Correlation between copy number variation genes and molecular subtypes

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 62 peak regions and 8 molecular subtypes across 150 patients, 47 significant findings detected with Q value < 0.25.

Amp Peak 1(1p34.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 2(1p22.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(1q21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 4(1q23.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Amp Peak 5(3p25.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 9(5p15.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 10(6p22.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(7p11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 14(8p11.23) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(8q22.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(8q24.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 18(10p15.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 19(11q13.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Amp Peak 23(17q11.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 24(17q12) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 25(19q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 26(19q13.43) cnvs correlated to 'CN_CNMF'.
Amp Peak 27(20q11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q37.1) cnvs correlated to 'CN_CNMF'.
Del Peak 6(3p21.31) cnvs correlated to 'MRNASEQ_CNMF'.
Del Peak 7(3p14.2) cnvs correlated to 'RPPA_CHIERARCHICAL' and 'MRNASEQ_CNMF'.
Del Peak 8(3p12.3) cnvs correlated to 'RPPA_CHIERARCHICAL'.
Del Peak 10(4q34.2) cnvs correlated to 'CN_CNMF'.
Del Peak 11(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 12(5q35.1) cnvs correlated to 'CN_CNMF'.
Del Peak 14(6q21) cnvs correlated to 'CN_CNMF'.
Del Peak 15(8p23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 16(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 17(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 19(10q23.31) cnvs correlated to 'CN_CNMF'.
Del Peak 20(11p15.5) cnvs correlated to 'CN_CNMF'.
Del Peak 22(13q14.2) cnvs correlated to 'CN_CNMF' and 'RPPA_CNMF'.
Del Peak 24(14q32.31) cnvs correlated to 'MIRSEQ_CNMF'.
Del Peak 25(15q13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 26(16p13.3) cnvs correlated to 'CN_CNMF'.
Del Peak 27(16q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 31(22q13.32) 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 62 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 47 significant findings detected.


		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	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test
Amp Peak 1(1p34 2)	0 (0%)	105	7.72e-07 (0.000376)	4.09e-05 (0.0194)	0.894 (1.00)	0.706 (1.00)	0.0633 (1.00)	0.0927 (1.00)	0.259 (1.00)	0.0481 (1.00)
Amp Peak 3(1q21 3)	0 (0%)	74	1.27e-08 (6.29e-06)	0.0004 (0.182)	0.0118 (1.00)	0.0511 (1.00)	0.0524 (1.00)	0.176 (1.00)	0.112 (1.00)	0.115 (1.00)
Amp Peak 4(1q23 3)	0 (0%)	68	7.96e-06 (0.0038)	0.0124 (1.00)	0.925 (1.00)	0.589 (1.00)	0.177 (1.00)	0.619 (1.00)	0.000496 (0.224)	0.00476 (1.00)
Amp Peak 5(3p25 2)	0 (0%)	80	6.76e-06 (0.00324)	0.00904 (1.00)	0.278 (1.00)	0.0393 (1.00)	0.000333 (0.153)	0.0311 (1.00)	0.00155 (0.687)	0.00323 (1.00)
Amp Peak 18(10p15 1)	0 (0%)	89	2.91e-09 (1.44e-06)	5.25e-06 (0.00252)	0.893 (1.00)	0.215 (1.00)	0.875 (1.00)	0.467 (1.00)	0.249 (1.00)	0.181 (1.00)
Amp Peak 19(11q13 3)	0 (0%)	90	8.05e-07 (0.000391)	0.218 (1.00)	0.554 (1.00)	0.597 (1.00)	0.123 (1.00)	0.928 (1.00)	0.000434 (0.197)	0.035 (1.00)
Amp Peak 23(17q11 2)	0 (0%)	82	3.59e-06 (0.00173)	0.00122 (0.544)	0.76 (1.00)	0.439 (1.00)	9.31e-05 (0.0439)	0.01 (1.00)	0.0196 (1.00)	0.0131 (1.00)
Amp Peak 24(17q12)	0 (0%)	87	0.000209 (0.097)	0.153 (1.00)	0.939 (1.00)	0.439 (1.00)	0.0411 (1.00)	0.211 (1.00)	0.0265 (1.00)	0.000217 (0.1)
Del Peak 7(3p14 2)	0 (0%)	102	0.0861 (1.00)	0.56 (1.00)	0.0759 (1.00)	0.000294 (0.135)	0.000489 (0.222)	0.00671 (1.00)	0.326 (1.00)	0.298 (1.00)
Del Peak 22(13q14 2)	0 (0%)	92	0.000254 (0.117)	0.986 (1.00)	0.000229 (0.106)	0.00875 (1.00)	0.00519 (1.00)	0.11 (1.00)	0.844 (1.00)	0.0599 (1.00)
Amp Peak 2(1p22 3)	0 (0%)	107	2.2e-08 (1.08e-05)	0.341 (1.00)	0.33 (1.00)	0.581 (1.00)	0.464 (1.00)	0.709 (1.00)	0.25 (1.00)	0.0771 (1.00)
Amp Peak 9(5p15 1)	0 (0%)	80	2.34e-06 (0.00113)	0.222 (1.00)	0.014 (1.00)	0.46 (1.00)	0.0265 (1.00)	0.0886 (1.00)	0.174 (1.00)	0.244 (1.00)
Amp Peak 10(6p22 3)	0 (0%)	89	8.2e-11 (4.07e-08)	0.00236 (1.00)	0.834 (1.00)	0.872 (1.00)	0.221 (1.00)	0.629 (1.00)	0.058 (1.00)	0.377 (1.00)
Amp Peak 13(7p11 2)	0 (0%)	70	6.99e-08 (3.44e-05)	0.000984 (0.44)	0.481 (1.00)	0.243 (1.00)	0.319 (1.00)	0.888 (1.00)	0.414 (1.00)	0.48 (1.00)
Amp Peak 14(8p11 23)	0 (0%)	101	0.000144 (0.067)	0.0745 (1.00)	0.0732 (1.00)	0.017 (1.00)	0.814 (1.00)	0.409 (1.00)	0.211 (1.00)	0.751 (1.00)
Amp Peak 16(8q22 3)	0 (0%)	57	2.25e-07 (0.000111)	0.00267 (1.00)	0.168 (1.00)	0.208 (1.00)	0.321 (1.00)	0.523 (1.00)	0.013 (1.00)	0.279 (1.00)
Amp Peak 17(8q24 21)	0 (0%)	61	0.000129 (0.0604)	0.0256 (1.00)	0.226 (1.00)	0.354 (1.00)	0.115 (1.00)	0.675 (1.00)	0.0281 (1.00)	0.597 (1.00)
Amp Peak 25(19q12)	0 (0%)	85	4.82e-05 (0.0229)	0.00271 (1.00)	0.37 (1.00)	0.936 (1.00)	0.645 (1.00)	0.463 (1.00)	0.372 (1.00)	0.318 (1.00)
Amp Peak 26(19q13 43)	0 (0%)	87	0.000105 (0.0491)	0.0258 (1.00)	0.778 (1.00)	0.767 (1.00)	0.14 (1.00)	0.461 (1.00)	0.152 (1.00)	0.0946 (1.00)
Amp Peak 27(20q11 21)	0 (0%)	46	2.07e-06 (0.001)	0.428 (1.00)	0.342 (1.00)	0.865 (1.00)	0.579 (1.00)	0.659 (1.00)	0.311 (1.00)	0.32 (1.00)
Del Peak 5(2q37 1)	0 (0%)	77	0.000526 (0.237)	0.0128 (1.00)	0.908 (1.00)	0.875 (1.00)	0.165 (1.00)	0.172 (1.00)	0.0434 (1.00)	0.109 (1.00)
Del Peak 6(3p21 31)	0 (0%)	103	0.179 (1.00)	0.12 (1.00)	0.00649 (1.00)	0.0023 (1.00)	0.000115 (0.0538)	0.0108 (1.00)	0.105 (1.00)	0.204 (1.00)
Del Peak 8(3p12 3)	0 (0%)	109	0.0107 (1.00)	0.455 (1.00)	0.0189 (1.00)	0.000495 (0.224)	0.00132 (0.587)	0.0877 (1.00)	0.418 (1.00)	0.633 (1.00)
Del Peak 10(4q34 2)	0 (0%)	85	7.79e-05 (0.0368)	0.374 (1.00)	0.422 (1.00)	0.875 (1.00)	0.387 (1.00)	0.452 (1.00)	0.121 (1.00)	0.0135 (1.00)
Del Peak 11(5q11 2)	0 (0%)	75	3.24e-07 (0.000159)	0.0336 (1.00)	0.814 (1.00)	0.474 (1.00)	0.271 (1.00)	0.668 (1.00)	0.167 (1.00)	0.151 (1.00)
Del Peak 12(5q35 1)	0 (0%)	78	0.000355 (0.162)	0.00394 (1.00)	0.567 (1.00)	0.568 (1.00)	0.501 (1.00)	0.282 (1.00)	0.0563 (1.00)	0.141 (1.00)
Del Peak 14(6q21)	0 (0%)	87	0.000367 (0.168)	0.0129 (1.00)	0.0799 (1.00)	0.272 (1.00)	0.569 (1.00)	0.0603 (1.00)	0.344 (1.00)	0.686 (1.00)
Del Peak 15(8p23 1)	0 (0%)	67	8.84e-06 (0.00422)	0.000649 (0.291)	0.169 (1.00)	0.446 (1.00)	0.438 (1.00)	0.846 (1.00)	0.0123 (1.00)	0.00835 (1.00)
Del Peak 16(9p23)	0 (0%)	84	0.000501 (0.226)	0.752 (1.00)	0.274 (1.00)	0.717 (1.00)	0.73 (1.00)	0.162 (1.00)	0.45 (1.00)	0.954 (1.00)
Del Peak 17(9p21 3)	0 (0%)	63	4.52e-07 (0.00022)	0.406 (1.00)	0.0718 (1.00)	0.93 (1.00)	0.379 (1.00)	0.0983 (1.00)	0.637 (1.00)	0.591 (1.00)
Del Peak 19(10q23 31)	0 (0%)	90	0.000115 (0.054)	0.0025 (1.00)	0.228 (1.00)	0.929 (1.00)	0.562 (1.00)	0.195 (1.00)	0.322 (1.00)	0.409 (1.00)
Del Peak 20(11p15 5)	0 (0%)	77	7.69e-05 (0.0364)	0.038 (1.00)	0.195 (1.00)	0.673 (1.00)	0.0596 (1.00)	0.0178 (1.00)	0.00472 (1.00)	0.0411 (1.00)
Del Peak 24(14q32 31)	0 (0%)	109	0.128 (1.00)	0.0272 (1.00)	0.805 (1.00)	0.843 (1.00)	0.407 (1.00)	0.862 (1.00)	0.00025 (0.115)	0.0843 (1.00)
Del Peak 25(15q13 1)	0 (0%)	95	4.32e-06 (0.00208)	0.00534 (1.00)	0.0829 (1.00)	0.46 (1.00)	0.0723 (1.00)	0.137 (1.00)	0.0942 (1.00)	0.116 (1.00)
Del Peak 26(16p13 3)	0 (0%)	96	3.5e-06 (0.00169)	0.00652 (1.00)	0.191 (1.00)	0.23 (1.00)	0.665 (1.00)	0.975 (1.00)	0.497 (1.00)	0.642 (1.00)
Del Peak 27(16q23 1)	0 (0%)	112	1.76e-05 (0.00837)	0.0434 (1.00)	0.232 (1.00)	0.753 (1.00)	0.118 (1.00)	0.358 (1.00)	0.0492 (1.00)	0.215 (1.00)
Del Peak 31(22q13 32)	0 (0%)	90	2.97e-07 (0.000145)	0.26 (1.00)	0.128 (1.00)	0.0675 (1.00)	0.0283 (1.00)	0.15 (1.00)	0.576 (1.00)	0.115 (1.00)
Amp Peak 6(3q26 32)	0 (0%)	66	0.00494 (1.00)	0.664 (1.00)	0.161 (1.00)	0.812 (1.00)	0.0558 (1.00)	0.953 (1.00)	0.495 (1.00)	0.62 (1.00)
Amp Peak 7(4p16 3)	0 (0%)	120	0.585 (1.00)	0.15 (1.00)	0.162 (1.00)	0.189 (1.00)	0.0903 (1.00)	0.135 (1.00)	0.117 (1.00)	0.324 (1.00)
Amp Peak 8(4q13 3)	0 (0%)	127	0.00397 (1.00)	0.16 (1.00)	0.517 (1.00)	0.867 (1.00)	0.922 (1.00)	0.643 (1.00)	0.23 (1.00)	0.169 (1.00)
Amp Peak 11(6q12)	0 (0%)	125	0.0102 (1.00)	0.627 (1.00)	1 (1.00)	1 (1.00)	0.255 (1.00)	0.606 (1.00)	0.172 (1.00)	0.00284 (1.00)
Amp Peak 12(6q21)	0 (0%)	132	0.0363 (1.00)	0.0512 (1.00)	0.621 (1.00)	0.584 (1.00)	0.0546 (1.00)	0.849 (1.00)	0.853 (1.00)	0.62 (1.00)
Amp Peak 15(8p11 21)	0 (0%)	100	0.00229 (1.00)	0.0126 (1.00)	0.596 (1.00)	0.637 (1.00)	0.275 (1.00)	0.618 (1.00)	0.0852 (1.00)	0.683 (1.00)
Amp Peak 20(12q15)	0 (0%)	102	0.00662 (1.00)	0.107 (1.00)	0.76 (1.00)	0.439 (1.00)	0.0608 (1.00)	0.157 (1.00)	0.232 (1.00)	0.0388 (1.00)
Amp Peak 21(13q34)	0 (0%)	95	0.0588 (1.00)	0.933 (1.00)	0.0164 (1.00)	0.0318 (1.00)	0.0221 (1.00)	0.501 (1.00)	0.212 (1.00)	0.641 (1.00)
Amp Peak 22(16p12 1)	0 (0%)	111	0.00842 (1.00)	0.112 (1.00)	0.0783 (1.00)	0.453 (1.00)	0.728 (1.00)	0.266 (1.00)	0.396 (1.00)	0.376 (1.00)
Amp Peak 28(22q11 23)	0 (0%)	115	0.126 (1.00)	0.383 (1.00)	0.837 (1.00)	0.0916 (1.00)	0.344 (1.00)	0.822 (1.00)	0.217 (1.00)	0.265 (1.00)
Del Peak 1(1p36 11)	0 (0%)	123	0.226 (1.00)	0.00499 (1.00)	0.0699 (1.00)	0.0114 (1.00)	0.684 (1.00)	0.099 (1.00)	0.763 (1.00)	0.276 (1.00)
Del Peak 2(1q32 1)	0 (0%)	122	0.0686 (1.00)	0.115 (1.00)	0.738 (1.00)	0.38 (1.00)	0.98 (1.00)	0.329 (1.00)	0.963 (1.00)	0.295 (1.00)
Del Peak 3(2q22 1)	0 (0%)	107	0.178 (1.00)	0.295 (1.00)	0.315 (1.00)	0.278 (1.00)	0.12 (1.00)	0.67 (1.00)	0.229 (1.00)	0.16 (1.00)
Del Peak 4(2q34)	0 (0%)	90	0.00149 (0.661)	0.137 (1.00)	0.309 (1.00)	0.472 (1.00)	0.511 (1.00)	0.468 (1.00)	0.0785 (1.00)	0.278 (1.00)
Del Peak 9(4q22 1)	0 (0%)	91	0.121 (1.00)	0.628 (1.00)	0.358 (1.00)	1 (1.00)	0.408 (1.00)	0.0884 (1.00)	0.886 (1.00)	0.508 (1.00)
Del Peak 13(6p25 3)	0 (0%)	111	0.122 (1.00)	0.271 (1.00)	0.135 (1.00)	0.66 (1.00)	0.232 (1.00)	0.426 (1.00)	0.658 (1.00)	0.927 (1.00)
Del Peak 18(10p12 1)	0 (0%)	121	0.101 (1.00)	0.769 (1.00)	0.455 (1.00)	0.906 (1.00)	0.18 (1.00)	0.119 (1.00)	0.283 (1.00)	0.2 (1.00)
Del Peak 21(11q25)	0 (0%)	103	0.00973 (1.00)	0.337 (1.00)	0.378 (1.00)	1 (1.00)	0.00528 (1.00)	0.213 (1.00)	0.0704 (1.00)	0.0599 (1.00)
Del Peak 23(14q12)	0 (0%)	107	0.00133 (0.592)	0.000941 (0.422)	0.805 (1.00)	0.598 (1.00)	0.194 (1.00)	0.261 (1.00)	0.0884 (1.00)	0.527 (1.00)
Del Peak 28(17p12)	0 (0%)	73	0.00217 (0.956)	0.0175 (1.00)	0.556 (1.00)	0.405 (1.00)	0.0394 (1.00)	0.377 (1.00)	0.192 (1.00)	0.777 (1.00)
Del Peak 29(18q23)	0 (0%)	87	0.0616 (1.00)	0.485 (1.00)	0.979 (1.00)	0.763 (1.00)	0.903 (1.00)	0.281 (1.00)	0.0308 (1.00)	0.0197 (1.00)
Del Peak 30(19p13 3)	0 (0%)	91	0.00274 (1.00)	0.0503 (1.00)	1 (1.00)	0.757 (1.00)	0.598 (1.00)	0.82 (1.00)	0.345 (1.00)	0.111 (1.00)
Del Peak 32(Xp11 3)	0 (0%)	110	0.15 (1.00)	0.0054 (1.00)	0.775 (1.00)	0.922 (1.00)	0.628 (1.00)	0.236 (1.00)	0.554 (1.00)	0.336 (1.00)
Del Peak 33(Xq21 33)	0 (0%)	115	0.211 (1.00)	0.0789 (1.00)	0.173 (1.00)	0.173 (1.00)	0.0242 (1.00)	0.0868 (1.00)	0.153 (1.00)	0.315 (1.00)
Del Peak 34(Xq23)	0 (0%)	117	0.297 (1.00)	0.0273 (1.00)	0.173 (1.00)	0.173 (1.00)	0.0109 (1.00)	0.0775 (1.00)	0.165 (1.00)	0.0924 (1.00)

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

P value = 7.72e-07 (Fisher's exact test), Q value = 0.00038

Table S1. Gene #1: 'Amp Peak 1(1p34.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 1(1P34.2) CNV	15	8	22
AMP PEAK 1(1P34.2) WILD-TYPE	30	61	14

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 4.09e-05 (Fisher's exact test), Q value = 0.019

Table S2. Gene #1: 'Amp Peak 1(1p34.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	50	39	25
AMP PEAK 1(1P34.2) CNV	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)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 2(1p22.3)' versus 'CN_CNMF'

P value = 2.2e-08 (Fisher's exact test), Q value = 1.1e-05

Table S3. Gene #2: 'Amp Peak 2(1p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 2(1P22.3) CNV	17	5	21
AMP PEAK 2(1P22.3) WILD-TYPE	28	64	15

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(1q21.3)' versus 'CN_CNMF'

P value = 1.27e-08 (Fisher's exact test), Q value = 6.3e-06

Table S4. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 3(1Q21.3) CNV	31	17	28
AMP PEAK 3(1Q21.3) WILD-TYPE	14	52	8

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(1q21.3)' versus 'METHLYATION_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.18

Table S5. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(1q23.3)' versus 'CN_CNMF'

P value = 7.96e-06 (Fisher's exact test), Q value = 0.0038

Table S6. Gene #4: 'Amp Peak 4(1q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 4(1Q23.3) CNV	33	23	26
AMP PEAK 4(1Q23.3) WILD-TYPE	12	46	10

Figure S6. Get High-res Image Gene #4: 'Amp Peak 4(1q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(1q23.3)' versus 'MIRSEQ_CNMF'

P value = 0.000496 (Fisher's exact test), Q value = 0.22

Table S7. Gene #4: 'Amp Peak 4(1q23.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	68	48
AMP PEAK 4(1Q23.3) CNV	28	29	25
AMP PEAK 4(1Q23.3) WILD-TYPE	6	39	23

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(1q23.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Amp Peak 5(3p25.2)' versus 'CN_CNMF'

P value = 6.76e-06 (Fisher's exact test), Q value = 0.0032

Table S8. Gene #5: 'Amp Peak 5(3p25.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 5(3P25.2) CNV	33	19	18
AMP PEAK 5(3P25.2) WILD-TYPE	12	50	18

Figure S8. Get High-res Image Gene #5: 'Amp Peak 5(3p25.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 5(3p25.2)' versus 'MRNASEQ_CNMF'

P value = 0.000333 (Fisher's exact test), Q value = 0.15

Table S9. Gene #5: 'Amp Peak 5(3p25.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	23	45	25
AMP PEAK 5(3P25.2) CNV	31	16	10	13
AMP PEAK 5(3P25.2) WILD-TYPE	24	7	35	12

Figure S9. Get High-res Image Gene #5: 'Amp Peak 5(3p25.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 9(5p15.1)' versus 'CN_CNMF'

P value = 2.34e-06 (Fisher's exact test), Q value = 0.0011

Table S10. Gene #9: 'Amp Peak 9(5p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 9(5P15.1) CNV	31	17	22
AMP PEAK 9(5P15.1) WILD-TYPE	14	52	14

Figure S10. Get High-res Image Gene #9: 'Amp Peak 9(5p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 10(6p22.3)' versus 'CN_CNMF'

P value = 8.2e-11 (Fisher's exact test), Q value = 4.1e-08

Table S11. Gene #10: 'Amp Peak 10(6p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 10(6P22.3) CNV	25	9	27
AMP PEAK 10(6P22.3) WILD-TYPE	20	60	9

Figure S11. Get High-res Image Gene #10: 'Amp Peak 10(6p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 13(7p11.2)' versus 'CN_CNMF'

P value = 6.99e-08 (Fisher's exact test), Q value = 3.4e-05

Table S12. Gene #13: 'Amp Peak 13(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 13(7P11.2) CNV	36	20	24
AMP PEAK 13(7P11.2) WILD-TYPE	9	49	12

Figure S12. Get High-res Image Gene #13: 'Amp Peak 13(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 14(8p11.23)' versus 'CN_CNMF'

P value = 0.000144 (Fisher's exact test), Q value = 0.067

Table S13. Gene #14: 'Amp Peak 14(8p11.23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 14(8P11.23) CNV	26	16	7
AMP PEAK 14(8P11.23) WILD-TYPE	19	53	29

Figure S13. Get High-res Image Gene #14: 'Amp Peak 14(8p11.23)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 16(8q22.3)' versus 'CN_CNMF'

P value = 2.25e-07 (Fisher's exact test), Q value = 0.00011

Table S14. Gene #16: 'Amp Peak 16(8q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 16(8Q22.3) CNV	42	34	17
AMP PEAK 16(8Q22.3) WILD-TYPE	3	35	19

Figure S14. Get High-res Image Gene #16: 'Amp Peak 16(8q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 17(8q24.21)' versus 'CN_CNMF'

P value = 0.000129 (Fisher's exact test), Q value = 0.06

Table S15. Gene #17: 'Amp Peak 17(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 17(8Q24.21) CNV	38	34	17
AMP PEAK 17(8Q24.21) WILD-TYPE	7	35	19

Figure S15. Get High-res Image Gene #17: 'Amp Peak 17(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 18(10p15.1)' versus 'CN_CNMF'

P value = 2.91e-09 (Fisher's exact test), Q value = 1.4e-06

Table S16. Gene #18: 'Amp Peak 18(10p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 18(10P15.1) CNV	30	10	21
AMP PEAK 18(10P15.1) WILD-TYPE	15	59	15

Figure S16. Get High-res Image Gene #18: 'Amp Peak 18(10p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 18(10p15.1)' versus 'METHLYATION_CNMF'

P value = 5.25e-06 (Fisher's exact test), Q value = 0.0025

Table S17. Gene #18: 'Amp Peak 18(10p15.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	36	50	39	25
AMP PEAK 18(10P15.1) CNV	28	15	12	6
AMP PEAK 18(10P15.1) WILD-TYPE	8	35	27	19

Figure S17. Get High-res Image Gene #18: 'Amp Peak 18(10p15.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 19(11q13.3)' versus 'CN_CNMF'

P value = 8.05e-07 (Fisher's exact test), Q value = 0.00039

Table S18. Gene #19: 'Amp Peak 19(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 19(11Q13.3) CNV	32	15	13
AMP PEAK 19(11Q13.3) WILD-TYPE	13	54	23

Figure S18. Get High-res Image Gene #19: 'Amp Peak 19(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 19(11q13.3)' versus 'MIRSEQ_CNMF'

P value = 0.000434 (Fisher's exact test), Q value = 0.2

Table S19. Gene #19: 'Amp Peak 19(11q13.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	68	48
AMP PEAK 19(11Q13.3) CNV	14	37	9
AMP PEAK 19(11Q13.3) WILD-TYPE	20	31	39

Figure S19. Get High-res Image Gene #19: 'Amp Peak 19(11q13.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Amp Peak 23(17q11.2)' versus 'CN_CNMF'

P value = 3.59e-06 (Fisher's exact test), Q value = 0.0017

Table S20. Gene #23: 'Amp Peak 23(17q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 23(17Q11.2) CNV	34	20	14
AMP PEAK 23(17Q11.2) WILD-TYPE	11	49	22

Figure S20. Get High-res Image Gene #23: 'Amp Peak 23(17q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 23(17q11.2)' versus 'MRNASEQ_CNMF'

P value = 9.31e-05 (Fisher's exact test), Q value = 0.044

Table S21. Gene #23: 'Amp Peak 23(17q11.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	23	45	25
AMP PEAK 23(17Q11.2) CNV	33	16	10	9
AMP PEAK 23(17Q11.2) WILD-TYPE	22	7	35	16

Figure S21. Get High-res Image Gene #23: 'Amp Peak 23(17q11.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 24(17q12)' versus 'CN_CNMF'

P value = 0.000209 (Fisher's exact test), Q value = 0.097

Table S22. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 24(17Q12) CNV	30	24	9
AMP PEAK 24(17Q12) WILD-TYPE	15	45	27

Figure S22. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 24(17q12)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000217 (Chi-square test), Q value = 0.1

Table S23. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	21	75	7	37	10
AMP PEAK 24(17Q12) CNV	17	31	0	10	5
AMP PEAK 24(17Q12) WILD-TYPE	4	44	7	27	5

Figure S23. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 25(19q12)' versus 'CN_CNMF'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.023

Table S24. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 25(19Q12) CNV	29	17	19
AMP PEAK 25(19Q12) WILD-TYPE	16	52	17

Figure S24. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 26(19q13.43)' versus 'CN_CNMF'

P value = 0.000105 (Fisher's exact test), Q value = 0.049

Table S25. Gene #26: 'Amp Peak 26(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 26(19Q13.43) CNV	29	17	17
AMP PEAK 26(19Q13.43) WILD-TYPE	16	52	19

Figure S25. Get High-res Image Gene #26: 'Amp Peak 26(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 27(20q11.21)' versus 'CN_CNMF'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.001

Table S26. Gene #27: 'Amp Peak 27(20q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
AMP PEAK 27(20Q11.21) CNV	41	34	29
AMP PEAK 27(20Q11.21) WILD-TYPE	4	35	7

Figure S26. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000526 (Fisher's exact test), Q value = 0.24

Table S27. Gene #33: 'Del Peak 5(2q37.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 5(2Q37.1) CNV	30	22	21
DEL PEAK 5(2Q37.1) WILD-TYPE	15	47	15

Figure S27. Get High-res Image Gene #33: 'Del Peak 5(2q37.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(3p21.31)' versus 'MRNASEQ_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.054

Table S28. Gene #34: 'Del Peak 6(3p21.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	23	45	25
DEL PEAK 6(3P21.31) CNV	13	9	23	1
DEL PEAK 6(3P21.31) WILD-TYPE	42	14	22	24

Figure S28. Get High-res Image Gene #34: 'Del Peak 6(3p21.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 7(3p14.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000294 (Fisher's exact test), Q value = 0.14

Table S29. Gene #35: 'Del Peak 7(3p14.2)' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	14	24
DEL PEAK 7(3P14.2) CNV	7	9	2
DEL PEAK 7(3P14.2) WILD-TYPE	6	5	22

Figure S29. Get High-res Image Gene #35: 'Del Peak 7(3p14.2)' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

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

P value = 0.000489 (Fisher's exact test), Q value = 0.22

Table S30. Gene #35: 'Del Peak 7(3p14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	23	45	25
DEL PEAK 7(3P14.2) CNV	14	6	24	2
DEL PEAK 7(3P14.2) WILD-TYPE	41	17	21	23

Figure S30. Get High-res Image Gene #35: 'Del Peak 7(3p14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 8(3p12.3)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000495 (Fisher's exact test), Q value = 0.22

Table S31. Gene #36: 'Del Peak 8(3p12.3)' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	14	24
DEL PEAK 8(3P12.3) CNV	6	9	2
DEL PEAK 8(3P12.3) WILD-TYPE	7	5	22

Figure S31. Get High-res Image Gene #36: 'Del Peak 8(3p12.3)' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'Del Peak 10(4q34.2)' versus 'CN_CNMF'

P value = 7.79e-05 (Fisher's exact test), Q value = 0.037

Table S32. Gene #38: 'Del Peak 10(4q34.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 10(4Q34.2) CNV	28	17	20
DEL PEAK 10(4Q34.2) WILD-TYPE	17	52	16

Figure S32. Get High-res Image Gene #38: 'Del Peak 10(4q34.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(5q11.2)' versus 'CN_CNMF'

P value = 3.24e-07 (Fisher's exact test), Q value = 0.00016

Table S33. Gene #39: 'Del Peak 11(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 11(5Q11.2) CNV	32	18	25
DEL PEAK 11(5Q11.2) WILD-TYPE	13	51	11

Figure S33. Get High-res Image Gene #39: 'Del Peak 11(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(5q35.1)' versus 'CN_CNMF'

P value = 0.000355 (Fisher's exact test), Q value = 0.16

Table S34. Gene #40: 'Del Peak 12(5q35.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 12(5Q35.1) CNV	29	21	22
DEL PEAK 12(5Q35.1) WILD-TYPE	16	48	14

Figure S34. Get High-res Image Gene #40: 'Del Peak 12(5q35.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000367 (Fisher's exact test), Q value = 0.17

Table S35. Gene #42: 'Del Peak 14(6q21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 14(6Q21) CNV	30	21	12
DEL PEAK 14(6Q21) WILD-TYPE	15	48	24

Figure S35. Get High-res Image Gene #42: 'Del Peak 14(6q21)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(8p23.1)' versus 'CN_CNMF'

P value = 8.84e-06 (Fisher's exact test), Q value = 0.0042

Table S36. Gene #43: 'Del Peak 15(8p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 15(8P23.1) CNV	28	25	30
DEL PEAK 15(8P23.1) WILD-TYPE	17	44	6

Figure S36. Get High-res Image Gene #43: 'Del Peak 15(8p23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(9p23)' versus 'CN_CNMF'

P value = 0.000501 (Fisher's exact test), Q value = 0.23

Table S37. Gene #44: 'Del Peak 16(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 16(9P23) CNV	23	37	6
DEL PEAK 16(9P23) WILD-TYPE	22	32	30

Figure S37. Get High-res Image Gene #44: 'Del Peak 16(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(9p21.3)' versus 'CN_CNMF'

P value = 4.52e-07 (Fisher's exact test), Q value = 0.00022

Table S38. Gene #45: 'Del Peak 17(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 17(9P21.3) CNV	31	49	7
DEL PEAK 17(9P21.3) WILD-TYPE	14	20	29

Figure S38. Get High-res Image Gene #45: 'Del Peak 17(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 19(10q23.31)' versus 'CN_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.054

Table S39. Gene #47: 'Del Peak 19(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 19(10Q23.31) CNV	25	15	20
DEL PEAK 19(10Q23.31) WILD-TYPE	20	54	16

Figure S39. Get High-res Image Gene #47: 'Del Peak 19(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(11p15.5)' versus 'CN_CNMF'

P value = 7.69e-05 (Fisher's exact test), Q value = 0.036

Table S40. Gene #48: 'Del Peak 20(11p15.5)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 20(11P15.5) CNV	34	25	14
DEL PEAK 20(11P15.5) WILD-TYPE	11	44	22

Figure S40. Get High-res Image Gene #48: 'Del Peak 20(11p15.5)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 22(13q14.2)' versus 'CN_CNMF'

P value = 0.000254 (Fisher's exact test), Q value = 0.12

Table S41. Gene #50: 'Del Peak 22(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 22(13Q14.2) CNV	22	15	21
DEL PEAK 22(13Q14.2) WILD-TYPE	23	54	15

Figure S41. Get High-res Image Gene #50: 'Del Peak 22(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 22(13q14.2)' versus 'RPPA_CNMF'

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

Table S42. Gene #50: 'Del Peak 22(13q14.2)' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	11	10	14	16
DEL PEAK 22(13Q14.2) CNV	2	6	1	12
DEL PEAK 22(13Q14.2) WILD-TYPE	9	4	13	4

Figure S42. Get High-res Image Gene #50: 'Del Peak 22(13q14.2)' versus Molecular Subtype #3: 'RPPA_CNMF'

'Del Peak 24(14q32.31)' versus 'MIRSEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.12

Table S43. Gene #52: 'Del Peak 24(14q32.31)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	34	68	48
DEL PEAK 24(14Q32.31) CNV	19	13	9
DEL PEAK 24(14Q32.31) WILD-TYPE	15	55	39

Figure S43. Get High-res Image Gene #52: 'Del Peak 24(14q32.31)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 25(15q13.1)' versus 'CN_CNMF'

P value = 4.32e-06 (Fisher's exact test), Q value = 0.0021

Table S44. Gene #53: 'Del Peak 25(15q13.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 25(15Q13.1) CNV	24	11	20
DEL PEAK 25(15Q13.1) WILD-TYPE	21	58	16

Figure S44. Get High-res Image Gene #53: 'Del Peak 25(15q13.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 26(16p13.3)' versus 'CN_CNMF'

P value = 3.5e-06 (Fisher's exact test), Q value = 0.0017

Table S45. Gene #54: 'Del Peak 26(16p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 26(16P13.3) CNV	21	11	22
DEL PEAK 26(16P13.3) WILD-TYPE	24	58	14

Figure S45. Get High-res Image Gene #54: 'Del Peak 26(16p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 27(16q23.1)' versus 'CN_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.0084

Table S46. Gene #55: 'Del Peak 27(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 27(16Q23.1) CNV	15	6	17
DEL PEAK 27(16Q23.1) WILD-TYPE	30	63	19

Figure S46. Get High-res Image Gene #55: 'Del Peak 27(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 31(22q13.32)' versus 'CN_CNMF'

P value = 2.97e-07 (Fisher's exact test), Q value = 0.00015

Table S47. Gene #59: 'Del Peak 31(22q13.32)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	69	36
DEL PEAK 31(22Q13.32) CNV	16	16	28
DEL PEAK 31(22Q13.32) WILD-TYPE	29	53	8

Figure S47. Get High-res Image Gene #59: 'Del Peak 31(22q13.32)' versus Molecular Subtype #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 = 62
Number of molecular subtypes = 8
Exclude regions that fewer than K tumors have alterations, K = 3

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

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

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.

References

[1] 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)

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

[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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