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 70 peak regions and 10 molecular subtypes across 561 patients, 118 significant findings detected with Q value < 0.25.

Amp Peak 1(1p36.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1q32.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(1q44) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(3q26.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(4q12) cnvs correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
Amp Peak 8(7p11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 9(7q11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Amp Peak 10(7q21.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Amp Peak 11(7q31.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 12(7q36.1) cnvs correlated to 'MRNA_CNMF', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Amp Peak 13(8q24.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Amp Peak 15(12p13.32) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(12q14.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(12q15) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(17q25.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(19p13.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'RPPA_CHIERARCHICAL'.
Amp Peak 23(19q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'RPPA_CHIERARCHICAL'.
Del Peak 7(2q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 8(2q37.1) cnvs correlated to 'MIR_CHIERARCHICAL'.
Del Peak 9(3p21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 10(3q13.31) cnvs correlated to 'CN_CNMF'.
Del Peak 11(3q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 14(4q34.3) cnvs correlated to 'CN_CNMF'.
Del Peak 15(5q35.2) cnvs correlated to 'MRNA_CNMF', 'MIR_CNMF', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 16(6q22.31) cnvs correlated to 'CN_CNMF'.
Del Peak 17(6q26) cnvs correlated to 'CN_CNMF'.
Del Peak 19(9p21.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 21(10p15.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 22(10p13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'RPPA_CNMF'.
Del Peak 23(10p11.23) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 24(10q23.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 25(10q26.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 26(11p15.5) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
Del Peak 27(11p11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 28(11q14.1) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 30(12q12) cnvs correlated to 'CN_CNMF'.
Del Peak 31(12q15) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 32(13q14.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
Del Peak 33(14q13.1) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 34(14q24.2) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 35(14q31.3) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 36(15q14) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 39(17p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 40(17p13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 41(17q11.2) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Del Peak 43(19q13.41) cnvs correlated to 'MRNA_CHIERARCHICAL'.
Del Peak 44(21q22.3) cnvs correlated to 'MIR_CNMF'.
Del Peak 46(Xp22.2) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 70 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 118 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
	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
Amp Peak 8(7p11 2)	0 (0%)	69	2.56e-11 (1.74e-08)	7.75e-10 (5.23e-07)	3.08e-07 (2e-04)	1.66e-12 (1.13e-09)	1.53e-20 (1.07e-17)	1.32e-06 (0.000844)	8.62e-06 (0.00534)	5.85e-05 (0.0353)	1.11e-05 (0.00685)	0.000357 (0.208)
Amp Peak 9(7q11 21)	0 (0%)	111	8.12e-06 (0.00505)	2.59e-06 (0.00163)	4.53e-06 (0.00285)	2.54e-09 (1.7e-06)	2.04e-09 (1.37e-06)	0.00585 (1.00)	0.00417 (1.00)	0.336 (1.00)	0.004 (1.00)	0.00143 (0.8)
Del Peak 22(10p13)	0 (0%)	103	6.24e-07 (0.000403)	1.44e-05 (0.00885)	0.00126 (0.714)	1.15e-07 (7.58e-05)	3.98e-15 (2.74e-12)	0.035 (1.00)	0.000132 (0.0789)	0.00458 (1.00)	0.0885 (1.00)	0.41 (1.00)
Del Peak 23(10p11 23)	0 (0%)	99	9.69e-10 (6.52e-07)	1.86e-07 (0.000122)	0.000199 (0.118)	9.32e-09 (6.21e-06)	3.97e-16 (2.75e-13)	0.027 (1.00)	0.000786 (0.45)	0.0175 (1.00)	0.0443 (1.00)	0.084 (1.00)
Del Peak 26(11p15 5)	0 (0%)	435	1.59e-09 (1.07e-06)	2.26e-07 (0.000147)	0.256 (1.00)	1.76e-06 (0.00112)	7.17e-15 (4.93e-12)	0.000309 (0.181)	0.268 (1.00)	0.0938 (1.00)	0.00119 (0.677)	0.263 (1.00)
Del Peak 36(15q14)	0 (0%)	413	7.11e-06 (0.00445)	3.39e-08 (2.25e-05)	0.012 (1.00)	2.14e-06 (0.00136)	3.91e-07 (0.000253)	0.00231 (1.00)	0.0699 (1.00)	0.0241 (1.00)	0.000352 (0.205)	0.158 (1.00)
Amp Peak 10(7q21 2)	0 (0%)	95	1.44e-05 (0.00887)	0.000314 (0.183)	0.0101 (1.00)	2.22e-06 (0.00141)	1.23e-10 (8.37e-08)	0.00363 (1.00)	0.0179 (1.00)	0.0964 (1.00)	0.0618 (1.00)	0.00474 (1.00)
Amp Peak 13(8q24 21)	0 (0%)	497	2e-07 (0.000131)	0.00011 (0.0662)	0.0368 (1.00)	5.61e-05 (0.0339)	3.99e-06 (0.00251)	0.0699 (1.00)	0.104 (1.00)	0.00574 (1.00)	0.131 (1.00)	0.345 (1.00)
Amp Peak 22(19p13 2)	0 (0%)	322	6.24e-13 (4.27e-10)	5.7e-07 (0.000369)	0.25 (1.00)	0.00455 (1.00)	8.93e-20 (6.2e-17)	0.017 (1.00)	0.0116 (1.00)	1.32e-05 (0.00815)	0.164 (1.00)	0.0199 (1.00)
Amp Peak 23(19q12)	0 (0%)	358	2.83e-11 (1.92e-08)	1.78e-09 (1.2e-06)	0.262 (1.00)	0.00206 (1.00)	3.21e-15 (2.22e-12)	0.0553 (1.00)	0.0174 (1.00)	0.000213 (0.125)	0.0823 (1.00)	0.0438 (1.00)
Del Peak 15(5q35 2)	0 (0%)	507	1.58e-05 (0.00968)	0.00244 (1.00)	0.000142 (0.0849)	1.46e-06 (0.00093)	6.24e-05 (0.0376)	0.00338 (1.00)	0.944 (1.00)	0.295 (1.00)	0.208 (1.00)	0.841 (1.00)
Del Peak 21(10p15 3)	0 (0%)	105	4.05e-06 (0.00255)	0.000151 (0.0901)	0.00631 (1.00)	1.66e-07 (0.000109)	5.18e-14 (3.55e-11)	0.035 (1.00)	0.00523 (1.00)	0.0278 (1.00)	0.0147 (1.00)	0.41 (1.00)
Del Peak 24(10q23 31)	0 (0%)	63	1.05e-06 (0.000673)	3.85e-05 (0.0235)	0.00337 (1.00)	3.85e-05 (0.0235)	4.77e-16 (3.3e-13)	0.196 (1.00)	0.0105 (1.00)	0.131 (1.00)	0.369 (1.00)	0.16 (1.00)
Del Peak 25(10q26 3)	0 (0%)	62	2.52e-07 (0.000164)	4.75e-06 (0.00298)	0.0514 (1.00)	3.31e-05 (0.0202)	1.73e-13 (1.18e-10)	0.0145 (1.00)	0.117 (1.00)	0.0761 (1.00)	0.25 (1.00)	0.378 (1.00)
Del Peak 27(11p11 2)	0 (0%)	461	2.01e-07 (0.000131)	0.00016 (0.0951)	0.941 (1.00)	1.27e-05 (0.00788)	6.78e-13 (4.63e-10)	0.000701 (0.403)	0.825 (1.00)	0.576 (1.00)	0.051 (1.00)	0.706 (1.00)
Amp Peak 12(7q36 1)	0 (0%)	98	5.21e-05 (0.0316)	0.00155 (0.868)	0.0567 (1.00)	3.8e-06 (0.0024)	1.66e-05 (0.0102)	0.00363 (1.00)	0.227 (1.00)	0.249 (1.00)	0.0292 (1.00)	0.00467 (1.00)
Del Peak 19(9p21 3)	0 (0%)	155	8.3e-06 (0.00515)	1.52e-07 (1e-04)	0.572 (1.00)	0.00351 (1.00)	1.24e-10 (8.37e-08)	0.0417 (1.00)	0.0878 (1.00)	0.0182 (1.00)	0.0274 (1.00)	0.00319 (1.00)
Del Peak 31(12q15)	0 (0%)	484	0.000128 (0.0766)	6.15e-05 (0.0371)	0.35 (1.00)	0.0448 (1.00)	6.36e-07 (0.000409)	0.514 (1.00)	0.527 (1.00)	0.724 (1.00)	0.585 (1.00)	0.943 (1.00)
Del Peak 32(13q14 2)	0 (0%)	325	1.56e-07 (0.000102)	3.87e-05 (0.0235)	0.135 (1.00)	0.184 (1.00)	3.48e-16 (2.42e-13)	0.0328 (1.00)	0.794 (1.00)	0.107 (1.00)	0.0921 (1.00)	0.193 (1.00)
Amp Peak 7(4q12)	0 (0%)	457	0.000491 (0.285)	1.44e-05 (0.00885)	0.472 (1.00)	0.0648 (1.00)	1.2e-07 (7.89e-05)	0.384 (1.00)	0.272 (1.00)	0.664 (1.00)	0.0487 (1.00)	0.403 (1.00)
Del Peak 28(11q14 1)	0 (0%)	467	1.29e-06 (0.000826)	0.0155 (1.00)	0.937 (1.00)	0.00299 (1.00)	5.38e-16 (3.72e-13)	0.259 (1.00)	0.552 (1.00)	0.5 (1.00)	0.0908 (1.00)	0.793 (1.00)
Del Peak 33(14q13 1)	0 (0%)	387	7.74e-06 (0.00482)	0.0092 (1.00)	0.577 (1.00)	0.234 (1.00)	2.64e-29 (1.84e-26)	0.108 (1.00)	0.577 (1.00)	0.367 (1.00)	0.291 (1.00)	0.742 (1.00)
Del Peak 34(14q24 2)	0 (0%)	392	1.26e-07 (8.29e-05)	0.000602 (0.348)	0.0408 (1.00)	0.915 (1.00)	1.24e-38 (8.66e-36)	0.0503 (1.00)	0.457 (1.00)	0.275 (1.00)	0.0497 (1.00)	0.142 (1.00)
Del Peak 35(14q31 3)	0 (0%)	406	5.12e-09 (3.42e-06)	0.00191 (1.00)	0.292 (1.00)	0.88 (1.00)	1.31e-40 (9.15e-38)	0.00996 (1.00)	0.515 (1.00)	0.108 (1.00)	0.222 (1.00)	0.0846 (1.00)
Del Peak 41(17q11 2)	0 (0%)	491	7.34e-06 (0.00458)	0.00135 (0.761)	0.00107 (0.607)	0.0209 (1.00)	1.05e-06 (0.000675)	0.496 (1.00)	0.00594 (1.00)	0.00512 (1.00)	0.539 (1.00)	0.104 (1.00)
Amp Peak 1(1p36 21)	0 (0%)	473	0.562 (1.00)	0.588 (1.00)	0.203 (1.00)	0.0216 (1.00)	4.4e-08 (2.92e-05)	0.473 (1.00)	0.048 (1.00)	0.0531 (1.00)	0.0967 (1.00)	0.0808 (1.00)
Amp Peak 2(1q32 1)	0 (0%)	409	0.913 (1.00)	0.354 (1.00)	0.253 (1.00)	0.177 (1.00)	4.62e-08 (3.06e-05)	0.623 (1.00)	0.84 (1.00)	0.335 (1.00)	0.475 (1.00)	0.095 (1.00)
Amp Peak 3(1q44)	0 (0%)	466	0.275 (1.00)	0.453 (1.00)	0.364 (1.00)	0.399 (1.00)	2.53e-08 (1.68e-05)	0.931 (1.00)	0.426 (1.00)	0.177 (1.00)	0.775 (1.00)	0.439 (1.00)
Amp Peak 5(3q26 33)	0 (0%)	453	0.018 (1.00)	0.0668 (1.00)	0.978 (1.00)	0.519 (1.00)	1.15e-06 (0.000737)	0.00452 (1.00)	0.0685 (1.00)	0.358 (1.00)	0.546 (1.00)	0.321 (1.00)
Amp Peak 11(7q31 2)	0 (0%)	103	0.00103 (0.589)	0.000736 (0.422)	0.00185 (1.00)	0.000489 (0.284)	2.55e-07 (0.000166)	0.0107 (1.00)	0.103 (1.00)	0.183 (1.00)	0.256 (1.00)	0.00355 (1.00)
Amp Peak 15(12p13 32)	0 (0%)	480	0.606 (1.00)	0.781 (1.00)	0.544 (1.00)	0.881 (1.00)	4.93e-05 (0.0299)	0.278 (1.00)	0.411 (1.00)	0.553 (1.00)	0.442 (1.00)	0.151 (1.00)
Amp Peak 16(12q14 1)	0 (0%)	430	0.077 (1.00)	0.116 (1.00)	0.181 (1.00)	0.126 (1.00)	2.51e-09 (1.68e-06)	0.525 (1.00)	0.0452 (1.00)	0.338 (1.00)	0.0335 (1.00)	0.0543 (1.00)
Amp Peak 17(12q15)	0 (0%)	469	0.655 (1.00)	0.5 (1.00)	0.569 (1.00)	0.312 (1.00)	1.15e-06 (0.000737)	0.563 (1.00)	0.273 (1.00)	0.649 (1.00)	0.333 (1.00)	0.349 (1.00)
Amp Peak 21(17q25 1)	0 (0%)	484	0.026 (1.00)	0.292 (1.00)	0.41 (1.00)	0.367 (1.00)	0.000122 (0.073)	0.937 (1.00)	0.13 (1.00)	0.292 (1.00)	1 (1.00)	0.417 (1.00)
Del Peak 7(2q22 1)	0 (0%)	517	0.00239 (1.00)	0.0314 (1.00)	0.453 (1.00)	0.0264 (1.00)	1.69e-06 (0.00108)	0.00338 (1.00)	0.478 (1.00)	0.86 (1.00)	0.181 (1.00)	0.21 (1.00)
Del Peak 8(2q37 1)	0 (0%)	505	0.0708 (1.00)	0.00906 (1.00)	0.242 (1.00)	0.000184 (0.109)	0.0065 (1.00)	0.0265 (1.00)	0.647 (1.00)	0.72 (1.00)	0.181 (1.00)	0.687 (1.00)
Del Peak 9(3p21 1)	0 (0%)	509	0.243 (1.00)	0.521 (1.00)	0.895 (1.00)	0.0786 (1.00)	0.000201 (0.118)	0.252 (1.00)	0.134 (1.00)	0.855 (1.00)	0.461 (1.00)	0.0959 (1.00)
Del Peak 10(3q13 31)	0 (0%)	506	0.514 (1.00)	0.863 (1.00)	0.977 (1.00)	0.305 (1.00)	7.21e-06 (0.0045)	0.405 (1.00)	0.87 (1.00)	0.797 (1.00)	1 (1.00)	0.0547 (1.00)
Del Peak 11(3q22 1)	0 (0%)	506	0.792 (1.00)	0.232 (1.00)	0.627 (1.00)	0.596 (1.00)	0.000293 (0.172)	0.198 (1.00)	0.859 (1.00)	0.892 (1.00)	1 (1.00)	0.103 (1.00)
Del Peak 14(4q34 3)	0 (0%)	471	0.00463 (1.00)	0.00535 (1.00)	0.16 (1.00)	0.0342 (1.00)	0.000189 (0.112)	0.152 (1.00)	0.0967 (1.00)	0.283 (1.00)	0.125 (1.00)	0.96 (1.00)
Del Peak 16(6q22 31)	0 (0%)	407	0.648 (1.00)	0.912 (1.00)	0.599 (1.00)	0.029 (1.00)	1.28e-11 (8.7e-09)	0.311 (1.00)	0.204 (1.00)	0.192 (1.00)	0.796 (1.00)	0.426 (1.00)
Del Peak 17(6q26)	0 (0%)	387	0.753 (1.00)	0.07 (1.00)	0.878 (1.00)	0.0806 (1.00)	6.21e-07 (0.000401)	0.617 (1.00)	0.0166 (1.00)	0.0111 (1.00)	0.761 (1.00)	0.292 (1.00)
Del Peak 30(12q12)	0 (0%)	485	0.00874 (1.00)	0.000734 (0.421)	0.295 (1.00)	0.0153 (1.00)	0.0002 (0.118)	0.299 (1.00)	0.137 (1.00)	0.489 (1.00)	0.941 (1.00)	0.868 (1.00)
Del Peak 39(17p13 2)	0 (0%)	477	0.00304 (1.00)	0.71 (1.00)	0.89 (1.00)	0.717 (1.00)	4.96e-10 (3.35e-07)	0.376 (1.00)	0.632 (1.00)	0.487 (1.00)	0.587 (1.00)	0.261 (1.00)
Del Peak 40(17p13 1)	0 (0%)	467	0.000432 (0.251)	0.34 (1.00)	0.894 (1.00)	0.749 (1.00)	4.73e-15 (3.25e-12)	0.133 (1.00)	0.709 (1.00)	0.447 (1.00)	0.645 (1.00)	0.295 (1.00)
Del Peak 43(19q13 41)	0 (0%)	462	0.00266 (1.00)	0.000155 (0.0922)	0.0027 (1.00)	0.00241 (1.00)	0.0013 (0.733)	0.778 (1.00)	0.0401 (1.00)	0.574 (1.00)	0.02 (1.00)	0.0941 (1.00)
Del Peak 44(21q22 3)	0 (0%)	502	0.00149 (0.833)	0.0627 (1.00)	8.73e-05 (0.0525)	0.000609 (0.351)	0.0738 (1.00)	0.0685 (1.00)	0.39 (1.00)	0.121 (1.00)	1 (1.00)	0.119 (1.00)
Del Peak 46(Xp22 2)	0 (0%)	438	0.00402 (1.00)	0.0359 (1.00)	0.101 (1.00)	0.216 (1.00)	8.52e-10 (5.74e-07)	0.00951 (1.00)	0.605 (1.00)	0.253 (1.00)	0.337 (1.00)	0.644 (1.00)
Amp Peak 4(2p24 3)	0 (0%)	516	0.0427 (1.00)	0.0134 (1.00)	0.772 (1.00)	0.377 (1.00)	0.000516 (0.298)	0.0574 (1.00)	0.209 (1.00)	0.112 (1.00)	0.93 (1.00)	1 (1.00)
Amp Peak 6(4p16 3)	0 (0%)	515	0.392 (1.00)	0.296 (1.00)	0.809 (1.00)	0.173 (1.00)	0.465 (1.00)	0.529 (1.00)	0.636 (1.00)	0.53 (1.00)	0.941 (1.00)	0.759 (1.00)
Amp Peak 14(11p13)	0 (0%)	535	0.693 (1.00)	0.858 (1.00)	0.337 (1.00)	0.439 (1.00)	0.468 (1.00)	0.181 (1.00)	0.265 (1.00)	0.112 (1.00)	0.602 (1.00)	1 (1.00)
Amp Peak 18(13q34)	0 (0%)	531	0.193 (1.00)	0.429 (1.00)	0.165 (1.00)	0.16 (1.00)	0.00606 (1.00)		0.0677 (1.00)	0.186 (1.00)	0.368 (1.00)	1 (1.00)
Amp Peak 19(14q32 33)	0 (0%)	528	0.38 (1.00)	0.71 (1.00)	0.0111 (1.00)	0.835 (1.00)	0.899 (1.00)	0.903 (1.00)	0.0394 (1.00)	0.275 (1.00)	0.0429 (1.00)	0.884 (1.00)
Amp Peak 20(17p13 2)	0 (0%)	516	0.0025 (1.00)	0.0223 (1.00)	0.0712 (1.00)	0.169 (1.00)	0.00741 (1.00)	0.865 (1.00)	0.0545 (1.00)	0.63 (1.00)	0.615 (1.00)	0.281 (1.00)
Amp Peak 24(21q21 1)	0 (0%)	495	0.00298 (1.00)	0.0068 (1.00)	0.0838 (1.00)	0.0589 (1.00)	0.00142 (0.8)	0.879 (1.00)	0.669 (1.00)	0.83 (1.00)	0.0967 (1.00)	0.0663 (1.00)
Del Peak 1(1p36 32)	0 (0%)	462	0.809 (1.00)	0.0378 (1.00)	0.505 (1.00)	0.243 (1.00)	0.619 (1.00)	0.339 (1.00)	0.545 (1.00)	0.561 (1.00)	0.252 (1.00)	0.0437 (1.00)
Del Peak 2(1p36 23)	0 (0%)	426	0.164 (1.00)	0.0495 (1.00)	0.317 (1.00)	0.298 (1.00)	0.000912 (0.52)	0.306 (1.00)	0.279 (1.00)	0.725 (1.00)	0.0632 (1.00)	0.103 (1.00)
Del Peak 3(1p32 3)	0 (0%)	502	0.306 (1.00)	0.542 (1.00)	0.982 (1.00)	0.856 (1.00)	0.143 (1.00)	0.822 (1.00)	0.706 (1.00)	0.63 (1.00)	0.803 (1.00)	0.159 (1.00)
Del Peak 4(1p22 1)	0 (0%)	514	0.865 (1.00)	0.875 (1.00)	0.736 (1.00)	0.188 (1.00)	0.159 (1.00)	0.579 (1.00)	0.888 (1.00)	0.372 (1.00)	1 (1.00)	0.015 (1.00)
Del Peak 5(1q42 11)	0 (0%)	514	0.285 (1.00)	0.892 (1.00)	0.418 (1.00)	0.472 (1.00)	0.501 (1.00)	0.412 (1.00)	0.161 (1.00)	0.00286 (1.00)	0.686 (1.00)	0.647 (1.00)
Del Peak 6(1q44)	0 (0%)	529	0.704 (1.00)	0.462 (1.00)	0.669 (1.00)	0.112 (1.00)	0.611 (1.00)	0.187 (1.00)	0.799 (1.00)	0.335 (1.00)	0.539 (1.00)	0.904 (1.00)
Del Peak 12(3q29)	0 (0%)	498	0.0901 (1.00)	0.222 (1.00)	0.575 (1.00)	0.891 (1.00)	0.00606 (1.00)	0.259 (1.00)	0.379 (1.00)	0.684 (1.00)	0.954 (1.00)	0.731 (1.00)
Del Peak 13(4p16 3)	0 (0%)	484	0.0567 (1.00)	0.00643 (1.00)	0.572 (1.00)	0.0997 (1.00)	0.0926 (1.00)	1 (1.00)	0.832 (1.00)	0.71 (1.00)	0.872 (1.00)	0.818 (1.00)
Del Peak 18(8p23 2)	0 (0%)	495	0.475 (1.00)	0.659 (1.00)	0.229 (1.00)	0.498 (1.00)	0.065 (1.00)	0.892 (1.00)	0.951 (1.00)	0.946 (1.00)	0.62 (1.00)	0.159 (1.00)
Del Peak 20(9q34 2)	0 (0%)	490	0.164 (1.00)	0.0442 (1.00)	0.797 (1.00)	0.261 (1.00)	0.312 (1.00)	0.652 (1.00)	0.113 (1.00)	0.241 (1.00)	0.442 (1.00)	0.0569 (1.00)
Del Peak 29(12p13 1)	0 (0%)	487	0.0266 (1.00)	0.00333 (1.00)	0.182 (1.00)	0.104 (1.00)	0.106 (1.00)	0.669 (1.00)	0.875 (1.00)	0.522 (1.00)	0.944 (1.00)	0.566 (1.00)
Del Peak 37(16p12 2)	0 (0%)	472	0.408 (1.00)	0.501 (1.00)	0.0455 (1.00)	0.737 (1.00)	0.104 (1.00)	0.243 (1.00)	0.405 (1.00)	0.535 (1.00)	0.443 (1.00)	0.422 (1.00)
Del Peak 38(16q23 3)	0 (0%)	466	0.0176 (1.00)	0.524 (1.00)	0.727 (1.00)	0.828 (1.00)	0.00533 (1.00)	0.752 (1.00)	0.0385 (1.00)	0.0802 (1.00)	0.528 (1.00)	0.468 (1.00)
Del Peak 42(18q22 3)	0 (0%)	482	0.254 (1.00)	0.131 (1.00)	0.466 (1.00)	0.461 (1.00)	0.00217 (1.00)	0.0928 (1.00)	0.0315 (1.00)	0.00134 (0.754)	0.159 (1.00)	0.697 (1.00)
Del Peak 45(22q13 32)	0 (0%)	353	0.804 (1.00)	0.191 (1.00)	0.0181 (1.00)	0.187 (1.00)	0.000823 (0.47)	0.774 (1.00)	0.915 (1.00)	0.941 (1.00)	0.0721 (1.00)	0.923 (1.00)

'Amp Peak 1(1p36.21)' versus 'CN_CNMF'

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

Table S1. Gene #1: 'Amp Peak 1(1p36.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 1(1P36.21) CNV	49	19	20
AMP PEAK 1(1P36.21) WILD-TYPE	112	169	192

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p36.21)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 2(1q32.1)' versus 'CN_CNMF'

P value = 4.62e-08 (Fisher's exact test), Q value = 3.1e-05

Table S2. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 2(1Q32.1) CNV	72	37	43
AMP PEAK 2(1Q32.1) WILD-TYPE	89	151	169

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 3(1q44)' versus 'CN_CNMF'

P value = 2.53e-08 (Fisher's exact test), Q value = 1.7e-05

Table S3. Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 3(1Q44) CNV	52	22	21
AMP PEAK 3(1Q44) WILD-TYPE	109	166	191

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 5(3q26.33)' versus 'CN_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00074

Table S4. Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 5(3Q26.33) CNV	53	31	24
AMP PEAK 5(3Q26.33) WILD-TYPE	108	157	188

Figure S4. Get High-res Image Gene #5: 'Amp Peak 5(3q26.33)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 7(4q12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.0089

Table S5. Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
AMP PEAK 7(4Q12) CNV	13	53	32
AMP PEAK 7(4Q12) WILD-TYPE	104	118	188

Figure S5. Get High-res Image Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 7(4q12)' versus 'CN_CNMF'

P value = 1.2e-07 (Fisher's exact test), Q value = 7.9e-05

Table S6. Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 7(4Q12) CNV	53	30	21
AMP PEAK 7(4Q12) WILD-TYPE	108	158	191

Figure S6. Get High-res Image Gene #7: 'Amp Peak 7(4q12)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 8(7p11.2)' versus 'MRNA_CNMF'

P value = 2.56e-11 (Fisher's exact test), Q value = 1.7e-08

Table S7. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 8(7P11.2) CNV	139	67	147	89
AMP PEAK 8(7P11.2) WILD-TYPE	8	29	5	24

Figure S7. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 8(7p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 7.75e-10 (Fisher's exact test), Q value = 5.2e-07

Table S8. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
AMP PEAK 8(7P11.2) CNV	112	125	205
AMP PEAK 8(7P11.2) WILD-TYPE	5	46	15

Figure S8. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 8(7p11.2)' versus 'MIR_CNMF'

P value = 3.08e-07 (Fisher's exact test), Q value = 2e-04

Table S9. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	155	73	104
AMP PEAK 8(7P11.2) CNV	136	122	59	95
AMP PEAK 8(7P11.2) WILD-TYPE	3	33	14	9

Figure S9. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #3: 'MIR_CNMF'

'Amp Peak 8(7p11.2)' versus 'MIR_CHIERARCHICAL'

P value = 1.66e-12 (Fisher's exact test), Q value = 1.1e-09

Table S10. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
AMP PEAK 8(7P11.2) CNV	173	146	93
AMP PEAK 8(7P11.2) WILD-TYPE	8	9	42

Figure S10. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 8(7p11.2)' versus 'CN_CNMF'

P value = 1.53e-20 (Fisher's exact test), Q value = 1.1e-17

Table S11. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 8(7P11.2) CNV	149	132	211
AMP PEAK 8(7P11.2) WILD-TYPE	12	56	1

Figure S11. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 8(7p11.2)' versus 'METHLYATION_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00084

Table S12. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	27	16	27
AMP PEAK 8(7P11.2) CNV	38	27	16	16
AMP PEAK 8(7P11.2) WILD-TYPE	1	0	0	11

Figure S12. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Amp Peak 8(7p11.2)' versus 'RPPA_CNMF'

P value = 8.62e-06 (Fisher's exact test), Q value = 0.0053

Table S13. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	58	44	45
AMP PEAK 8(7P11.2) CNV	49	42	44	44
AMP PEAK 8(7P11.2) WILD-TYPE	5	16	0	1

Figure S13. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #7: 'RPPA_CNMF'

'Amp Peak 8(7p11.2)' versus 'RPPA_CHIERARCHICAL'

P value = 5.85e-05 (Fisher's exact test), Q value = 0.035

Table S14. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	33	104
AMP PEAK 8(7P11.2) CNV	64	31	84
AMP PEAK 8(7P11.2) WILD-TYPE	0	2	20

Figure S14. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'Amp Peak 8(7p11.2)' versus 'MRNASEQ_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0068

Table S15. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
AMP PEAK 8(7P11.2) CNV	31	66	34
AMP PEAK 8(7P11.2) WILD-TYPE	13	1	2

Figure S15. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'Amp Peak 8(7p11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000357 (Fisher's exact test), Q value = 0.21

Table S16. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	21	60
AMP PEAK 8(7P11.2) CNV	64	21	46
AMP PEAK 8(7P11.2) WILD-TYPE	2	0	14

Figure S16. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 9(7q11.21)' versus 'MRNA_CNMF'

P value = 8.12e-06 (Fisher's exact test), Q value = 0.005

Table S17. Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 9(7Q11.21) CNV	133	63	124	82
AMP PEAK 9(7Q11.21) WILD-TYPE	14	33	28	31

Figure S17. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 9(7q11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 2.59e-06 (Fisher's exact test), Q value = 0.0016

Table S18. Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
AMP PEAK 9(7Q11.21) CNV	95	114	193
AMP PEAK 9(7Q11.21) WILD-TYPE	22	57	27

Figure S18. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 9(7q11.21)' versus 'MIR_CNMF'

P value = 4.53e-06 (Fisher's exact test), Q value = 0.0028

Table S19. Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	155	73	104
AMP PEAK 9(7Q11.21) CNV	126	111	49	90
AMP PEAK 9(7Q11.21) WILD-TYPE	13	44	24	14

Figure S19. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #3: 'MIR_CNMF'

'Amp Peak 9(7q11.21)' versus 'MIR_CHIERARCHICAL'

P value = 2.54e-09 (Fisher's exact test), Q value = 1.7e-06

Table S20. Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
AMP PEAK 9(7Q11.21) CNV	157	137	82
AMP PEAK 9(7Q11.21) WILD-TYPE	24	18	53

Figure S20. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 9(7q11.21)' versus 'CN_CNMF'

P value = 2.04e-09 (Fisher's exact test), Q value = 1.4e-06

Table S21. Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 9(7Q11.21) CNV	144	122	184
AMP PEAK 9(7Q11.21) WILD-TYPE	17	66	28

Figure S21. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 10(7q21.2)' versus 'MRNA_CNMF'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.0089

Table S22. Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 10(7Q21.2) CNV	131	63	134	90
AMP PEAK 10(7Q21.2) WILD-TYPE	16	33	18	23

Figure S22. Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 10(7q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000314 (Fisher's exact test), Q value = 0.18

Table S23. Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
AMP PEAK 10(7Q21.2) CNV	101	124	193
AMP PEAK 10(7Q21.2) WILD-TYPE	16	47	27

Figure S23. Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 10(7q21.2)' versus 'MIR_CHIERARCHICAL'

P value = 2.22e-06 (Fisher's exact test), Q value = 0.0014

Table S24. Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
AMP PEAK 10(7Q21.2) CNV	162	133	91
AMP PEAK 10(7Q21.2) WILD-TYPE	19	22	44

Figure S24. Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 10(7q21.2)' versus 'CN_CNMF'

P value = 1.23e-10 (Fisher's exact test), Q value = 8.4e-08

Table S25. Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 10(7Q21.2) CNV	145	127	194
AMP PEAK 10(7Q21.2) WILD-TYPE	16	61	18

Figure S25. Get High-res Image Gene #10: 'Amp Peak 10(7q21.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 11(7q31.2)' versus 'CN_CNMF'

P value = 2.55e-07 (Fisher's exact test), Q value = 0.00017

Table S26. Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 11(7Q31.2) CNV	141	129	188
AMP PEAK 11(7Q31.2) WILD-TYPE	20	59	24

Figure S26. Get High-res Image Gene #11: 'Amp Peak 11(7q31.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 12(7q36.1)' versus 'MRNA_CNMF'

P value = 5.21e-05 (Fisher's exact test), Q value = 0.032

Table S27. Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 12(7Q36.1) CNV	131	63	131	91
AMP PEAK 12(7Q36.1) WILD-TYPE	16	33	21	22

Figure S27. Get High-res Image Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 12(7q36.1)' versus 'MIR_CHIERARCHICAL'

P value = 3.8e-06 (Fisher's exact test), Q value = 0.0024

Table S28. Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
AMP PEAK 12(7Q36.1) CNV	162	131	91
AMP PEAK 12(7Q36.1) WILD-TYPE	19	24	44

Figure S28. Get High-res Image Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Amp Peak 12(7q36.1)' versus 'CN_CNMF'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.01

Table S29. Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 12(7Q36.1) CNV	139	135	189
AMP PEAK 12(7Q36.1) WILD-TYPE	22	53	23

Figure S29. Get High-res Image Gene #12: 'Amp Peak 12(7q36.1)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 2e-07 (Fisher's exact test), Q value = 0.00013

Table S30. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 13(8Q24.21) CNV	8	24	6	19
AMP PEAK 13(8Q24.21) WILD-TYPE	139	72	146	94

Figure S30. 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 = 0.00011 (Fisher's exact test), Q value = 0.066

Table S31. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
AMP PEAK 13(8Q24.21) CNV	7	34	16
AMP PEAK 13(8Q24.21) WILD-TYPE	110	137	204

Figure S31. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 5.61e-05 (Fisher's exact test), Q value = 0.034

Table S32. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
AMP PEAK 13(8Q24.21) CNV	12	12	30
AMP PEAK 13(8Q24.21) WILD-TYPE	169	143	105

Figure S32. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

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

P value = 3.99e-06 (Fisher's exact test), Q value = 0.0025

Table S33. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 13(8Q24.21) CNV	31	25	8
AMP PEAK 13(8Q24.21) WILD-TYPE	130	163	204

Figure S33. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 15(12p13.32)' versus 'CN_CNMF'

P value = 4.93e-05 (Fisher's exact test), Q value = 0.03

Table S34. Gene #15: 'Amp Peak 15(12p13.32)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 15(12P13.32) CNV	40	23	18
AMP PEAK 15(12P13.32) WILD-TYPE	121	165	194

Figure S34. Get High-res Image Gene #15: 'Amp Peak 15(12p13.32)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 16(12q14.1)' versus 'CN_CNMF'

P value = 2.51e-09 (Fisher's exact test), Q value = 1.7e-06

Table S35. Gene #16: 'Amp Peak 16(12q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 16(12Q14.1) CNV	67	28	36
AMP PEAK 16(12Q14.1) WILD-TYPE	94	160	176

Figure S35. Get High-res Image Gene #16: 'Amp Peak 16(12q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 17(12q15)' versus 'CN_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00074

Table S36. Gene #17: 'Amp Peak 17(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 17(12Q15) CNV	48	20	24
AMP PEAK 17(12Q15) WILD-TYPE	113	168	188

Figure S36. Get High-res Image Gene #17: 'Amp Peak 17(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 21(17q25.1)' versus 'CN_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.073

Table S37. Gene #21: 'Amp Peak 21(17q25.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 21(17Q25.1) CNV	38	21	18
AMP PEAK 21(17Q25.1) WILD-TYPE	123	167	194

Figure S37. Get High-res Image Gene #21: 'Amp Peak 21(17q25.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 22(19p13.2)' versus 'MRNA_CNMF'

P value = 6.24e-13 (Fisher's exact test), Q value = 4.3e-10

Table S38. Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 22(19P13.2) CNV	56	36	101	24
AMP PEAK 22(19P13.2) WILD-TYPE	91	60	51	89

Figure S38. Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(19p13.2)' versus 'MRNA_CHIERARCHICAL'

P value = 5.7e-07 (Fisher's exact test), Q value = 0.00037

Table S39. Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
AMP PEAK 22(19P13.2) CNV	72	51	94
AMP PEAK 22(19P13.2) WILD-TYPE	45	120	126

Figure S39. Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 22(19p13.2)' versus 'CN_CNMF'

P value = 8.93e-20 (Fisher's exact test), Q value = 6.2e-17

Table S40. Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 22(19P13.2) CNV	48	48	143
AMP PEAK 22(19P13.2) WILD-TYPE	113	140	69

Figure S40. Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 22(19p13.2)' versus 'RPPA_CHIERARCHICAL'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.0081

Table S41. Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	33	104
AMP PEAK 22(19P13.2) CNV	42	8	34
AMP PEAK 22(19P13.2) WILD-TYPE	22	25	70

Figure S41. Get High-res Image Gene #22: 'Amp Peak 22(19p13.2)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'Amp Peak 23(19q12)' versus 'MRNA_CNMF'

P value = 2.83e-11 (Fisher's exact test), Q value = 1.9e-08

Table S42. Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 23(19Q12) CNV	55	28	84	16
AMP PEAK 23(19Q12) WILD-TYPE	92	68	68	97

Figure S42. Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 23(19q12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.78e-09 (Fisher's exact test), Q value = 1.2e-06

Table S43. Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
AMP PEAK 23(19Q12) CNV	62	32	89
AMP PEAK 23(19Q12) WILD-TYPE	55	139	131

Figure S43. Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(19q12)' versus 'CN_CNMF'

P value = 3.21e-15 (Fisher's exact test), Q value = 2.2e-12

Table S44. Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
AMP PEAK 23(19Q12) CNV	38	43	122
AMP PEAK 23(19Q12) WILD-TYPE	123	145	90

Figure S44. Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #5: 'CN_CNMF'

'Amp Peak 23(19q12)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000213 (Fisher's exact test), Q value = 0.13

Table S45. Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	33	104
AMP PEAK 23(19Q12) CNV	35	7	27
AMP PEAK 23(19Q12) WILD-TYPE	29	26	77

Figure S45. Get High-res Image Gene #23: 'Amp Peak 23(19q12)' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'Del Peak 7(2q22.1)' versus 'CN_CNMF'

P value = 1.69e-06 (Fisher's exact test), Q value = 0.0011

Table S46. Gene #31: 'Del Peak 7(2q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 7(2Q22.1) CNV	26	14	4
DEL PEAK 7(2Q22.1) WILD-TYPE	135	174	208

Figure S46. Get High-res Image Gene #31: 'Del Peak 7(2q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 8(2q37.1)' versus 'MIR_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.11

Table S47. Gene #32: 'Del Peak 8(2q37.1)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
DEL PEAK 8(2Q37.1) CNV	13	9	27
DEL PEAK 8(2Q37.1) WILD-TYPE	168	146	108

Figure S47. Get High-res Image Gene #32: 'Del Peak 8(2q37.1)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 9(3p21.1)' versus 'CN_CNMF'

P value = 0.000201 (Fisher's exact test), Q value = 0.12

Table S48. Gene #33: 'Del Peak 9(3p21.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 9(3P21.1) CNV	23	22	7
DEL PEAK 9(3P21.1) WILD-TYPE	138	166	205

Figure S48. Get High-res Image Gene #33: 'Del Peak 9(3p21.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 10(3q13.31)' versus 'CN_CNMF'

P value = 7.21e-06 (Fisher's exact test), Q value = 0.0045

Table S49. Gene #34: 'Del Peak 10(3q13.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 10(3Q13.31) CNV	27	22	6
DEL PEAK 10(3Q13.31) WILD-TYPE	134	166	206

Figure S49. Get High-res Image Gene #34: 'Del Peak 10(3q13.31)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 11(3q22.1)' versus 'CN_CNMF'

P value = 0.000293 (Fisher's exact test), Q value = 0.17

Table S50. Gene #35: 'Del Peak 11(3q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 11(3Q22.1) CNV	24	23	8
DEL PEAK 11(3Q22.1) WILD-TYPE	137	165	204

Figure S50. Get High-res Image Gene #35: 'Del Peak 11(3q22.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 14(4q34.3)' versus 'CN_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.11

Table S51. Gene #38: 'Del Peak 14(4q34.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 14(4Q34.3) CNV	41	29	20
DEL PEAK 14(4Q34.3) WILD-TYPE	120	159	192

Figure S51. Get High-res Image Gene #38: 'Del Peak 14(4q34.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 15(5q35.2)' versus 'MRNA_CNMF'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.0097

Table S52. Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 15(5Q35.2) CNV	8	22	7	15
DEL PEAK 15(5Q35.2) WILD-TYPE	139	74	145	98

Figure S52. Get High-res Image Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 15(5q35.2)' versus 'MIR_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.085

Table S53. Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	155	73	104
DEL PEAK 15(5Q35.2) CNV	4	26	11	7
DEL PEAK 15(5Q35.2) WILD-TYPE	135	129	62	97

Figure S53. Get High-res Image Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #3: 'MIR_CNMF'

'Del Peak 15(5q35.2)' versus 'MIR_CHIERARCHICAL'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.00093

Table S54. Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
DEL PEAK 15(5Q35.2) CNV	14	5	29
DEL PEAK 15(5Q35.2) WILD-TYPE	167	150	106

Figure S54. Get High-res Image Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 15(5q35.2)' versus 'CN_CNMF'

P value = 6.24e-05 (Fisher's exact test), Q value = 0.038

Table S55. Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 15(5Q35.2) CNV	18	29	7
DEL PEAK 15(5Q35.2) WILD-TYPE	143	159	205

Figure S55. Get High-res Image Gene #39: 'Del Peak 15(5q35.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 16(6q22.31)' versus 'CN_CNMF'

P value = 1.28e-11 (Fisher's exact test), Q value = 8.7e-09

Table S56. Gene #40: 'Del Peak 16(6q22.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 16(6Q22.31) CNV	79	34	41
DEL PEAK 16(6Q22.31) WILD-TYPE	82	154	171

Figure S56. Get High-res Image Gene #40: 'Del Peak 16(6q22.31)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 17(6q26)' versus 'CN_CNMF'

P value = 6.21e-07 (Fisher's exact test), Q value = 4e-04

Table S57. Gene #41: 'Del Peak 17(6q26)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 17(6Q26) CNV	76	40	58
DEL PEAK 17(6Q26) WILD-TYPE	85	148	154

Figure S57. Get High-res Image Gene #41: 'Del Peak 17(6q26)' versus Molecular Subtype #5: 'CN_CNMF'

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

P value = 8.3e-06 (Fisher's exact test), Q value = 0.0052

Table S58. Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 19(9P21.3) CNV	100	62	133	75
DEL PEAK 19(9P21.3) WILD-TYPE	47	34	19	38

Figure S58. Get High-res Image Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 1.52e-07 (Fisher's exact test), Q value = 1e-04

Table S59. Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 19(9P21.3) CNV	107	112	151
DEL PEAK 19(9P21.3) WILD-TYPE	10	59	69

Figure S59. Get High-res Image Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

P value = 1.24e-10 (Fisher's exact test), Q value = 8.4e-08

Table S60. Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 19(9P21.3) CNV	108	112	186
DEL PEAK 19(9P21.3) WILD-TYPE	53	76	26

Figure S60. Get High-res Image Gene #43: 'Del Peak 19(9p21.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 21(10p15.3)' versus 'MRNA_CNMF'

P value = 4.05e-06 (Fisher's exact test), Q value = 0.0025

Table S61. Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 21(10P15.3) CNV	129	63	134	82
DEL PEAK 21(10P15.3) WILD-TYPE	18	33	18	31

Figure S61. Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 21(10p15.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000151 (Fisher's exact test), Q value = 0.09

Table S62. Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 21(10P15.3) CNV	104	120	184
DEL PEAK 21(10P15.3) WILD-TYPE	13	51	36

Figure S62. Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 21(10p15.3)' versus 'MIR_CHIERARCHICAL'

P value = 1.66e-07 (Fisher's exact test), Q value = 0.00011

Table S63. Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
DEL PEAK 21(10P15.3) CNV	157	136	86
DEL PEAK 21(10P15.3) WILD-TYPE	24	19	49

Figure S63. Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 21(10p15.3)' versus 'CN_CNMF'

P value = 5.18e-14 (Fisher's exact test), Q value = 3.6e-11

Table S64. Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 21(10P15.3) CNV	137	120	199
DEL PEAK 21(10P15.3) WILD-TYPE	24	68	13

Figure S64. Get High-res Image Gene #45: 'Del Peak 21(10p15.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 22(10p13)' versus 'MRNA_CNMF'

P value = 6.24e-07 (Fisher's exact test), Q value = 4e-04

Table S65. Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 22(10P13) CNV	131	65	135	79
DEL PEAK 22(10P13) WILD-TYPE	16	31	17	34

Figure S65. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 22(10p13)' versus 'MRNA_CHIERARCHICAL'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.0089

Table S66. Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 22(10P13) CNV	104	118	188
DEL PEAK 22(10P13) WILD-TYPE	13	53	32

Figure S66. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 22(10p13)' versus 'MIR_CHIERARCHICAL'

P value = 1.15e-07 (Fisher's exact test), Q value = 7.6e-05

Table S67. Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
DEL PEAK 22(10P13) CNV	157	138	87
DEL PEAK 22(10P13) WILD-TYPE	24	17	48

Figure S67. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 22(10p13)' versus 'CN_CNMF'

P value = 3.98e-15 (Fisher's exact test), Q value = 2.7e-12

Table S68. Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 22(10P13) CNV	137	120	201
DEL PEAK 22(10P13) WILD-TYPE	24	68	11

Figure S68. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 22(10p13)' versus 'RPPA_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.079

Table S69. Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	58	44	45
DEL PEAK 22(10P13) CNV	50	38	42	37
DEL PEAK 22(10P13) WILD-TYPE	4	20	2	8

Figure S69. Get High-res Image Gene #46: 'Del Peak 22(10p13)' versus Molecular Subtype #7: 'RPPA_CNMF'

'Del Peak 23(10p11.23)' versus 'MRNA_CNMF'

P value = 9.69e-10 (Fisher's exact test), Q value = 6.5e-07

Table S70. Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 23(10P11.23) CNV	130	61	142	83
DEL PEAK 23(10P11.23) WILD-TYPE	17	35	10	30

Figure S70. Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 23(10p11.23)' versus 'MRNA_CHIERARCHICAL'

P value = 1.86e-07 (Fisher's exact test), Q value = 0.00012

Table S71. Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 23(10P11.23) CNV	110	119	187
DEL PEAK 23(10P11.23) WILD-TYPE	7	52	33

Figure S71. Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 23(10p11.23)' versus 'MIR_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.12

Table S72. Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	155	73	104
DEL PEAK 23(10P11.23) CNV	129	117	55	86
DEL PEAK 23(10P11.23) WILD-TYPE	10	38	18	18

Figure S72. Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #3: 'MIR_CNMF'

'Del Peak 23(10p11.23)' versus 'MIR_CHIERARCHICAL'

P value = 9.32e-09 (Fisher's exact test), Q value = 6.2e-06

Table S73. Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
DEL PEAK 23(10P11.23) CNV	162	138	87
DEL PEAK 23(10P11.23) WILD-TYPE	19	17	48

Figure S73. Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 23(10p11.23)' versus 'CN_CNMF'

P value = 3.97e-16 (Fisher's exact test), Q value = 2.8e-13

Table S74. Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 23(10P11.23) CNV	138	121	203
DEL PEAK 23(10P11.23) WILD-TYPE	23	67	9

Figure S74. Get High-res Image Gene #47: 'Del Peak 23(10p11.23)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 24(10q23.31)' versus 'MRNA_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00067

Table S75. Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 24(10Q23.31) CNV	136	75	147	91
DEL PEAK 24(10Q23.31) WILD-TYPE	11	21	5	22

Figure S75. Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 24(10q23.31)' versus 'MRNA_CHIERARCHICAL'

P value = 3.85e-05 (Fisher's exact test), Q value = 0.023

Table S76. Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 24(10Q23.31) CNV	113	137	199
DEL PEAK 24(10Q23.31) WILD-TYPE	4	34	21

Figure S76. Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 24(10q23.31)' versus 'MIR_CHIERARCHICAL'

P value = 3.85e-05 (Fisher's exact test), Q value = 0.023

Table S77. Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
DEL PEAK 24(10Q23.31) CNV	169	144	105
DEL PEAK 24(10Q23.31) WILD-TYPE	12	11	30

Figure S77. Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 24(10q23.31)' versus 'CN_CNMF'

P value = 4.77e-16 (Fisher's exact test), Q value = 3.3e-13

Table S78. Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 24(10Q23.31) CNV	149	139	210
DEL PEAK 24(10Q23.31) WILD-TYPE	12	49	2

Figure S78. Get High-res Image Gene #48: 'Del Peak 24(10q23.31)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 25(10q26.3)' versus 'MRNA_CNMF'

P value = 2.52e-07 (Fisher's exact test), Q value = 0.00016

Table S79. Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 25(10Q26.3) CNV	136	75	148	91
DEL PEAK 25(10Q26.3) WILD-TYPE	11	21	4	22

Figure S79. Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 25(10q26.3)' versus 'MRNA_CHIERARCHICAL'

P value = 4.75e-06 (Fisher's exact test), Q value = 0.003

Table S80. Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 25(10Q26.3) CNV	115	138	197
DEL PEAK 25(10Q26.3) WILD-TYPE	2	33	23

Figure S80. Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 25(10q26.3)' versus 'MIR_CHIERARCHICAL'

P value = 3.31e-05 (Fisher's exact test), Q value = 0.02

Table S81. Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
DEL PEAK 25(10Q26.3) CNV	172	140	106
DEL PEAK 25(10Q26.3) WILD-TYPE	9	15	29

Figure S81. Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 25(10q26.3)' versus 'CN_CNMF'

P value = 1.73e-13 (Fisher's exact test), Q value = 1.2e-10

Table S82. Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 25(10Q26.3) CNV	148	142	209
DEL PEAK 25(10Q26.3) WILD-TYPE	13	46	3

Figure S82. Get High-res Image Gene #49: 'Del Peak 25(10q26.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 26(11p15.5)' versus 'MRNA_CNMF'

P value = 1.59e-09 (Fisher's exact test), Q value = 1.1e-06

Table S83. Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 26(11P15.5) CNV	32	42	13	32
DEL PEAK 26(11P15.5) WILD-TYPE	115	54	139	81

Figure S83. Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 26(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 2.26e-07 (Fisher's exact test), Q value = 0.00015

Table S84. Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 26(11P15.5) CNV	10	61	48
DEL PEAK 26(11P15.5) WILD-TYPE	107	110	172

Figure S84. Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 26(11p15.5)' versus 'MIR_CHIERARCHICAL'

P value = 1.76e-06 (Fisher's exact test), Q value = 0.0011

Table S85. Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
DEL PEAK 26(11P15.5) CNV	31	28	55
DEL PEAK 26(11P15.5) WILD-TYPE	150	127	80

Figure S85. Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 26(11p15.5)' versus 'CN_CNMF'

P value = 7.17e-15 (Fisher's exact test), Q value = 4.9e-12

Table S86. Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 26(11P15.5) CNV	62	51	13
DEL PEAK 26(11P15.5) WILD-TYPE	99	137	199

Figure S86. Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 26(11p15.5)' versus 'METHLYATION_CNMF'

P value = 0.000309 (Fisher's exact test), Q value = 0.18

Table S87. Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	27	16	27
DEL PEAK 26(11P15.5) CNV	0	4	1	9
DEL PEAK 26(11P15.5) WILD-TYPE	39	23	15	18

Figure S87. Get High-res Image Gene #50: 'Del Peak 26(11p15.5)' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'Del Peak 27(11p11.2)' versus 'MRNA_CNMF'

P value = 2.01e-07 (Fisher's exact test), Q value = 0.00013

Table S88. Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 27(11P11.2) CNV	26	34	10	24
DEL PEAK 27(11P11.2) WILD-TYPE	121	62	142	89

Figure S88. Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 27(11p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.095

Table S89. Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 27(11P11.2) CNV	10	47	37
DEL PEAK 27(11P11.2) WILD-TYPE	107	124	183

Figure S89. Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 27(11p11.2)' versus 'MIR_CHIERARCHICAL'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.0079

Table S90. Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
DEL PEAK 27(11P11.2) CNV	19	28	43
DEL PEAK 27(11P11.2) WILD-TYPE	162	127	92

Figure S90. Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 27(11p11.2)' versus 'CN_CNMF'

P value = 6.78e-13 (Fisher's exact test), Q value = 4.6e-10

Table S91. Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 27(11P11.2) CNV	54	36	10
DEL PEAK 27(11P11.2) WILD-TYPE	107	152	202

Figure S91. Get High-res Image Gene #51: 'Del Peak 27(11p11.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 28(11q14.1)' versus 'MRNA_CNMF'

P value = 1.29e-06 (Fisher's exact test), Q value = 0.00083

Table S92. Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 28(11Q14.1) CNV	29	33	12	14
DEL PEAK 28(11Q14.1) WILD-TYPE	118	63	140	99

Figure S92. Get High-res Image Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 28(11q14.1)' versus 'CN_CNMF'

P value = 5.38e-16 (Fisher's exact test), Q value = 3.7e-13

Table S93. Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 28(11Q14.1) CNV	60	24	10
DEL PEAK 28(11Q14.1) WILD-TYPE	101	164	202

Figure S93. Get High-res Image Gene #52: 'Del Peak 28(11q14.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 30(12q12)' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S94. Gene #54: 'Del Peak 30(12q12)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 30(12Q12) CNV	35	26	15
DEL PEAK 30(12Q12) WILD-TYPE	126	162	197

Figure S94. Get High-res Image Gene #54: 'Del Peak 30(12q12)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 31(12q15)' versus 'MRNA_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.077

Table S95. Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 31(12Q15) CNV	20	21	7	21
DEL PEAK 31(12Q15) WILD-TYPE	127	75	145	92

Figure S95. Get High-res Image Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 31(12q15)' versus 'MRNA_CHIERARCHICAL'

P value = 6.15e-05 (Fisher's exact test), Q value = 0.037

Table S96. Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 31(12Q15) CNV	4	35	30
DEL PEAK 31(12Q15) WILD-TYPE	113	136	190

Figure S96. Get High-res Image Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 31(12q15)' versus 'CN_CNMF'

P value = 6.36e-07 (Fisher's exact test), Q value = 0.00041

Table S97. Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 31(12Q15) CNV	40	25	12
DEL PEAK 31(12Q15) WILD-TYPE	121	163	200

Figure S97. Get High-res Image Gene #55: 'Del Peak 31(12q15)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 32(13q14.2)' versus 'MRNA_CNMF'

P value = 1.56e-07 (Fisher's exact test), Q value = 1e-04

Table S98. Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 32(13Q14.2) CNV	81	45	36	53
DEL PEAK 32(13Q14.2) WILD-TYPE	66	51	116	60

Figure S98. Get High-res Image Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 32(13q14.2)' versus 'MRNA_CHIERARCHICAL'

P value = 3.87e-05 (Fisher's exact test), Q value = 0.024

Table S99. Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 32(13Q14.2) CNV	29	78	108
DEL PEAK 32(13Q14.2) WILD-TYPE	88	93	112

Figure S99. Get High-res Image Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 32(13q14.2)' versus 'CN_CNMF'

P value = 3.48e-16 (Fisher's exact test), Q value = 2.4e-13

Table S100. Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 32(13Q14.2) CNV	101	90	45
DEL PEAK 32(13Q14.2) WILD-TYPE	60	98	167

Figure S100. Get High-res Image Gene #56: 'Del Peak 32(13q14.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 33(14q13.1)' versus 'MRNA_CNMF'

P value = 7.74e-06 (Fisher's exact test), Q value = 0.0048

Table S101. Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 33(14Q13.1) CNV	55	39	25	44
DEL PEAK 33(14Q13.1) WILD-TYPE	92	57	127	69

Figure S101. Get High-res Image Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 33(14q13.1)' versus 'CN_CNMF'

P value = 2.64e-29 (Fisher's exact test), Q value = 1.8e-26

Table S102. Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 33(14Q13.1) CNV	103	51	20
DEL PEAK 33(14Q13.1) WILD-TYPE	58	137	192

Figure S102. Get High-res Image Gene #57: 'Del Peak 33(14q13.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 34(14q24.2)' versus 'MRNA_CNMF'

P value = 1.26e-07 (Fisher's exact test), Q value = 8.3e-05

Table S103. Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 34(14Q24.2) CNV	52	42	22	46
DEL PEAK 34(14Q24.2) WILD-TYPE	95	54	130	67

Figure S103. Get High-res Image Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 34(14q24.2)' versus 'CN_CNMF'

P value = 1.24e-38 (Fisher's exact test), Q value = 8.7e-36

Table S104. Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 34(14Q24.2) CNV	107	51	11
DEL PEAK 34(14Q24.2) WILD-TYPE	54	137	201

Figure S104. Get High-res Image Gene #58: 'Del Peak 34(14q24.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 35(14q31.3)' versus 'MRNA_CNMF'

P value = 5.12e-09 (Fisher's exact test), Q value = 3.4e-06

Table S105. Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 35(14Q31.3) CNV	52	38	16	42
DEL PEAK 35(14Q31.3) WILD-TYPE	95	58	136	71

Figure S105. Get High-res Image Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(14q31.3)' versus 'CN_CNMF'

P value = 1.31e-40 (Fisher's exact test), Q value = 9.2e-38

Table S106. Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 35(14Q31.3) CNV	102	47	6
DEL PEAK 35(14Q31.3) WILD-TYPE	59	141	206

Figure S106. Get High-res Image Gene #59: 'Del Peak 35(14q31.3)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 36(15q14)' versus 'MRNA_CNMF'

P value = 7.11e-06 (Fisher's exact test), Q value = 0.0045

Table S107. Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 36(15Q14) CNV	35	38	23	43
DEL PEAK 36(15Q14) WILD-TYPE	112	58	129	70

Figure S107. Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 36(15q14)' versus 'MRNA_CHIERARCHICAL'

P value = 3.39e-08 (Fisher's exact test), Q value = 2.3e-05

Table S108. Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 36(15Q14) CNV	14	72	53
DEL PEAK 36(15Q14) WILD-TYPE	103	99	167

Figure S108. Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 36(15q14)' versus 'MIR_CHIERARCHICAL'

P value = 2.14e-06 (Fisher's exact test), Q value = 0.0014

Table S109. Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	181	155	135
DEL PEAK 36(15Q14) CNV	50	23	56
DEL PEAK 36(15Q14) WILD-TYPE	131	132	79

Figure S109. Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'Del Peak 36(15q14)' versus 'CN_CNMF'

P value = 3.91e-07 (Fisher's exact test), Q value = 0.00025

Table S110. Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 36(15Q14) CNV	68	43	37
DEL PEAK 36(15Q14) WILD-TYPE	93	145	175

Figure S110. Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 36(15q14)' versus 'MRNASEQ_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.2

Table S111. Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	67	36
DEL PEAK 36(15Q14) CNV	24	14	7
DEL PEAK 36(15Q14) WILD-TYPE	20	53	29

Figure S111. Get High-res Image Gene #60: 'Del Peak 36(15q14)' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'Del Peak 39(17p13.2)' versus 'CN_CNMF'

P value = 4.96e-10 (Fisher's exact test), Q value = 3.4e-07

Table S112. Gene #63: 'Del Peak 39(17p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 39(17P13.2) CNV	42	34	8
DEL PEAK 39(17P13.2) WILD-TYPE	119	154	204

Figure S112. Get High-res Image Gene #63: 'Del Peak 39(17p13.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 40(17p13.1)' versus 'CN_CNMF'

P value = 4.73e-15 (Fisher's exact test), Q value = 3.3e-12

Table S113. Gene #64: 'Del Peak 40(17p13.1)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 40(17P13.1) CNV	52	36	6
DEL PEAK 40(17P13.1) WILD-TYPE	109	152	206

Figure S113. Get High-res Image Gene #64: 'Del Peak 40(17p13.1)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 41(17q11.2)' versus 'MRNA_CNMF'

P value = 7.34e-06 (Fisher's exact test), Q value = 0.0046

Table S114. Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 41(17Q11.2) CNV	35	9	12	5
DEL PEAK 41(17Q11.2) WILD-TYPE	112	87	140	108

Figure S114. Get High-res Image Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 41(17q11.2)' versus 'CN_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00068

Table S115. Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 41(17Q11.2) CNV	30	32	8
DEL PEAK 41(17Q11.2) WILD-TYPE	131	156	204

Figure S115. Get High-res Image Gene #65: 'Del Peak 41(17q11.2)' versus Molecular Subtype #5: 'CN_CNMF'

'Del Peak 43(19q13.41)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000155 (Fisher's exact test), Q value = 0.092

Table S116. Gene #67: 'Del Peak 43(19q13.41)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	117	171	220
DEL PEAK 43(19Q13.41) CNV	12	48	32
DEL PEAK 43(19Q13.41) WILD-TYPE	105	123	188

Figure S116. Get High-res Image Gene #67: 'Del Peak 43(19q13.41)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 44(21q22.3)' versus 'MIR_CNMF'

P value = 8.73e-05 (Fisher's exact test), Q value = 0.052

Table S117. Gene #68: 'Del Peak 44(21q22.3)' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	139	155	73	104
DEL PEAK 44(21Q22.3) CNV	8	32	8	5
DEL PEAK 44(21Q22.3) WILD-TYPE	131	123	65	99

Figure S117. Get High-res Image Gene #68: 'Del Peak 44(21q22.3)' versus Molecular Subtype #3: 'MIR_CNMF'

'Del Peak 46(Xp22.2)' versus 'CN_CNMF'

P value = 8.52e-10 (Fisher's exact test), Q value = 5.7e-07

Table S118. Gene #70: 'Del Peak 46(Xp22.2)' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	161	188	212
DEL PEAK 46(XP22.2) CNV	65	29	29
DEL PEAK 46(XP22.2) WILD-TYPE	96	159	183

Figure S118. Get High-res Image Gene #70: 'Del Peak 46(Xp22.2)' versus Molecular Subtype #5: 'CN_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = GBM-TP.transferedmergedcluster.txt
Number of patients = 561
Number of copy number variation regions = 70
Number of molecular subtypes = 10
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

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] 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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