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 68 peak regions and 10 molecular subtypes across 413 patients, 150 significant findings detected with Q value < 0.25.

Amp Peak 1(2q33.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(5p13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 4(6p21.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(8p11.23) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(8p11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(8q12.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 8(8q24.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(11p15.5) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
Amp Peak 11(13q12.13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 12(13q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 13(16p11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 14(16q12.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
Amp Peak 15(17q12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 16(17q24.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 17(19p13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 19(20p12.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 20(20p11.23) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(20p11.21) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 22(20q11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 23(20q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Amp Peak 24(20q13.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 1(1p36.11) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 2(1p33) cnvs correlated to 'CN_CNMF'.
Del Peak 3(1p13.1) cnvs correlated to 'CN_CNMF'.
Del Peak 4(1q43) cnvs correlated to 'CN_CNMF'.
Del Peak 6(3p26.1) cnvs correlated to 'CN_CNMF'.
Del Peak 9(4p16.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 10(4q22.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 11(4q35.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 13(5q21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 14(5q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 15(6p25.3) cnvs correlated to 'CN_CNMF'.
Del Peak 18(8p23.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 19(8p22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
Del Peak 20(8p11.22) cnvs correlated to 'CN_CNMF'.
Del Peak 21(8p11.21) cnvs correlated to 'CN_CNMF'.
Del Peak 22(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 23(10p15.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(10q21.1) cnvs correlated to 'CN_CNMF'.
Del Peak 25(10q23.31) cnvs correlated to 'CN_CNMF'.
Del Peak 26(10q25.2) cnvs correlated to 'CN_CNMF'.
Del Peak 27(12p13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 28(13q14.13) cnvs correlated to 'CN_CNMF'.
Del Peak 29(14q32.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
Del Peak 30(15q11.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 31(15q21.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 32(15q22.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 35(17p12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 37(18p11.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 38(18q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 39(18q21.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 40(18q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 42(20p12.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 43(21q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 44(22q13.32) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 68 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 150 significant findings detected.


		Molecular subtypes	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 22(20q11 21)	0 (0%)	117	1.07e-10 (6.69e-08)	2.86e-11 (1.8e-08)	1.54e-43 (1.04e-40)	2.19e-09 (1.34e-06)	0.0201 (1.00)	0.000108 (0.06)	1.47e-14 (9.62e-12)	3.85e-12 (2.47e-09)	0.443 (1.00)	1 (1.00)
Amp Peak 23(20q12)	0 (0%)	116	9.28e-12 (5.91e-09)	1.82e-11 (1.15e-08)	6.28e-43 (4.24e-40)	1.58e-08 (9.58e-06)	0.00771 (1.00)	2.18e-05 (0.0125)	5.48e-14 (3.59e-11)	1.34e-11 (8.53e-09)	0.406 (1.00)	0.948 (1.00)
Amp Peak 24(20q13 32)	0 (0%)	113	2.87e-10 (1.79e-07)	6.27e-12 (4e-09)	3.18e-43 (2.15e-40)	1.58e-08 (9.58e-06)	0.00832 (1.00)	1.3e-05 (0.00749)	5.48e-14 (3.59e-11)	1.34e-11 (8.53e-09)	0.414 (1.00)	0.96 (1.00)
Del Peak 35(17p12)	0 (0%)	184	6.12e-08 (3.66e-05)	1.6e-06 (0.000933)	2.81e-35 (1.89e-32)	1.8e-09 (1.11e-06)	0.0465 (1.00)	7.42e-05 (0.0416)	1.06e-10 (6.61e-08)	3.2e-08 (1.92e-05)	0.363 (1.00)	0.729 (1.00)
Del Peak 38(18q12 2)	0 (0%)	166	8.37e-11 (5.25e-08)	1.08e-09 (6.69e-07)	1.87e-45 (1.27e-42)	8.98e-16 (5.9e-13)	0.0214 (1.00)	0.000421 (0.226)	7.66e-16 (5.04e-13)	1.07e-08 (6.52e-06)	0.449 (1.00)	0.865 (1.00)
Del Peak 39(18q21 2)	0 (0%)	153	3.06e-10 (1.91e-07)	6.85e-10 (4.25e-07)	1.51e-45 (1.03e-42)	3.29e-12 (2.11e-09)	0.0109 (1.00)	0.000225 (0.122)	8.74e-13 (5.66e-10)	7.14e-07 (0.000421)	0.0517 (1.00)	0.901 (1.00)
Del Peak 40(18q22 1)	0 (0%)	153	6.92e-11 (4.35e-08)	3.65e-09 (2.23e-06)	1.58e-47 (1.07e-44)	2.02e-12 (1.3e-09)	0.0178 (1.00)	0.000224 (0.122)	4.05e-12 (2.59e-09)	2.76e-07 (0.000164)	0.0746 (1.00)	0.912 (1.00)
Amp Peak 11(13q12 13)	0 (0%)	163	7.21e-08 (4.31e-05)	5.27e-06 (0.00307)	5.04e-36 (3.39e-33)	0.00027 (0.146)	0.0709 (1.00)	0.0124 (1.00)	1.27e-06 (0.000745)	0.000196 (0.107)	0.459 (1.00)	0.798 (1.00)
Del Peak 37(18p11 31)	0 (0%)	193	1.51e-12 (9.71e-10)	3.65e-09 (2.23e-06)	1.93e-42 (1.3e-39)	3.11e-13 (2.02e-10)	0.0023 (1.00)	0.00104 (0.527)	3.11e-17 (2.06e-14)	8.19e-10 (5.07e-07)	0.48 (1.00)	0.841 (1.00)
Amp Peak 12(13q22 1)	0 (0%)	159	6.34e-05 (0.0358)	5.43e-05 (0.0307)	7.2e-33 (4.83e-30)	0.00051 (0.27)	0.152 (1.00)	0.0444 (1.00)	1.15e-06 (0.000674)	7.67e-05 (0.0429)	0.272 (1.00)	0.977 (1.00)
Amp Peak 13(16p11 2)	0 (0%)	297	0.000447 (0.237)	0.000375 (0.202)	8.55e-19 (5.67e-16)	0.0212 (1.00)	0.373 (1.00)	0.033 (1.00)	0.000429 (0.229)	0.00838 (1.00)	0.771 (1.00)	0.809 (1.00)
Amp Peak 21(20p11 21)	0 (0%)	183	0.000692 (0.359)	4.27e-05 (0.0243)	4e-23 (2.67e-20)	0.00113 (0.572)	0.0624 (1.00)	0.0394 (1.00)	2.41e-07 (0.000143)	1.39e-06 (0.000812)	0.174 (1.00)	0.509 (1.00)
Del Peak 11(4q35 1)	0 (0%)	276	0.000128 (0.0703)	0.00928 (1.00)	1.05e-13 (6.82e-11)	7.69e-05 (0.043)	0.173 (1.00)	0.146 (1.00)	0.000239 (0.129)	0.000527 (0.278)	0.416 (1.00)	0.235 (1.00)
Del Peak 19(8p22)	0 (0%)	228	0.00115 (0.579)	0.000958 (0.489)	2.41e-30 (1.61e-27)	3.46e-07 (0.000205)	0.0649 (1.00)	0.00013 (0.0714)	2.16e-05 (0.0124)	0.000656 (0.343)	0.115 (1.00)	0.832 (1.00)
Del Peak 29(14q32 11)	0 (0%)	280	2.12e-05 (0.0122)	0.00011 (0.061)	1.61e-20 (1.07e-17)	0.000707 (0.366)	0.00347 (1.00)	0.0236 (1.00)	7.3e-05 (0.041)	0.00084 (0.431)	0.319 (1.00)	0.0612 (1.00)
Del Peak 30(15q11 2)	0 (0%)	253	0.000422 (0.226)	0.00683 (1.00)	1.2e-21 (7.98e-19)	0.00432 (1.00)	0.0746 (1.00)	0.07 (1.00)	2.09e-06 (0.00122)	0.000117 (0.0647)	0.877 (1.00)	0.893 (1.00)
Del Peak 32(15q22 33)	0 (0%)	268	0.000758 (0.391)	0.00327 (1.00)	2.48e-21 (1.65e-18)	0.000435 (0.231)	0.141 (1.00)	0.0512 (1.00)	3.07e-08 (1.84e-05)	7.55e-06 (0.00437)	0.949 (1.00)	0.365 (1.00)
Amp Peak 9(11p15 5)	0 (0%)	327	1.38e-05 (0.00795)	0.000201 (0.11)	1.54e-09 (9.48e-07)	0.000612 (0.321)	0.00156 (0.777)	0.00358 (1.00)	0.00193 (0.959)	0.00845 (1.00)	0.117 (1.00)	0.201 (1.00)
Amp Peak 14(16q12 1)	0 (0%)	311	3.02e-05 (0.0173)	0.000126 (0.0696)	1.67e-20 (1.11e-17)	0.0511 (1.00)	0.619 (1.00)	0.081 (1.00)	0.000642 (0.336)	0.00254 (1.00)	0.902 (1.00)	0.93 (1.00)
Del Peak 1(1p36 11)	0 (0%)	263	6.81e-05 (0.0384)	0.00576 (1.00)	6.32e-17 (4.17e-14)	0.000792 (0.408)	0.0155 (1.00)	0.0238 (1.00)	0.000347 (0.187)	0.0012 (0.604)	0.409 (1.00)	0.0624 (1.00)
Del Peak 9(4p16 2)	0 (0%)	292	0.00194 (0.963)	0.0107 (1.00)	1.16e-12 (7.47e-10)	0.011 (1.00)	0.442 (1.00)	0.0866 (1.00)	0.000237 (0.129)	0.000107 (0.0594)	0.376 (1.00)	0.206 (1.00)
Del Peak 10(4q22 1)	0 (0%)	287	0.000585 (0.308)	0.00864 (1.00)	8.5e-12 (5.42e-09)	0.00207 (1.00)	0.516 (1.00)	0.391 (1.00)	9.23e-05 (0.0515)	2.81e-05 (0.0161)	0.21 (1.00)	0.518 (1.00)
Del Peak 31(15q21 1)	0 (0%)	262	0.013 (1.00)	0.0411 (1.00)	8.15e-18 (5.39e-15)	0.00747 (1.00)	0.0441 (1.00)	0.0657 (1.00)	2.03e-07 (0.000121)	2.05e-05 (0.0118)	0.979 (1.00)	0.621 (1.00)
Amp Peak 15(17q12)	0 (0%)	312	0.0989 (1.00)	0.0852 (1.00)	7.53e-07 (0.000443)	0.0164 (1.00)	0.582 (1.00)	0.00276 (1.00)	4.59e-05 (0.026)	0.0142 (1.00)	0.0121 (1.00)	0.986 (1.00)
Amp Peak 16(17q24 1)	0 (0%)	321	0.0519 (1.00)	0.00821 (1.00)	1.61e-08 (9.69e-06)	0.0123 (1.00)	0.304 (1.00)	0.00527 (1.00)	6.04e-06 (0.00351)	0.00312 (1.00)	0.00254 (1.00)	0.781 (1.00)
Del Peak 18(8p23 3)	0 (0%)	242	0.00276 (1.00)	0.000603 (0.316)	6.84e-26 (4.58e-23)	3.61e-06 (0.00211)	0.0514 (1.00)	0.00096 (0.489)	0.000672 (0.35)	0.00231 (1.00)	0.154 (1.00)	0.848 (1.00)
Del Peak 42(20p12 1)	0 (0%)	334	0.0656 (1.00)	0.173 (1.00)	1.38e-13 (8.97e-11)	0.00404 (1.00)	0.323 (1.00)	0.278 (1.00)	0.00015 (0.082)	0.00674 (1.00)	0.0931 (1.00)	0.101 (1.00)
Del Peak 44(22q13 32)	0 (0%)	275	0.000428 (0.229)	0.000747 (0.386)	9.76e-13 (6.32e-10)	0.0049 (1.00)	0.306 (1.00)	0.218 (1.00)	0.00222 (1.00)	0.00106 (0.537)	0.394 (1.00)	0.069 (1.00)
Amp Peak 1(2q33 1)	0 (0%)	334	0.0734 (1.00)	0.105 (1.00)	3.05e-05 (0.0174)	0.258 (1.00)	0.245 (1.00)	0.0652 (1.00)	0.000516 (0.272)	0.0137 (1.00)	0.277 (1.00)	0.258 (1.00)
Amp Peak 2(5p13 2)	0 (0%)	332	0.334 (1.00)	0.469 (1.00)	0.000202 (0.11)	0.15 (1.00)	0.00999 (1.00)	0.724 (1.00)	0.0864 (1.00)	0.0696 (1.00)	0.927 (1.00)	0.581 (1.00)
Amp Peak 4(6p21 1)	0 (0%)	324	0.0902 (1.00)	0.000996 (0.506)	3.37e-09 (2.06e-06)	0.17 (1.00)	0.83 (1.00)	0.178 (1.00)	0.00644 (1.00)	0.033 (1.00)	0.776 (1.00)	0.258 (1.00)
Amp Peak 5(8p11 23)	0 (0%)	269	0.444 (1.00)	0.231 (1.00)	2.99e-13 (1.94e-10)	0.868 (1.00)	0.864 (1.00)	0.733 (1.00)	0.211 (1.00)	0.783 (1.00)	0.179 (1.00)	0.189 (1.00)
Amp Peak 6(8p11 21)	0 (0%)	240	0.355 (1.00)	0.129 (1.00)	4.51e-10 (2.8e-07)	0.886 (1.00)	0.27 (1.00)	0.00672 (1.00)	0.421 (1.00)	0.606 (1.00)	0.502 (1.00)	0.218 (1.00)
Amp Peak 7(8q12 1)	0 (0%)	198	0.15 (1.00)	0.0646 (1.00)	9.31e-12 (5.92e-09)	0.0383 (1.00)	0.0228 (1.00)	0.00068 (0.354)	0.0141 (1.00)	0.228 (1.00)	0.126 (1.00)	0.295 (1.00)
Amp Peak 8(8q24 21)	0 (0%)	174	0.203 (1.00)	0.107 (1.00)	7.86e-14 (5.13e-11)	0.0102 (1.00)	0.103 (1.00)	0.0104 (1.00)	0.00636 (1.00)	0.445 (1.00)	0.404 (1.00)	0.215 (1.00)
Amp Peak 17(19p13 2)	0 (0%)	348	0.0535 (1.00)	0.0345 (1.00)	4.82e-05 (0.0273)	0.283 (1.00)	0.734 (1.00)	0.341 (1.00)	0.501 (1.00)	0.539 (1.00)	0.204 (1.00)	0.385 (1.00)
Amp Peak 19(20p12 3)	0 (0%)	229	0.00188 (0.936)	0.000844 (0.432)	1.86e-12 (1.2e-09)	0.434 (1.00)	0.0113 (1.00)	0.478 (1.00)	0.0305 (1.00)	0.00972 (1.00)	0.597 (1.00)	0.195 (1.00)
Amp Peak 20(20p11 23)	0 (0%)	208	0.0267 (1.00)	0.000792 (0.408)	1.26e-16 (8.32e-14)	0.105 (1.00)	0.0479 (1.00)	0.183 (1.00)	0.000513 (0.271)	0.00104 (0.527)	0.455 (1.00)	0.212 (1.00)
Del Peak 2(1p33)	0 (0%)	306	0.0246 (1.00)	0.532 (1.00)	1.09e-11 (6.91e-09)	0.00668 (1.00)	0.556 (1.00)	0.395 (1.00)	0.0051 (1.00)	0.0141 (1.00)	0.893 (1.00)	0.0519 (1.00)
Del Peak 3(1p13 1)	0 (0%)	310	0.115 (1.00)	0.374 (1.00)	6.85e-10 (4.25e-07)	0.185 (1.00)	0.56 (1.00)	0.89 (1.00)	0.0836 (1.00)	0.00481 (1.00)	0.868 (1.00)	0.379 (1.00)
Del Peak 4(1q43)	0 (0%)	369	0.0983 (1.00)	0.458 (1.00)	6.98e-06 (0.00405)	0.105 (1.00)	0.393 (1.00)	0.664 (1.00)	0.0312 (1.00)	0.0114 (1.00)	0.335 (1.00)	0.301 (1.00)
Del Peak 6(3p26 1)	0 (0%)	353	0.0994 (1.00)	0.304 (1.00)	0.00043 (0.229)	0.268 (1.00)	0.942 (1.00)	0.861 (1.00)	0.539 (1.00)	0.0883 (1.00)	0.541 (1.00)	0.958 (1.00)
Del Peak 12(5q11 2)	0 (0%)	322	0.00129 (0.648)	0.00378 (1.00)	4.94e-09 (3.01e-06)	0.0339 (1.00)	0.048 (1.00)	0.0118 (1.00)	0.00142 (0.711)	0.00781 (1.00)	0.835 (1.00)	0.215 (1.00)
Del Peak 13(5q21 3)	0 (0%)	296	0.118 (1.00)	0.0281 (1.00)	1.14e-09 (7.04e-07)	0.0359 (1.00)	0.0651 (1.00)	0.0971 (1.00)	0.00438 (1.00)	0.0104 (1.00)	0.654 (1.00)	0.36 (1.00)
Del Peak 14(5q23 1)	0 (0%)	306	0.0628 (1.00)	0.0356 (1.00)	1.57e-08 (9.52e-06)	0.087 (1.00)	0.044 (1.00)	0.15 (1.00)	0.0219 (1.00)	0.0126 (1.00)	0.622 (1.00)	0.246 (1.00)
Del Peak 15(6p25 3)	0 (0%)	359	0.971 (1.00)	0.792 (1.00)	0.000102 (0.0571)	0.0527 (1.00)	0.337 (1.00)	0.828 (1.00)	0.353 (1.00)	0.788 (1.00)	0.406 (1.00)	0.453 (1.00)
Del Peak 20(8p11 22)	0 (0%)	333	0.213 (1.00)	0.118 (1.00)	8.88e-09 (5.4e-06)	0.0614 (1.00)	0.049 (1.00)	0.00534 (1.00)	0.0993 (1.00)	0.0804 (1.00)	0.359 (1.00)	0.831 (1.00)
Del Peak 21(8p11 21)	0 (0%)	370	0.0231 (1.00)	0.351 (1.00)	5.81e-07 (0.000343)	0.366 (1.00)	0.156 (1.00)	0.024 (1.00)	0.483 (1.00)	0.308 (1.00)	0.0997 (1.00)	0.549 (1.00)
Del Peak 22(9p21 3)	0 (0%)	357	0.251 (1.00)	0.264 (1.00)	4.51e-05 (0.0256)	0.204 (1.00)	0.768 (1.00)	0.214 (1.00)	0.0637 (1.00)	0.127 (1.00)	0.904 (1.00)	0.663 (1.00)
Del Peak 23(10p15 3)	0 (0%)	345	0.261 (1.00)	0.141 (1.00)	2.25e-08 (1.35e-05)	0.0291 (1.00)	0.0673 (1.00)	0.104 (1.00)	0.126 (1.00)	0.034 (1.00)	0.68 (1.00)	0.566 (1.00)
Del Peak 24(10q21 1)	0 (0%)	331	0.00928 (1.00)	0.0374 (1.00)	2.24e-11 (1.41e-08)	0.194 (1.00)	0.277 (1.00)	0.144 (1.00)	0.191 (1.00)	0.0431 (1.00)	0.887 (1.00)	0.831 (1.00)
Del Peak 25(10q23 31)	0 (0%)	319	0.249 (1.00)	0.0829 (1.00)	3.46e-07 (0.000205)	0.0801 (1.00)	0.123 (1.00)	0.375 (1.00)	0.0348 (1.00)	0.165 (1.00)	0.885 (1.00)	0.985 (1.00)
Del Peak 26(10q25 2)	0 (0%)	320	0.172 (1.00)	0.0105 (1.00)	1.91e-11 (1.21e-08)	0.0139 (1.00)	0.03 (1.00)	0.319 (1.00)	0.00312 (1.00)	0.0025 (1.00)	0.921 (1.00)	0.593 (1.00)
Del Peak 27(12p13 2)	0 (0%)	369	0.0404 (1.00)	0.00796 (1.00)	9.87e-08 (5.89e-05)	0.207 (1.00)	0.383 (1.00)	0.87 (1.00)	0.0262 (1.00)	0.00369 (1.00)	0.695 (1.00)	0.973 (1.00)
Del Peak 28(13q14 13)	0 (0%)	395	0.395 (1.00)	0.876 (1.00)	0.000128 (0.0703)	0.153 (1.00)	0.212 (1.00)	0.34 (1.00)	0.228 (1.00)	0.452 (1.00)	0.614 (1.00)	0.834 (1.00)
Del Peak 43(21q11 2)	0 (0%)	288	0.00298 (1.00)	0.0933 (1.00)	3.37e-09 (2.06e-06)	0.0302 (1.00)	0.236 (1.00)	0.455 (1.00)	0.000897 (0.458)	0.0187 (1.00)	0.923 (1.00)	0.47 (1.00)
Amp Peak 3(5q22 3)	0 (0%)	373	0.78 (1.00)	0.629 (1.00)	0.0293 (1.00)	0.875 (1.00)	0.394 (1.00)	0.494 (1.00)	0.165 (1.00)	0.112 (1.00)	0.693 (1.00)	0.839 (1.00)
Amp Peak 10(12p13 33)	0 (0%)	309	0.463 (1.00)	0.882 (1.00)	0.0612 (1.00)	0.247 (1.00)	0.429 (1.00)	0.958 (1.00)	0.334 (1.00)	0.977 (1.00)	0.304 (1.00)	0.173 (1.00)
Amp Peak 18(19q13 11)	0 (0%)	330	0.332 (1.00)	0.0177 (1.00)	0.002 (0.988)	0.517 (1.00)	0.173 (1.00)	0.688 (1.00)	0.0736 (1.00)	0.167 (1.00)	0.417 (1.00)	0.491 (1.00)
Del Peak 5(2q37 2)	0 (0%)	392	0.928 (1.00)	0.0598 (1.00)	0.977 (1.00)	0.701 (1.00)	0.23 (1.00)	0.208 (1.00)	1 (1.00)	0.184 (1.00)	0.447 (1.00)	0.447 (1.00)
Del Peak 7(3p14 2)	0 (0%)	338	0.466 (1.00)	0.744 (1.00)	0.205 (1.00)	0.735 (1.00)	0.566 (1.00)	0.29 (1.00)	0.632 (1.00)	0.483 (1.00)	0.203 (1.00)	0.536 (1.00)
Del Peak 8(3q26 31)	0 (0%)	374	0.122 (1.00)	0.605 (1.00)	0.00818 (1.00)	0.497 (1.00)	0.288 (1.00)	0.369 (1.00)	0.458 (1.00)	0.0223 (1.00)	0.15 (1.00)	0.939 (1.00)
Del Peak 16(6q26)	0 (0%)	353	0.383 (1.00)	0.304 (1.00)	0.157 (1.00)	0.356 (1.00)	0.189 (1.00)	0.355 (1.00)	0.873 (1.00)	0.697 (1.00)	0.797 (1.00)	0.53 (1.00)
Del Peak 17(7q31 1)	0 (0%)	402	1 (1.00)	0.504 (1.00)	0.816 (1.00)	0.795 (1.00)	0.354 (1.00)	0.219 (1.00)	0.49 (1.00)	1 (1.00)	1 (1.00)	0.564 (1.00)
Del Peak 33(16p13 3)	0 (0%)	368	0.334 (1.00)	0.155 (1.00)	0.208 (1.00)	0.376 (1.00)	0.418 (1.00)	0.913 (1.00)	0.62 (1.00)	0.572 (1.00)	0.842 (1.00)	0.739 (1.00)
Del Peak 34(16q23 1)	0 (0%)	364	0.259 (1.00)	0.00785 (1.00)	0.131 (1.00)	0.337 (1.00)	0.489 (1.00)	0.821 (1.00)	0.0421 (1.00)	0.0701 (1.00)	0.977 (1.00)	0.505 (1.00)
Del Peak 36(17q24 3)	0 (0%)	354	0.102 (1.00)	0.676 (1.00)	0.00348 (1.00)	0.0118 (1.00)	0.874 (1.00)	0.338 (1.00)	0.00329 (1.00)	0.0329 (1.00)	0.681 (1.00)	0.979 (1.00)
Del Peak 41(19p13 3)	0 (0%)	356	0.268 (1.00)	0.198 (1.00)	0.00362 (1.00)	0.565 (1.00)	0.88 (1.00)	0.0676 (1.00)	0.0512 (1.00)	0.0244 (1.00)	0.582 (1.00)	0.0166 (1.00)

'Amp Peak 1(2q33.1)' versus 'CN_CNMF'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.017

Table S1. Gene #1: 'Amp Peak 1(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 1(2Q33.1) CNV	49	18	8	4
AMP PEAK 1(2Q33.1) WILD-TYPE	121	169	24	20

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(5p13.2)' versus 'CN_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.11

Table S2. Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 2(5P13.2) CNV	46	20	10	5
AMP PEAK 2(5P13.2) WILD-TYPE	124	167	22	19

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(6p21.1)' versus 'CN_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.1e-06

Table S3. Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 4(6P21.1) CNV	61	16	8	4
AMP PEAK 4(6P21.1) WILD-TYPE	109	171	24	20

Figure S3. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(8p11.23)' versus 'CN_CNMF'

P value = 2.99e-13 (Fisher's exact test), Q value = 1.9e-10

Table S4. Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 5(8P11.23) CNV	56	47	17	24
AMP PEAK 5(8P11.23) WILD-TYPE	114	140	15	0

Figure S4. Get High-res Image Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(8p11.21)' versus 'CN_CNMF'

P value = 4.51e-10 (Fisher's exact test), Q value = 2.8e-07

Table S5. Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 6(8P11.21) CNV	75	55	21	22
AMP PEAK 6(8P11.21) WILD-TYPE	95	132	11	2

Figure S5. Get High-res Image Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(8q12.1)' versus 'CN_CNMF'

P value = 9.31e-12 (Fisher's exact test), Q value = 5.9e-09

Table S6. Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 7(8Q12.1) CNV	106	64	23	22
AMP PEAK 7(8Q12.1) WILD-TYPE	64	123	9	2

Figure S6. Get High-res Image Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 7.86e-14 (Fisher's exact test), Q value = 5.1e-11

Table S7. Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 8(8Q24.21) CNV	119	73	23	24
AMP PEAK 8(8Q24.21) WILD-TYPE	51	114	9	0

Figure S7. Get High-res Image Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(11p15.5)' versus 'MRNA_CNMF'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0079

Table S8. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
AMP PEAK 9(11P15.5) CNV	1	17	3	13
AMP PEAK 9(11P15.5) WILD-TYPE	30	45	27	10

Figure S8. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 9(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000201 (Fisher's exact test), Q value = 0.11

Table S9. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
AMP PEAK 9(11P15.5) CNV	14	2	18
AMP PEAK 9(11P15.5) WILD-TYPE	42	42	28

Figure S9. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 9(11p15.5)' versus 'CN_CNMF'

P value = 1.54e-09 (Fisher's exact test), Q value = 9.5e-07

Table S10. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 9(11P15.5) CNV	54	17	14	1
AMP PEAK 9(11P15.5) WILD-TYPE	116	170	18	23

Figure S10. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNA_CNMF'

P value = 7.21e-08 (Fisher's exact test), Q value = 4.3e-05

Table S11. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
AMP PEAK 11(13Q12.13) CNV	14	52	8	18
AMP PEAK 11(13Q12.13) WILD-TYPE	17	10	22	5

Figure S11. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNA_CHIERARCHICAL'

P value = 5.27e-06 (Fisher's exact test), Q value = 0.0031

Table S12. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
AMP PEAK 11(13Q12.13) CNV	39	15	38
AMP PEAK 11(13Q12.13) WILD-TYPE	17	29	8

Figure S12. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 11(13q12.13)' versus 'CN_CNMF'

P value = 5.04e-36 (Fisher's exact test), Q value = 3.4e-33

Table S13. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 11(13Q12.13) CNV	158	57	18	17
AMP PEAK 11(13Q12.13) WILD-TYPE	12	130	14	7

Figure S13. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(13q12.13)' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.15

Table S14. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
AMP PEAK 11(13Q12.13) CNV	79	42	33
AMP PEAK 11(13Q12.13) WILD-TYPE	26	44	30

Figure S14. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNASEQ_CNMF'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.00075

Table S15. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 11(13Q12.13) CNV	22	46	26	16
AMP PEAK 11(13Q12.13) WILD-TYPE	9	13	21	38

Figure S15. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000196 (Fisher's exact test), Q value = 0.11

Table S16. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 11(13Q12.13) CNV	16	43	51
AMP PEAK 11(13Q12.13) WILD-TYPE	33	19	29

Figure S16. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(13q22.1)' versus 'MRNA_CNMF'

P value = 6.34e-05 (Fisher's exact test), Q value = 0.036

Table S17. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
AMP PEAK 12(13Q22.1) CNV	15	49	10	17
AMP PEAK 12(13Q22.1) WILD-TYPE	16	13	20	6

Figure S17. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 5.43e-05 (Fisher's exact test), Q value = 0.031

Table S18. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
AMP PEAK 12(13Q22.1) CNV	38	16	37
AMP PEAK 12(13Q22.1) WILD-TYPE	18	28	9

Figure S18. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(13q22.1)' versus 'CN_CNMF'

P value = 7.2e-33 (Fisher's exact test), Q value = 4.8e-30

Table S19. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 12(13Q22.1) CNV	158	63	17	16
AMP PEAK 12(13Q22.1) WILD-TYPE	12	124	15	8

Figure S19. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNASEQ_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00067

Table S20. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 12(13Q22.1) CNV	22	49	25	19
AMP PEAK 12(13Q22.1) WILD-TYPE	9	10	22	35

Figure S20. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.67e-05 (Fisher's exact test), Q value = 0.043

Table S21. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 12(13Q22.1) CNV	17	46	52
AMP PEAK 12(13Q22.1) WILD-TYPE	32	16	28

Figure S21. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(16p11.2)' versus 'MRNA_CNMF'

P value = 0.000447 (Fisher's exact test), Q value = 0.24

Table S22. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
AMP PEAK 13(16P11.2) CNV	5	23	3	13
AMP PEAK 13(16P11.2) WILD-TYPE	26	39	27	10

Figure S22. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 13(16p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000375 (Fisher's exact test), Q value = 0.2

Table S23. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
AMP PEAK 13(16P11.2) CNV	13	7	24
AMP PEAK 13(16P11.2) WILD-TYPE	43	37	22

Figure S23. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 13(16p11.2)' versus 'CN_CNMF'

P value = 8.55e-19 (Fisher's exact test), Q value = 5.7e-16

Table S24. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 13(16P11.2) CNV	88	18	8	2
AMP PEAK 13(16P11.2) WILD-TYPE	82	169	24	22

Figure S24. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(16p11.2)' versus 'MRNASEQ_CNMF'

P value = 0.000429 (Fisher's exact test), Q value = 0.23

Table S25. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 13(16P11.2) CNV	8	24	13	4
AMP PEAK 13(16P11.2) WILD-TYPE	23	35	34	50

Figure S25. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 14(16q12.1)' versus 'MRNA_CNMF'

P value = 3.02e-05 (Fisher's exact test), Q value = 0.017

Table S26. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
AMP PEAK 14(16Q12.1) CNV	3	21	2	13
AMP PEAK 14(16Q12.1) WILD-TYPE	28	41	28	10

Figure S26. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 14(16q12.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000126 (Fisher's exact test), Q value = 0.07

Table S27. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
AMP PEAK 14(16Q12.1) CNV	13	4	22
AMP PEAK 14(16Q12.1) WILD-TYPE	43	40	24

Figure S27. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 14(16q12.1)' versus 'CN_CNMF'

P value = 1.67e-20 (Fisher's exact test), Q value = 1.1e-17

Table S28. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 14(16Q12.1) CNV	82	12	7	1
AMP PEAK 14(16Q12.1) WILD-TYPE	88	175	25	23

Figure S28. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(17q12)' versus 'CN_CNMF'

P value = 7.53e-07 (Fisher's exact test), Q value = 0.00044

Table S29. Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 15(17Q12) CNV	62	23	8	8
AMP PEAK 15(17Q12) WILD-TYPE	108	164	24	16

Figure S29. Get High-res Image Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(17q12)' versus 'MRNASEQ_CNMF'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.026

Table S30. Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 15(17Q12) CNV	8	26	6	5
AMP PEAK 15(17Q12) WILD-TYPE	23	33	41	49

Figure S30. Get High-res Image Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 16(17q24.1)' versus 'CN_CNMF'

P value = 1.61e-08 (Fisher's exact test), Q value = 9.7e-06

Table S31. Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 16(17Q24.1) CNV	59	17	8	8
AMP PEAK 16(17Q24.1) WILD-TYPE	111	170	24	16

Figure S31. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(17q24.1)' versus 'MRNASEQ_CNMF'

P value = 6.04e-06 (Fisher's exact test), Q value = 0.0035

Table S32. Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 16(17Q24.1) CNV	9	26	4	5
AMP PEAK 16(17Q24.1) WILD-TYPE	22	33	43	49

Figure S32. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 17(19p13.2)' versus 'CN_CNMF'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.027

Table S33. Gene #17: 'Amp Peak 17(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 17(19P13.2) CNV	39	13	8	5
AMP PEAK 17(19P13.2) WILD-TYPE	131	174	24	19

Figure S33. Get High-res Image Gene #17: 'Amp Peak 17(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(20p12.3)' versus 'CN_CNMF'

P value = 1.86e-12 (Fisher's exact test), Q value = 1.2e-09

Table S34. Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 19(20P12.3) CNV	83	58	31	12
AMP PEAK 19(20P12.3) WILD-TYPE	87	129	1	12

Figure S34. Get High-res Image Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(20p11.23)' versus 'CN_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 8.3e-14

Table S35. Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 20(20P11.23) CNV	102	58	32	13
AMP PEAK 20(20P11.23) WILD-TYPE	68	129	0	11

Figure S35. Get High-res Image Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(20p11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 4.27e-05 (Fisher's exact test), Q value = 0.024

Table S36. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
AMP PEAK 21(20P11.21) CNV	38	12	31
AMP PEAK 21(20P11.21) WILD-TYPE	18	32	15

Figure S36. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 21(20p11.21)' versus 'CN_CNMF'

P value = 4e-23 (Fisher's exact test), Q value = 2.7e-20

Table S37. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 21(20P11.21) CNV	126	58	32	14
AMP PEAK 21(20P11.21) WILD-TYPE	44	129	0	10

Figure S37. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(20p11.21)' versus 'MRNASEQ_CNMF'

P value = 2.41e-07 (Fisher's exact test), Q value = 0.00014

Table S38. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 21(20P11.21) CNV	19	44	24	12
AMP PEAK 21(20P11.21) WILD-TYPE	12	15	23	42

Figure S38. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(20p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.39e-06 (Fisher's exact test), Q value = 0.00081

Table S39. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 21(20P11.21) CNV	10	40	49
AMP PEAK 21(20P11.21) WILD-TYPE	39	22	31

Figure S39. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'MRNA_CNMF'

P value = 1.07e-10 (Fisher's exact test), Q value = 6.7e-08

Table S40. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
AMP PEAK 22(20Q11.21) CNV	12	59	14	20
AMP PEAK 22(20Q11.21) WILD-TYPE	19	3	16	3

Figure S40. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(20q11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 2.86e-11 (Fisher's exact test), Q value = 1.8e-08

Table S41. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
AMP PEAK 22(20Q11.21) CNV	50	14	41
AMP PEAK 22(20Q11.21) WILD-TYPE	6	30	5

Figure S41. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'CN_CNMF'

P value = 1.54e-43 (Fisher's exact test), Q value = 1e-40

Table S42. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 22(20Q11.21) CNV	167	74	32	23
AMP PEAK 22(20Q11.21) WILD-TYPE	3	113	0	1

Figure S42. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(20q11.21)' versus 'METHLYATION_CNMF'

P value = 2.19e-09 (Fisher's exact test), Q value = 1.3e-06

Table S43. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
AMP PEAK 22(20Q11.21) CNV	96	46	40
AMP PEAK 22(20Q11.21) WILD-TYPE	9	40	23

Figure S43. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(20q11.21)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.06

Table S44. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 22(20Q11.21) CNV	13	29	53	133
AMP PEAK 22(20Q11.21) WILD-TYPE	13	27	10	47

Figure S44. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'MRNASEQ_CNMF'

P value = 1.47e-14 (Fisher's exact test), Q value = 9.6e-12

Table S45. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 22(20Q11.21) CNV	23	58	34	17
AMP PEAK 22(20Q11.21) WILD-TYPE	8	1	13	37

Figure S45. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(20q11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.85e-12 (Fisher's exact test), Q value = 2.5e-09

Table S46. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 22(20Q11.21) CNV	14	56	62
AMP PEAK 22(20Q11.21) WILD-TYPE	35	6	18

Figure S46. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'MRNA_CNMF'

P value = 9.28e-12 (Fisher's exact test), Q value = 5.9e-09

Table S47. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
AMP PEAK 23(20Q12) CNV	11	59	13	20
AMP PEAK 23(20Q12) WILD-TYPE	20	3	17	3

Figure S47. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 23(20q12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.82e-11 (Fisher's exact test), Q value = 1.1e-08

Table S48. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
AMP PEAK 23(20Q12) CNV	49	13	41
AMP PEAK 23(20Q12) WILD-TYPE	7	31	5

Figure S48. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'CN_CNMF'

P value = 6.28e-43 (Fisher's exact test), Q value = 4.2e-40

Table S49. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 23(20Q12) CNV	167	75	32	23
AMP PEAK 23(20Q12) WILD-TYPE	3	112	0	1

Figure S49. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(20q12)' versus 'METHLYATION_CNMF'

P value = 1.58e-08 (Fisher's exact test), Q value = 9.6e-06

Table S50. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
AMP PEAK 23(20Q12) CNV	96	48	41
AMP PEAK 23(20Q12) WILD-TYPE	9	38	22

Figure S50. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(20q12)' versus 'RPPA_CHIERARCHICAL'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.012

Table S51. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 23(20Q12) CNV	13	29	55	132
AMP PEAK 23(20Q12) WILD-TYPE	13	27	8	48

Figure S51. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'MRNASEQ_CNMF'

P value = 5.48e-14 (Fisher's exact test), Q value = 3.6e-11

Table S52. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 23(20Q12) CNV	23	58	35	18
AMP PEAK 23(20Q12) WILD-TYPE	8	1	12	36

Figure S52. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 23(20q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-11 (Fisher's exact test), Q value = 8.5e-09

Table S53. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 23(20Q12) CNV	15	56	63
AMP PEAK 23(20Q12) WILD-TYPE	34	6	17

Figure S53. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'MRNA_CNMF'

P value = 2.87e-10 (Fisher's exact test), Q value = 1.8e-07

Table S54. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
AMP PEAK 24(20Q13.32) CNV	12	59	15	20
AMP PEAK 24(20Q13.32) WILD-TYPE	19	3	15	3

Figure S54. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(20q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 6.27e-12 (Fisher's exact test), Q value = 4e-09

Table S55. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
AMP PEAK 24(20Q13.32) CNV	51	14	41
AMP PEAK 24(20Q13.32) WILD-TYPE	5	30	5

Figure S55. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'CN_CNMF'

P value = 3.18e-43 (Fisher's exact test), Q value = 2.1e-40

Table S56. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
AMP PEAK 24(20Q13.32) CNV	168	77	32	23
AMP PEAK 24(20Q13.32) WILD-TYPE	2	110	0	1

Figure S56. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(20q13.32)' versus 'METHLYATION_CNMF'

P value = 1.58e-08 (Fisher's exact test), Q value = 9.6e-06

Table S57. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
AMP PEAK 24(20Q13.32) CNV	96	48	41
AMP PEAK 24(20Q13.32) WILD-TYPE	9	38	22

Figure S57. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(20q13.32)' versus 'RPPA_CHIERARCHICAL'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0075

Table S58. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
AMP PEAK 24(20Q13.32) CNV	13	29	55	135
AMP PEAK 24(20Q13.32) WILD-TYPE	13	27	8	45

Figure S58. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'MRNASEQ_CNMF'

P value = 5.48e-14 (Fisher's exact test), Q value = 3.6e-11

Table S59. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
AMP PEAK 24(20Q13.32) CNV	23	58	35	18
AMP PEAK 24(20Q13.32) WILD-TYPE	8	1	12	36

Figure S59. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(20q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-11 (Fisher's exact test), Q value = 8.5e-09

Table S60. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
AMP PEAK 24(20Q13.32) CNV	15	56	63
AMP PEAK 24(20Q13.32) WILD-TYPE	34	6	17

Figure S60. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 6.81e-05 (Fisher's exact test), Q value = 0.038

Table S61. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
DEL PEAK 1(1P36.11) CNV	9	35	3	11
DEL PEAK 1(1P36.11) WILD-TYPE	22	27	27	12

Figure S61. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

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

P value = 6.32e-17 (Fisher's exact test), Q value = 4.2e-14

Table S62. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 1(1P36.11) CNV	91	28	22	9
DEL PEAK 1(1P36.11) WILD-TYPE	79	159	10	15

Figure S62. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 0.000347 (Fisher's exact test), Q value = 0.19

Table S63. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 1(1P36.11) CNV	11	31	17	8
DEL PEAK 1(1P36.11) WILD-TYPE	20	28	30	46

Figure S63. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p33)' versus 'CN_CNMF'

P value = 1.09e-11 (Fisher's exact test), Q value = 6.9e-09

Table S64. Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 2(1P33) CNV	69	20	15	3
DEL PEAK 2(1P33) WILD-TYPE	101	167	17	21

Figure S64. Get High-res Image Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(1p13.1)' versus 'CN_CNMF'

P value = 6.85e-10 (Fisher's exact test), Q value = 4.3e-07

Table S65. Gene #27: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 3(1P13.1) CNV	66	23	13	1
DEL PEAK 3(1P13.1) WILD-TYPE	104	164	19	23

Figure S65. Get High-res Image Gene #27: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(1q43)' versus 'CN_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.004

Table S66. Gene #28: 'Del Peak 4(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 4(1Q43) CNV	32	7	5	0
DEL PEAK 4(1Q43) WILD-TYPE	138	180	27	24

Figure S66. Get High-res Image Gene #28: 'Del Peak 4(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(3p26.1)' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.23

Table S67. Gene #30: 'Del Peak 6(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 6(3P26.1) CNV	36	14	8	2
DEL PEAK 6(3P26.1) WILD-TYPE	134	173	24	22

Figure S67. Get High-res Image Gene #30: 'Del Peak 6(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4p16.2)' versus 'CN_CNMF'

P value = 1.16e-12 (Fisher's exact test), Q value = 7.5e-10

Table S68. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 9(4P16.2) CNV	73	23	19	6
DEL PEAK 9(4P16.2) WILD-TYPE	97	164	13	18

Figure S68. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4p16.2)' versus 'MRNASEQ_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.13

Table S69. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 9(4P16.2) CNV	9	24	16	4
DEL PEAK 9(4P16.2) WILD-TYPE	22	35	31	50

Figure S69. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 9(4p16.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.059

Table S70. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 9(4P16.2) CNV	3	23	27
DEL PEAK 9(4P16.2) WILD-TYPE	46	39	53

Figure S70. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(4q22.1)' versus 'CN_CNMF'

P value = 8.5e-12 (Fisher's exact test), Q value = 5.4e-09

Table S71. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 10(4Q22.1) CNV	77	28	18	3
DEL PEAK 10(4Q22.1) WILD-TYPE	93	159	14	21

Figure S71. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4q22.1)' versus 'MRNASEQ_CNMF'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.052

Table S72. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 10(4Q22.1) CNV	9	28	15	5
DEL PEAK 10(4Q22.1) WILD-TYPE	22	31	32	49

Figure S72. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(4q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.016

Table S73. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 10(4Q22.1) CNV	3	25	29
DEL PEAK 10(4Q22.1) WILD-TYPE	46	37	51

Figure S73. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(4q35.1)' versus 'MRNA_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.07

Table S74. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
DEL PEAK 11(4Q35.1) CNV	7	30	3	13
DEL PEAK 11(4Q35.1) WILD-TYPE	24	32	27	10

Figure S74. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 11(4q35.1)' versus 'CN_CNMF'

P value = 1.05e-13 (Fisher's exact test), Q value = 6.8e-11

Table S75. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 11(4Q35.1) CNV	88	28	16	5
DEL PEAK 11(4Q35.1) WILD-TYPE	82	159	16	19

Figure S75. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q35.1)' versus 'METHLYATION_CNMF'

P value = 7.69e-05 (Fisher's exact test), Q value = 0.043

Table S76. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 11(4Q35.1) CNV	46	13	20
DEL PEAK 11(4Q35.1) WILD-TYPE	59	73	43

Figure S76. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(4q35.1)' versus 'MRNASEQ_CNMF'

P value = 0.000239 (Fisher's exact test), Q value = 0.13

Table S77. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 11(4Q35.1) CNV	11	30	15	7
DEL PEAK 11(4Q35.1) WILD-TYPE	20	29	32	47

Figure S77. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(5q11.2)' versus 'CN_CNMF'

P value = 4.94e-09 (Fisher's exact test), Q value = 3e-06

Table S78. Gene #36: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 12(5Q11.2) CNV	60	16	9	6
DEL PEAK 12(5Q11.2) WILD-TYPE	110	171	23	18

Figure S78. Get High-res Image Gene #36: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(5q21.3)' versus 'CN_CNMF'

P value = 1.14e-09 (Fisher's exact test), Q value = 7e-07

Table S79. Gene #37: 'Del Peak 13(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 13(5Q21.3) CNV	71	24	14	8
DEL PEAK 13(5Q21.3) WILD-TYPE	99	163	18	16

Figure S79. Get High-res Image Gene #37: 'Del Peak 13(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(5q23.1)' versus 'CN_CNMF'

P value = 1.57e-08 (Fisher's exact test), Q value = 9.5e-06

Table S80. Gene #38: 'Del Peak 14(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 14(5Q23.1) CNV	64	22	13	8
DEL PEAK 14(5Q23.1) WILD-TYPE	106	165	19	16

Figure S80. Get High-res Image Gene #38: 'Del Peak 14(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(6p25.3)' versus 'CN_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.057

Table S81. Gene #39: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 15(6P25.3) CNV	13	23	9	9
DEL PEAK 15(6P25.3) WILD-TYPE	157	164	23	15

Figure S81. Get High-res Image Gene #39: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p23.3)' versus 'CN_CNMF'

P value = 6.84e-26 (Fisher's exact test), Q value = 4.6e-23

Table S82. Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 18(8P23.3) CNV	119	32	6	14
DEL PEAK 18(8P23.3) WILD-TYPE	51	155	26	10

Figure S82. Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p23.3)' versus 'METHLYATION_CNMF'

P value = 3.61e-06 (Fisher's exact test), Q value = 0.0021

Table S83. Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 18(8P23.3) CNV	62	21	22
DEL PEAK 18(8P23.3) WILD-TYPE	43	65	41

Figure S83. Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(8p22)' versus 'CN_CNMF'

P value = 2.41e-30 (Fisher's exact test), Q value = 1.6e-27

Table S84. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 19(8P22) CNV	129	33	8	15
DEL PEAK 19(8P22) WILD-TYPE	41	154	24	9

Figure S84. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(8p22)' versus 'METHLYATION_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00021

Table S85. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 19(8P22) CNV	69	24	24
DEL PEAK 19(8P22) WILD-TYPE	36	62	39

Figure S85. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(8p22)' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.071

Table S86. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 19(8P22) CNV	5	15	38	82
DEL PEAK 19(8P22) WILD-TYPE	21	41	25	98

Figure S86. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(8p22)' versus 'MRNASEQ_CNMF'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.012

Table S87. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 19(8P22) CNV	17	38	21	11
DEL PEAK 19(8P22) WILD-TYPE	14	21	26	43

Figure S87. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 20(8p11.22)' versus 'CN_CNMF'

P value = 8.88e-09 (Fisher's exact test), Q value = 5.4e-06

Table S88. Gene #44: 'Del Peak 20(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 20(8P11.22) CNV	58	18	3	1
DEL PEAK 20(8P11.22) WILD-TYPE	112	169	29	23

Figure S88. Get High-res Image Gene #44: 'Del Peak 20(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(8p11.21)' versus 'CN_CNMF'

P value = 5.81e-07 (Fisher's exact test), Q value = 0.00034

Table S89. Gene #45: 'Del Peak 21(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 21(8P11.21) CNV	35	7	1	0
DEL PEAK 21(8P11.21) WILD-TYPE	135	180	31	24

Figure S89. Get High-res Image Gene #45: 'Del Peak 21(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(9p21.3)' versus 'CN_CNMF'

P value = 4.51e-05 (Fisher's exact test), Q value = 0.026

Table S90. Gene #46: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 22(9P21.3) CNV	35	10	7	4
DEL PEAK 22(9P21.3) WILD-TYPE	135	177	25	20

Figure S90. Get High-res Image Gene #46: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(10p15.3)' versus 'CN_CNMF'

P value = 2.25e-08 (Fisher's exact test), Q value = 1.4e-05

Table S91. Gene #47: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 23(10P15.3) CNV	38	12	15	3
DEL PEAK 23(10P15.3) WILD-TYPE	132	175	17	21

Figure S91. Get High-res Image Gene #47: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(10q21.1)' versus 'CN_CNMF'

P value = 2.24e-11 (Fisher's exact test), Q value = 1.4e-08

Table S92. Gene #48: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 24(10Q21.1) CNV	48	12	17	5
DEL PEAK 24(10Q21.1) WILD-TYPE	122	175	15	19

Figure S92. Get High-res Image Gene #48: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(10q23.31)' versus 'CN_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00021

Table S93. Gene #49: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 25(10Q23.31) CNV	53	21	15	5
DEL PEAK 25(10Q23.31) WILD-TYPE	117	166	17	19

Figure S93. Get High-res Image Gene #49: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10q25.2)' versus 'CN_CNMF'

P value = 1.91e-11 (Fisher's exact test), Q value = 1.2e-08

Table S94. Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 26(10Q25.2) CNV	57	16	17	3
DEL PEAK 26(10Q25.2) WILD-TYPE	113	171	15	21

Figure S94. Get High-res Image Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(12p13.2)' versus 'CN_CNMF'

P value = 9.87e-08 (Fisher's exact test), Q value = 5.9e-05

Table S95. Gene #51: 'Del Peak 27(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 27(12P13.2) CNV	34	4	5	1
DEL PEAK 27(12P13.2) WILD-TYPE	136	183	27	23

Figure S95. Get High-res Image Gene #51: 'Del Peak 27(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(13q14.13)' versus 'CN_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.07

Table S96. Gene #52: 'Del Peak 28(13q14.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 28(13Q14.13) CNV	1	9	6	2
DEL PEAK 28(13Q14.13) WILD-TYPE	169	178	26	22

Figure S96. Get High-res Image Gene #52: 'Del Peak 28(13q14.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNA_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.012

Table S97. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
DEL PEAK 29(14Q32.11) CNV	7	35	3	11
DEL PEAK 29(14Q32.11) WILD-TYPE	24	27	27	12

Figure S97. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.061

Table S98. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
DEL PEAK 29(14Q32.11) CNV	22	7	27
DEL PEAK 29(14Q32.11) WILD-TYPE	34	37	19

Figure S98. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 29(14q32.11)' versus 'CN_CNMF'

P value = 1.61e-20 (Fisher's exact test), Q value = 1.1e-17

Table S99. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 29(14Q32.11) CNV	98	22	10	3
DEL PEAK 29(14Q32.11) WILD-TYPE	72	165	22	21

Figure S99. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNASEQ_CNMF'

P value = 7.3e-05 (Fisher's exact test), Q value = 0.041

Table S100. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 29(14Q32.11) CNV	11	28	13	5
DEL PEAK 29(14Q32.11) WILD-TYPE	20	31	34	49

Figure S100. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(15q11.2)' versus 'MRNA_CNMF'

P value = 0.000422 (Fisher's exact test), Q value = 0.23

Table S101. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
DEL PEAK 30(15Q11.2) CNV	8	35	5	12
DEL PEAK 30(15Q11.2) WILD-TYPE	23	27	25	11

Figure S101. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 30(15q11.2)' versus 'CN_CNMF'

P value = 1.2e-21 (Fisher's exact test), Q value = 8e-19

Table S102. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 30(15Q11.2) CNV	104	29	22	5
DEL PEAK 30(15Q11.2) WILD-TYPE	66	158	10	19

Figure S102. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(15q11.2)' versus 'MRNASEQ_CNMF'

P value = 2.09e-06 (Fisher's exact test), Q value = 0.0012

Table S103. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 30(15Q11.2) CNV	13	32	19	5
DEL PEAK 30(15Q11.2) WILD-TYPE	18	27	28	49

Figure S103. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(15q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000117 (Fisher's exact test), Q value = 0.065

Table S104. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 30(15Q11.2) CNV	6	29	34
DEL PEAK 30(15Q11.2) WILD-TYPE	43	33	46

Figure S104. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q21.1)' versus 'CN_CNMF'

P value = 8.15e-18 (Fisher's exact test), Q value = 5.4e-15

Table S105. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 31(15Q21.1) CNV	97	30	20	4
DEL PEAK 31(15Q21.1) WILD-TYPE	73	157	12	20

Figure S105. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(15q21.1)' versus 'MRNASEQ_CNMF'

P value = 2.03e-07 (Fisher's exact test), Q value = 0.00012

Table S106. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 31(15Q21.1) CNV	12	31	17	3
DEL PEAK 31(15Q21.1) WILD-TYPE	19	28	30	51

Figure S106. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(15q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.012

Table S107. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 31(15Q21.1) CNV	4	28	31
DEL PEAK 31(15Q21.1) WILD-TYPE	45	34	49

Figure S107. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(15q22.33)' versus 'CN_CNMF'

P value = 2.48e-21 (Fisher's exact test), Q value = 1.7e-18

Table S108. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 32(15Q22.33) CNV	96	23	21	5
DEL PEAK 32(15Q22.33) WILD-TYPE	74	164	11	19

Figure S108. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(15q22.33)' versus 'METHLYATION_CNMF'

P value = 0.000435 (Fisher's exact test), Q value = 0.23

Table S109. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 32(15Q22.33) CNV	49	17	22
DEL PEAK 32(15Q22.33) WILD-TYPE	56	69	41

Figure S109. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(15q22.33)' versus 'MRNASEQ_CNMF'

P value = 3.07e-08 (Fisher's exact test), Q value = 1.8e-05

Table S110. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 32(15Q22.33) CNV	13	33	17	3
DEL PEAK 32(15Q22.33) WILD-TYPE	18	26	30	51

Figure S110. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(15q22.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.55e-06 (Fisher's exact test), Q value = 0.0044

Table S111. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 32(15Q22.33) CNV	4	29	33
DEL PEAK 32(15Q22.33) WILD-TYPE	45	33	47

Figure S111. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'MRNA_CNMF'

P value = 6.12e-08 (Fisher's exact test), Q value = 3.7e-05

Table S112. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
DEL PEAK 35(17P12) CNV	10	49	7	16
DEL PEAK 35(17P12) WILD-TYPE	21	13	23	7

Figure S112. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(17p12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.6e-06 (Fisher's exact test), Q value = 0.00093

Table S113. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
DEL PEAK 35(17P12) CNV	36	11	35
DEL PEAK 35(17P12) WILD-TYPE	20	33	11

Figure S113. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'CN_CNMF'

P value = 2.81e-35 (Fisher's exact test), Q value = 1.9e-32

Table S114. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 35(17P12) CNV	146	43	24	16
DEL PEAK 35(17P12) WILD-TYPE	24	144	8	8

Figure S114. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(17p12)' versus 'METHLYATION_CNMF'

P value = 1.8e-09 (Fisher's exact test), Q value = 1.1e-06

Table S115. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 35(17P12) CNV	82	30	29
DEL PEAK 35(17P12) WILD-TYPE	23	56	34

Figure S115. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(17p12)' versus 'RPPA_CHIERARCHICAL'

P value = 7.42e-05 (Fisher's exact test), Q value = 0.042

Table S116. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 35(17P12) CNV	8	19	43	106
DEL PEAK 35(17P12) WILD-TYPE	18	37	20	74

Figure S116. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'MRNASEQ_CNMF'

P value = 1.06e-10 (Fisher's exact test), Q value = 6.6e-08

Table S117. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 35(17P12) CNV	20	49	23	11
DEL PEAK 35(17P12) WILD-TYPE	11	10	24	43

Figure S117. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(17p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.2e-08 (Fisher's exact test), Q value = 1.9e-05

Table S118. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 35(17P12) CNV	11	48	44
DEL PEAK 35(17P12) WILD-TYPE	38	14	36

Figure S118. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(18p11.31)' versus 'MRNA_CNMF'

P value = 1.51e-12 (Fisher's exact test), Q value = 9.7e-10

Table S119. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
DEL PEAK 37(18P11.31) CNV	6	51	5	16
DEL PEAK 37(18P11.31) WILD-TYPE	25	11	25	7

Figure S119. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNA_CHIERARCHICAL'

P value = 3.65e-09 (Fisher's exact test), Q value = 2.2e-06

Table S120. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
DEL PEAK 37(18P11.31) CNV	36	7	35
DEL PEAK 37(18P11.31) WILD-TYPE	20	37	11

Figure S120. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 37(18p11.31)' versus 'CN_CNMF'

P value = 1.93e-42 (Fisher's exact test), Q value = 1.3e-39

Table S121. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 37(18P11.31) CNV	145	34	28	13
DEL PEAK 37(18P11.31) WILD-TYPE	25	153	4	11

Figure S121. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(18p11.31)' versus 'METHLYATION_CNMF'

P value = 3.11e-13 (Fisher's exact test), Q value = 2e-10

Table S122. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 37(18P11.31) CNV	83	22	31
DEL PEAK 37(18P11.31) WILD-TYPE	22	64	32

Figure S122. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNASEQ_CNMF'

P value = 3.11e-17 (Fisher's exact test), Q value = 2.1e-14

Table S123. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 37(18P11.31) CNV	17	52	24	5
DEL PEAK 37(18P11.31) WILD-TYPE	14	7	23	49

Figure S123. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.19e-10 (Fisher's exact test), Q value = 5.1e-07

Table S124. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 37(18P11.31) CNV	7	45	46
DEL PEAK 37(18P11.31) WILD-TYPE	42	17	34

Figure S124. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'MRNA_CNMF'

P value = 8.37e-11 (Fisher's exact test), Q value = 5.2e-08

Table S125. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
DEL PEAK 38(18Q12.2) CNV	8	53	8	17
DEL PEAK 38(18Q12.2) WILD-TYPE	23	9	22	6

Figure S125. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 38(18q12.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.08e-09 (Fisher's exact test), Q value = 6.7e-07

Table S126. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
DEL PEAK 38(18Q12.2) CNV	39	9	38
DEL PEAK 38(18Q12.2) WILD-TYPE	17	35	8

Figure S126. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'CN_CNMF'

P value = 1.87e-45 (Fisher's exact test), Q value = 1.3e-42

Table S127. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 38(18Q12.2) CNV	157	44	27	19
DEL PEAK 38(18Q12.2) WILD-TYPE	13	143	5	5

Figure S127. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(18q12.2)' versus 'METHLYATION_CNMF'

P value = 8.98e-16 (Fisher's exact test), Q value = 5.9e-13

Table S128. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 38(18Q12.2) CNV	93	29	31
DEL PEAK 38(18Q12.2) WILD-TYPE	12	57	32

Figure S128. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(18q12.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000421 (Fisher's exact test), Q value = 0.23

Table S129. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 38(18Q12.2) CNV	9	22	43	113
DEL PEAK 38(18Q12.2) WILD-TYPE	17	34	20	67

Figure S129. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'MRNASEQ_CNMF'

P value = 7.66e-16 (Fisher's exact test), Q value = 5e-13

Table S130. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 38(18Q12.2) CNV	21	53	28	8
DEL PEAK 38(18Q12.2) WILD-TYPE	10	6	19	46

Figure S130. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(18q12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-08 (Fisher's exact test), Q value = 6.5e-06

Table S131. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 38(18Q12.2) CNV	11	48	51
DEL PEAK 38(18Q12.2) WILD-TYPE	38	14	29

Figure S131. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'MRNA_CNMF'

P value = 3.06e-10 (Fisher's exact test), Q value = 1.9e-07

Table S132. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
DEL PEAK 39(18Q21.2) CNV	8	53	9	17
DEL PEAK 39(18Q21.2) WILD-TYPE	23	9	21	6

Figure S132. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 39(18q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 6.85e-10 (Fisher's exact test), Q value = 4.3e-07

Table S133. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
DEL PEAK 39(18Q21.2) CNV	40	9	38
DEL PEAK 39(18Q21.2) WILD-TYPE	16	35	8

Figure S133. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'CN_CNMF'

P value = 1.51e-45 (Fisher's exact test), Q value = 1e-42

Table S134. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 39(18Q21.2) CNV	161	51	28	20
DEL PEAK 39(18Q21.2) WILD-TYPE	9	136	4	4

Figure S134. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 39(18q21.2)' versus 'METHLYATION_CNMF'

P value = 3.29e-12 (Fisher's exact test), Q value = 2.1e-09

Table S135. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 39(18Q21.2) CNV	94	38	33
DEL PEAK 39(18Q21.2) WILD-TYPE	11	48	30

Figure S135. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 39(18q21.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000225 (Fisher's exact test), Q value = 0.12

Table S136. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 39(18Q21.2) CNV	10	24	46	120
DEL PEAK 39(18Q21.2) WILD-TYPE	16	32	17	60

Figure S136. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'MRNASEQ_CNMF'

P value = 8.74e-13 (Fisher's exact test), Q value = 5.7e-10

Table S137. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 39(18Q21.2) CNV	21	54	29	13
DEL PEAK 39(18Q21.2) WILD-TYPE	10	5	18	41

Figure S137. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 39(18q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.14e-07 (Fisher's exact test), Q value = 0.00042

Table S138. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 39(18Q21.2) CNV	15	49	53
DEL PEAK 39(18Q21.2) WILD-TYPE	34	13	27

Figure S138. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'MRNA_CNMF'

P value = 6.92e-11 (Fisher's exact test), Q value = 4.3e-08

Table S139. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
DEL PEAK 40(18Q22.1) CNV	8	54	9	17
DEL PEAK 40(18Q22.1) WILD-TYPE	23	8	21	6

Figure S139. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(18q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 3.65e-09 (Fisher's exact test), Q value = 2.2e-06

Table S140. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	44	46
DEL PEAK 40(18Q22.1) CNV	40	10	38
DEL PEAK 40(18Q22.1) WILD-TYPE	16	34	8

Figure S140. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'CN_CNMF'

P value = 1.58e-47 (Fisher's exact test), Q value = 1.1e-44

Table S141. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 40(18Q22.1) CNV	162	50	29	19
DEL PEAK 40(18Q22.1) WILD-TYPE	8	137	3	5

Figure S141. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(18q22.1)' versus 'METHLYATION_CNMF'

P value = 2.02e-12 (Fisher's exact test), Q value = 1.3e-09

Table S142. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	86	63
DEL PEAK 40(18Q22.1) CNV	94	38	32
DEL PEAK 40(18Q22.1) WILD-TYPE	11	48	31

Figure S142. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 40(18q22.1)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000224 (Fisher's exact test), Q value = 0.12

Table S143. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	26	56	63	180
DEL PEAK 40(18Q22.1) CNV	10	24	45	122
DEL PEAK 40(18Q22.1) WILD-TYPE	16	32	18	58

Figure S143. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'MRNASEQ_CNMF'

P value = 4.05e-12 (Fisher's exact test), Q value = 2.6e-09

Table S144. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 40(18Q22.1) CNV	21	54	29	14
DEL PEAK 40(18Q22.1) WILD-TYPE	10	5	18	40

Figure S144. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(18q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-07 (Fisher's exact test), Q value = 0.00016

Table S145. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	49	62	80
DEL PEAK 40(18Q22.1) CNV	15	50	53
DEL PEAK 40(18Q22.1) WILD-TYPE	34	12	27

Figure S145. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(20p12.1)' versus 'CN_CNMF'

P value = 1.38e-13 (Fisher's exact test), Q value = 9e-11

Table S146. Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 42(20P12.1) CNV	61	12	0	6
DEL PEAK 42(20P12.1) WILD-TYPE	109	175	32	18

Figure S146. Get High-res Image Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 42(20p12.1)' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.082

Table S147. Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	59	47	54
DEL PEAK 42(20P12.1) CNV	8	24	7	4
DEL PEAK 42(20P12.1) WILD-TYPE	23	35	40	50

Figure S147. Get High-res Image Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 43(21q11.2)' versus 'CN_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.1e-06

Table S148. Gene #67: 'Del Peak 43(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 43(21Q11.2) CNV	72	30	18	5
DEL PEAK 43(21Q11.2) WILD-TYPE	98	157	14	19

Figure S148. Get High-res Image Gene #67: 'Del Peak 43(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(22q13.32)' versus 'MRNA_CNMF'

P value = 0.000428 (Fisher's exact test), Q value = 0.23

Table S149. Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	31	62	30	23
DEL PEAK 44(22Q13.32) CNV	8	34	4	10
DEL PEAK 44(22Q13.32) WILD-TYPE	23	28	26	13

Figure S149. Get High-res Image Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 44(22q13.32)' versus 'CN_CNMF'

P value = 9.76e-13 (Fisher's exact test), Q value = 6.3e-10

Table S150. Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	170	187	32	24
DEL PEAK 44(22Q13.32) CNV	85	28	17	8
DEL PEAK 44(22Q13.32) WILD-TYPE	85	159	15	16

Figure S150. Get High-res Image Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #3: '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 = COAD-TP.transferedmergedcluster.txt
Number of patients = 413
Number of copy number variation regions = 68
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

Made with Nozzle