Correlation between copy number variation genes and molecular subtypes

Bladder Urothelial Carcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

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/C15H7DJK

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 66 peak regions and 10 molecular subtypes across 182 patients, 49 significant findings detected with Q value < 0.25.

Amp Peak 1(1p34.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(1q23.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(3p25.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_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(7p21.1) 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'.
Amp Peak 24(17q11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 25(17q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 26(19q12) cnvs correlated to 'CN_CNMF'.
Amp Peak 27(19q13.43) cnvs correlated to 'CN_CNMF'.
Amp Peak 28(20q11.21) 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 'MRNASEQ_CNMF'.
Del Peak 7(3p14.2) cnvs correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 8(3p12.3) cnvs correlated to 'MRNASEQ_CNMF'.
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(6q27) cnvs correlated to 'CN_CNMF'.
Del Peak 16(8p23.3) cnvs correlated to 'CN_CNMF'.
Del Peak 17(8p12) cnvs correlated to 'CN_CNMF'.
Del Peak 18(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 19(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 20(9q22.33) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 22(10q23.31) cnvs correlated to 'CN_CNMF'.
Del Peak 23(11p15.5) cnvs correlated to 'CN_CNMF'.
Del Peak 25(13q14.2) cnvs correlated to 'CN_CNMF'.
Del Peak 26(14q12) cnvs correlated to 'CN_CNMF'.
Del Peak 28(15q13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 29(16p13.3) cnvs correlated to 'CN_CNMF'.
Del Peak 30(16q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 31(17p12) cnvs correlated to 'CN_CNMF'.
Del Peak 34(22q13.31) 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 66 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 49 significant findings detected.


		Molecular subtypes	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	Fisher's exact test	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)	0 (0%)	103	7.28e-07 (0.000467)	0.0188 (1.00)	0.129 (1.00)	0.0469 (1.00)	1.83e-05 (0.0115)	3.93e-05 (0.0244)	0.00046 (0.281)	2.44e-05 (0.0153)	0.00017 (0.105)	3.74e-05 (0.0233)
Del Peak 7(3p14 2)	0 (0%)	126	0.103 (1.00)	0.362 (1.00)	0.0776 (1.00)	0.065 (1.00)	4.22e-05 (0.0261)	0.00037 (0.227)	0.635 (1.00)	0.333 (1.00)	0.533 (1.00)	0.252 (1.00)
Del Peak 20(9q22 33)	0 (0%)	106	0.000357 (0.219)	0.00136 (0.812)	0.0845 (1.00)	0.00214 (1.00)	0.00186 (1.00)	3.74e-05 (0.0233)	0.451 (1.00)	0.154 (1.00)	0.0296 (1.00)	0.0643 (1.00)
Amp Peak 1(1p34 3)	0 (0%)	129	2.03e-05 (0.0128)	0.0589 (1.00)	0.134 (1.00)	0.517 (1.00)	0.298 (1.00)	0.236 (1.00)	0.0111 (1.00)	0.462 (1.00)	0.315 (1.00)	0.343 (1.00)
Amp Peak 2(1q21 3)	0 (0%)	89	1e-08 (6.59e-06)	0.256 (1.00)	0.226 (1.00)	0.208 (1.00)	0.0155 (1.00)	0.12 (1.00)	0.0691 (1.00)	0.284 (1.00)	0.238 (1.00)	0.134 (1.00)
Amp Peak 3(1q23 3)	0 (0%)	83	7.89e-07 (0.000506)	0.0378 (1.00)	0.536 (1.00)	0.353 (1.00)	0.0288 (1.00)	0.452 (1.00)	0.00127 (0.764)	0.000605 (0.367)	0.00378 (1.00)	0.00276 (1.00)
Amp Peak 7(4q13 3)	0 (0%)	150	1.95e-05 (0.0123)	0.111 (1.00)	0.505 (1.00)	0.88 (1.00)	0.97 (1.00)	0.531 (1.00)	0.237 (1.00)	0.487 (1.00)	0.244 (1.00)	0.688 (1.00)
Amp Peak 8(5p15 1)	0 (0%)	95	4.4e-08 (2.88e-05)	0.374 (1.00)	0.00244 (1.00)	0.0487 (1.00)	0.00127 (0.764)	0.0202 (1.00)	0.277 (1.00)	0.188 (1.00)	0.441 (1.00)	0.339 (1.00)
Amp Peak 9(6p22 3)	0 (0%)	110	4.61e-13 (3.05e-10)	0.0745 (1.00)	0.299 (1.00)	0.54 (1.00)	0.183 (1.00)	0.98 (1.00)	0.201 (1.00)	0.539 (1.00)	0.426 (1.00)	0.416 (1.00)
Amp Peak 12(7p21 1)	0 (0%)	93	3.63e-05 (0.0227)	0.00373 (1.00)	0.194 (1.00)	0.551 (1.00)	0.0945 (1.00)	0.411 (1.00)	0.379 (1.00)	0.127 (1.00)	0.416 (1.00)	0.658 (1.00)
Amp Peak 13(7p11 2)	0 (0%)	91	3.64e-07 (0.000236)	0.00276 (1.00)	0.0872 (1.00)	0.958 (1.00)	0.331 (1.00)	0.838 (1.00)	0.549 (1.00)	0.448 (1.00)	0.229 (1.00)	0.347 (1.00)
Amp Peak 14(8p11 23)	0 (0%)	126	0.000202 (0.124)	0.185 (1.00)	0.711 (1.00)	0.82 (1.00)	0.759 (1.00)	0.71 (1.00)	0.279 (1.00)	0.744 (1.00)	0.366 (1.00)	0.664 (1.00)
Amp Peak 16(8q22 3)	0 (0%)	66	6.69e-07 (0.00043)	0.00738 (1.00)	0.029 (1.00)	0.0902 (1.00)	0.67 (1.00)	0.367 (1.00)	0.0265 (1.00)	0.132 (1.00)	0.0115 (1.00)	0.0342 (1.00)
Amp Peak 17(8q24 21)	0 (0%)	72	0.000322 (0.198)	0.0165 (1.00)	0.0323 (1.00)	0.141 (1.00)	0.46 (1.00)	0.663 (1.00)	0.0648 (1.00)	0.255 (1.00)	0.102 (1.00)	0.165 (1.00)
Amp Peak 18(10p15 1)	0 (0%)	103	1.64e-09 (1.08e-06)	0.265 (1.00)	0.326 (1.00)	0.684 (1.00)	0.443 (1.00)	0.0654 (1.00)	0.251 (1.00)	0.123 (1.00)	0.0799 (1.00)	0.427 (1.00)
Amp Peak 24(17q11 2)	0 (0%)	101	3.89e-06 (0.00248)	0.00222 (1.00)	0.0592 (1.00)	0.127 (1.00)	0.000601 (0.366)	0.00223 (1.00)	0.00671 (1.00)	0.00688 (1.00)	0.000889 (0.537)	0.00138 (0.823)
Amp Peak 25(17q12)	0 (0%)	106	2.89e-05 (0.0181)	0.115 (1.00)	0.123 (1.00)	0.0329 (1.00)	0.0238 (1.00)	0.025 (1.00)	0.00211 (1.00)	0.00752 (1.00)	0.00196 (1.00)	0.00224 (1.00)
Amp Peak 26(19q12)	0 (0%)	106	5.95e-08 (3.89e-05)	0.115 (1.00)	0.782 (1.00)	0.907 (1.00)	0.703 (1.00)	0.381 (1.00)	0.268 (1.00)	0.183 (1.00)	0.133 (1.00)	0.405 (1.00)
Amp Peak 27(19q13 43)	0 (0%)	109	4.02e-06 (0.00255)	0.00935 (1.00)	0.399 (1.00)	0.555 (1.00)	0.378 (1.00)	0.721 (1.00)	0.28 (1.00)	0.0308 (1.00)	0.0557 (1.00)	0.0598 (1.00)
Amp Peak 28(20q11 21)	0 (0%)	63	1.09e-06 (0.000696)	0.132 (1.00)	0.688 (1.00)	0.0682 (1.00)	0.329 (1.00)	0.201 (1.00)	0.176 (1.00)	0.156 (1.00)	0.0292 (1.00)	0.438 (1.00)
Del Peak 4(2q34)	0 (0%)	106	5.95e-08 (3.89e-05)	0.0557 (1.00)	0.451 (1.00)	0.214 (1.00)	0.293 (1.00)	0.158 (1.00)	0.127 (1.00)	0.27 (1.00)	0.164 (1.00)	0.132 (1.00)
Del Peak 5(2q37 1)	0 (0%)	92	8.88e-08 (5.78e-05)	0.00405 (1.00)	0.467 (1.00)	0.279 (1.00)	0.07 (1.00)	0.122 (1.00)	0.0795 (1.00)	0.112 (1.00)	0.0982 (1.00)	0.0797 (1.00)
Del Peak 6(3p21 31)	0 (0%)	127	0.333 (1.00)	0.187 (1.00)	0.0296 (1.00)	0.0317 (1.00)	1.83e-05 (0.0116)	0.000531 (0.324)	0.0563 (1.00)	0.12 (1.00)	0.186 (1.00)	0.169 (1.00)
Del Peak 8(3p12 3)	0 (0%)	134	0.0879 (1.00)	0.713 (1.00)	0.419 (1.00)	0.0483 (1.00)	9.86e-05 (0.061)	0.00372 (1.00)	0.252 (1.00)	0.437 (1.00)	0.796 (1.00)	0.536 (1.00)
Del Peak 10(4q34 2)	0 (0%)	106	0.000198 (0.122)	0.653 (1.00)	0.453 (1.00)	0.821 (1.00)	0.402 (1.00)	0.724 (1.00)	0.0272 (1.00)	0.0157 (1.00)	0.0357 (1.00)	0.0137 (1.00)
Del Peak 11(5q11 2)	0 (0%)	91	6.93e-08 (4.52e-05)	0.0461 (1.00)	0.969 (1.00)	0.422 (1.00)	0.0586 (1.00)	0.523 (1.00)	0.164 (1.00)	0.0884 (1.00)	0.22 (1.00)	0.11 (1.00)
Del Peak 12(5q35 1)	0 (0%)	94	3.19e-06 (0.00203)	0.00428 (1.00)	0.341 (1.00)	0.29 (1.00)	0.423 (1.00)	0.175 (1.00)	0.108 (1.00)	0.197 (1.00)	0.425 (1.00)	0.34 (1.00)
Del Peak 14(6q21)	0 (0%)	101	4.05e-07 (0.000262)	0.0132 (1.00)	0.843 (1.00)	0.63 (1.00)	0.564 (1.00)	0.0353 (1.00)	0.164 (1.00)	0.232 (1.00)	0.203 (1.00)	0.587 (1.00)
Del Peak 15(6q27)	0 (0%)	101	3.89e-06 (0.00248)	0.00128 (0.767)	0.657 (1.00)	0.63 (1.00)	0.459 (1.00)	0.0638 (1.00)	0.0407 (1.00)	0.109 (1.00)	0.203 (1.00)	0.366 (1.00)
Del Peak 16(8p23 3)	0 (0%)	83	2.61e-09 (1.72e-06)	0.111 (1.00)	0.523 (1.00)	0.234 (1.00)	0.00415 (1.00)	0.019 (1.00)	0.0178 (1.00)	0.1 (1.00)	0.0455 (1.00)	0.0233 (1.00)
Del Peak 17(8p12)	0 (0%)	94	5.6e-07 (0.000361)	0.389 (1.00)	0.548 (1.00)	0.514 (1.00)	0.0345 (1.00)	0.246 (1.00)	0.0227 (1.00)	0.0118 (1.00)	0.113 (1.00)	0.0247 (1.00)
Del Peak 18(9p23)	0 (0%)	102	1.24e-05 (0.00785)	0.447 (1.00)	0.235 (1.00)	0.198 (1.00)	0.702 (1.00)	0.228 (1.00)	0.272 (1.00)	0.71 (1.00)	0.388 (1.00)	0.936 (1.00)
Del Peak 19(9p21 3)	0 (0%)	76	9.6e-08 (6.24e-05)	0.749 (1.00)	0.415 (1.00)	0.00241 (1.00)	0.445 (1.00)	0.385 (1.00)	0.609 (1.00)	0.462 (1.00)	0.564 (1.00)	0.835 (1.00)
Del Peak 22(10q23 31)	0 (0%)	107	3.46e-05 (0.0217)	0.00268 (1.00)	0.644 (1.00)	0.689 (1.00)	0.0845 (1.00)	0.133 (1.00)	0.306 (1.00)	0.144 (1.00)	0.132 (1.00)	0.0996 (1.00)
Del Peak 23(11p15 5)	0 (0%)	95	2.02e-06 (0.00129)	0.00982 (1.00)	0.348 (1.00)	0.779 (1.00)	0.0403 (1.00)	0.00875 (1.00)	0.00174 (1.00)	0.0129 (1.00)	0.00415 (1.00)	0.339 (1.00)
Del Peak 25(13q14 2)	0 (0%)	108	2.83e-07 (0.000184)	0.415 (1.00)	0.00849 (1.00)	0.00336 (1.00)	0.0136 (1.00)	0.0682 (1.00)	0.923 (1.00)	0.843 (1.00)	0.308 (1.00)	0.392 (1.00)
Del Peak 26(14q12)	0 (0%)	131	0.000211 (0.13)	0.257 (1.00)	0.149 (1.00)	0.0899 (1.00)	0.0528 (1.00)	0.05 (1.00)	0.0317 (1.00)	0.0405 (1.00)	0.0491 (1.00)	0.0912 (1.00)
Del Peak 28(15q13 1)	0 (0%)	113	5.64e-07 (0.000363)	0.00899 (1.00)	0.286 (1.00)	0.456 (1.00)	0.105 (1.00)	0.303 (1.00)	0.0453 (1.00)	0.0478 (1.00)	0.0573 (1.00)	0.0314 (1.00)
Del Peak 29(16p13 3)	0 (0%)	112	3.8e-07 (0.000246)	0.285 (1.00)	0.192 (1.00)	0.202 (1.00)	0.719 (1.00)	0.486 (1.00)	0.96 (1.00)	0.644 (1.00)	0.644 (1.00)	0.586 (1.00)
Del Peak 30(16q23 1)	0 (0%)	136	3.18e-06 (0.00203)	0.0327 (1.00)	0.427 (1.00)	0.107 (1.00)	0.0635 (1.00)	0.903 (1.00)	0.032 (1.00)	0.102 (1.00)	0.134 (1.00)	0.119 (1.00)
Del Peak 31(17p12)	0 (0%)	89	4.06e-05 (0.0252)	0.0535 (1.00)	0.201 (1.00)	0.444 (1.00)	0.049 (1.00)	0.087 (1.00)	0.306 (1.00)	0.883 (1.00)	0.562 (1.00)	0.673 (1.00)
Del Peak 34(22q13 31)	0 (0%)	108	4.8e-09 (3.15e-06)	0.0792 (1.00)	0.329 (1.00)	0.00512 (1.00)	0.127 (1.00)	0.286 (1.00)	0.98 (1.00)	0.13 (1.00)	0.456 (1.00)	0.374 (1.00)
Amp Peak 5(3q26 32)	0 (0%)	84	0.00127 (0.764)	0.768 (1.00)	0.389 (1.00)	0.161 (1.00)	0.0105 (1.00)	0.961 (1.00)	0.704 (1.00)	0.395 (1.00)	0.486 (1.00)	0.0843 (1.00)
Amp Peak 6(4p16 3)	0 (0%)	142	0.0709 (1.00)	0.222 (1.00)	0.0275 (1.00)	0.00757 (1.00)	0.0516 (1.00)	0.0144 (1.00)	0.0427 (1.00)	0.13 (1.00)	0.0287 (1.00)	0.466 (1.00)
Amp Peak 10(6q12)	0 (0%)	152	0.0231 (1.00)	0.713 (1.00)	0.762 (1.00)	0.0376 (1.00)	0.0475 (1.00)	0.552 (1.00)	0.432 (1.00)	0.017 (1.00)	0.605 (1.00)	0.729 (1.00)
Amp Peak 11(6q21)	0 (0%)	164	0.00716 (1.00)	0.435 (1.00)	0.482 (1.00)	0.1 (1.00)	0.0698 (1.00)	0.359 (1.00)	0.403 (1.00)	0.618 (1.00)	0.898 (1.00)	0.584 (1.00)
Amp Peak 15(8p11 21)	0 (0%)	125	0.0006 (0.366)	0.00144 (0.855)	0.944 (1.00)	0.955 (1.00)	0.215 (1.00)	0.797 (1.00)	0.16 (1.00)	0.486 (1.00)	0.179 (1.00)	0.106 (1.00)
Amp Peak 19(11q13 3)	0 (0%)	112	0.000645 (0.391)	0.202 (1.00)	0.269 (1.00)	0.0742 (1.00)	0.0622 (1.00)	1 (1.00)	0.0941 (1.00)	0.056 (1.00)	0.685 (1.00)	0.912 (1.00)
Amp Peak 20(11q22 1)	0 (0%)	149	0.272 (1.00)	0.319 (1.00)	0.641 (1.00)	0.271 (1.00)	0.339 (1.00)	0.188 (1.00)	0.39 (1.00)	0.113 (1.00)	0.569 (1.00)	0.514 (1.00)
Amp Peak 21(12q15)	0 (0%)	125	0.00567 (1.00)	0.235 (1.00)	0.0497 (1.00)	0.0268 (1.00)	0.0801 (1.00)	0.109 (1.00)	0.118 (1.00)	0.0198 (1.00)	0.0183 (1.00)	0.0275 (1.00)
Amp Peak 22(13q22 1)	0 (0%)	126	0.236 (1.00)	0.493 (1.00)	0.944 (1.00)	0.887 (1.00)	0.717 (1.00)	0.812 (1.00)	0.555 (1.00)	0.708 (1.00)	0.691 (1.00)	0.95 (1.00)
Amp Peak 23(16p12 1)	0 (0%)	136	0.00157 (0.93)	0.609 (1.00)	0.387 (1.00)	0.438 (1.00)	0.421 (1.00)	0.356 (1.00)	0.514 (1.00)	0.802 (1.00)	0.925 (1.00)	0.371 (1.00)
Amp Peak 29(22q11 23)	0 (0%)	142	0.0127 (1.00)	0.0617 (1.00)	0.592 (1.00)	0.714 (1.00)	0.965 (1.00)	0.552 (1.00)	0.23 (1.00)	0.538 (1.00)	0.972 (1.00)	0.56 (1.00)
Del Peak 1(1p36 11)	0 (0%)	146	0.624 (1.00)	0.188 (1.00)	0.335 (1.00)	0.0259 (1.00)	0.334 (1.00)	0.0299 (1.00)	0.914 (1.00)	0.428 (1.00)	0.552 (1.00)	0.352 (1.00)
Del Peak 2(1q32 1)	0 (0%)	149	0.0198 (1.00)	0.502 (1.00)	0.581 (1.00)	0.727 (1.00)	0.765 (1.00)	0.0231 (1.00)	0.724 (1.00)	0.607 (1.00)	0.167 (1.00)	0.773 (1.00)
Del Peak 3(2q22 1)	0 (0%)	128	0.00138 (0.824)	0.371 (1.00)	0.206 (1.00)	0.54 (1.00)	0.0469 (1.00)	0.203 (1.00)	0.344 (1.00)	0.607 (1.00)	0.11 (1.00)	0.42 (1.00)
Del Peak 9(4q22 1)	0 (0%)	112	0.0422 (1.00)	0.328 (1.00)	0.513 (1.00)	0.427 (1.00)	0.0641 (1.00)	0.02 (1.00)	0.358 (1.00)	0.875 (1.00)	0.0319 (1.00)	0.113 (1.00)
Del Peak 13(6p25 3)	0 (0%)	135	0.0631 (1.00)	0.11 (1.00)	0.808 (1.00)	0.678 (1.00)	0.11 (1.00)	0.531 (1.00)	0.145 (1.00)	0.513 (1.00)	0.539 (1.00)	0.281 (1.00)
Del Peak 21(10p11 22)	0 (0%)	146	0.57 (1.00)	0.071 (1.00)	0.744 (1.00)	0.588 (1.00)	0.032 (1.00)	0.142 (1.00)	0.192 (1.00)	0.052 (1.00)	0.215 (1.00)	0.122 (1.00)
Del Peak 24(11q25)	0 (0%)	118	0.00974 (1.00)	0.0531 (1.00)	0.853 (1.00)	0.8 (1.00)	0.0348 (1.00)	0.0515 (1.00)	0.376 (1.00)	0.237 (1.00)	0.315 (1.00)	0.767 (1.00)
Del Peak 27(14q24 1)	0 (0%)	129	0.00199 (1.00)	0.188 (1.00)	0.542 (1.00)	0.233 (1.00)	0.0281 (1.00)	0.00185 (1.00)	0.00116 (0.702)	0.00708 (1.00)	0.0091 (1.00)	0.0151 (1.00)
Del Peak 32(18q23)	0 (0%)	110	0.0158 (1.00)	0.267 (1.00)	0.599 (1.00)	1 (1.00)	0.485 (1.00)	0.336 (1.00)	0.00966 (1.00)	0.00474 (1.00)	0.166 (1.00)	0.134 (1.00)
Del Peak 33(19p13 3)	0 (0%)	112	0.00164 (0.972)	0.742 (1.00)	0.82 (1.00)	0.723 (1.00)	0.475 (1.00)	0.606 (1.00)	0.219 (1.00)	0.264 (1.00)	0.219 (1.00)	0.475 (1.00)
Del Peak 35(Xp11 3)	0 (0%)	134	0.00303 (1.00)	0.039 (1.00)	0.358 (1.00)	0.468 (1.00)	0.182 (1.00)	0.421 (1.00)	0.202 (1.00)	1 (1.00)	0.045 (1.00)	0.271 (1.00)
Del Peak 36(Xq21 33)	0 (0%)	140	0.00308 (1.00)	0.00174 (1.00)	0.963 (1.00)	0.137 (1.00)	0.0482 (1.00)	0.377 (1.00)	0.178 (1.00)	0.434 (1.00)	0.0641 (1.00)	0.116 (1.00)
Del Peak 37(Xq23)	0 (0%)	143	0.018 (1.00)	0.000741 (0.448)	0.996 (1.00)	0.212 (1.00)	0.0875 (1.00)	0.379 (1.00)	0.101 (1.00)	0.303 (1.00)	0.0334 (1.00)	0.0671 (1.00)

'Amp Peak 1(1p34.3)' versus 'CN_CNMF'

P value = 2.03e-05 (Fisher's exact test), Q value = 0.013

Table S1. Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 1(1P34.3) CNV	19	11	23
AMP PEAK 1(1P34.3) WILD-TYPE	36	71	22

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1e-08 (Fisher's exact test), Q value = 6.6e-06

Table S2. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 2(1Q21.3) CNV	37	22	34
AMP PEAK 2(1Q21.3) WILD-TYPE	18	60	11

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 7.89e-07 (Fisher's exact test), Q value = 0.00051

Table S3. Gene #3: 'Amp Peak 3(1q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 3(1Q23.3) CNV	40	27	32
AMP PEAK 3(1Q23.3) WILD-TYPE	15	55	13

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(1q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 7.28e-07 (Fisher's exact test), Q value = 0.00047

Table S4. Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 4(3P25.2) CNV	37	19	23
AMP PEAK 4(3P25.2) WILD-TYPE	18	63	22

Figure S4. Get High-res Image Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(3p25.2)' versus 'MRNASEQ_CNMF'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.012

Table S5. Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	52	35	63
AMP PEAK 4(3P25.2) CNV	19	9	17	34
AMP PEAK 4(3P25.2) WILD-TYPE	10	43	18	29

Figure S5. Get High-res Image Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 3.93e-05 (Fisher's exact test), Q value = 0.024

Table S6. Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	67	76
AMP PEAK 4(3P25.2) CNV	22	38	19
AMP PEAK 4(3P25.2) WILD-TYPE	14	29	57

Figure S6. Get High-res Image Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.44e-05 (Fisher's exact test), Q value = 0.015

Table S7. Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	138	8
AMP PEAK 4(3P25.2) CNV	27	51	1
AMP PEAK 4(3P25.2) WILD-TYPE	9	87	7

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 4(3p25.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.11

Table S8. Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	79	70
AMP PEAK 4(3P25.2) CNV	25	27	27
AMP PEAK 4(3P25.2) WILD-TYPE	8	52	43

Figure S8. Get High-res Image Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 4(3p25.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.74e-05 (Fisher's exact test), Q value = 0.023

Table S9. Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	97	26
AMP PEAK 4(3P25.2) CNV	27	31	21
AMP PEAK 4(3P25.2) WILD-TYPE	32	66	5

Figure S9. Get High-res Image Gene #4: 'Amp Peak 4(3p25.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 1.95e-05 (Fisher's exact test), Q value = 0.012

Table S10. Gene #7: 'Amp Peak 7(4q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 7(4Q13.3) CNV	21	6	5
AMP PEAK 7(4Q13.3) WILD-TYPE	34	76	40

Figure S10. Get High-res Image Gene #7: 'Amp Peak 7(4q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 4.4e-08 (Fisher's exact test), Q value = 2.9e-05

Table S11. Gene #8: 'Amp Peak 8(5p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 8(5P15.1) CNV	38	20	29
AMP PEAK 8(5P15.1) WILD-TYPE	17	62	16

Figure S11. Get High-res Image Gene #8: 'Amp Peak 8(5p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 4.61e-13 (Fisher's exact test), Q value = 3e-10

Table S12. Gene #9: 'Amp Peak 9(6p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 9(6P22.3) CNV	28	10	34
AMP PEAK 9(6P22.3) WILD-TYPE	27	72	11

Figure S12. Get High-res Image Gene #9: 'Amp Peak 9(6p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 12(7p21.1)' versus 'CN_CNMF'

P value = 3.63e-05 (Fisher's exact test), Q value = 0.023

Table S13. Gene #12: 'Amp Peak 12(7p21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 12(7P21.1) CNV	36	25	28
AMP PEAK 12(7P21.1) WILD-TYPE	19	57	17

Figure S13. Get High-res Image Gene #12: 'Amp Peak 12(7p21.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 3.64e-07 (Fisher's exact test), Q value = 0.00024

Table S14. Gene #13: 'Amp Peak 13(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 13(7P11.2) CNV	39	23	29
AMP PEAK 13(7P11.2) WILD-TYPE	16	59	16

Figure S14. 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 = 0.000202 (Fisher's exact test), Q value = 0.12

Table S15. Gene #14: 'Amp Peak 14(8p11.23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 14(8P11.23) CNV	29	18	9
AMP PEAK 14(8P11.23) WILD-TYPE	26	64	36

Figure S15. 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 = 6.69e-07 (Fisher's exact test), Q value = 0.00043

Table S16. Gene #16: 'Amp Peak 16(8q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 16(8Q22.3) CNV	50	43	23
AMP PEAK 16(8Q22.3) WILD-TYPE	5	39	22

Figure S16. 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 = 0.000322 (Fisher's exact test), Q value = 0.2

Table S17. Gene #17: 'Amp Peak 17(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 17(8Q24.21) CNV	45	43	22
AMP PEAK 17(8Q24.21) WILD-TYPE	10	39	23

Figure S17. 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 = 1.64e-09 (Fisher's exact test), Q value = 1.1e-06

Table S18. Gene #18: 'Amp Peak 18(10p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 18(10P15.1) CNV	34	15	30
AMP PEAK 18(10P15.1) WILD-TYPE	21	67	15

Figure S18. Get High-res Image Gene #18: 'Amp Peak 18(10p15.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 24(17q11.2)' versus 'CN_CNMF'

P value = 3.89e-06 (Fisher's exact test), Q value = 0.0025

Table S19. Gene #24: 'Amp Peak 24(17q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 24(17Q11.2) CNV	39	23	19
AMP PEAK 24(17Q11.2) WILD-TYPE	16	59	26

Figure S19. Get High-res Image Gene #24: 'Amp Peak 24(17q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 25(17q12)' versus 'CN_CNMF'

P value = 2.89e-05 (Fisher's exact test), Q value = 0.018

Table S20. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 25(17Q12) CNV	37	26	13
AMP PEAK 25(17Q12) WILD-TYPE	18	56	32

Figure S20. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 26(19q12)' versus 'CN_CNMF'

P value = 5.95e-08 (Fisher's exact test), Q value = 3.9e-05

Table S21. Gene #26: 'Amp Peak 26(19q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 26(19Q12) CNV	36	16	24
AMP PEAK 26(19Q12) WILD-TYPE	19	66	21

Figure S21. Get High-res Image Gene #26: 'Amp Peak 26(19q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 27(19q13.43)' versus 'CN_CNMF'

P value = 4.02e-06 (Fisher's exact test), Q value = 0.0025

Table S22. Gene #27: 'Amp Peak 27(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 27(19Q13.43) CNV	35	18	20
AMP PEAK 27(19Q13.43) WILD-TYPE	20	64	25

Figure S22. Get High-res Image Gene #27: 'Amp Peak 27(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 28(20q11.21)' versus 'CN_CNMF'

P value = 1.09e-06 (Fisher's exact test), Q value = 7e-04

Table S23. Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
AMP PEAK 28(20Q11.21) CNV	46	37	36
AMP PEAK 28(20Q11.21) WILD-TYPE	9	45	9

Figure S23. Get High-res Image Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 5.95e-08 (Fisher's exact test), Q value = 3.9e-05

Table S24. Gene #33: 'Del Peak 4(2q34)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 4(2Q34) CNV	36	16	24
DEL PEAK 4(2Q34) WILD-TYPE	19	66	21

Figure S24. Get High-res Image Gene #33: 'Del Peak 4(2q34)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 8.88e-08 (Fisher's exact test), Q value = 5.8e-05

Table S25. Gene #34: 'Del Peak 5(2q37.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 5(2Q37.1) CNV	40	22	28
DEL PEAK 5(2Q37.1) WILD-TYPE	15	60	17

Figure S25. Get High-res Image Gene #34: 'Del Peak 5(2q37.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.83e-05 (Fisher's exact test), Q value = 0.012

Table S26. Gene #35: 'Del Peak 6(3p21.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	52	35	63
DEL PEAK 6(3P21.31) CNV	10	27	2	15
DEL PEAK 6(3P21.31) WILD-TYPE	19	25	33	48

Figure S26. Get High-res Image Gene #35: 'Del Peak 6(3p21.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 4.22e-05 (Fisher's exact test), Q value = 0.026

Table S27. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	52	35	63
DEL PEAK 7(3P14.2) CNV	7	28	3	16
DEL PEAK 7(3P14.2) WILD-TYPE	22	24	32	47

Figure S27. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 0.00037 (Fisher's exact test), Q value = 0.23

Table S28. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	67	76
DEL PEAK 7(3P14.2) CNV	3	18	33
DEL PEAK 7(3P14.2) WILD-TYPE	33	49	43

Figure S28. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 9.86e-05 (Fisher's exact test), Q value = 0.061

Table S29. Gene #37: 'Del Peak 8(3p12.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	52	35	63
DEL PEAK 8(3P12.3) CNV	9	24	2	12
DEL PEAK 8(3P12.3) WILD-TYPE	20	28	33	51

Figure S29. Get High-res Image Gene #37: 'Del Peak 8(3p12.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 0.000198 (Fisher's exact test), Q value = 0.12

Table S30. Gene #39: 'Del Peak 10(4q34.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 10(4Q34.2) CNV	28	21	27
DEL PEAK 10(4Q34.2) WILD-TYPE	27	61	18

Figure S30. Get High-res Image Gene #39: 'Del Peak 10(4q34.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 6.93e-08 (Fisher's exact test), Q value = 4.5e-05

Table S31. Gene #40: 'Del Peak 11(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 11(5Q11.2) CNV	39	22	30
DEL PEAK 11(5Q11.2) WILD-TYPE	16	60	15

Figure S31. Get High-res Image Gene #40: 'Del Peak 11(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 3.19e-06 (Fisher's exact test), Q value = 0.002

Table S32. Gene #41: 'Del Peak 12(5q35.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 12(5Q35.1) CNV	37	23	28
DEL PEAK 12(5Q35.1) WILD-TYPE	18	59	17

Figure S32. Get High-res Image Gene #41: 'Del Peak 12(5q35.1)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 4.05e-07 (Fisher's exact test), Q value = 0.00026

Table S33. Gene #43: 'Del Peak 14(6q21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 14(6Q21) CNV	41	24	16
DEL PEAK 14(6Q21) WILD-TYPE	14	58	29

Figure S33. Get High-res Image Gene #43: 'Del Peak 14(6q21)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 3.89e-06 (Fisher's exact test), Q value = 0.0025

Table S34. Gene #44: 'Del Peak 15(6q27)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 15(6Q27) CNV	39	23	19
DEL PEAK 15(6Q27) WILD-TYPE	16	59	26

Figure S34. Get High-res Image Gene #44: 'Del Peak 15(6q27)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.61e-09 (Fisher's exact test), Q value = 1.7e-06

Table S35. Gene #45: 'Del Peak 16(8p23.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 16(8P23.3) CNV	34	26	39
DEL PEAK 16(8P23.3) WILD-TYPE	21	56	6

Figure S35. Get High-res Image Gene #45: 'Del Peak 16(8p23.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(8p12)' versus 'CN_CNMF'

P value = 5.6e-07 (Fisher's exact test), Q value = 0.00036

Table S36. Gene #46: 'Del Peak 17(8p12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 17(8P12) CNV	29	24	35
DEL PEAK 17(8P12) WILD-TYPE	26	58	10

Figure S36. Get High-res Image Gene #46: 'Del Peak 17(8p12)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 18(9p23)' versus 'CN_CNMF'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0078

Table S37. Gene #47: 'Del Peak 18(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 18(9P23) CNV	33	40	7
DEL PEAK 18(9P23) WILD-TYPE	22	42	38

Figure S37. Get High-res Image Gene #47: 'Del Peak 18(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 9.6e-08 (Fisher's exact test), Q value = 6.2e-05

Table S38. Gene #48: 'Del Peak 19(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 19(9P21.3) CNV	40	56	10
DEL PEAK 19(9P21.3) WILD-TYPE	15	26	35

Figure S38. Get High-res Image Gene #48: 'Del Peak 19(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(9q22.33)' versus 'CN_CNMF'

P value = 0.000357 (Fisher's exact test), Q value = 0.22

Table S39. Gene #49: 'Del Peak 20(9q22.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 20(9Q22.33) CNV	30	38	8
DEL PEAK 20(9Q22.33) WILD-TYPE	25	44	37

Figure S39. Get High-res Image Gene #49: 'Del Peak 20(9q22.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(9q22.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.74e-05 (Fisher's exact test), Q value = 0.023

Table S40. Gene #49: 'Del Peak 20(9q22.33)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	67	76
DEL PEAK 20(9Q22.33) CNV	21	36	17
DEL PEAK 20(9Q22.33) WILD-TYPE	15	31	59

Figure S40. Get High-res Image Gene #49: 'Del Peak 20(9q22.33)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 22(10q23.31)' versus 'CN_CNMF'

P value = 3.46e-05 (Fisher's exact test), Q value = 0.022

Table S41. Gene #51: 'Del Peak 22(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 22(10Q23.31) CNV	31	19	25
DEL PEAK 22(10Q23.31) WILD-TYPE	24	63	20

Figure S41. Get High-res Image Gene #51: 'Del Peak 22(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 23(11p15.5)' versus 'CN_CNMF'

P value = 2.02e-06 (Fisher's exact test), Q value = 0.0013

Table S42. Gene #52: 'Del Peak 23(11p15.5)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 23(11P15.5) CNV	42	29	16
DEL PEAK 23(11P15.5) WILD-TYPE	13	53	29

Figure S42. Get High-res Image Gene #52: 'Del Peak 23(11p15.5)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(13q14.2)' versus 'CN_CNMF'

P value = 2.83e-07 (Fisher's exact test), Q value = 0.00018

Table S43. Gene #54: 'Del Peak 25(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 25(13Q14.2) CNV	29	16	29
DEL PEAK 25(13Q14.2) WILD-TYPE	26	66	16

Figure S43. Get High-res Image Gene #54: 'Del Peak 25(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 26(14q12)' versus 'CN_CNMF'

P value = 0.000211 (Fisher's exact test), Q value = 0.13

Table S44. Gene #55: 'Del Peak 26(14q12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 26(14Q12) CNV	27	17	7
DEL PEAK 26(14Q12) WILD-TYPE	28	65	38

Figure S44. Get High-res Image Gene #55: 'Del Peak 26(14q12)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 28(15q13.1)' versus 'CN_CNMF'

P value = 5.64e-07 (Fisher's exact test), Q value = 0.00036

Table S45. Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 28(15Q13.1) CNV	30	14	25
DEL PEAK 28(15Q13.1) WILD-TYPE	25	68	20

Figure S45. Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 29(16p13.3)' versus 'CN_CNMF'

P value = 3.8e-07 (Fisher's exact test), Q value = 0.00025

Table S46. Gene #58: 'Del Peak 29(16p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 29(16P13.3) CNV	26	15	29
DEL PEAK 29(16P13.3) WILD-TYPE	29	67	16

Figure S46. Get High-res Image Gene #58: 'Del Peak 29(16p13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 30(16q23.1)' versus 'CN_CNMF'

P value = 3.18e-06 (Fisher's exact test), Q value = 0.002

Table S47. Gene #59: 'Del Peak 30(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 30(16Q23.1) CNV	19	7	20
DEL PEAK 30(16Q23.1) WILD-TYPE	36	75	25

Figure S47. Get High-res Image Gene #59: 'Del Peak 30(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 31(17p12)' versus 'CN_CNMF'

P value = 4.06e-05 (Fisher's exact test), Q value = 0.025

Table S48. Gene #60: 'Del Peak 31(17p12)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 31(17P12) CNV	40	28	25
DEL PEAK 31(17P12) WILD-TYPE	15	54	20

Figure S48. Get High-res Image Gene #60: 'Del Peak 31(17p12)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 34(22q13.31)' versus 'CN_CNMF'

P value = 4.8e-09 (Fisher's exact test), Q value = 3.2e-06

Table S49. Gene #63: 'Del Peak 34(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	82	45
DEL PEAK 34(22Q13.31) CNV	21	18	35
DEL PEAK 34(22Q13.31) WILD-TYPE	34	64	10

Figure S49. Get High-res Image Gene #63: 'Del Peak 34(22q13.31)' 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 = 182
Number of copy number variation regions = 66
Number of molecular subtypes = 10
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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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