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 69 peak regions and 14 molecular subtypes across 569 patients, 71 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(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 20(14q32.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(15q26.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 23(18q11.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 24(19p13.12) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
Amp Peak 25(19q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 26(19q13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 27(20p13) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 28(20q11.21) cnvs correlated to 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 29(20q13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 31(Xp11.23) cnvs correlated to 'CN_CNMF'.
Amp Peak 32(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 'CN_CNMF'.
Del Peak 6(3p26.2) cnvs correlated to 'CN_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 'CN_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 'MRNA_CHIERARCHICAL' and '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 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 69 regions and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 71 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	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	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 13(8q24 21)	0 (0%)	122	1.12e-07 (0.000105)	1.23e-05 (0.0113)	0.229 (1.00)	0.00313 (1.00)	2.31e-17 (2.22e-14)	0.00417 (1.00)	0.96 (1.00)	0.595 (1.00)	4.52e-07 (0.00042)	2.46e-05 (0.0226)	0.142 (1.00)	0.0406 (1.00)	0.15 (1.00)	0.114 (1.00)
Amp Peak 28(20q11 21)	0 (0%)	237	0.00328 (1.00)	0.00181 (1.00)	0.185 (1.00)	0.000105 (0.0951)	2.61e-24 (2.52e-21)	2.9e-11 (2.75e-08)	0.14 (1.00)	0.0392 (1.00)	0.000138 (0.124)	0.599 (1.00)	0.543 (1.00)	0.251 (1.00)	0.678 (1.00)	0.608 (1.00)
Amp Peak 24(19p13 12)	0 (0%)	263	0.000474 (0.421)	3.22e-07 (3e-04)	0.0461 (1.00)	0.052 (1.00)	1.02e-13 (9.83e-11)	2.61e-06 (0.00241)	0.000662 (0.584)	0.00378 (1.00)	0.215 (1.00)	0.27 (1.00)	0.482 (1.00)	0.595 (1.00)	0.923 (1.00)	0.613 (1.00)
Del Peak 11(6q27)	0 (0%)	188	0.151 (1.00)	0.0214 (1.00)	0.346 (1.00)	0.0164 (1.00)	3.86e-09 (3.64e-06)	2.56e-05 (0.0235)	0.428 (1.00)	0.917 (1.00)	2.69e-05 (0.0246)	0.25 (1.00)	0.457 (1.00)	0.945 (1.00)	0.526 (1.00)	0.512 (1.00)
Amp Peak 3(1q42 2)	0 (0%)	257	0.0422 (1.00)	0.051 (1.00)	0.941 (1.00)	0.0063 (1.00)	5.98e-09 (5.63e-06)	3.36e-05 (0.0307)	0.279 (1.00)	0.207 (1.00)	0.62 (1.00)	0.418 (1.00)	0.183 (1.00)	0.27 (1.00)	0.421 (1.00)	0.271 (1.00)
Amp Peak 14(10p15 3)	0 (0%)	328	0.865 (1.00)	0.585 (1.00)	0.0698 (1.00)	0.255 (1.00)	2.5e-12 (2.4e-09)	0.000149 (0.134)	0.562 (1.00)	0.408 (1.00)	0.344 (1.00)	0.306 (1.00)	0.465 (1.00)	0.945 (1.00)	0.764 (1.00)	0.893 (1.00)
Amp Peak 17(12p13 33)	0 (0%)	251	0.0385 (1.00)	0.141 (1.00)	0.29 (1.00)	0.0108 (1.00)	9.98e-11 (9.46e-08)	0.00022 (0.198)	0.314 (1.00)	0.614 (1.00)	0.0124 (1.00)	0.137 (1.00)	0.32 (1.00)	0.921 (1.00)	0.685 (1.00)	0.462 (1.00)
Amp Peak 18(12p12 1)	0 (0%)	268	0.246 (1.00)	0.109 (1.00)	0.843 (1.00)	0.0968 (1.00)	1.63e-13 (1.57e-10)	4.88e-05 (0.0444)	0.819 (1.00)	0.493 (1.00)	0.0214 (1.00)	0.133 (1.00)	0.202 (1.00)	0.7 (1.00)	0.488 (1.00)	0.507 (1.00)
Amp Peak 25(19q12)	0 (0%)	255	0.148 (1.00)	0.00608 (1.00)	0.0402 (1.00)	0.147 (1.00)	2.25e-29 (2.17e-26)	1.28e-09 (1.21e-06)	0.0803 (1.00)	0.82 (1.00)	0.551 (1.00)	0.86 (1.00)	0.335 (1.00)	0.596 (1.00)	0.811 (1.00)	0.631 (1.00)
Amp Peak 26(19q13 2)	0 (0%)	331	0.994 (1.00)	0.859 (1.00)	0.654 (1.00)	0.307 (1.00)	6.2e-12 (5.93e-09)	0.000162 (0.146)	0.457 (1.00)	0.382 (1.00)	0.458 (1.00)	0.985 (1.00)	1 (1.00)	0.379 (1.00)	0.836 (1.00)	0.358 (1.00)
Amp Peak 27(20p13)	0 (0%)	259	0.444 (1.00)	0.0582 (1.00)	0.133 (1.00)	0.0302 (1.00)	1.43e-11 (1.36e-08)	2.97e-05 (0.0271)	0.321 (1.00)	0.971 (1.00)	0.0716 (1.00)	0.686 (1.00)	0.242 (1.00)	0.896 (1.00)	0.0764 (1.00)	0.873 (1.00)
Amp Peak 29(20q13 33)	0 (0%)	177	0.00782 (1.00)	0.0175 (1.00)	0.599 (1.00)	0.00326 (1.00)	6.66e-18 (6.42e-15)	1.66e-06 (0.00154)	0.899 (1.00)	0.56 (1.00)	0.008 (1.00)	0.793 (1.00)	0.476 (1.00)	0.604 (1.00)	0.659 (1.00)	0.322 (1.00)
Del Peak 22(12q24 33)	0 (0%)	352	0.000809 (0.712)	0.000106 (0.0962)	0.216 (1.00)	0.0891 (1.00)	4.83e-10 (4.58e-07)	0.0206 (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)	0.0885 (1.00)	0.00668 (1.00)
Del Peak 23(13q14 2)	0 (0%)	214	0.00909 (1.00)	0.0184 (1.00)	0.723 (1.00)	0.683 (1.00)	1.29e-06 (0.0012)	3.31e-05 (0.0302)	0.0014 (1.00)	0.000807 (0.711)	0.0989 (1.00)	0.25 (1.00)	0.375 (1.00)	0.891 (1.00)	0.0293 (1.00)	0.751 (1.00)
Del Peak 25(15q15 1)	0 (0%)	212	0.0446 (1.00)	0.0143 (1.00)	0.0111 (1.00)	0.00626 (1.00)	2.28e-11 (2.17e-08)	1.96e-05 (0.018)	0.121 (1.00)	0.0456 (1.00)	0.018 (1.00)	0.768 (1.00)	0.464 (1.00)	0.676 (1.00)	0.372 (1.00)	0.676 (1.00)
Amp Peak 1(1p34 3)	0 (0%)	287	0.33 (1.00)	0.424 (1.00)	0.148 (1.00)	0.134 (1.00)	2.72e-06 (0.00252)	0.232 (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)	0.0826 (1.00)	0.265 (1.00)
Amp Peak 2(1q21 3)	0 (0%)	213	0.201 (1.00)	0.193 (1.00)	0.687 (1.00)	0.15 (1.00)	1.52e-11 (1.45e-08)	0.000547 (0.486)	0.0601 (1.00)	0.00999 (1.00)	0.628 (1.00)	0.28 (1.00)	0.916 (1.00)	0.972 (1.00)	0.436 (1.00)	0.917 (1.00)
Amp Peak 4(2p23 2)	0 (0%)	330	0.34 (1.00)	0.428 (1.00)	0.582 (1.00)	0.0135 (1.00)	5.72e-09 (5.39e-06)	0.0064 (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)	0.789 (1.00)	0.163 (1.00)
Amp Peak 5(2q31 2)	0 (0%)	319	0.0649 (1.00)	0.0667 (1.00)	0.0744 (1.00)	0.052 (1.00)	2.18e-11 (2.08e-08)	0.00511 (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)	0.377 (1.00)	0.665 (1.00)
Amp Peak 6(3q26 2)	0 (0%)	96	0.0134 (1.00)	0.00598 (1.00)	0.907 (1.00)	0.438 (1.00)	2.9e-11 (2.75e-08)	0.0361 (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)	0.591 (1.00)	0.368 (1.00)
Amp Peak 7(4p16 3)	0 (0%)	413	0.969 (1.00)	0.311 (1.00)	0.0518 (1.00)	0.694 (1.00)	4.24e-05 (0.0386)	0.0183 (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)	0.781 (1.00)	0.763 (1.00)
Amp Peak 8(4q13 3)	0 (0%)	463	0.868 (1.00)	0.878 (1.00)	0.354 (1.00)	0.175 (1.00)	1.06e-05 (0.00982)	0.385 (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)	0.963 (1.00)	0.408 (1.00)
Amp Peak 9(5p15 33)	0 (0%)	270	0.911 (1.00)	0.988 (1.00)	0.625 (1.00)	0.54 (1.00)	1.33e-07 (0.000125)	0.0847 (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)	0.168 (1.00)	0.414 (1.00)
Amp Peak 10(6p22 3)	0 (0%)	278	0.164 (1.00)	0.0703 (1.00)	0.249 (1.00)	0.156 (1.00)	1.59e-08 (1.49e-05)	0.0888 (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)	0.277 (1.00)	0.495 (1.00)
Amp Peak 11(7q36 3)	0 (0%)	265	0.0984 (1.00)	0.0902 (1.00)	0.262 (1.00)	0.588 (1.00)	1.25e-05 (0.0115)	0.244 (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)	0.121 (1.00)	0.188 (1.00)
Amp Peak 12(8p11 21)	0 (0%)	367	0.0437 (1.00)	0.0288 (1.00)	0.102 (1.00)	0.292 (1.00)	3.5e-07 (0.000326)	0.02 (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)	0.839 (1.00)	0.789 (1.00)
Amp Peak 16(11q14 1)	0 (0%)	318	0.00345 (1.00)	0.0324 (1.00)	0.847 (1.00)	0.294 (1.00)	5.31e-09 (5.01e-06)	0.00993 (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)	0.132 (1.00)	0.827 (1.00)
Amp Peak 20(14q32 33)	0 (0%)	418	0.38 (1.00)	0.422 (1.00)	0.198 (1.00)	0.823 (1.00)	0.000278 (0.249)	0.327 (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)	0.558 (1.00)	0.37 (1.00)
Amp Peak 21(15q26 3)	0 (0%)	412	0.0696 (1.00)	0.258 (1.00)	0.503 (1.00)	0.689 (1.00)	2.42e-09 (2.29e-06)	0.703 (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)	0.182 (1.00)	0.265 (1.00)
Amp Peak 23(18q11 2)	0 (0%)	430	0.943 (1.00)	0.868 (1.00)	0.976 (1.00)	0.527 (1.00)	3.4e-07 (0.000317)	0.00548 (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)	0.453 (1.00)	0.628 (1.00)
Amp Peak 31(Xp11 23)	0 (0%)	406	0.835 (1.00)	0.488 (1.00)	0.298 (1.00)	0.308 (1.00)	7.15e-06 (0.00661)	0.000426 (0.38)	0.703 (1.00)	0.222 (1.00)	0.286 (1.00)	0.216 (1.00)	0.365 (1.00)	0.879 (1.00)	0.566 (1.00)	0.629 (1.00)
Amp Peak 32(Xq28)	0 (0%)	345	0.136 (1.00)	0.277 (1.00)	0.832 (1.00)	0.117 (1.00)	4.73e-05 (0.043)	0.103 (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)	0.928 (1.00)	0.135 (1.00)
Del Peak 1(1p36 11)	0 (0%)	304	0.825 (1.00)	0.734 (1.00)	0.0385 (1.00)	0.326 (1.00)	1.88e-06 (0.00174)	0.0889 (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)	0.225 (1.00)	0.388 (1.00)
Del Peak 2(1q32 3)	0 (0%)	474	0.0793 (1.00)	0.596 (1.00)	0.477 (1.00)	0.11 (1.00)	3.05e-07 (0.000285)	0.342 (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)	1 (1.00)	0.509 (1.00)
Del Peak 5(2q37 3)	0 (0%)	395	0.0227 (1.00)	0.0381 (1.00)	0.612 (1.00)	0.0017 (1.00)	3.6e-05 (0.0329)	0.108 (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)	0.0624 (1.00)	0.00536 (1.00)
Del Peak 6(3p26 2)	0 (0%)	359	0.127 (1.00)	0.101 (1.00)	0.00412 (1.00)	0.0222 (1.00)	6.47e-05 (0.0587)	0.000355 (0.318)	0.97 (1.00)	0.0949 (1.00)	0.00312 (1.00)	0.674 (1.00)	0.628 (1.00)	0.611 (1.00)	1 (1.00)	0.545 (1.00)
Del Peak 9(5q11 2)	0 (0%)	228	0.896 (1.00)	0.487 (1.00)	0.425 (1.00)	0.206 (1.00)	4.69e-08 (4.4e-05)	0.000664 (0.586)	0.731 (1.00)	0.852 (1.00)	0.182 (1.00)	0.128 (1.00)	0.0341 (1.00)	0.000558 (0.495)	0.0373 (1.00)	0.00219 (1.00)
Del Peak 10(5q13 2)	0 (0%)	163	0.617 (1.00)	0.44 (1.00)	0.888 (1.00)	0.809 (1.00)	2.07e-12 (1.98e-09)	0.0936 (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)	0.203 (1.00)	0.0309 (1.00)
Del Peak 12(7p22 1)	0 (0%)	322	0.349 (1.00)	0.665 (1.00)	0.678 (1.00)	0.66 (1.00)	2.78e-13 (2.67e-10)	0.643 (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)	0.295 (1.00)	0.412 (1.00)
Del Peak 13(8p23 3)	0 (0%)	188	0.0579 (1.00)	0.275 (1.00)	0.629 (1.00)	0.0185 (1.00)	1.1e-11 (1.05e-08)	0.0395 (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)	0.311 (1.00)	0.115 (1.00)
Del Peak 14(8p21 2)	0 (0%)	171	0.0385 (1.00)	0.417 (1.00)	0.233 (1.00)	0.00956 (1.00)	1.1e-08 (1.04e-05)	0.109 (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)	0.614 (1.00)	0.486 (1.00)
Del Peak 15(9p24 3)	0 (0%)	314	0.000427 (0.38)	0.014 (1.00)	0.772 (1.00)	0.00914 (1.00)	0.0217 (1.00)	0.000119 (0.107)	0.452 (1.00)	0.597 (1.00)	0.0726 (1.00)	0.0746 (1.00)	0.0879 (1.00)	0.137 (1.00)	0.152 (1.00)	0.194 (1.00)
Del Peak 16(9q34 13)	0 (0%)	232	0.0223 (1.00)	0.0219 (1.00)	1 (1.00)	0.0188 (1.00)	2.94e-07 (0.000275)	0.0338 (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)	0.0924 (1.00)	0.0697 (1.00)
Del Peak 18(10q23 31)	0 (0%)	349	0.351 (1.00)	0.0544 (1.00)	0.000556 (0.493)	0.0125 (1.00)	0.000247 (0.221)	0.0019 (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)	0.396 (1.00)	0.421 (1.00)
Del Peak 19(10q26 3)	0 (0%)	380	0.00487 (1.00)	0.000602 (0.533)	0.25 (1.00)	0.405 (1.00)	1.08e-05 (0.00996)	0.13 (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)	0.151 (1.00)	0.142 (1.00)
Del Peak 20(11p15 5)	0 (0%)	231	0.107 (1.00)	0.451 (1.00)	0.729 (1.00)	0.0477 (1.00)	6.76e-12 (6.46e-09)	0.00882 (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)	0.145 (1.00)	0.0363 (1.00)
Del Peak 24(14q23 3)	0 (0%)	271	0.111 (1.00)	0.64 (1.00)	0.828 (1.00)	0.854 (1.00)	0.000143 (0.129)	0.562 (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)	0.66 (1.00)	0.763 (1.00)
Del Peak 28(16q23 1)	0 (0%)	127	0.0916 (1.00)	0.197 (1.00)	0.143 (1.00)	0.32 (1.00)	5.1e-05 (0.0463)	0.603 (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)	0.0288 (1.00)	0.0282 (1.00)
Del Peak 34(19q13 43)	0 (0%)	289	0.0166 (1.00)	0.0024 (1.00)	0.0789 (1.00)	0.157 (1.00)	0.000816 (0.717)	6.95e-05 (0.0629)	0.178 (1.00)	0.278 (1.00)	0.555 (1.00)	0.154 (1.00)	0.527 (1.00)	0.455 (1.00)	0.6 (1.00)	0.578 (1.00)
Amp Peak 15(10q22 3)	0 (0%)	393	0.488 (1.00)	0.397 (1.00)	0.607 (1.00)	0.0601 (1.00)	0.285 (1.00)	0.755 (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)	0.638 (1.00)	0.482 (1.00)
Amp Peak 19(14q11 2)	0 (0%)	425	0.00905 (1.00)	0.0239 (1.00)	0.323 (1.00)	0.00145 (1.00)	0.0393 (1.00)	0.154 (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)	0.135 (1.00)	0.186 (1.00)
Amp Peak 22(17q25 3)	0 (0%)	362	0.437 (1.00)	0.717 (1.00)	0.913 (1.00)	0.123 (1.00)	0.00573 (1.00)	0.752 (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)	0.134 (1.00)	0.0414 (1.00)
Amp Peak 30(22q12 2)	0 (0%)	481	0.698 (1.00)	0.581 (1.00)	0.0836 (1.00)	0.359 (1.00)	0.00187 (1.00)	0.00104 (0.912)	1 (1.00)	0.0575 (1.00)	0.0986 (1.00)	0.195 (1.00)	0.101 (1.00)	0.0114 (1.00)	0.0681 (1.00)	0.0222 (1.00)
Del Peak 3(2p25 3)	0 (0%)	451	0.946 (1.00)	0.982 (1.00)	0.454 (1.00)	0.489 (1.00)	0.345 (1.00)	0.676 (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)	0.686 (1.00)	0.548 (1.00)
Del Peak 4(2q22 1)	0 (0%)	435	0.0862 (1.00)	0.225 (1.00)	0.867 (1.00)	0.15 (1.00)	0.0327 (1.00)	0.516 (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)	0.433 (1.00)	0.275 (1.00)
Del Peak 7(4q22 1)	0 (0%)	186	0.0399 (1.00)	0.11 (1.00)	0.927 (1.00)	0.00966 (1.00)	0.0751 (1.00)	0.359 (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)	0.0572 (1.00)	0.073 (1.00)
Del Peak 8(4q34 3)	0 (0%)	157	0.0319 (1.00)	0.0266 (1.00)	0.0222 (1.00)	0.0134 (1.00)	0.283 (1.00)	0.56 (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)	0.0522 (1.00)	0.544 (1.00)
Del Peak 17(10p15 3)	0 (0%)	448	0.141 (1.00)	0.0623 (1.00)	0.0968 (1.00)	0.0865 (1.00)	0.0721 (1.00)	0.283 (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)	0.11 (1.00)	0.117 (1.00)
Del Peak 21(11q25)	0 (0%)	374	0.715 (1.00)	0.641 (1.00)	0.175 (1.00)	0.38 (1.00)	0.0957 (1.00)	0.531 (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)	0.735 (1.00)	0.0859 (1.00)
Del Peak 26(16p13 3)	0 (0%)	266	0.554 (1.00)	0.11 (1.00)	0.167 (1.00)	0.462 (1.00)	0.062 (1.00)	0.49 (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)	0.549 (1.00)	0.852 (1.00)
Del Peak 27(16q22 1)	0 (0%)	118	0.47 (1.00)	0.709 (1.00)	0.0303 (1.00)	0.925 (1.00)	0.000316 (0.283)	0.683 (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)	0.0719 (1.00)	0.104 (1.00)
Del Peak 29(17p12)	0 (0%)	88	0.202 (1.00)	0.208 (1.00)	0.619 (1.00)	0.591 (1.00)	0.936 (1.00)	0.4 (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)	0.594 (1.00)	0.473 (1.00)
Del Peak 30(17q11 2)	0 (0%)	103	0.911 (1.00)	0.129 (1.00)	0.735 (1.00)	0.477 (1.00)	0.000626 (0.553)	0.00116 (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)	0.282 (1.00)	0.476 (1.00)
Del Peak 31(18q23)	0 (0%)	196	1 (1.00)	0.986 (1.00)	0.188 (1.00)	0.434 (1.00)	0.00594 (1.00)	0.285 (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)	0.268 (1.00)	0.174 (1.00)
Del Peak 32(19p13 3)	0 (0%)	67	0.214 (1.00)	0.00934 (1.00)	0.943 (1.00)	0.462 (1.00)	0.00124 (1.00)	0.0438 (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)	0.531 (1.00)	1 (1.00)
Del Peak 33(19q13 33)	0 (0%)	274	0.000437 (0.389)	0.000381 (0.34)	0.0634 (1.00)	0.138 (1.00)	0.0286 (1.00)	0.00262 (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)	0.268 (1.00)	0.188 (1.00)
Del Peak 35(21q22 3)	0 (0%)	348	0.319 (1.00)	0.481 (1.00)	0.705 (1.00)	0.241 (1.00)	0.783 (1.00)	0.285 (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)	0.532 (1.00)	0.533 (1.00)
Del Peak 36(22q13 32)	0 (0%)	76	0.108 (1.00)	0.033 (1.00)	0.0229 (1.00)	0.0717 (1.00)	0.00805 (1.00)	0.151 (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)	0.0133 (1.00)	0.429 (1.00)
Del Peak 37(Xp21 1)	0 (0%)	205	0.332 (1.00)	0.717 (1.00)	0.12 (1.00)	0.643 (1.00)	0.1 (1.00)	0.025 (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)	0.576 (1.00)	0.405 (1.00)

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

P value = 2.72e-06 (Fisher's exact test), Q value = 0.0025

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 1(1P34.3) CNV	55	114	113
AMP PEAK 1(1P34.3) WILD-TYPE	111	90	86

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 = 1.52e-11 (Fisher's exact test), Q value = 1.4e-08

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 2(1Q21.3) CNV	83	111	162
AMP PEAK 2(1Q21.3) WILD-TYPE	83	93	37

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

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

P value = 5.98e-09 (Fisher's exact test), Q value = 5.6e-06

Table S3. Gene #3: 'Amp Peak 3(1q42.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 3(1Q42.2) CNV	85	85	142
AMP PEAK 3(1Q42.2) WILD-TYPE	81	119	57

Figure S3. 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 = 3.36e-05 (Fisher's exact test), Q value = 0.031

Table S4. Gene #3: 'Amp Peak 3(1q42.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 3(1Q42.2) CNV	119	86	107
AMP PEAK 3(1Q42.2) WILD-TYPE	53	89	114

Figure S4. 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 = 5.72e-09 (Fisher's exact test), Q value = 5.4e-06

Table S5. Gene #4: 'Amp Peak 4(2p23.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 4(2P23.2) CNV	41	86	112
AMP PEAK 4(2P23.2) WILD-TYPE	125	118	87

Figure S5. 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 = 2.18e-11 (Fisher's exact test), Q value = 2.1e-08

Table S6. Gene #5: 'Amp Peak 5(2q31.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 5(2Q31.2) CNV	37	100	113
AMP PEAK 5(2Q31.2) WILD-TYPE	129	104	86

Figure S6. 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 = 2.9e-11 (Fisher's exact test), Q value = 2.8e-08

Table S7. Gene #6: 'Amp Peak 6(3q26.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 6(3Q26.2) CNV	110	177	186
AMP PEAK 6(3Q26.2) WILD-TYPE	56	27	13

Figure S7. 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 = 4.24e-05 (Fisher's exact test), Q value = 0.039

Table S8. Gene #7: 'Amp Peak 7(4p16.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 7(4P16.3) CNV	30	78	48
AMP PEAK 7(4P16.3) WILD-TYPE	136	126	151

Figure S8. 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 = 1.06e-05 (Fisher's exact test), Q value = 0.0098

Table S9. Gene #8: 'Amp Peak 8(4q13.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 8(4Q13.3) CNV	13	54	39
AMP PEAK 8(4Q13.3) WILD-TYPE	153	150	160

Figure S9. 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 = 1.33e-07 (Fisher's exact test), Q value = 0.00012

Table S10. Gene #9: 'Amp Peak 9(5p15.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 9(5P15.33) CNV	57	120	122
AMP PEAK 9(5P15.33) WILD-TYPE	109	84	77

Figure S10. 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 = 1.59e-08 (Fisher's exact test), Q value = 1.5e-05

Table S11. Gene #10: 'Amp Peak 10(6p22.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 10(6P22.3) CNV	53	125	113
AMP PEAK 10(6P22.3) WILD-TYPE	113	79	86

Figure S11. 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 = 1.25e-05 (Fisher's exact test), Q value = 0.012

Table S12. Gene #11: 'Amp Peak 11(7q36.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 11(7Q36.3) CNV	63	121	120
AMP PEAK 11(7Q36.3) WILD-TYPE	103	83	79

Figure S12. 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 = 3.5e-07 (Fisher's exact test), Q value = 0.00033

Table S13. Gene #12: 'Amp Peak 12(8p11.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 12(8P11.21) CNV	36	69	97
AMP PEAK 12(8P11.21) WILD-TYPE	130	135	102

Figure S13. 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 = 1.12e-07 (Fisher's exact test), Q value = 0.00011

Table S14. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	215	216	126
AMP PEAK 13(8Q24.21) CNV	142	186	110
AMP PEAK 13(8Q24.21) WILD-TYPE	73	30	16

Figure S14. 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 = 1.23e-05 (Fisher's exact test), Q value = 0.011

Table S15. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	210	219
AMP PEAK 13(8Q24.21) CNV	114	144	180
AMP PEAK 13(8Q24.21) WILD-TYPE	14	66	39

Figure S15. 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 = 2.31e-17 (Fisher's exact test), Q value = 2.2e-14

Table S16. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 13(8Q24.21) CNV	108	197	142
AMP PEAK 13(8Q24.21) WILD-TYPE	58	7	57

Figure S16. 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 = 0.00042

Table S17. 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 S17. 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 S18. 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 S18. 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 = 2.5e-12 (Fisher's exact test), Q value = 2.4e-09

Table S19. Gene #14: 'Amp Peak 14(10p15.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 14(10P15.3) CNV	44	73	124
AMP PEAK 14(10P15.3) WILD-TYPE	122	131	75

Figure S19. 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 = 0.000149 (Fisher's exact test), Q value = 0.13

Table S20. Gene #14: 'Amp Peak 14(10p15.3)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 14(10P15.3) CNV	95	60	85
AMP PEAK 14(10P15.3) WILD-TYPE	77	115	136

Figure S20. 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 = 5.31e-09 (Fisher's exact test), Q value = 5e-06

Table S21. Gene #16: 'Amp Peak 16(11q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 16(11Q14.1) CNV	46	121	84
AMP PEAK 16(11Q14.1) WILD-TYPE	120	83	115

Figure S21. 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 = 9.98e-11 (Fisher's exact test), Q value = 9.5e-08

Table S22. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 17(12P13.33) CNV	63	110	145
AMP PEAK 17(12P13.33) WILD-TYPE	103	94	54

Figure S22. 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 = 0.00022 (Fisher's exact test), Q value = 0.2

Table S23. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 17(12P13.33) CNV	117	96	105
AMP PEAK 17(12P13.33) WILD-TYPE	55	79	116

Figure S23. 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 = 1.63e-13 (Fisher's exact test), Q value = 1.6e-10

Table S24. Gene #18: 'Amp Peak 18(12p12.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 18(12P12.1) CNV	58	97	146
AMP PEAK 18(12P12.1) WILD-TYPE	108	107	53

Figure S24. 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 = 4.88e-05 (Fisher's exact test), Q value = 0.044

Table S25. Gene #18: 'Amp Peak 18(12p12.1)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 18(12P12.1) CNV	115	86	100
AMP PEAK 18(12P12.1) WILD-TYPE	57	89	121

Figure S25. Get High-res Image Gene #18: 'Amp Peak 18(12p12.1)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 20(14q32.33)' versus 'CN_CNMF'

P value = 0.000278 (Fisher's exact test), Q value = 0.25

Table S26. Gene #20: 'Amp Peak 20(14q32.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 20(14Q32.33) CNV	44	72	35
AMP PEAK 20(14Q32.33) WILD-TYPE	122	132	164

Figure S26. Get High-res Image Gene #20: 'Amp Peak 20(14q32.33)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 21(15q26.3)' versus 'CN_CNMF'

P value = 2.42e-09 (Fisher's exact test), Q value = 2.3e-06

Table S27. Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 21(15Q26.3) CNV	30	89	38
AMP PEAK 21(15Q26.3) WILD-TYPE	136	115	161

Figure S27. Get High-res Image Gene #21: 'Amp Peak 21(15q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 23(18q11.2)' versus 'CN_CNMF'

P value = 3.4e-07 (Fisher's exact test), Q value = 0.00032

Table S28. Gene #23: 'Amp Peak 23(18q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 23(18Q11.2) CNV	22	43	74
AMP PEAK 23(18Q11.2) WILD-TYPE	144	161	125

Figure S28. Get High-res Image Gene #23: 'Amp Peak 23(18q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 24(19p13.12)' versus 'MRNA_CHIERARCHICAL'

P value = 3.22e-07 (Fisher's exact test), Q value = 3e-04

Table S29. Gene #24: 'Amp Peak 24(19p13.12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	210	219
AMP PEAK 24(19P13.12) CNV	44	136	120
AMP PEAK 24(19P13.12) WILD-TYPE	84	74	99

Figure S29. Get High-res Image Gene #24: 'Amp Peak 24(19p13.12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(19p13.12)' versus 'CN_CNMF'

P value = 1.02e-13 (Fisher's exact test), Q value = 9.8e-11

Table S30. Gene #24: 'Amp Peak 24(19p13.12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 24(19P13.12) CNV	67	89	150
AMP PEAK 24(19P13.12) WILD-TYPE	99	115	49

Figure S30. Get High-res Image Gene #24: 'Amp Peak 24(19p13.12)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 24(19p13.12)' versus 'METHLYATION_CNMF'

P value = 2.61e-06 (Fisher's exact test), Q value = 0.0024

Table S31. Gene #24: 'Amp Peak 24(19p13.12)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 24(19P13.12) CNV	117	72	116
AMP PEAK 24(19P13.12) WILD-TYPE	55	103	105

Figure S31. Get High-res Image Gene #24: 'Amp Peak 24(19p13.12)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

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

P value = 2.25e-29 (Fisher's exact test), Q value = 2.2e-26

Table S32. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 25(19Q12) CNV	60	82	172
AMP PEAK 25(19Q12) WILD-TYPE	106	122	27

Figure S32. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.28e-09 (Fisher's exact test), Q value = 1.2e-06

Table S33. Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 25(19Q12) CNV	125	68	121
AMP PEAK 25(19Q12) WILD-TYPE	47	107	100

Figure S33. Get High-res Image Gene #25: 'Amp Peak 25(19q12)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 26(19q13.2)' versus 'CN_CNMF'

P value = 6.2e-12 (Fisher's exact test), Q value = 5.9e-09

Table S34. Gene #26: 'Amp Peak 26(19q13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 26(19Q13.2) CNV	46	69	123
AMP PEAK 26(19Q13.2) WILD-TYPE	120	135	76

Figure S34. Get High-res Image Gene #26: 'Amp Peak 26(19q13.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 26(19q13.2)' versus 'METHLYATION_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.15

Table S35. Gene #26: 'Amp Peak 26(19q13.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 26(19Q13.2) CNV	92	55	91
AMP PEAK 26(19Q13.2) WILD-TYPE	80	120	130

Figure S35. Get High-res Image Gene #26: 'Amp Peak 26(19q13.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 27(20p13)' versus 'CN_CNMF'

P value = 1.43e-11 (Fisher's exact test), Q value = 1.4e-08

Table S36. Gene #27: 'Amp Peak 27(20p13)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 27(20P13) CNV	66	97	147
AMP PEAK 27(20P13) WILD-TYPE	100	107	52

Figure S36. Get High-res Image Gene #27: 'Amp Peak 27(20p13)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 27(20p13)' versus 'METHLYATION_CNMF'

P value = 2.97e-05 (Fisher's exact test), Q value = 0.027

Table S37. Gene #27: 'Amp Peak 27(20p13)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 27(20P13) CNV	118	81	110
AMP PEAK 27(20P13) WILD-TYPE	54	94	111

Figure S37. Get High-res Image Gene #27: 'Amp Peak 27(20p13)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

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

P value = 0.000105 (Chi-square test), Q value = 0.095

Table S38. Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	65	115	125	99	57	94
AMP PEAK 28(20Q11.21) CNV	37	54	71	50	39	73
AMP PEAK 28(20Q11.21) WILD-TYPE	28	61	54	49	18	21

Figure S38. Get High-res Image Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

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

P value = 2.61e-24 (Fisher's exact test), Q value = 2.5e-21

Table S39. Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 28(20Q11.21) CNV	69	91	172
AMP PEAK 28(20Q11.21) WILD-TYPE	97	113	27

Figure S39. Get High-res Image Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 2.9e-11 (Fisher's exact test), Q value = 2.8e-08

Table S40. Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 28(20Q11.21) CNV	137	89	106
AMP PEAK 28(20Q11.21) WILD-TYPE	35	86	115

Figure S40. Get High-res Image Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

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

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

Table S41. Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	100	67	91
AMP PEAK 28(20Q11.21) CNV	60	27	67
AMP PEAK 28(20Q11.21) WILD-TYPE	40	40	24

Figure S41. Get High-res Image Gene #28: 'Amp Peak 28(20q11.21)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'Amp Peak 29(20q13.33)' versus 'CN_CNMF'

P value = 6.66e-18 (Fisher's exact test), Q value = 6.4e-15

Table S42. Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 29(20Q13.33) CNV	82	131	179
AMP PEAK 29(20Q13.33) WILD-TYPE	84	73	20

Figure S42. Get High-res Image Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 29(20q13.33)' versus 'METHLYATION_CNMF'

P value = 1.66e-06 (Fisher's exact test), Q value = 0.0015

Table S43. Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
AMP PEAK 29(20Q13.33) CNV	144	109	139
AMP PEAK 29(20Q13.33) WILD-TYPE	28	66	82

Figure S43. Get High-res Image Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 31(Xp11.23)' versus 'CN_CNMF'

P value = 7.15e-06 (Fisher's exact test), Q value = 0.0066

Table S44. Gene #31: 'Amp Peak 31(Xp11.23)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 31(XP11.23) CNV	29	54	80
AMP PEAK 31(XP11.23) WILD-TYPE	137	150	119

Figure S44. Get High-res Image Gene #31: 'Amp Peak 31(Xp11.23)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 32(Xq28)' versus 'CN_CNMF'

P value = 4.73e-05 (Fisher's exact test), Q value = 0.043

Table S45. Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
AMP PEAK 32(XQ28) CNV	44	100	80
AMP PEAK 32(XQ28) WILD-TYPE	122	104	119

Figure S45. Get High-res Image Gene #32: 'Amp Peak 32(Xq28)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.88e-06 (Fisher's exact test), Q value = 0.0017

Table S46. Gene #33: 'Del Peak 1(1p36.11)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 1(1P36.11) CNV	87	114	64
DEL PEAK 1(1P36.11) WILD-TYPE	79	90	135

Figure S46. Get High-res Image Gene #33: 'Del Peak 1(1p36.11)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 3.05e-07 (Fisher's exact test), Q value = 0.00029

Table S47. Gene #34: 'Del Peak 2(1q32.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 2(1Q32.3) CNV	16	58	21
DEL PEAK 2(1Q32.3) WILD-TYPE	150	146	178

Figure S47. Get High-res Image Gene #34: 'Del Peak 2(1q32.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 3.6e-05 (Fisher's exact test), Q value = 0.033

Table S48. Gene #37: 'Del Peak 5(2q37.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 5(2Q37.3) CNV	34	85	55
DEL PEAK 5(2Q37.3) WILD-TYPE	132	119	144

Figure S48. Get High-res Image Gene #37: 'Del Peak 5(2q37.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 6.47e-05 (Fisher's exact test), Q value = 0.059

Table S49. Gene #38: 'Del Peak 6(3p26.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 6(3P26.2) CNV	44	70	96
DEL PEAK 6(3P26.2) WILD-TYPE	122	134	103

Figure S49. Get High-res Image Gene #38: 'Del Peak 6(3p26.2)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 4.69e-08 (Fisher's exact test), Q value = 4.4e-05

Table S50. Gene #41: 'Del Peak 9(5q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 9(5Q11.2) CNV	69	143	129
DEL PEAK 9(5Q11.2) WILD-TYPE	97	61	70

Figure S50. Get High-res Image Gene #41: 'Del Peak 9(5q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 2.07e-12 (Fisher's exact test), Q value = 2e-09

Table S51. Gene #42: 'Del Peak 10(5q13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 10(5Q13.2) CNV	87	177	142
DEL PEAK 10(5Q13.2) WILD-TYPE	79	27	57

Figure S51. Get High-res Image Gene #42: 'Del Peak 10(5q13.2)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 3.86e-09 (Fisher's exact test), Q value = 3.6e-06

Table S52. Gene #43: 'Del Peak 11(6q27)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 11(6Q27) CNV	122	159	100
DEL PEAK 11(6Q27) WILD-TYPE	44	45	99

Figure S52. Get High-res Image Gene #43: 'Del Peak 11(6q27)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 2.56e-05 (Fisher's exact test), Q value = 0.023

Table S53. Gene #43: 'Del Peak 11(6q27)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 11(6Q27) CNV	92	133	155
DEL PEAK 11(6Q27) WILD-TYPE	80	42	66

Figure S53. Get High-res Image Gene #43: '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 S54. Gene #43: '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 S54. Get High-res Image Gene #43: 'Del Peak 11(6q27)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

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

P value = 2.78e-13 (Fisher's exact test), Q value = 2.7e-10

Table S55. Gene #44: 'Del Peak 12(7p22.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 12(7P22.1) CNV	47	131	69
DEL PEAK 12(7P22.1) WILD-TYPE	119	73	130

Figure S55. Get High-res Image Gene #44: 'Del Peak 12(7p22.1)' versus Molecular Subtype #5: 'CN_CNMF'

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

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

Table S56. Gene #45: 'Del Peak 13(8p23.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 13(8P23.3) CNV	75	161	145
DEL PEAK 13(8P23.3) WILD-TYPE	91	43	54

Figure S56. Get High-res Image Gene #45: 'Del Peak 13(8p23.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.1e-08 (Fisher's exact test), Q value = 1e-05

Table S57. Gene #46: 'Del Peak 14(8p21.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 14(8P21.2) CNV	86	163	149
DEL PEAK 14(8P21.2) WILD-TYPE	80	41	50

Figure S57. Get High-res Image Gene #46: 'Del Peak 14(8p21.2)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 0.000119 (Fisher's exact test), Q value = 0.11

Table S58. Gene #47: 'Del Peak 15(9p24.3)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 15(9P24.3) CNV	92	88	75
DEL PEAK 15(9P24.3) WILD-TYPE	80	87	146

Figure S58. Get High-res Image Gene #47: 'Del Peak 15(9p24.3)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

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

P value = 2.94e-07 (Fisher's exact test), Q value = 0.00027

Table S59. Gene #48: 'Del Peak 16(9q34.13)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 16(9Q34.13) CNV	87	102	148
DEL PEAK 16(9Q34.13) WILD-TYPE	79	102	51

Figure S59. Get High-res Image Gene #48: 'Del Peak 16(9q34.13)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 0.000247 (Fisher's exact test), Q value = 0.22

Table S60. Gene #50: 'Del Peak 18(10q23.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 18(10Q23.31) CNV	43	91	86
DEL PEAK 18(10Q23.31) WILD-TYPE	123	113	113

Figure S60. Get High-res Image Gene #50: 'Del Peak 18(10q23.31)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.08e-05 (Fisher's exact test), Q value = 0.01

Table S61. Gene #51: 'Del Peak 19(10q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 19(10Q26.3) CNV	32	85	72
DEL PEAK 19(10Q26.3) WILD-TYPE	134	119	127

Figure S61. Get High-res Image Gene #51: 'Del Peak 19(10q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 6.76e-12 (Fisher's exact test), Q value = 6.5e-09

Table S62. Gene #52: 'Del Peak 20(11p15.5)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 20(11P15.5) CNV	75	160	103
DEL PEAK 20(11P15.5) WILD-TYPE	91	44	96

Figure S62. Get High-res Image Gene #52: 'Del Peak 20(11p15.5)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 0.000106 (Fisher's exact test), Q value = 0.096

Table S63. Gene #54: 'Del Peak 22(12q24.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	210	219
DEL PEAK 22(12Q24.33) CNV	50	58	104
DEL PEAK 22(12Q24.33) WILD-TYPE	78	152	115

Figure S63. Get High-res Image Gene #54: 'Del Peak 22(12q24.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 4.83e-10 (Fisher's exact test), Q value = 4.6e-07

Table S64. Gene #54: 'Del Peak 22(12q24.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 22(12Q24.33) CNV	55	113	49
DEL PEAK 22(12Q24.33) WILD-TYPE	111	91	150

Figure S64. Get High-res Image Gene #54: 'Del Peak 22(12q24.33)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.29e-06 (Fisher's exact test), Q value = 0.0012

Table S65. Gene #55: 'Del Peak 23(13q14.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 23(13Q14.2) CNV	83	154	118
DEL PEAK 23(13Q14.2) WILD-TYPE	83	50	81

Figure S65. Get High-res Image Gene #55: 'Del Peak 23(13q14.2)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 3.31e-05 (Fisher's exact test), Q value = 0.03

Table S66. Gene #55: 'Del Peak 23(13q14.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 23(13Q14.2) CNV	109	87	159
DEL PEAK 23(13Q14.2) WILD-TYPE	63	88	62

Figure S66. Get High-res Image Gene #55: 'Del Peak 23(13q14.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

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

P value = 0.000143 (Fisher's exact test), Q value = 0.13

Table S67. Gene #56: 'Del Peak 24(14q23.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 24(14Q23.3) CNV	69	103	126
DEL PEAK 24(14Q23.3) WILD-TYPE	97	101	73

Figure S67. Get High-res Image Gene #56: 'Del Peak 24(14q23.3)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 2.28e-11 (Fisher's exact test), Q value = 2.2e-08

Table S68. Gene #57: 'Del Peak 25(15q15.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 25(15Q15.1) CNV	79	117	161
DEL PEAK 25(15Q15.1) WILD-TYPE	87	87	38

Figure S68. Get High-res Image Gene #57: 'Del Peak 25(15q15.1)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 1.96e-05 (Fisher's exact test), Q value = 0.018

Table S69. Gene #57: 'Del Peak 25(15q15.1)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 25(15Q15.1) CNV	132	96	129
DEL PEAK 25(15Q15.1) WILD-TYPE	40	79	92

Figure S69. Get High-res Image Gene #57: 'Del Peak 25(15q15.1)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

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

P value = 5.1e-05 (Fisher's exact test), Q value = 0.046

Table S70. Gene #60: 'Del Peak 28(16q23.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	204	199
DEL PEAK 28(16Q23.1) CNV	109	164	169
DEL PEAK 28(16Q23.1) WILD-TYPE	57	40	30

Figure S70. Get High-res Image Gene #60: 'Del Peak 28(16q23.1)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 6.95e-05 (Fisher's exact test), Q value = 0.063

Table S71. Gene #66: 'Del Peak 34(19q13.43)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	175	221
DEL PEAK 34(19Q13.43) CNV	104	65	111
DEL PEAK 34(19Q13.43) WILD-TYPE	68	110	110

Figure S71. Get High-res Image Gene #66: '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 = 569
Number of copy number variation regions = 69
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

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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