13	7	13	20	6	9
AMP PEAK 22(17Q11.2) WILD-TYPE	1	46	11	9	7	8

Figure S17. Get High-res Image Gene #22: 'Amp Peak 22(17q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 22(17q11.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.064

Table S18. Gene #22: 'Amp Peak 22(17q11.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	33	38
AMP PEAK 22(17Q11.2) MUTATED	33	11	9
AMP PEAK 22(17Q11.2) WILD-TYPE	17	22	29

Figure S18. Get High-res Image Gene #22: 'Amp Peak 22(17q11.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Amp Peak 24(19q12) mutation analysis' versus 'CN_CNMF'

P value = 6.35e-06 (Chi-square test), Q value = 0.0031

Table S19. Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 24(19Q12) MUTATED	9	9	19	13	5	10
AMP PEAK 24(19Q12) WILD-TYPE	5	44	5	16	8	7

Figure S19. Get High-res Image Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 25(19q13.43) mutation analysis' versus 'CN_CNMF'

P value = 9.08e-05 (Chi-square test), Q value = 0.043

Table S20. Gene #25: 'Amp Peak 25(19q13.43) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
AMP PEAK 25(19Q13.43) MUTATED	10	9	16	14	5	9
AMP PEAK 25(19Q13.43) WILD-TYPE	4	44	8	15	8	8

Figure S20. Get High-res Image Gene #25: 'Amp Peak 25(19q13.43) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 4(2q34) mutation analysis' versus 'CN_CNMF'

P value = 3.53e-06 (Chi-square test), Q value = 0.0017

Table S21. Gene #31: 'Del Peak 4(2q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 4(2Q34) MUTATED	5	9	19	9	8	10
DEL PEAK 4(2Q34) WILD-TYPE	9	44	5	20	5	7

Figure S21. Get High-res Image Gene #31: 'Del Peak 4(2q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 5(2q37.1) mutation analysis' versus 'CN_CNMF'

P value = 3.3e-05 (Chi-square test), Q value = 0.016

Table S22. Gene #32: 'Del Peak 5(2q37.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 5(2Q37.1) MUTATED	7	13	20	13	8	12
DEL PEAK 5(2Q37.1) WILD-TYPE	7	40	4	16	5	5

Figure S22. Get High-res Image Gene #32: 'Del Peak 5(2q37.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 6(3p21.31) mutation analysis' versus 'CN_CNMF'

P value = 0.000394 (Chi-square test), Q value = 0.18

Table S23. Gene #33: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 6(3P21.31) MUTATED	4	10	13	14	6	0
DEL PEAK 6(3P21.31) WILD-TYPE	10	43	11	15	7	17

Figure S23. Get High-res Image Gene #33: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000507 (Chi-square test), Q value = 0.23

Table S24. Gene #34: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 7(3P14.2) MUTATED	7	10	13	12	6	0
DEL PEAK 7(3P14.2) WILD-TYPE	7	43	11	17	7	17

Figure S24. Get High-res Image Gene #34: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 7(3p14.2) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000425 (Fisher's exact test), Q value = 0.2

Table S25. Gene #34: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	33	38
DEL PEAK 7(3P14.2) MUTATED	14	4	21
DEL PEAK 7(3P14.2) WILD-TYPE	36	29	17

Figure S25. Get High-res Image Gene #34: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 14(6q21) mutation analysis' versus 'CN_CNMF'

P value = 7.29e-07 (Chi-square test), Q value = 0.00036

Table S26. Gene #41: 'Del Peak 14(6q21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 14(6Q21) MUTATED	6	7	13	16	6	15
DEL PEAK 14(6Q21) WILD-TYPE	8	46	11	13	7	2

Figure S26. Get High-res Image Gene #41: 'Del Peak 14(6q21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(6q27) mutation analysis' versus 'CN_CNMF'

P value = 2.04e-06 (Chi-square test), Q value = 0.001

Table S27. Gene #42: 'Del Peak 15(6q27) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 15(6Q27) MUTATED	9	8	11	14	5	15
DEL PEAK 15(6Q27) WILD-TYPE	5	45	13	15	8	2

Figure S27. Get High-res Image Gene #42: 'Del Peak 15(6q27) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 16(8p23.3) mutation analysis' versus 'CN_CNMF'

P value = 2.1e-08 (Chi-square test), Q value = 1.1e-05

Table S28. Gene #43: 'Del Peak 16(8p23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 16(8P23.3) MUTATED	12	23	20	3	11	11
DEL PEAK 16(8P23.3) WILD-TYPE	2	30	4	26	2	6

Figure S28. Get High-res Image Gene #43: 'Del Peak 16(8p23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 16(8p23.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.24e-05 (Fisher's exact test), Q value = 0.025

Table S29. Gene #43: 'Del Peak 16(8p23.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	50	39	25
DEL PEAK 16(8P23.3) MUTATED	28	30	10	12
DEL PEAK 16(8P23.3) WILD-TYPE	8	20	29	13

Figure S29. Get High-res Image Gene #43: 'Del Peak 16(8p23.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 17(8p21.1) mutation analysis' versus 'CN_CNMF'

P value = 1.53e-09 (Chi-square test), Q value = 7.7e-07

Table S30. Gene #44: 'Del Peak 17(8p21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 17(8P21.1) MUTATED	11	22	21	4	12	14
DEL PEAK 17(8P21.1) WILD-TYPE	3	31	3	25	1	3

Figure S30. Get High-res Image Gene #44: 'Del Peak 17(8p21.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 17(8p21.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.2e-05 (Fisher's exact test), Q value = 0.025

Table S31. Gene #44: 'Del Peak 17(8p21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	50	39	25
DEL PEAK 17(8P21.1) MUTATED	31	28	14	11
DEL PEAK 17(8P21.1) WILD-TYPE	5	22	25	14

Figure S31. Get High-res Image Gene #44: 'Del Peak 17(8p21.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 19(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000482 (Chi-square test), Q value = 0.22

Table S32. Gene #46: 'Del Peak 19(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 19(9P21.3) MUTATED	8	28	16	24	1	9
DEL PEAK 19(9P21.3) WILD-TYPE	6	25	8	5	12	8

Figure S32. Get High-res Image Gene #46: 'Del Peak 19(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 22(11p15.5) mutation analysis' versus 'CN_CNMF'

P value = 5.12e-06 (Chi-square test), Q value = 0.0025

Table S33. Gene #49: 'Del Peak 22(11p15.5) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 22(11P15.5) MUTATED	9	14	19	16	2	13
DEL PEAK 22(11P15.5) WILD-TYPE	5	39	5	13	11	4

Figure S33. Get High-res Image Gene #49: 'Del Peak 22(11p15.5) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 22(11p15.5) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000152 (Fisher's exact test), Q value = 0.072

Table S34. Gene #49: 'Del Peak 22(11p15.5) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	18	64
DEL PEAK 22(11P15.5) MUTATED	14	3	42
DEL PEAK 22(11P15.5) WILD-TYPE	25	15	22

Figure S34. Get High-res Image Gene #49: 'Del Peak 22(11p15.5) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 23(11q25) mutation analysis' versus 'CN_CNMF'

P value = 4.26e-05 (Chi-square test), Q value = 0.021

Table S35. Gene #50: 'Del Peak 23(11q25) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 23(11Q25) MUTATED	7	5	14	14	2	5
DEL PEAK 23(11Q25) WILD-TYPE	7	48	10	15	11	12

Figure S35. Get High-res Image Gene #50: 'Del Peak 23(11q25) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 24(13q14.2) mutation analysis' versus 'CN_CNMF'

P value = 0.000135 (Chi-square test), Q value = 0.064

Table S36. Gene #51: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 24(13Q14.2) MUTATED	3	12	15	10	11	7
DEL PEAK 24(13Q14.2) WILD-TYPE	11	41	9	19	2	10

Figure S36. Get High-res Image Gene #51: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 24(13q14.2) mutation analysis' versus 'RPPA_CNMF'

P value = 0.000229 (Fisher's exact test), Q value = 0.11

Table S37. Gene #51: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	11	10	14	16
DEL PEAK 24(13Q14.2) MUTATED	2	6	1	12
DEL PEAK 24(13Q14.2) WILD-TYPE	9	4	13	4

Figure S37. Get High-res Image Gene #51: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #3: 'RPPA_CNMF'

'Del Peak 24(13q14.2) mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000117 (Fisher's exact test), Q value = 0.056

Table S38. Gene #51: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	17	21
DEL PEAK 24(13Q14.2) MUTATED	3	14	4
DEL PEAK 24(13Q14.2) WILD-TYPE	10	3	17

Figure S38. Get High-res Image Gene #51: 'Del Peak 24(13q14.2) mutation analysis' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'Del Peak 26(14q32.31) mutation analysis' versus 'CN_CNMF'

P value = 5.95e-05 (Chi-square test), Q value = 0.029

Table S39. Gene #53: 'Del Peak 26(14q32.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 26(14Q32.31) MUTATED	10	5	5	8	5	8
DEL PEAK 26(14Q32.31) WILD-TYPE	4	48	19	21	8	9

Figure S39. Get High-res Image Gene #53: 'Del Peak 26(14q32.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 26(14q32.31) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000136 (Fisher's exact test), Q value = 0.064

Table S40. Gene #53: 'Del Peak 26(14q32.31) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	66	37
DEL PEAK 26(14Q32.31) MUTATED	18	11	8
DEL PEAK 26(14Q32.31) WILD-TYPE	13	55	29

Figure S40. Get High-res Image Gene #53: 'Del Peak 26(14q32.31) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Del Peak 27(15q13.1) mutation analysis' versus 'CN_CNMF'

P value = 0.000301 (Chi-square test), Q value = 0.14

Table S41. Gene #54: 'Del Peak 27(15q13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 27(15Q13.1) MUTATED	10	14	14	4	7	5
DEL PEAK 27(15Q13.1) WILD-TYPE	4	39	10	25	6	12

Figure S41. Get High-res Image Gene #54: 'Del Peak 27(15q13.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 29(16q23.1) mutation analysis' versus 'CN_CNMF'

P value = 1.99e-05 (Chi-square test), Q value = 0.0097

Table S42. Gene #56: 'Del Peak 29(16q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 29(16Q23.1) MUTATED	8	7	2	5	6	10
DEL PEAK 29(16Q23.1) WILD-TYPE	6	46	22	24	7	7

Figure S42. Get High-res Image Gene #56: 'Del Peak 29(16q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 30(17p12) mutation analysis' versus 'CN_CNMF'

P value = 2.91e-08 (Chi-square test), Q value = 1.5e-05

Table S43. Gene #57: 'Del Peak 30(17p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	14	53	24	29	13	17
DEL PEAK 30(17P12) MUTATED	11	11	17	21	3	14
DEL PEAK 30(17P12) WILD-TYPE	3	42	7	8	10	3

Figure S43. Get High-res Image Gene #57: 'Del Peak 30(17p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = BLCA-TP.transferedmergedcluster.txt
Number of patients = 150
Number of copy number variation regions = 63
Number of molecular subtypes = 8
Exclude regions that fewer than K tumors have alterations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

[4] GISTIC_version2

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