Correlation between copy number variation genes and molecular subtypes

Ovarian Serous Cystadenocarcinoma (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/C1RR1WK7

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 70 peak regions and 14 molecular subtypes across 570 patients, 76 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' and 'METHLYATION_CNMF'.
Amp Peak 3(1q42.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 4(2p23.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(2q31.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(3q26.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(4p16.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(4q13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 10(6p22.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(7q36.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 12(8p11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(8q24.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 14(10p15.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 16(11q14.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(12p13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 18(12p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 19(12q15) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 21(14q32.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(15q26.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 24(18q11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 25(19p13.12) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
Amp Peak 26(19q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 27(19q13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 28(20p13) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 29(20q11.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 30(20q13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 32(Xp11.23) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 33(Xq28) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.11) cnvs correlated to 'CN_CNMF'.
Del Peak 2(1q32.3) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q37.3) cnvs correlated to 'MIR_CHIERARCHICAL' and 'CN_CNMF'.
Del Peak 6(3p26.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 9(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 10(5q13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 11(6q27) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 12(7p22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 13(8p23.3) cnvs correlated to 'CN_CNMF'.
Del Peak 14(8p21.2) cnvs correlated to 'CN_CNMF'.
Del Peak 15(9p24.3) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 16(9q34.13) cnvs correlated to 'CN_CNMF'.
Del Peak 18(10q23.31) cnvs correlated to 'MIR_CNMF'.
Del Peak 19(10q26.3) cnvs correlated to 'CN_CNMF'.
Del Peak 20(11p15.5) cnvs correlated to 'CN_CNMF'.
Del Peak 22(12q24.33) cnvs correlated to 'CN_CNMF'.
Del Peak 23(13q14.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 24(14q23.3) cnvs correlated to 'CN_CNMF'.
Del Peak 25(15q15.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 27(16q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 28(16q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 34(19q13.43) cnvs correlated to 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 70 regions and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 76 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	MIR CNMF	MIR CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	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	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 13(8q24 21)	0 (0%)	122	3.97e-07 (0.000376)	1.57e-05 (0.0146)	0.254 (1.00)	0.000789 (0.704)	1.76e-17 (1.72e-14)	0.00265 (1.00)	0.96 (1.00)	0.595 (1.00)	4.52e-07 (0.000427)	2.46e-05 (0.0228)	0.142 (1.00)	0.0406 (1.00)	0.084 (1.00)	0.0836 (1.00)
Amp Peak 25(19p13 12)	0 (0%)	264	0.000811 (0.722)	3.24e-06 (0.00305)	0.0212 (1.00)	0.0645 (1.00)	6.6e-13 (6.42e-10)	1.43e-06 (0.00135)	0.000662 (0.594)	0.00378 (1.00)	0.215 (1.00)	0.27 (1.00)	0.482 (1.00)	0.595 (1.00)	0.961 (1.00)	0.656 (1.00)
Amp Peak 29(20q11 21)	0 (0%)	237	0.0051 (1.00)	0.000464 (0.419)	0.261 (1.00)	0.0129 (1.00)	1.43e-25 (1.4e-22)	4.06e-12 (3.94e-09)	0.14 (1.00)	0.0392 (1.00)	0.000138 (0.125)	0.599 (1.00)	0.543 (1.00)	0.251 (1.00)	0.968 (1.00)	0.573 (1.00)
Del Peak 11(6q27)	0 (0%)	189	0.14 (1.00)	0.0058 (1.00)	0.555 (1.00)	0.566 (1.00)	8.46e-09 (8.08e-06)	2.35e-05 (0.0218)	0.428 (1.00)	0.917 (1.00)	2.69e-05 (0.0249)	0.25 (1.00)	0.457 (1.00)	0.945 (1.00)	0.311 (1.00)	0.0927 (1.00)
Amp Peak 2(1q21 3)	0 (0%)	213	0.186 (1.00)	0.112 (1.00)	0.536 (1.00)	0.188 (1.00)	2.93e-11 (2.84e-08)	0.000103 (0.0938)	0.0601 (1.00)	0.00999 (1.00)	0.628 (1.00)	0.28 (1.00)	0.916 (1.00)	0.972 (1.00)	0.784 (1.00)	0.978 (1.00)
Amp Peak 3(1q42 2)	0 (0%)	257	0.0204 (1.00)	0.0435 (1.00)	0.873 (1.00)	0.128 (1.00)	5.55e-09 (5.31e-06)	5.89e-06 (0.0055)	0.279 (1.00)	0.207 (1.00)	0.62 (1.00)	0.418 (1.00)	0.183 (1.00)	0.27 (1.00)	0.258 (1.00)	0.219 (1.00)
Amp Peak 14(10p15 3)	0 (0%)	329	0.877 (1.00)	0.377 (1.00)	0.0732 (1.00)	0.121 (1.00)	4.15e-12 (4.03e-09)	2.85e-05 (0.0264)	0.562 (1.00)	0.408 (1.00)	0.344 (1.00)	0.306 (1.00)	0.465 (1.00)	0.945 (1.00)	0.798 (1.00)	0.652 (1.00)
Amp Peak 17(12p13 33)	0 (0%)	251	0.0281 (1.00)	0.0239 (1.00)	0.162 (1.00)	0.0802 (1.00)	1.02e-10 (9.86e-08)	3.04e-05 (0.0281)	0.314 (1.00)	0.614 (1.00)	0.0124 (1.00)	0.137 (1.00)	0.32 (1.00)	0.921 (1.00)	0.657 (1.00)	0.357 (1.00)
Amp Peak 18(12p12 1)	0 (0%)	268	0.325 (1.00)	0.145 (1.00)	0.889 (1.00)	0.142 (1.00)	9.05e-15 (8.84e-12)	5.73e-06 (0.00536)	0.819 (1.00)	0.493 (1.00)	0.0214 (1.00)	0.133 (1.00)	0.202 (1.00)	0.7 (1.00)	0.504 (1.00)	0.581 (1.00)
Amp Peak 19(12q15)	0 (0%)	359	0.0045 (1.00)	0.00276 (1.00)	0.853 (1.00)	0.325 (1.00)	1.43e-08 (1.36e-05)	3.16e-05 (0.0291)	0.204 (1.00)	0.328 (1.00)	0.00324 (1.00)	0.00034 (0.307)	0.665 (1.00)	0.62 (1.00)	0.717 (1.00)	0.54 (1.00)
Amp Peak 26(19q12)	0 (0%)	255	0.0646 (1.00)	0.00134 (1.00)	0.0316 (1.00)	0.541 (1.00)	9.11e-29 (8.93e-26)	2.19e-10 (2.11e-07)	0.0803 (1.00)	0.82 (1.00)	0.551 (1.00)	0.86 (1.00)	0.335 (1.00)	0.596 (1.00)	0.738 (1.00)	0.438 (1.00)
Amp Peak 27(19q13 2)	0 (0%)	331	0.922 (1.00)	0.733 (1.00)	0.481 (1.00)	0.753 (1.00)	2.38e-13 (2.32e-10)	7.33e-05 (0.0672)	0.457 (1.00)	0.382 (1.00)	0.458 (1.00)	0.985 (1.00)	1 (1.00)	0.379 (1.00)	0.664 (1.00)	0.374 (1.00)
Amp Peak 28(20p13)	0 (0%)	259	0.257 (1.00)	0.154 (1.00)	0.174 (1.00)	0.0563 (1.00)	1.18e-11 (1.14e-08)	3.25e-05 (0.03)	0.321 (1.00)	0.971 (1.00)	0.0716 (1.00)	0.686 (1.00)	0.242 (1.00)	0.896 (1.00)	0.723 (1.00)	0.299 (1.00)
Amp Peak 30(20q13 33)	0 (0%)	177	0.0096 (1.00)	0.00373 (1.00)	0.739 (1.00)	0.364 (1.00)	1.82e-17 (1.78e-14)	8.5e-08 (8.09e-05)	0.899 (1.00)	0.56 (1.00)	0.008 (1.00)	0.793 (1.00)	0.476 (1.00)	0.604 (1.00)	0.689 (1.00)	0.319 (1.00)
Amp Peak 32(Xp11 23)	0 (0%)	406	0.943 (1.00)	0.306 (1.00)	0.286 (1.00)	0.0383 (1.00)	3.29e-06 (0.00309)	8.73e-05 (0.0799)	0.703 (1.00)	0.222 (1.00)	0.286 (1.00)	0.216 (1.00)	0.365 (1.00)	0.879 (1.00)	0.467 (1.00)	0.72 (1.00)
Del Peak 5(2q37 3)	0 (0%)	396	0.016 (1.00)	0.0633 (1.00)	0.526 (1.00)	9.03e-05 (0.0825)	3.33e-05 (0.0307)	0.124 (1.00)	0.725 (1.00)	0.894 (1.00)	0.0199 (1.00)	0.0289 (1.00)	0.0187 (1.00)	0.0125 (1.00)	0.0728 (1.00)	0.0275 (1.00)
Del Peak 6(3p26 2)	0 (0%)	359	0.146 (1.00)	0.0352 (1.00)	0.0152 (1.00)	0.108 (1.00)	7.95e-05 (0.0728)	0.000226 (0.205)	0.97 (1.00)	0.0949 (1.00)	0.00312 (1.00)	0.674 (1.00)	0.628 (1.00)	0.611 (1.00)	0.959 (1.00)	0.0249 (1.00)
Del Peak 23(13q14 2)	0 (0%)	215	0.00355 (1.00)	0.0252 (1.00)	0.612 (1.00)	0.885 (1.00)	6.63e-07 (0.000626)	4.32e-05 (0.0397)	0.0014 (1.00)	0.000807 (0.719)	0.0989 (1.00)	0.25 (1.00)	0.375 (1.00)	0.891 (1.00)	0.451 (1.00)	0.657 (1.00)
Del Peak 25(15q15 1)	0 (0%)	212	0.0287 (1.00)	0.0195 (1.00)	0.0111 (1.00)	0.00618 (1.00)	2.12e-11 (2.05e-08)	7.21e-06 (0.00672)	0.121 (1.00)	0.0456 (1.00)	0.018 (1.00)	0.768 (1.00)	0.464 (1.00)	0.676 (1.00)	0.243 (1.00)	0.214 (1.00)
Amp Peak 1(1p34 3)	0 (0%)	288	0.285 (1.00)	0.138 (1.00)	0.072 (1.00)	0.2 (1.00)	4.75e-06 (0.00445)	0.153 (1.00)	0.121 (1.00)	0.784 (1.00)	0.602 (1.00)	0.104 (1.00)	0.0694 (1.00)	0.0922 (1.00)	0.0479 (1.00)	0.536 (1.00)
Amp Peak 4(2p23 2)	0 (0%)	330	0.302 (1.00)	0.169 (1.00)	0.409 (1.00)	0.0501 (1.00)	2.19e-08 (2.08e-05)	0.00449 (1.00)	0.223 (1.00)	0.658 (1.00)	0.0316 (1.00)	0.751 (1.00)	0.911 (1.00)	0.115 (1.00)	0.96 (1.00)	0.638 (1.00)
Amp Peak 5(2q31 2)	0 (0%)	319	0.0474 (1.00)	0.0865 (1.00)	0.151 (1.00)	0.325 (1.00)	1.9e-10 (1.83e-07)	0.00277 (1.00)	0.0575 (1.00)	0.507 (1.00)	0.229 (1.00)	0.522 (1.00)	0.456 (1.00)	0.664 (1.00)	0.218 (1.00)	0.0856 (1.00)
Amp Peak 6(3q26 2)	0 (0%)	96	0.00705 (1.00)	0.057 (1.00)	0.637 (1.00)	0.0954 (1.00)	4.01e-11 (3.87e-08)	0.0835 (1.00)	0.554 (1.00)	0.553 (1.00)	0.0166 (1.00)	0.0463 (1.00)	0.123 (1.00)	0.432 (1.00)	0.562 (1.00)	0.659 (1.00)
Amp Peak 7(4p16 3)	0 (0%)	414	0.955 (1.00)	0.473 (1.00)	0.0447 (1.00)	0.927 (1.00)	0.000103 (0.0938)	0.0421 (1.00)	0.244 (1.00)	0.769 (1.00)	0.75 (1.00)	0.455 (1.00)	0.644 (1.00)	0.664 (1.00)	0.676 (1.00)	0.422 (1.00)
Amp Peak 8(4q13 3)	0 (0%)	464	0.887 (1.00)	0.98 (1.00)	0.245 (1.00)	0.934 (1.00)	4.59e-06 (0.0043)	0.117 (1.00)	0.312 (1.00)	0.149 (1.00)	0.148 (1.00)	0.935 (1.00)	0.976 (1.00)	0.108 (1.00)	0.829 (1.00)	0.48 (1.00)
Amp Peak 9(5p15 33)	0 (0%)	270	0.667 (1.00)	0.928 (1.00)	0.862 (1.00)	0.0404 (1.00)	2.26e-07 (0.000215)	0.0614 (1.00)	0.982 (1.00)	0.477 (1.00)	0.175 (1.00)	0.927 (1.00)	0.0138 (1.00)	0.436 (1.00)	0.0677 (1.00)	0.382 (1.00)
Amp Peak 10(6p22 3)	0 (0%)	278	0.0861 (1.00)	0.0425 (1.00)	0.67 (1.00)	0.417 (1.00)	1.69e-09 (1.61e-06)	0.127 (1.00)	0.0709 (1.00)	0.053 (1.00)	0.833 (1.00)	0.0709 (1.00)	0.304 (1.00)	0.434 (1.00)	0.124 (1.00)	0.295 (1.00)
Amp Peak 11(7q36 3)	0 (0%)	265	0.0677 (1.00)	0.0359 (1.00)	0.513 (1.00)	0.953 (1.00)	7.02e-06 (0.00655)	0.412 (1.00)	0.0683 (1.00)	0.242 (1.00)	0.962 (1.00)	0.764 (1.00)	0.165 (1.00)	0.143 (1.00)	0.0227 (1.00)	0.211 (1.00)
Amp Peak 12(8p11 21)	0 (0%)	367	0.0688 (1.00)	0.136 (1.00)	0.117 (1.00)	0.263 (1.00)	8.83e-08 (8.39e-05)	0.00351 (1.00)	0.0365 (1.00)	0.262 (1.00)	0.352 (1.00)	0.216 (1.00)	0.905 (1.00)	0.672 (1.00)	0.599 (1.00)	0.693 (1.00)
Amp Peak 16(11q14 1)	0 (0%)	319	0.00648 (1.00)	0.005 (1.00)	0.563 (1.00)	0.213 (1.00)	1.19e-09 (1.14e-06)	0.0211 (1.00)	0.6 (1.00)	0.222 (1.00)	0.00378 (1.00)	0.00405 (1.00)	0.205 (1.00)	0.827 (1.00)	0.233 (1.00)	0.9 (1.00)
Amp Peak 21(14q32 33)	0 (0%)	419	0.271 (1.00)	0.0496 (1.00)	0.742 (1.00)	0.287 (1.00)	0.000155 (0.14)	0.318 (1.00)	1 (1.00)	0.671 (1.00)	0.185 (1.00)	0.578 (1.00)	0.508 (1.00)	0.78 (1.00)	0.513 (1.00)	0.584 (1.00)
Amp Peak 22(15q26 3)	0 (0%)	413	0.0908 (1.00)	0.196 (1.00)	0.82 (1.00)	0.725 (1.00)	8.69e-10 (8.34e-07)	0.757 (1.00)	0.978 (1.00)	0.253 (1.00)	0.157 (1.00)	0.945 (1.00)	0.119 (1.00)	0.363 (1.00)	0.181 (1.00)	0.404 (1.00)
Amp Peak 24(18q11 2)	0 (0%)	431	0.876 (1.00)	0.699 (1.00)	0.819 (1.00)	0.614 (1.00)	1.83e-06 (0.00172)	0.00932 (1.00)	0.205 (1.00)	0.453 (1.00)	0.0427 (1.00)	0.109 (1.00)	0.313 (1.00)	0.825 (1.00)	0.317 (1.00)	0.469 (1.00)
Amp Peak 33(Xq28)	0 (0%)	346	0.137 (1.00)	0.384 (1.00)	0.702 (1.00)	0.464 (1.00)	1.93e-05 (0.0179)	0.115 (1.00)	0.359 (1.00)	0.791 (1.00)	0.549 (1.00)	0.435 (1.00)	0.917 (1.00)	0.0119 (1.00)	0.891 (1.00)	0.821 (1.00)
Del Peak 1(1p36 11)	0 (0%)	304	0.907 (1.00)	0.694 (1.00)	0.125 (1.00)	0.606 (1.00)	3.32e-06 (0.00312)	0.0462 (1.00)	0.189 (1.00)	0.416 (1.00)	0.961 (1.00)	0.807 (1.00)	0.221 (1.00)	0.144 (1.00)	0.345 (1.00)	0.161 (1.00)
Del Peak 2(1q32 3)	0 (0%)	475	0.0823 (1.00)	0.237 (1.00)	0.467 (1.00)	0.459 (1.00)	3.46e-07 (0.000327)	0.227 (1.00)	0.781 (1.00)	0.105 (1.00)	0.115 (1.00)	0.33 (1.00)	0.897 (1.00)	0.57 (1.00)	0.958 (1.00)	0.857 (1.00)
Del Peak 9(5q11 2)	0 (0%)	228	0.77 (1.00)	0.593 (1.00)	0.198 (1.00)	0.264 (1.00)	2.69e-07 (0.000255)	0.000528 (0.476)	0.731 (1.00)	0.852 (1.00)	0.182 (1.00)	0.128 (1.00)	0.0341 (1.00)	0.000558 (0.503)	0.0153 (1.00)	0.0119 (1.00)
Del Peak 10(5q13 2)	0 (0%)	163	0.699 (1.00)	0.499 (1.00)	0.847 (1.00)	0.477 (1.00)	3.89e-11 (3.76e-08)	0.122 (1.00)	0.762 (1.00)	0.824 (1.00)	0.354 (1.00)	0.00303 (1.00)	0.121 (1.00)	0.00885 (1.00)	0.103 (1.00)	0.0683 (1.00)
Del Peak 12(7p22 1)	0 (0%)	323	0.26 (1.00)	0.694 (1.00)	0.61 (1.00)	0.827 (1.00)	1.4e-13 (1.37e-10)	0.802 (1.00)	0.801 (1.00)	0.782 (1.00)	0.282 (1.00)	0.104 (1.00)	0.328 (1.00)	0.564 (1.00)	0.668 (1.00)	0.564 (1.00)
Del Peak 13(8p23 3)	0 (0%)	188	0.101 (1.00)	0.26 (1.00)	0.788 (1.00)	0.00314 (1.00)	5.63e-11 (5.43e-08)	0.15 (1.00)	0.873 (1.00)	0.616 (1.00)	0.895 (1.00)	0.6 (1.00)	0.235 (1.00)	0.159 (1.00)	0.187 (1.00)	0.402 (1.00)
Del Peak 14(8p21 2)	0 (0%)	171	0.0658 (1.00)	0.248 (1.00)	0.116 (1.00)	0.00222 (1.00)	1.35e-08 (1.29e-05)	0.202 (1.00)	0.794 (1.00)	0.848 (1.00)	0.36 (1.00)	0.25 (1.00)	0.541 (1.00)	0.484 (1.00)	0.901 (1.00)	0.976 (1.00)
Del Peak 15(9p24 3)	0 (0%)	315	0.000905 (0.804)	0.00583 (1.00)	0.679 (1.00)	0.0112 (1.00)	0.0123 (1.00)	6.6e-05 (0.0606)	0.452 (1.00)	0.597 (1.00)	0.0726 (1.00)	0.0746 (1.00)	0.0879 (1.00)	0.137 (1.00)	0.059 (1.00)	0.133 (1.00)
Del Peak 16(9q34 13)	0 (0%)	232	0.0166 (1.00)	0.0196 (1.00)	0.915 (1.00)	0.0157 (1.00)	6.63e-07 (0.000626)	0.0578 (1.00)	0.344 (1.00)	0.371 (1.00)	0.272 (1.00)	1 (1.00)	0.0371 (1.00)	0.0995 (1.00)	0.102 (1.00)	0.057 (1.00)
Del Peak 18(10q23 31)	0 (0%)	350	0.222 (1.00)	0.00258 (1.00)	0.000124 (0.113)	0.719 (1.00)	0.000662 (0.594)	0.0012 (1.00)	0.036 (1.00)	0.0121 (1.00)	0.961 (1.00)	0.502 (1.00)	0.0735 (1.00)	0.383 (1.00)	0.0836 (1.00)	0.165 (1.00)
Del Peak 19(10q26 3)	0 (0%)	381	0.00621 (1.00)	0.000636 (0.572)	0.154 (1.00)	0.26 (1.00)	1.53e-05 (0.0142)	0.155 (1.00)	0.0924 (1.00)	0.0135 (1.00)	0.0603 (1.00)	0.122 (1.00)	0.0163 (1.00)	0.221 (1.00)	0.0513 (1.00)	0.233 (1.00)
Del Peak 20(11p15 5)	0 (0%)	231	0.0704 (1.00)	0.279 (1.00)	0.769 (1.00)	0.242 (1.00)	1.89e-11 (1.83e-08)	0.0249 (1.00)	0.963 (1.00)	0.596 (1.00)	0.717 (1.00)	0.272 (1.00)	0.129 (1.00)	0.024 (1.00)	0.157 (1.00)	0.284 (1.00)
Del Peak 22(12q24 33)	0 (0%)	353	0.000695 (0.623)	0.00058 (0.522)	0.212 (1.00)	0.00404 (1.00)	2.18e-09 (2.08e-06)	0.0154 (1.00)	0.381 (1.00)	0.502 (1.00)	0.07 (1.00)	0.00314 (1.00)	0.0172 (1.00)	0.00569 (1.00)	0.0211 (1.00)	0.00977 (1.00)
Del Peak 24(14q23 3)	0 (0%)	272	0.0295 (1.00)	0.116 (1.00)	0.596 (1.00)	0.815 (1.00)	6.12e-05 (0.0563)	0.537 (1.00)	0.185 (1.00)	0.247 (1.00)	0.856 (1.00)	0.201 (1.00)	0.803 (1.00)	0.662 (1.00)	0.585 (1.00)	0.209 (1.00)
Del Peak 27(16q22 1)	0 (0%)	118	0.492 (1.00)	0.894 (1.00)	0.0376 (1.00)	0.372 (1.00)	0.000257 (0.233)	0.576 (1.00)	0.552 (1.00)	0.359 (1.00)	0.303 (1.00)	0.305 (1.00)	0.412 (1.00)	0.126 (1.00)	0.0747 (1.00)	0.19 (1.00)
Del Peak 28(16q23 1)	0 (0%)	127	0.121 (1.00)	0.228 (1.00)	0.122 (1.00)	0.171 (1.00)	0.000129 (0.117)	0.604 (1.00)	0.602 (1.00)	0.925 (1.00)	0.395 (1.00)	0.449 (1.00)	0.0892 (1.00)	0.0393 (1.00)	0.0668 (1.00)	0.0569 (1.00)
Del Peak 34(19q13 43)	0 (0%)	290	0.0432 (1.00)	0.00799 (1.00)	0.155 (1.00)	0.0508 (1.00)	0.00464 (1.00)	0.000108 (0.0981)	0.178 (1.00)	0.278 (1.00)	0.555 (1.00)	0.154 (1.00)	0.527 (1.00)	0.455 (1.00)	0.427 (1.00)	0.619 (1.00)
Amp Peak 15(10q22 3)	0 (0%)	394	0.786 (1.00)	0.693 (1.00)	0.652 (1.00)	0.116 (1.00)	0.355 (1.00)	0.993 (1.00)	0.527 (1.00)	0.978 (1.00)	0.0749 (1.00)	0.332 (1.00)	0.112 (1.00)	0.151 (1.00)	0.69 (1.00)	0.336 (1.00)
Amp Peak 20(14q11 2)	0 (0%)	426	0.00723 (1.00)	0.0334 (1.00)	0.374 (1.00)	0.00451 (1.00)	0.0458 (1.00)	0.228 (1.00)	0.393 (1.00)	0.288 (1.00)	0.255 (1.00)	0.333 (1.00)	0.234 (1.00)	0.335 (1.00)	0.267 (1.00)	0.279 (1.00)
Amp Peak 23(17q25 3)	0 (0%)	362	0.531 (1.00)	0.847 (1.00)	0.831 (1.00)	0.125 (1.00)	0.00258 (1.00)	0.904 (1.00)	0.0936 (1.00)	0.112 (1.00)	0.0162 (1.00)	0.0241 (1.00)	0.406 (1.00)	0.169 (1.00)	0.332 (1.00)	0.134 (1.00)
Amp Peak 31(22q12 2)	0 (0%)	482	0.491 (1.00)	0.487 (1.00)	0.105 (1.00)	0.0165 (1.00)	0.000725 (0.648)	0.00145 (1.00)	1 (1.00)	0.0575 (1.00)	0.0986 (1.00)	0.195 (1.00)	0.101 (1.00)	0.0114 (1.00)	0.0489 (1.00)	0.0395 (1.00)
Del Peak 3(2p25 3)	0 (0%)	452	0.982 (1.00)	0.928 (1.00)	0.213 (1.00)	0.524 (1.00)	0.286 (1.00)	0.739 (1.00)	0.149 (1.00)	0.112 (1.00)	0.0501 (1.00)	0.734 (1.00)	0.905 (1.00)	0.506 (1.00)	0.933 (1.00)	0.553 (1.00)
Del Peak 4(2q22 1)	0 (0%)	436	0.115 (1.00)	0.299 (1.00)	0.416 (1.00)	0.00732 (1.00)	0.0383 (1.00)	0.361 (1.00)	0.281 (1.00)	0.71 (1.00)	0.983 (1.00)	0.357 (1.00)	0.567 (1.00)	0.574 (1.00)	0.565 (1.00)	0.154 (1.00)
Del Peak 7(4q22 1)	0 (0%)	186	0.0502 (1.00)	0.316 (1.00)	0.907 (1.00)	0.253 (1.00)	0.0458 (1.00)	0.58 (1.00)	0.0593 (1.00)	0.00908 (1.00)	0.109 (1.00)	0.424 (1.00)	0.195 (1.00)	0.00733 (1.00)	0.0227 (1.00)	0.119 (1.00)
Del Peak 8(4q34 3)	0 (0%)	157	0.0215 (1.00)	0.0239 (1.00)	0.0108 (1.00)	0.368 (1.00)	0.283 (1.00)	0.694 (1.00)	0.429 (1.00)	0.211 (1.00)	0.0851 (1.00)	0.0303 (1.00)	0.337 (1.00)	0.177 (1.00)	0.117 (1.00)	0.252 (1.00)
Del Peak 17(10p15 3)	0 (0%)	449	0.094 (1.00)	0.103 (1.00)	0.0364 (1.00)	0.0426 (1.00)	0.101 (1.00)	0.36 (1.00)	0.283 (1.00)	0.0688 (1.00)	0.0145 (1.00)	0.0607 (1.00)	0.255 (1.00)	0.338 (1.00)	0.113 (1.00)	0.288 (1.00)
Del Peak 21(11q25)	0 (0%)	374	0.8 (1.00)	0.321 (1.00)	0.27 (1.00)	0.462 (1.00)	0.0529 (1.00)	0.554 (1.00)	0.32 (1.00)	0.175 (1.00)	0.931 (1.00)	0.877 (1.00)	0.597 (1.00)	0.138 (1.00)	0.589 (1.00)	0.212 (1.00)
Del Peak 26(16p13 3)	0 (0%)	267	0.467 (1.00)	0.0692 (1.00)	0.124 (1.00)	0.183 (1.00)	0.0759 (1.00)	0.414 (1.00)	0.921 (1.00)	0.239 (1.00)	0.508 (1.00)	0.786 (1.00)	0.204 (1.00)	0.852 (1.00)	0.0969 (1.00)	0.813 (1.00)
Del Peak 29(17p12)	0 (0%)	89	0.181 (1.00)	0.0213 (1.00)	0.943 (1.00)	0.862 (1.00)	0.802 (1.00)	0.289 (1.00)	0.938 (1.00)	0.362 (1.00)	0.187 (1.00)	0.515 (1.00)	0.61 (1.00)	0.621 (1.00)	0.551 (1.00)	0.833 (1.00)
Del Peak 30(17q11 2)	0 (0%)	104	0.951 (1.00)	0.0434 (1.00)	0.765 (1.00)	0.0766 (1.00)	0.000711 (0.637)	0.00498 (1.00)	0.767 (1.00)	0.0666 (1.00)	0.377 (1.00)	0.571 (1.00)	0.202 (1.00)	0.565 (1.00)	0.0398 (1.00)	0.427 (1.00)
Del Peak 31(18q23)	0 (0%)	197	1 (1.00)	0.98 (1.00)	0.0884 (1.00)	0.178 (1.00)	0.00208 (1.00)	0.439 (1.00)	0.228 (1.00)	0.275 (1.00)	0.22 (1.00)	0.398 (1.00)	0.689 (1.00)	0.689 (1.00)	0.123 (1.00)	0.793 (1.00)
Del Peak 32(19p13 3)	0 (0%)	68	0.386 (1.00)	0.0294 (1.00)	0.852 (1.00)	0.54 (1.00)	0.0024 (1.00)	0.0127 (1.00)	0.592 (1.00)	0.229 (1.00)	0.333 (1.00)	0.0157 (1.00)	0.476 (1.00)	0.85 (1.00)	0.44 (1.00)	0.899 (1.00)
Del Peak 33(19q13 33)	0 (0%)	275	0.00188 (1.00)	0.000765 (0.683)	0.0222 (1.00)	0.159 (1.00)	0.081 (1.00)	0.00585 (1.00)	0.0342 (1.00)	0.214 (1.00)	0.00784 (1.00)	0.0844 (1.00)	0.259 (1.00)	0.151 (1.00)	0.244 (1.00)	0.432 (1.00)
Del Peak 35(21q22 3)	0 (0%)	348	0.435 (1.00)	0.533 (1.00)	0.535 (1.00)	0.578 (1.00)	0.755 (1.00)	0.266 (1.00)	0.579 (1.00)	0.626 (1.00)	0.189 (1.00)	0.272 (1.00)	0.74 (1.00)	0.652 (1.00)	0.185 (1.00)	0.411 (1.00)
Del Peak 36(22q13 32)	0 (0%)	76	0.109 (1.00)	0.0478 (1.00)	0.0436 (1.00)	0.0258 (1.00)	0.0149 (1.00)	0.0667 (1.00)	0.0711 (1.00)	0.349 (1.00)	0.068 (1.00)	0.18 (1.00)	0.0236 (1.00)	0.296 (1.00)	0.0202 (1.00)	0.48 (1.00)
Del Peak 37(Xp21 1)	0 (0%)	206	0.276 (1.00)	0.881 (1.00)	0.12 (1.00)	0.452 (1.00)	0.0818 (1.00)	0.0285 (1.00)	0.323 (1.00)	0.0434 (1.00)	0.908 (1.00)	0.409 (1.00)	0.936 (1.00)	0.43 (1.00)	0.702 (1.00)	0.476 (1.00)

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

P value = 4.75e-06 (Fisher's exact test), Q value = 0.0044

Table S1. Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 1(1P34.3) CNV	55	116	111
AMP PEAK 1(1P34.3) WILD-TYPE	110	89	89

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 2.93e-11 (Fisher's exact test), Q value = 2.8e-08

Table S2. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 2(1Q21.3) CNV	81	114	162
AMP PEAK 2(1Q21.3) WILD-TYPE	84	91	38

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 0.000103 (Fisher's exact test), Q value = 0.094

Table S3. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 2(1Q21.3) CNV	135	88	134
AMP PEAK 2(1Q21.3) WILD-TYPE	47	80	85

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 3(1q42.2)' versus 'CN_CNMF'

P value = 5.55e-09 (Fisher's exact test), Q value = 5.3e-06

Table S4. Gene #3: 'Amp Peak 3(1q42.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 3(1Q42.2) CNV	84	86	143
AMP PEAK 3(1Q42.2) WILD-TYPE	81	119	57

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(1q42.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 3(1q42.2)' versus 'METHLYATION_CNMF'

P value = 5.89e-06 (Fisher's exact test), Q value = 0.0055

Table S5. Gene #3: 'Amp Peak 3(1q42.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 3(1Q42.2) CNV	127	82	104
AMP PEAK 3(1Q42.2) WILD-TYPE	55	86	115

Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(1q42.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 4(2p23.2)' versus 'CN_CNMF'

P value = 2.19e-08 (Fisher's exact test), Q value = 2.1e-05

Table S6. Gene #4: 'Amp Peak 4(2p23.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 4(2P23.2) CNV	42	86	112
AMP PEAK 4(2P23.2) WILD-TYPE	123	119	88

Figure S6. Get High-res Image Gene #4: 'Amp Peak 4(2p23.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 5(2q31.2)' versus 'CN_CNMF'

P value = 1.9e-10 (Fisher's exact test), Q value = 1.8e-07

Table S7. Gene #5: 'Amp Peak 5(2q31.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 5(2Q31.2) CNV	38	102	111
AMP PEAK 5(2Q31.2) WILD-TYPE	127	103	89

Figure S7. Get High-res Image Gene #5: 'Amp Peak 5(2q31.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 6(3q26.2)' versus 'CN_CNMF'

P value = 4.01e-11 (Fisher's exact test), Q value = 3.9e-08

Table S8. Gene #6: 'Amp Peak 6(3q26.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 6(3Q26.2) CNV	109	179	186
AMP PEAK 6(3Q26.2) WILD-TYPE	56	26	14

Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(3q26.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 7(4p16.3)' versus 'CN_CNMF'

P value = 0.000103 (Fisher's exact test), Q value = 0.094

Table S9. Gene #7: 'Amp Peak 7(4p16.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 7(4P16.3) CNV	30	77	49
AMP PEAK 7(4P16.3) WILD-TYPE	135	128	151

Figure S9. Get High-res Image Gene #7: 'Amp Peak 7(4p16.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 8(4q13.3)' versus 'CN_CNMF'

P value = 4.59e-06 (Fisher's exact test), Q value = 0.0043

Table S10. Gene #8: 'Amp Peak 8(4q13.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 8(4Q13.3) CNV	12	54	40
AMP PEAK 8(4Q13.3) WILD-TYPE	153	151	160

Figure S10. Get High-res Image Gene #8: 'Amp Peak 8(4q13.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 9(5p15.33)' versus 'CN_CNMF'

P value = 2.26e-07 (Fisher's exact test), Q value = 0.00021

Table S11. Gene #9: 'Amp Peak 9(5p15.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 9(5P15.33) CNV	57	123	120
AMP PEAK 9(5P15.33) WILD-TYPE	108	82	80

Figure S11. Get High-res Image Gene #9: 'Amp Peak 9(5p15.33)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.69e-09 (Fisher's exact test), Q value = 1.6e-06

Table S12. Gene #10: 'Amp Peak 10(6p22.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 10(6P22.3) CNV	51	128	113
AMP PEAK 10(6P22.3) WILD-TYPE	114	77	87

Figure S12. Get High-res Image Gene #10: 'Amp Peak 10(6p22.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 11(7q36.3)' versus 'CN_CNMF'

P value = 7.02e-06 (Fisher's exact test), Q value = 0.0066

Table S13. Gene #11: 'Amp Peak 11(7q36.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 11(7Q36.3) CNV	62	122	121
AMP PEAK 11(7Q36.3) WILD-TYPE	103	83	79

Figure S13. Get High-res Image Gene #11: 'Amp Peak 11(7q36.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 12(8p11.21)' versus 'CN_CNMF'

P value = 8.83e-08 (Fisher's exact test), Q value = 8.4e-05

Table S14. Gene #12: 'Amp Peak 12(8p11.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 12(8P11.21) CNV	35	69	99
AMP PEAK 12(8P11.21) WILD-TYPE	130	136	101

Figure S14. Get High-res Image Gene #12: 'Amp Peak 12(8p11.21)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 13(8q24.21)' versus 'MRNA_CNMF'

P value = 3.97e-07 (Fisher's exact test), Q value = 0.00038

Table S15. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	209	133
AMP PEAK 13(8Q24.21) CNV	144	179	116
AMP PEAK 13(8Q24.21) WILD-TYPE	72	30	17

Figure S15. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 13(8q24.21)' versus 'MRNA_CHIERARCHICAL'

P value = 1.57e-05 (Fisher's exact test), Q value = 0.015

Table S16. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	195	128
AMP PEAK 13(8Q24.21) CNV	192	133	114
AMP PEAK 13(8Q24.21) WILD-TYPE	43	62	14

Figure S16. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 13(8q24.21)' versus 'CN_CNMF'

P value = 1.76e-17 (Fisher's exact test), Q value = 1.7e-14

Table S17. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 13(8Q24.21) CNV	107	198	143
AMP PEAK 13(8Q24.21) WILD-TYPE	58	7	57

Figure S17. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 13(8q24.21)' versus 'MRNASEQ_CNMF'

P value = 4.52e-07 (Fisher's exact test), Q value = 0.00043

Table S18. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	67	91
AMP PEAK 13(8Q24.21) CNV	90	61	56
AMP PEAK 13(8Q24.21) WILD-TYPE	10	6	35

Figure S18. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'Amp Peak 13(8q24.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.46e-05 (Fisher's exact test), Q value = 0.023

Table S19. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	110	38
AMP PEAK 13(8Q24.21) CNV	74	97	36
AMP PEAK 13(8Q24.21) WILD-TYPE	36	13	2

Figure S19. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 14(10p15.3)' versus 'CN_CNMF'

P value = 4.15e-12 (Fisher's exact test), Q value = 4e-09

Table S20. Gene #14: 'Amp Peak 14(10p15.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 14(10P15.3) CNV	44	73	124
AMP PEAK 14(10P15.3) WILD-TYPE	121	132	76

Figure S20. Get High-res Image Gene #14: 'Amp Peak 14(10p15.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 14(10p15.3)' versus 'METHLYATION_CNMF'

P value = 2.85e-05 (Fisher's exact test), Q value = 0.026

Table S21. Gene #14: 'Amp Peak 14(10p15.3)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 14(10P15.3) CNV	102	59	79
AMP PEAK 14(10P15.3) WILD-TYPE	80	109	140

Figure S21. Get High-res Image Gene #14: 'Amp Peak 14(10p15.3)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 16(11q14.1)' versus 'CN_CNMF'

P value = 1.19e-09 (Fisher's exact test), Q value = 1.1e-06

Table S22. Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 16(11Q14.1) CNV	45	123	83
AMP PEAK 16(11Q14.1) WILD-TYPE	120	82	117

Figure S22. Get High-res Image Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 17(12p13.33)' versus 'CN_CNMF'

P value = 1.02e-10 (Fisher's exact test), Q value = 9.9e-08

Table S23. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 17(12P13.33) CNV	63	110	146
AMP PEAK 17(12P13.33) WILD-TYPE	102	95	54

Figure S23. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 17(12p13.33)' versus 'METHLYATION_CNMF'

P value = 3.04e-05 (Fisher's exact test), Q value = 0.028

Table S24. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 17(12P13.33) CNV	125	93	101
AMP PEAK 17(12P13.33) WILD-TYPE	57	75	118

Figure S24. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 18(12p12.1)' versus 'CN_CNMF'

P value = 9.05e-15 (Fisher's exact test), Q value = 8.8e-12

Table S25. Gene #18: 'Amp Peak 18(12p12.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 18(12P12.1) CNV	57	96	149
AMP PEAK 18(12P12.1) WILD-TYPE	108	109	51

Figure S25. Get High-res Image Gene #18: 'Amp Peak 18(12p12.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 18(12p12.1)' versus 'METHLYATION_CNMF'

P value = 5.73e-06 (Fisher's exact test), Q value = 0.0054

Table S26. Gene #18: 'Amp Peak 18(12p12.1)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 18(12P12.1) CNV	123	83	96
AMP PEAK 18(12P12.1) WILD-TYPE	59	85	123

Figure S26. Get High-res Image Gene #18: 'Amp Peak 18(12p12.1)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 19(12q15)' versus 'CN_CNMF'

P value = 1.43e-08 (Fisher's exact test), Q value = 1.4e-05

Table S27. Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 19(12Q15) CNV	50	54	107
AMP PEAK 19(12Q15) WILD-TYPE	115	151	93

Figure S27. Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 19(12q15)' versus 'METHLYATION_CNMF'

P value = 3.16e-05 (Fisher's exact test), Q value = 0.029

Table S28. Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 19(12Q15) CNV	91	57	62
AMP PEAK 19(12Q15) WILD-TYPE	91	111	157

Figure S28. Get High-res Image Gene #19: 'Amp Peak 19(12q15)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 21(14q32.33)' versus 'CN_CNMF'

P value = 0.000155 (Fisher's exact test), Q value = 0.14

Table S29. Gene #21: 'Amp Peak 21(14q32.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 21(14Q32.33) CNV	45	72	34
AMP PEAK 21(14Q32.33) WILD-TYPE	120	133	166

Figure S29. Get High-res Image Gene #21: 'Amp Peak 21(14q32.33)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 22(15q26.3)' versus 'CN_CNMF'

P value = 8.69e-10 (Fisher's exact test), Q value = 8.3e-07

Table S30. Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 22(15Q26.3) CNV	29	90	38
AMP PEAK 22(15Q26.3) WILD-TYPE	136	115	162

Figure S30. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 24(18q11.2)' versus 'CN_CNMF'

P value = 1.83e-06 (Fisher's exact test), Q value = 0.0017

Table S31. Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 24(18Q11.2) CNV	22	45	72
AMP PEAK 24(18Q11.2) WILD-TYPE	143	160	128

Figure S31. Get High-res Image Gene #24: 'Amp Peak 24(18q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 25(19p13.12)' versus 'MRNA_CHIERARCHICAL'

P value = 3.24e-06 (Fisher's exact test), Q value = 0.003

Table S32. Gene #25: 'Amp Peak 25(19p13.12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	235	195	128
AMP PEAK 25(19P13.12) CNV	132	123	45
AMP PEAK 25(19P13.12) WILD-TYPE	103	72	83

Figure S32. Get High-res Image Gene #25: 'Amp Peak 25(19p13.12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 25(19p13.12)' versus 'CN_CNMF'

P value = 6.6e-13 (Fisher's exact test), Q value = 6.4e-10

Table S33. Gene #25: 'Amp Peak 25(19p13.12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 25(19P13.12) CNV	66	91	149
AMP PEAK 25(19P13.12) WILD-TYPE	99	114	51

Figure S33. Get High-res Image Gene #25: 'Amp Peak 25(19p13.12)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 25(19p13.12)' versus 'METHLYATION_CNMF'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0013

Table S34. Gene #25: 'Amp Peak 25(19p13.12)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 25(19P13.12) CNV	124	69	112
AMP PEAK 25(19P13.12) WILD-TYPE	58	99	107

Figure S34. Get High-res Image Gene #25: 'Amp Peak 25(19p13.12)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

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

P value = 9.11e-29 (Fisher's exact test), Q value = 8.9e-26

Table S35. Gene #26: 'Amp Peak 26(19q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 26(19Q12) CNV	58	85	172
AMP PEAK 26(19Q12) WILD-TYPE	107	120	28

Figure S35. Get High-res Image Gene #26: 'Amp Peak 26(19q12)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 2.19e-10 (Fisher's exact test), Q value = 2.1e-07

Table S36. Gene #26: 'Amp Peak 26(19q12)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 26(19Q12) CNV	133	64	118
AMP PEAK 26(19Q12) WILD-TYPE	49	104	101

Figure S36. Get High-res Image Gene #26: 'Amp Peak 26(19q12)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 27(19q13.2)' versus 'CN_CNMF'

P value = 2.38e-13 (Fisher's exact test), Q value = 2.3e-10

Table S37. Gene #27: 'Amp Peak 27(19q13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 27(19Q13.2) CNV	44	69	126
AMP PEAK 27(19Q13.2) WILD-TYPE	121	136	74

Figure S37. Get High-res Image Gene #27: 'Amp Peak 27(19q13.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 27(19q13.2)' versus 'METHLYATION_CNMF'

P value = 7.33e-05 (Fisher's exact test), Q value = 0.067

Table S38. Gene #27: 'Amp Peak 27(19q13.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 27(19Q13.2) CNV	97	51	91
AMP PEAK 27(19Q13.2) WILD-TYPE	85	117	128

Figure S38. Get High-res Image Gene #27: 'Amp Peak 27(19q13.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 28(20p13)' versus 'CN_CNMF'

P value = 1.18e-11 (Fisher's exact test), Q value = 1.1e-08

Table S39. Gene #28: 'Amp Peak 28(20p13)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 28(20P13) CNV	66	97	148
AMP PEAK 28(20P13) WILD-TYPE	99	108	52

Figure S39. Get High-res Image Gene #28: 'Amp Peak 28(20p13)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 28(20p13)' versus 'METHLYATION_CNMF'

P value = 3.25e-05 (Fisher's exact test), Q value = 0.03

Table S40. Gene #28: 'Amp Peak 28(20p13)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 28(20P13) CNV	124	78	108
AMP PEAK 28(20P13) WILD-TYPE	58	90	111

Figure S40. Get High-res Image Gene #28: 'Amp Peak 28(20p13)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 29(20q11.21)' versus 'CN_CNMF'

P value = 1.43e-25 (Fisher's exact test), Q value = 1.4e-22

Table S41. Gene #29: 'Amp Peak 29(20q11.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 29(20Q11.21) CNV	66	93	174
AMP PEAK 29(20Q11.21) WILD-TYPE	99	112	26

Figure S41. Get High-res Image Gene #29: 'Amp Peak 29(20q11.21)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 29(20q11.21)' versus 'METHLYATION_CNMF'

P value = 4.06e-12 (Fisher's exact test), Q value = 3.9e-09

Table S42. Gene #29: 'Amp Peak 29(20q11.21)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 29(20Q11.21) CNV	145	85	103
AMP PEAK 29(20Q11.21) WILD-TYPE	37	83	116

Figure S42. Get High-res Image Gene #29: 'Amp Peak 29(20q11.21)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 29(20q11.21)' versus 'MRNASEQ_CNMF'

P value = 0.000138 (Fisher's exact test), Q value = 0.12

Table S43. Gene #29: 'Amp Peak 29(20q11.21)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	67	91
AMP PEAK 29(20Q11.21) CNV	60	27	67
AMP PEAK 29(20Q11.21) WILD-TYPE	40	40	24

Figure S43. Get High-res Image Gene #29: 'Amp Peak 29(20q11.21)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'Amp Peak 30(20q13.33)' versus 'CN_CNMF'

P value = 1.82e-17 (Fisher's exact test), Q value = 1.8e-14

Table S44. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 30(20Q13.33) CNV	81	133	179
AMP PEAK 30(20Q13.33) WILD-TYPE	84	72	21

Figure S44. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 30(20q13.33)' versus 'METHLYATION_CNMF'

P value = 8.5e-08 (Fisher's exact test), Q value = 8.1e-05

Table S45. Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 30(20Q13.33) CNV	154	104	135
AMP PEAK 30(20Q13.33) WILD-TYPE	28	64	84

Figure S45. Get High-res Image Gene #30: 'Amp Peak 30(20q13.33)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 32(Xp11.23)' versus 'CN_CNMF'

P value = 3.29e-06 (Fisher's exact test), Q value = 0.0031

Table S46. Gene #32: 'Amp Peak 32(Xp11.23)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 32(XP11.23) CNV	28	55	81
AMP PEAK 32(XP11.23) WILD-TYPE	137	150	119

Figure S46. Get High-res Image Gene #32: 'Amp Peak 32(Xp11.23)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 32(Xp11.23)' versus 'METHLYATION_CNMF'

P value = 8.73e-05 (Fisher's exact test), Q value = 0.08

Table S47. Gene #32: 'Amp Peak 32(Xp11.23)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
AMP PEAK 32(XP11.23) CNV	74	35	55
AMP PEAK 32(XP11.23) WILD-TYPE	108	133	164

Figure S47. Get High-res Image Gene #32: 'Amp Peak 32(Xp11.23)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 33(Xq28)' versus 'CN_CNMF'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.018

Table S48. Gene #33: 'Amp Peak 33(Xq28)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
AMP PEAK 33(XQ28) CNV	42	100	82
AMP PEAK 33(XQ28) WILD-TYPE	123	105	118

Figure S48. Get High-res Image Gene #33: 'Amp Peak 33(Xq28)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 1(1p36.11)' versus 'CN_CNMF'

P value = 3.32e-06 (Fisher's exact test), Q value = 0.0031

Table S49. Gene #34: 'Del Peak 1(1p36.11)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 1(1P36.11) CNV	88	113	65
DEL PEAK 1(1P36.11) WILD-TYPE	77	92	135

Figure S49. Get High-res Image Gene #34: 'Del Peak 1(1p36.11)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 2(1q32.3)' versus 'CN_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00033

Table S50. Gene #35: 'Del Peak 2(1q32.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 2(1Q32.3) CNV	16	58	21
DEL PEAK 2(1Q32.3) WILD-TYPE	149	147	179

Figure S50. Get High-res Image Gene #35: 'Del Peak 2(1q32.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 5(2q37.3)' versus 'MIR_CHIERARCHICAL'

P value = 9.03e-05 (Fisher's exact test), Q value = 0.082

Table S51. Gene #38: 'Del Peak 5(2q37.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	179	220	157
DEL PEAK 5(2Q37.3) CNV	37	89	45
DEL PEAK 5(2Q37.3) WILD-TYPE	142	131	112

Figure S51. Get High-res Image Gene #38: 'Del Peak 5(2q37.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 5(2q37.3)' versus 'CN_CNMF'

P value = 3.33e-05 (Fisher's exact test), Q value = 0.031

Table S52. Gene #38: 'Del Peak 5(2q37.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 5(2Q37.3) CNV	35	86	53
DEL PEAK 5(2Q37.3) WILD-TYPE	130	119	147

Figure S52. Get High-res Image Gene #38: 'Del Peak 5(2q37.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 6(3p26.2)' versus 'CN_CNMF'

P value = 7.95e-05 (Fisher's exact test), Q value = 0.073

Table S53. Gene #39: 'Del Peak 6(3p26.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 6(3P26.2) CNV	45	69	97
DEL PEAK 6(3P26.2) WILD-TYPE	120	136	103

Figure S53. Get High-res Image Gene #39: 'Del Peak 6(3p26.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 6(3p26.2)' versus 'METHLYATION_CNMF'

P value = 0.000226 (Fisher's exact test), Q value = 0.2

Table S54. Gene #39: 'Del Peak 6(3p26.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
DEL PEAK 6(3P26.2) CNV	89	49	72
DEL PEAK 6(3P26.2) WILD-TYPE	93	119	147

Figure S54. Get High-res Image Gene #39: 'Del Peak 6(3p26.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Del Peak 9(5q11.2)' versus 'CN_CNMF'

P value = 2.69e-07 (Fisher's exact test), Q value = 0.00026

Table S55. Gene #42: 'Del Peak 9(5q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 9(5Q11.2) CNV	70	142	130
DEL PEAK 9(5Q11.2) WILD-TYPE	95	63	70

Figure S55. Get High-res Image Gene #42: 'Del Peak 9(5q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 10(5q13.2)' versus 'CN_CNMF'

P value = 3.89e-11 (Fisher's exact test), Q value = 3.8e-08

Table S56. Gene #43: 'Del Peak 10(5q13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 10(5Q13.2) CNV	88	176	143
DEL PEAK 10(5Q13.2) WILD-TYPE	77	29	57

Figure S56. Get High-res Image Gene #43: 'Del Peak 10(5q13.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 11(6q27)' versus 'CN_CNMF'

P value = 8.46e-09 (Fisher's exact test), Q value = 8.1e-06

Table S57. Gene #44: 'Del Peak 11(6q27)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 11(6Q27) CNV	121	159	101
DEL PEAK 11(6Q27) WILD-TYPE	44	46	99

Figure S57. Get High-res Image Gene #44: 'Del Peak 11(6q27)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 11(6q27)' versus 'METHLYATION_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.022

Table S58. Gene #44: 'Del Peak 11(6q27)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
DEL PEAK 11(6Q27) CNV	98	128	154
DEL PEAK 11(6Q27) WILD-TYPE	84	40	65

Figure S58. Get High-res Image Gene #44: 'Del Peak 11(6q27)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Del Peak 11(6q27)' versus 'MRNASEQ_CNMF'

P value = 2.69e-05 (Fisher's exact test), Q value = 0.025

Table S59. Gene #44: 'Del Peak 11(6q27)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	67	91
DEL PEAK 11(6Q27) CNV	68	51	39
DEL PEAK 11(6Q27) WILD-TYPE	32	16	52

Figure S59. Get High-res Image Gene #44: 'Del Peak 11(6q27)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'Del Peak 12(7p22.1)' versus 'CN_CNMF'

P value = 1.4e-13 (Fisher's exact test), Q value = 1.4e-10

Table S60. Gene #45: 'Del Peak 12(7p22.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 12(7P22.1) CNV	47	132	68
DEL PEAK 12(7P22.1) WILD-TYPE	118	73	132

Figure S60. Get High-res Image Gene #45: 'Del Peak 12(7p22.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 13(8p23.3)' versus 'CN_CNMF'

P value = 5.63e-11 (Fisher's exact test), Q value = 5.4e-08

Table S61. Gene #46: 'Del Peak 13(8p23.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 13(8P23.3) CNV	76	162	144
DEL PEAK 13(8P23.3) WILD-TYPE	89	43	56

Figure S61. Get High-res Image Gene #46: 'Del Peak 13(8p23.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 14(8p21.2)' versus 'CN_CNMF'

P value = 1.35e-08 (Fisher's exact test), Q value = 1.3e-05

Table S62. Gene #47: 'Del Peak 14(8p21.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 14(8P21.2) CNV	86	165	148
DEL PEAK 14(8P21.2) WILD-TYPE	79	40	52

Figure S62. Get High-res Image Gene #47: 'Del Peak 14(8p21.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 15(9p24.3)' versus 'METHLYATION_CNMF'

P value = 6.6e-05 (Fisher's exact test), Q value = 0.061

Table S63. Gene #48: 'Del Peak 15(9p24.3)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
DEL PEAK 15(9P24.3) CNV	96	86	73
DEL PEAK 15(9P24.3) WILD-TYPE	86	82	146

Figure S63. Get High-res Image Gene #48: 'Del Peak 15(9p24.3)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Del Peak 16(9q34.13)' versus 'CN_CNMF'

P value = 6.63e-07 (Fisher's exact test), Q value = 0.00063

Table S64. Gene #49: 'Del Peak 16(9q34.13)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 16(9Q34.13) CNV	86	104	148
DEL PEAK 16(9Q34.13) WILD-TYPE	79	101	52

Figure S64. Get High-res Image Gene #49: 'Del Peak 16(9q34.13)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 18(10q23.31)' versus 'MIR_CNMF'

P value = 0.000124 (Fisher's exact test), Q value = 0.11

Table S65. Gene #51: 'Del Peak 18(10q23.31)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	244	147
DEL PEAK 18(10Q23.31) CNV	59	116	39
DEL PEAK 18(10Q23.31) WILD-TYPE	106	128	108

Figure S65. Get High-res Image Gene #51: 'Del Peak 18(10q23.31)' versus Molecular Subtype #3: 'MIR_CNMF'

'Del Peak 19(10q26.3)' versus 'CN_CNMF'

P value = 1.53e-05 (Fisher's exact test), Q value = 0.014

Table S66. Gene #52: 'Del Peak 19(10q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 19(10Q26.3) CNV	32	85	72
DEL PEAK 19(10Q26.3) WILD-TYPE	133	120	128

Figure S66. Get High-res Image Gene #52: 'Del Peak 19(10q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.89e-11 (Fisher's exact test), Q value = 1.8e-08

Table S67. Gene #53: 'Del Peak 20(11p15.5)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 20(11P15.5) CNV	75	160	104
DEL PEAK 20(11P15.5) WILD-TYPE	90	45	96

Figure S67. Get High-res Image Gene #53: 'Del Peak 20(11p15.5)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 22(12q24.33)' versus 'CN_CNMF'

P value = 2.18e-09 (Fisher's exact test), Q value = 2.1e-06

Table S68. Gene #55: 'Del Peak 22(12q24.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 22(12Q24.33) CNV	55	112	50
DEL PEAK 22(12Q24.33) WILD-TYPE	110	93	150

Figure S68. Get High-res Image Gene #55: 'Del Peak 22(12q24.33)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 23(13q14.2)' versus 'CN_CNMF'

P value = 6.63e-07 (Fisher's exact test), Q value = 0.00063

Table S69. Gene #56: 'Del Peak 23(13q14.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 23(13Q14.2) CNV	84	156	115
DEL PEAK 23(13Q14.2) WILD-TYPE	81	49	85

Figure S69. Get High-res Image Gene #56: 'Del Peak 23(13q14.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 23(13q14.2)' versus 'METHLYATION_CNMF'

P value = 4.32e-05 (Fisher's exact test), Q value = 0.04

Table S70. Gene #56: 'Del Peak 23(13q14.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
DEL PEAK 23(13Q14.2) CNV	115	83	157
DEL PEAK 23(13Q14.2) WILD-TYPE	67	85	62

Figure S70. Get High-res Image Gene #56: 'Del Peak 23(13q14.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Del Peak 24(14q23.3)' versus 'CN_CNMF'

P value = 6.12e-05 (Fisher's exact test), Q value = 0.056

Table S71. Gene #57: 'Del Peak 24(14q23.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 24(14Q23.3) CNV	67	104	127
DEL PEAK 24(14Q23.3) WILD-TYPE	98	101	73

Figure S71. Get High-res Image Gene #57: 'Del Peak 24(14q23.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 25(15q15.1)' versus 'CN_CNMF'

P value = 2.12e-11 (Fisher's exact test), Q value = 2.1e-08

Table S72. Gene #58: 'Del Peak 25(15q15.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 25(15Q15.1) CNV	79	117	162
DEL PEAK 25(15Q15.1) WILD-TYPE	86	88	38

Figure S72. Get High-res Image Gene #58: 'Del Peak 25(15q15.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 25(15q15.1)' versus 'METHLYATION_CNMF'

P value = 7.21e-06 (Fisher's exact test), Q value = 0.0067

Table S73. Gene #58: 'Del Peak 25(15q15.1)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
DEL PEAK 25(15Q15.1) CNV	140	92	126
DEL PEAK 25(15Q15.1) WILD-TYPE	42	76	93

Figure S73. Get High-res Image Gene #58: 'Del Peak 25(15q15.1)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Del Peak 27(16q22.1)' versus 'CN_CNMF'

P value = 0.000257 (Fisher's exact test), Q value = 0.23

Table S74. Gene #60: 'Del Peak 27(16q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 27(16Q22.1) CNV	113	168	171
DEL PEAK 27(16Q22.1) WILD-TYPE	52	37	29

Figure S74. Get High-res Image Gene #60: 'Del Peak 27(16q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 28(16q23.1)' versus 'CN_CNMF'

P value = 0.000129 (Fisher's exact test), Q value = 0.12

Table S75. Gene #61: 'Del Peak 28(16q23.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	205	200
DEL PEAK 28(16Q23.1) CNV	109	166	168
DEL PEAK 28(16Q23.1) WILD-TYPE	56	39	32

Figure S75. Get High-res Image Gene #61: 'Del Peak 28(16q23.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 34(19q13.43)' versus 'METHLYATION_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.098

Table S76. Gene #67: 'Del Peak 34(19q13.43)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	182	168	219
DEL PEAK 34(19Q13.43) CNV	107	61	112
DEL PEAK 34(19Q13.43) WILD-TYPE	75	107	107

Figure S76. Get High-res Image Gene #67: 'Del Peak 34(19q13.43)' versus Molecular Subtype #6: 'METHLYATION_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 = OV-TP.transferedmergedcluster.txt
Number of patients = 570
Number of copy number variation regions = 70
Number of molecular subtypes = 14
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

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] 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)

[3] GISTIC_version2

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