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 48 peak regions and 12 molecular subtypes across 269 patients, 116 significant findings detected with Q value < 0.25.

Amp Peak 1(1q22) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1q32.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 6(7p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 7(7q32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 8(8q24.12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 9(10p15.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 11(12p13.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 12(12p12.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 13(12q14.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 14(13q33.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 15(17q25.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(18q23) cnvs correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 17(19p13.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 18(19q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Amp Peak 19(Xp22.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 20(Xp11.22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 1(1p36.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 2(1p32.3) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 4(2p25.3) cnvs correlated to 'CN_CNMF'.
Del Peak 5(2q37.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 6(2q37.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 7(3p21.1) cnvs correlated to 'CN_CNMF' and 'RPPA_CNMF'.
Del Peak 8(4q35.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 9(5q35.2) cnvs correlated to 'CN_CNMF'.
Del Peak 11(6q24.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Del Peak 12(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 13(10q26.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 14(11p15.5) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 15(11q25) cnvs correlated to 'CN_CNMF'.
Del Peak 16(12q12) cnvs correlated to 'CN_CNMF'.
Del Peak 17(13q14.2) cnvs correlated to 'CN_CNMF'.
Del Peak 18(13q21.2) cnvs correlated to 'CN_CNMF'.
Del Peak 19(13q22.1) cnvs correlated to 'CN_CNMF'.
Del Peak 20(13q34) cnvs correlated to 'CN_CNMF'.
Del Peak 21(14q24.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
Del Peak 25(19q13.42) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 26(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 27(Xp22.2) cnvs correlated to 'CN_CNMF'.
Del Peak 28(Xq21.1) 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 48 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 116 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	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test
Del Peak 1(1p36 31)	0 (0%)	173	0.000549 (0.239)	5.86e-05 (0.0274)	8.49e-14 (4.53e-11)	4.92e-43 (2.7e-40)	0.000732 (0.313)	0.54 (1.00)	7.9e-06 (0.00382)	3.23e-23 (1.75e-20)	8.86e-06 (0.00426)	0.000303 (0.134)	1.15e-08 (5.91e-06)	0.000104 (0.0479)
Del Peak 2(1p32 3)	0 (0%)	181	0.0286 (1.00)	0.000173 (0.0782)	2.21e-17 (1.19e-14)	2.3e-48 (1.27e-45)	0.000477 (0.209)	0.235 (1.00)	2.73e-09 (1.42e-06)	3.06e-27 (1.67e-24)	5.78e-08 (2.93e-05)	3.2e-05 (0.0151)	1.54e-09 (8.09e-07)	1.09e-06 (0.00054)
Del Peak 13(10q26 3)	0 (0%)	188	0.179 (1.00)	0.022 (1.00)	6.21e-19 (3.35e-16)	1.3e-20 (7.03e-18)	1.56e-07 (7.9e-05)	0.000214 (0.0967)	2.13e-08 (1.08e-05)	2.92e-09 (1.52e-06)	0.00461 (1.00)	5.98e-06 (0.00292)	4.5e-09 (2.32e-06)	1.26e-11 (6.69e-09)
Del Peak 25(19q13 42)	0 (0%)	133	0.0353 (1.00)	0.127 (1.00)	1.55e-15 (8.27e-13)	9.49e-28 (5.17e-25)	0.00212 (0.877)	0.6 (1.00)	7.99e-07 (0.000399)	9.06e-15 (4.84e-12)	8.24e-05 (0.0382)	0.000298 (0.132)	2.28e-05 (0.0108)	5.19e-08 (2.64e-05)
Amp Peak 6(7p11 2)	0 (0%)	196	0.864 (1.00)	0.726 (1.00)	2.06e-29 (1.12e-26)	4.41e-16 (2.36e-13)	0.000113 (0.052)	0.00626 (1.00)	1.96e-05 (0.00933)	0.000756 (0.322)	0.00133 (0.558)	6.43e-06 (0.00312)	4.5e-07 (0.000226)	3.1e-12 (1.65e-09)
Amp Peak 18(19q13 2)	0 (0%)	250	0.369 (1.00)	0.194 (1.00)	7.29e-07 (0.000365)	1.01e-05 (0.00485)	0.0381 (1.00)	0.34 (1.00)	0.000122 (0.0558)	0.00316 (1.00)	0.00251 (1.00)	0.00397 (1.00)	5.25e-06 (0.00258)	5.89e-06 (0.00288)
Del Peak 12(9p21 3)	0 (0%)	170	0.333 (1.00)	0.0153 (1.00)	3.04e-11 (1.61e-08)	2.66e-08 (1.36e-05)	8.67e-06 (0.00418)	9.22e-05 (0.0425)	0.0237 (1.00)	0.00935 (1.00)	0.177 (1.00)	0.206 (1.00)	0.0574 (1.00)	0.000199 (0.0899)
Del Peak 26(22q13 31)	0 (0%)	229	0.25 (1.00)	0.0588 (1.00)	1.41e-09 (7.41e-07)	2.85e-06 (0.00141)	6.75e-05 (0.0315)	0.0187 (1.00)	6.92e-06 (0.00336)	3.77e-05 (0.0178)	0.011 (1.00)	0.0269 (1.00)	0.0161 (1.00)	0.00779 (1.00)
Amp Peak 2(1q32 1)	0 (0%)	242			2.14e-07 (0.000108)	2.28e-06 (0.00113)	0.104 (1.00)	0.846 (1.00)	0.00996 (1.00)	0.249 (1.00)	0.618 (1.00)	8.96e-05 (0.0415)	0.0219 (1.00)	2.79e-05 (0.0132)
Amp Peak 7(7q32 3)	0 (0%)	169	0.764 (1.00)	0.755 (1.00)	5.19e-23 (2.81e-20)	2.11e-08 (1.08e-05)	0.00814 (1.00)	0.0242 (1.00)	0.000267 (0.119)	0.0012 (0.507)	0.068 (1.00)	0.00428 (1.00)	0.00282 (1.00)	1.02e-05 (0.00489)
Amp Peak 8(8q24 12)	0 (0%)	214	0.37 (1.00)	0.164 (1.00)	2.32e-12 (1.23e-09)	5.52e-09 (2.85e-06)	0.0287 (1.00)	0.884 (1.00)	0.225 (1.00)	0.00715 (1.00)	0.221 (1.00)	0.18 (1.00)	0.000257 (0.115)	0.00178 (0.736)
Amp Peak 9(10p15 3)	0 (0%)	228	0.526 (1.00)	0.207 (1.00)	1e-09 (5.27e-07)	2.97e-09 (1.54e-06)	0.0343 (1.00)	0.244 (1.00)	0.352 (1.00)	0.000605 (0.262)	0.0993 (1.00)	0.225 (1.00)	0.000284 (0.126)	0.0465 (1.00)
Amp Peak 12(12p12 1)	0 (0%)	241	1 (1.00)	0.0138 (1.00)	4.75e-06 (0.00234)	0.0256 (1.00)	0.169 (1.00)	0.688 (1.00)	0.000601 (0.261)	0.000392 (0.173)	0.00479 (1.00)	0.023 (1.00)	6.84e-05 (0.0318)	0.161 (1.00)
Amp Peak 20(Xp11 22)	0 (0%)	231	0.651 (1.00)	0.892 (1.00)	1.84e-09 (9.65e-07)	1.54e-06 (0.000762)	0.0268 (1.00)	0.143 (1.00)	0.0835 (1.00)	0.000355 (0.156)	0.132 (1.00)	0.0575 (1.00)	0.292 (1.00)	0.0226 (1.00)
Del Peak 6(2q37 3)	0 (0%)	229	0.18 (1.00)	0.116 (1.00)	6.07e-06 (0.00296)	1.8e-07 (9.09e-05)	0.0119 (1.00)	0.0217 (1.00)	0.227 (1.00)	0.00405 (1.00)	0.589 (1.00)	0.155 (1.00)	0.231 (1.00)	0.000114 (0.0522)
Del Peak 14(11p15 5)	0 (0%)	212	0.642 (1.00)	0.000741 (0.316)	1.88e-09 (9.8e-07)	2.11e-10 (1.11e-07)	0.146 (1.00)	0.849 (1.00)	0.00267 (1.00)	2.62e-05 (0.0124)	0.229 (1.00)	0.364 (1.00)	0.147 (1.00)	0.378 (1.00)
Amp Peak 11(12p13 32)	0 (0%)	226	0.864 (1.00)	0.0486 (1.00)	1.69e-10 (8.94e-08)	5.16e-05 (0.0243)	0.116 (1.00)	0.218 (1.00)	0.0218 (1.00)	0.00214 (0.88)	0.0142 (1.00)	0.0371 (1.00)	0.000803 (0.341)	0.0776 (1.00)
Amp Peak 16(18q23)	0 (0%)	257			0.00133 (0.558)	0.0268 (1.00)	0.000132 (0.0601)	1 (1.00)	0.00594 (1.00)	0.00296 (1.00)	0.0543 (1.00)	0.322 (1.00)	0.00027 (0.12)	0.083 (1.00)
Amp Peak 17(19p13 3)	0 (0%)	209	0.186 (1.00)	0.41 (1.00)	9.09e-05 (0.042)	1.07e-08 (5.5e-06)	0.867 (1.00)	0.684 (1.00)	0.654 (1.00)	0.0121 (1.00)	0.449 (1.00)	0.238 (1.00)	0.0396 (1.00)	0.0125 (1.00)
Del Peak 5(2q37 1)	0 (0%)	236	0.651 (1.00)	0.164 (1.00)	9.7e-07 (0.000483)	1.93e-05 (0.00922)	0.00223 (0.915)	0.024 (1.00)	0.0249 (1.00)	0.00127 (0.534)	0.14 (1.00)	0.0122 (1.00)	0.0829 (1.00)	0.00226 (0.924)
Del Peak 7(3p21 1)	0 (0%)	241	1 (1.00)	0.00815 (1.00)	5.04e-07 (0.000253)	0.0121 (1.00)	0.000478 (0.209)	0.152 (1.00)	0.0154 (1.00)	0.00381 (1.00)	0.00597 (1.00)	0.0491 (1.00)	0.0728 (1.00)	0.0197 (1.00)
Del Peak 8(4q35 2)	0 (0%)	193	1 (1.00)	0.602 (1.00)	9.34e-09 (4.8e-06)	9.66e-07 (0.000482)	0.0826 (1.00)	0.069 (1.00)	0.00371 (1.00)	0.00855 (1.00)	0.195 (1.00)	0.349 (1.00)	0.0051 (1.00)	0.00737 (1.00)
Del Peak 11(6q24 3)	0 (0%)	224	0.0479 (1.00)	0.194 (1.00)	0.000134 (0.0611)	0.00125 (0.527)	0.165 (1.00)	0.273 (1.00)	0.674 (1.00)	0.0882 (1.00)	0.000171 (0.0778)	0.532 (1.00)	0.507 (1.00)	0.102 (1.00)
Del Peak 21(14q24 3)	0 (0%)	208	0.303 (1.00)	0.171 (1.00)	5.54e-05 (0.026)	0.049 (1.00)	0.00299 (1.00)	0.0193 (1.00)	0.00638 (1.00)	0.071 (1.00)	0.000514 (0.224)	0.00345 (1.00)	0.0747 (1.00)	0.00259 (1.00)
Amp Peak 1(1q22)	0 (0%)	242			0.000254 (0.114)	0.133 (1.00)	0.251 (1.00)	0.403 (1.00)	0.169 (1.00)	0.312 (1.00)	0.937 (1.00)	0.309 (1.00)	0.134 (1.00)	0.499 (1.00)
Amp Peak 13(12q14 1)	0 (0%)	250			1.97e-05 (0.00939)	0.101 (1.00)	0.0228 (1.00)	0.881 (1.00)	0.0291 (1.00)	0.423 (1.00)	0.0543 (1.00)	0.192 (1.00)	0.325 (1.00)	0.011 (1.00)
Amp Peak 14(13q33 3)	0 (0%)	254			0.000431 (0.189)	0.00549 (1.00)	0.187 (1.00)	0.293 (1.00)	0.426 (1.00)	0.0806 (1.00)	0.861 (1.00)	0.666 (1.00)	0.408 (1.00)	0.263 (1.00)
Amp Peak 15(17q25 1)	0 (0%)	253	0.0889 (1.00)	0.0468 (1.00)	7.64e-06 (0.0037)	0.274 (1.00)	0.208 (1.00)	1 (1.00)	0.468 (1.00)	0.725 (1.00)	0.0163 (1.00)	0.389 (1.00)	0.00944 (1.00)	0.83 (1.00)
Amp Peak 19(Xp22 33)	0 (0%)	251			0.000241 (0.109)	0.00225 (0.923)	0.341 (1.00)	0.34 (1.00)	0.154 (1.00)	0.0225 (1.00)	0.779 (1.00)	0.00885 (1.00)	0.59 (1.00)	0.306 (1.00)
Del Peak 4(2p25 3)	0 (0%)	245	0.369 (1.00)	0.407 (1.00)	1.97e-06 (0.000973)	0.00447 (1.00)	0.195 (1.00)	1 (1.00)	0.455 (1.00)	0.0729 (1.00)	0.453 (1.00)	0.815 (1.00)	0.56 (1.00)	0.144 (1.00)
Del Peak 9(5q35 2)	0 (0%)	235	0.446 (1.00)	0.0182 (1.00)	4.08e-09 (2.11e-06)	0.00166 (0.687)	0.0994 (1.00)	0.941 (1.00)	0.0663 (1.00)	0.00913 (1.00)	0.393 (1.00)	0.502 (1.00)	0.00637 (1.00)	0.261 (1.00)
Del Peak 15(11q25)	0 (0%)	248			0.000243 (0.109)	0.00609 (1.00)	0.406 (1.00)	0.424 (1.00)	0.11 (1.00)	0.041 (1.00)	0.442 (1.00)	0.174 (1.00)	0.725 (1.00)	0.207 (1.00)
Del Peak 16(12q12)	0 (0%)	234	1 (1.00)	0.0879 (1.00)	5.28e-06 (0.00259)	0.000714 (0.306)	0.505 (1.00)	0.882 (1.00)	0.115 (1.00)	0.0148 (1.00)	0.922 (1.00)	0.956 (1.00)	0.471 (1.00)	0.607 (1.00)
Del Peak 17(13q14 2)	0 (0%)	192	0.18 (1.00)	0.000618 (0.267)	3.93e-30 (2.16e-27)	0.0078 (1.00)	0.0343 (1.00)	0.813 (1.00)	0.339 (1.00)	0.13 (1.00)	0.203 (1.00)	0.289 (1.00)	0.308 (1.00)	0.283 (1.00)
Del Peak 18(13q21 2)	0 (0%)	189	0.18 (1.00)	0.000618 (0.267)	1.52e-29 (8.31e-27)	0.00278 (1.00)	0.0185 (1.00)	0.713 (1.00)	0.145 (1.00)	0.0611 (1.00)	0.0754 (1.00)	0.229 (1.00)	0.34 (1.00)	0.29 (1.00)
Del Peak 19(13q22 1)	0 (0%)	192	0.438 (1.00)	0.000774 (0.329)	2.75e-25 (1.49e-22)	0.0163 (1.00)	0.00899 (1.00)	0.788 (1.00)	0.457 (1.00)	0.13 (1.00)	0.138 (1.00)	0.452 (1.00)	0.611 (1.00)	0.421 (1.00)
Del Peak 20(13q34)	0 (0%)	212	0.508 (1.00)	0.106 (1.00)	5.37e-17 (2.89e-14)	0.263 (1.00)	0.0856 (1.00)	0.524 (1.00)	0.454 (1.00)	0.161 (1.00)	0.0935 (1.00)	0.239 (1.00)	0.605 (1.00)	0.699 (1.00)
Del Peak 27(Xp22 2)	0 (0%)	211	0.839 (1.00)	0.131 (1.00)	6.73e-09 (3.46e-06)	0.128 (1.00)	0.0439 (1.00)	0.0294 (1.00)	0.965 (1.00)	0.0676 (1.00)	0.491 (1.00)	0.119 (1.00)	0.81 (1.00)	0.0436 (1.00)
Del Peak 28(Xq21 1)	0 (0%)	234	0.73 (1.00)	0.00107 (0.453)	5.92e-05 (0.0276)	0.118 (1.00)	0.0289 (1.00)	0.0495 (1.00)	0.523 (1.00)	0.0143 (1.00)	0.119 (1.00)	0.176 (1.00)	0.0416 (1.00)	0.884 (1.00)
Amp Peak 3(3p24 3)	0 (0%)	255			0.0312 (1.00)	0.933 (1.00)	0.907 (1.00)	0.0322 (1.00)	0.0815 (1.00)	0.252 (1.00)	0.735 (1.00)	0.643 (1.00)	0.63 (1.00)	0.621 (1.00)
Amp Peak 4(3q26 32)	0 (0%)	255			0.000655 (0.282)	0.118 (1.00)	0.0147 (1.00)	0.68 (1.00)	0.548 (1.00)	0.434 (1.00)	0.176 (1.00)	0.643 (1.00)	0.119 (1.00)	0.276 (1.00)
Amp Peak 5(4q12)	0 (0%)	255			0.0014 (0.584)	0.258 (1.00)	0.0204 (1.00)	0.737 (1.00)	0.696 (1.00)	0.372 (1.00)	0.0996 (1.00)	0.33 (1.00)	0.191 (1.00)	0.529 (1.00)
Amp Peak 10(11q23 3)	0 (0%)	224	0.225 (1.00)	0.025 (1.00)	0.185 (1.00)	0.122 (1.00)	0.101 (1.00)	0.141 (1.00)	0.603 (1.00)	0.599 (1.00)	0.579 (1.00)	0.627 (1.00)	0.0579 (1.00)	0.246 (1.00)
Del Peak 3(1q43)	0 (0%)	254			0.0604 (1.00)	0.228 (1.00)	0.101 (1.00)	0.567 (1.00)	0.894 (1.00)	0.186 (1.00)	0.559 (1.00)	0.666 (1.00)	0.638 (1.00)	0.557 (1.00)
Del Peak 10(6p25 3)	0 (0%)	241			0.0551 (1.00)	0.359 (1.00)	0.161 (1.00)	0.808 (1.00)	0.429 (1.00)	0.24 (1.00)	0.574 (1.00)	0.705 (1.00)	0.164 (1.00)	0.109 (1.00)
Del Peak 22(17q25 3)	0 (0%)	252			0.00155 (0.645)	0.216 (1.00)	0.247 (1.00)	0.161 (1.00)	0.778 (1.00)	0.161 (1.00)	0.204 (1.00)	0.153 (1.00)	0.716 (1.00)	0.341 (1.00)
Del Peak 23(18p11 32)	0 (0%)	227	0.321 (1.00)	0.316 (1.00)	0.0604 (1.00)	0.125 (1.00)	0.43 (1.00)	0.0609 (1.00)	1 (1.00)	1 (1.00)	0.609 (1.00)	0.785 (1.00)	0.682 (1.00)	0.689 (1.00)
Del Peak 24(18q23)	0 (0%)	226	0.321 (1.00)	0.316 (1.00)	0.134 (1.00)	0.0651 (1.00)	0.46 (1.00)	0.115 (1.00)	0.383 (1.00)	0.822 (1.00)	0.672 (1.00)	0.421 (1.00)	0.516 (1.00)	0.247 (1.00)

'Amp Peak 1(1q22)' versus 'CN_CNMF'

P value = 0.000254 (Fisher's exact test), Q value = 0.11

Table S1. Gene #1: 'Amp Peak 1(1q22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 1(1Q22) CNV	5	9	11	2
AMP PEAK 1(1Q22) WILD-TYPE	47	48	43	104

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q22)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.14e-07 (Fisher's exact test), Q value = 0.00011

Table S2. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 2(1Q32.1) CNV	2	15	9	1
AMP PEAK 2(1Q32.1) WILD-TYPE	50	42	45	105

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 2.28e-06 (Fisher's exact test), Q value = 0.0011

Table S3. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
AMP PEAK 2(1Q32.1) CNV	9	15	2	1
AMP PEAK 2(1Q32.1) WILD-TYPE	113	27	64	33

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 8.96e-05 (Fisher's exact test), Q value = 0.041

Table S4. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	145	109
AMP PEAK 2(1Q32.1) CNV	7	9	11
AMP PEAK 2(1Q32.1) WILD-TYPE	7	136	98

Figure S4. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

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

P value = 2.79e-05 (Fisher's exact test), Q value = 0.013

Table S5. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	105	121
AMP PEAK 2(1Q32.1) CNV	13	4	10
AMP PEAK 2(1Q32.1) WILD-TYPE	29	101	111

Figure S5. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 6(7p11.2)' versus 'CN_CNMF'

P value = 2.06e-29 (Fisher's exact test), Q value = 1.1e-26

Table S6. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 6(7P11.2) CNV	4	50	12	7
AMP PEAK 6(7P11.2) WILD-TYPE	48	7	42	99

Figure S6. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(7p11.2)' versus 'METHLYATION_CNMF'

P value = 4.41e-16 (Fisher's exact test), Q value = 2.4e-13

Table S7. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
AMP PEAK 6(7P11.2) CNV	22	35	8	6
AMP PEAK 6(7P11.2) WILD-TYPE	100	7	58	28

Figure S7. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 6(7p11.2)' versus 'RPPA_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.052

Table S8. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 6(7P11.2) CNV	13	30	12	12
AMP PEAK 6(7P11.2) WILD-TYPE	39	32	56	62

Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 6(7p11.2)' versus 'MRNASEQ_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.0093

Table S9. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	78	97
AMP PEAK 6(7P11.2) CNV	42	15	16
AMP PEAK 6(7P11.2) WILD-TYPE	52	63	81

Figure S9. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 6(7p11.2)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.43e-06 (Fisher's exact test), Q value = 0.0031

Table S10. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	145	109
AMP PEAK 6(7P11.2) CNV	11	43	18
AMP PEAK 6(7P11.2) WILD-TYPE	3	102	91

Figure S10. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(7p11.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.5e-07 (Chi-square test), Q value = 0.00023

Table S11. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	44	48	35	71	27	31	4	8
AMP PEAK 6(7P11.2) CNV	7	28	11	11	2	11	2	0
AMP PEAK 6(7P11.2) WILD-TYPE	37	20	24	60	25	20	2	8

Figure S11. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 6(7p11.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.1e-12 (Fisher's exact test), Q value = 1.6e-09

Table S12. Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	105	121
AMP PEAK 6(7P11.2) CNV	31	24	17
AMP PEAK 6(7P11.2) WILD-TYPE	11	81	104

Figure S12. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 7(7q32.3)' versus 'CN_CNMF'

P value = 5.19e-23 (Fisher's exact test), Q value = 2.8e-20

Table S13. Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 7(7Q32.3) CNV	13	53	17	17
AMP PEAK 7(7Q32.3) WILD-TYPE	39	4	37	89

Figure S13. Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(7q32.3)' versus 'METHLYATION_CNMF'

P value = 2.11e-08 (Fisher's exact test), Q value = 1.1e-05

Table S14. Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
AMP PEAK 7(7Q32.3) CNV	45	32	15	6
AMP PEAK 7(7Q32.3) WILD-TYPE	77	10	51	28

Figure S14. Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 7(7q32.3)' versus 'MRNASEQ_CNMF'

P value = 0.000267 (Fisher's exact test), Q value = 0.12

Table S15. Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	78	97
AMP PEAK 7(7Q32.3) CNV	50	25	25
AMP PEAK 7(7Q32.3) WILD-TYPE	44	53	72

Figure S15. Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 7(7q32.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.0049

Table S16. Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	105	121
AMP PEAK 7(7Q32.3) CNV	29	37	33
AMP PEAK 7(7Q32.3) WILD-TYPE	13	68	88

Figure S16. Get High-res Image Gene #7: 'Amp Peak 7(7q32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 8(8q24.12)' versus 'CN_CNMF'

P value = 2.32e-12 (Fisher's exact test), Q value = 1.2e-09

Table S17. Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 8(8Q24.12) CNV	17	11	25	2
AMP PEAK 8(8Q24.12) WILD-TYPE	35	46	29	104

Figure S17. Get High-res Image Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 8(8q24.12)' versus 'METHLYATION_CNMF'

P value = 5.52e-09 (Fisher's exact test), Q value = 2.8e-06

Table S18. Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
AMP PEAK 8(8Q24.12) CNV	46	4	3	2
AMP PEAK 8(8Q24.12) WILD-TYPE	76	38	63	32

Figure S18. Get High-res Image Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 8(8q24.12)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000257 (Chi-square test), Q value = 0.12

Table S19. Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	44	48	35	71	27	31	4	8
AMP PEAK 8(8Q24.12) CNV	17	6	10	9	1	8	3	1
AMP PEAK 8(8Q24.12) WILD-TYPE	27	42	25	62	26	23	1	7

Figure S19. Get High-res Image Gene #8: 'Amp Peak 8(8q24.12)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 9(10p15.3)' versus 'CN_CNMF'

P value = 1e-09 (Fisher's exact test), Q value = 5.3e-07

Table S20. Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 9(10P15.3) CNV	19	5	15	2
AMP PEAK 9(10P15.3) WILD-TYPE	33	52	39	104

Figure S20. Get High-res Image Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(10p15.3)' versus 'METHLYATION_CNMF'

P value = 2.97e-09 (Fisher's exact test), Q value = 1.5e-06

Table S21. Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
AMP PEAK 9(10P15.3) CNV	36	1	0	4
AMP PEAK 9(10P15.3) WILD-TYPE	86	41	66	30

Figure S21. Get High-res Image Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 9(10p15.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000284 (Chi-square test), Q value = 0.13

Table S22. Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	44	48	35	71	27	31	4	8
AMP PEAK 9(10P15.3) CNV	12	3	10	7	2	3	3	1
AMP PEAK 9(10P15.3) WILD-TYPE	32	45	25	64	25	28	1	7

Figure S22. Get High-res Image Gene #9: 'Amp Peak 9(10p15.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 11(12p13.32)' versus 'CN_CNMF'

P value = 1.69e-10 (Fisher's exact test), Q value = 8.9e-08

Table S23. Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 11(12P13.32) CNV	20	8	14	1
AMP PEAK 11(12P13.32) WILD-TYPE	32	49	40	105

Figure S23. Get High-res Image Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(12p13.32)' versus 'METHLYATION_CNMF'

P value = 5.16e-05 (Fisher's exact test), Q value = 0.024

Table S24. Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
AMP PEAK 11(12P13.32) CNV	33	5	2	3
AMP PEAK 11(12P13.32) WILD-TYPE	89	37	64	31

Figure S24. Get High-res Image Gene #11: 'Amp Peak 11(12p13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

P value = 4.75e-06 (Fisher's exact test), Q value = 0.0023

Table S25. Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 12(12P12.1) CNV	12	5	10	1
AMP PEAK 12(12P12.1) WILD-TYPE	40	52	44	105

Figure S25. Get High-res Image Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(12p12.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000392 (Fisher's exact test), Q value = 0.17

Table S26. Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	141	92
AMP PEAK 12(12P12.1) CNV	2	24	2
AMP PEAK 12(12P12.1) WILD-TYPE	34	117	90

Figure S26. Get High-res Image Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(12p12.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.84e-05 (Chi-square test), Q value = 0.032

Table S27. Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	44	48	35	71	27	31	4	8
AMP PEAK 12(12P12.1) CNV	7	6	7	1	2	2	3	0
AMP PEAK 12(12P12.1) WILD-TYPE	37	42	28	70	25	29	1	8

Figure S27. Get High-res Image Gene #12: 'Amp Peak 12(12p12.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 13(12q14.1)' versus 'CN_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.0094

Table S28. Gene #13: 'Amp Peak 13(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 13(12Q14.1) CNV	1	6	11	1
AMP PEAK 13(12Q14.1) WILD-TYPE	51	51	43	105

Figure S28. Get High-res Image Gene #13: 'Amp Peak 13(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 14(13q33.3)' versus 'CN_CNMF'

P value = 0.000431 (Fisher's exact test), Q value = 0.19

Table S29. Gene #14: 'Amp Peak 14(13q33.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 14(13Q33.3) CNV	5	3	7	0
AMP PEAK 14(13Q33.3) WILD-TYPE	47	54	47	106

Figure S29. Get High-res Image Gene #14: 'Amp Peak 14(13q33.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(17q25.1)' versus 'CN_CNMF'

P value = 7.64e-06 (Fisher's exact test), Q value = 0.0037

Table S30. Gene #15: 'Amp Peak 15(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 15(17Q25.1) CNV	1	1	12	2
AMP PEAK 15(17Q25.1) WILD-TYPE	51	56	42	104

Figure S30. Get High-res Image Gene #15: 'Amp Peak 15(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(18q23)' versus 'RPPA_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.06

Table S31. Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
AMP PEAK 16(18Q23) CNV	3	8	0	0
AMP PEAK 16(18Q23) WILD-TYPE	49	54	68	74

Figure S31. Get High-res Image Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 16(18q23)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Chi-square test), Q value = 0.12

Table S32. Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	44	48	35	71	27	31	4	8
AMP PEAK 16(18Q23) CNV	1	3	4	1	0	1	2	0
AMP PEAK 16(18Q23) WILD-TYPE	43	45	31	70	27	30	2	8

Figure S32. Get High-res Image Gene #16: 'Amp Peak 16(18q23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 17(19p13.3)' versus 'CN_CNMF'

P value = 9.09e-05 (Fisher's exact test), Q value = 0.042

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 17(19P13.3) CNV	2	17	8	33
AMP PEAK 17(19P13.3) WILD-TYPE	50	40	46	73

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

'Amp Peak 17(19p13.3)' versus 'METHLYATION_CNMF'

P value = 1.07e-08 (Fisher's exact test), Q value = 5.5e-06

Table S34. Gene #17: 'Amp Peak 17(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
AMP PEAK 17(19P13.3) CNV	10	14	29	3
AMP PEAK 17(19P13.3) WILD-TYPE	112	28	37	31

Figure S34. Get High-res Image Gene #17: 'Amp Peak 17(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 18(19q13.2)' versus 'CN_CNMF'

P value = 7.29e-07 (Fisher's exact test), Q value = 0.00037

Table S35. Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 18(19Q13.2) CNV	0	14	3	2
AMP PEAK 18(19Q13.2) WILD-TYPE	52	43	51	104

Figure S35. Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 18(19q13.2)' versus 'METHLYATION_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0048

Table S36. Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
AMP PEAK 18(19Q13.2) CNV	6	11	0	1
AMP PEAK 18(19Q13.2) WILD-TYPE	116	31	66	33

Figure S36. Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 18(19q13.2)' versus 'MRNASEQ_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.056

Table S37. Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	78	97
AMP PEAK 18(19Q13.2) CNV	15	3	1
AMP PEAK 18(19Q13.2) WILD-TYPE	79	75	96

Figure S37. Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 18(19q13.2)' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.25e-06 (Chi-square test), Q value = 0.0026

Table S38. Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	44	48	35	71	27	31	4	8
AMP PEAK 18(19Q13.2) CNV	2	13	1	3	0	0	0	0
AMP PEAK 18(19Q13.2) WILD-TYPE	42	35	34	68	27	31	4	8

Figure S38. Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 18(19q13.2)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.89e-06 (Fisher's exact test), Q value = 0.0029

Table S39. Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	105	121
AMP PEAK 18(19Q13.2) CNV	11	6	2
AMP PEAK 18(19Q13.2) WILD-TYPE	31	99	119

Figure S39. Get High-res Image Gene #18: 'Amp Peak 18(19q13.2)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Amp Peak 19(Xp22.33)' versus 'CN_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.11

Table S40. Gene #19: 'Amp Peak 19(Xp22.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 19(XP22.33) CNV	7	6	5	0
AMP PEAK 19(XP22.33) WILD-TYPE	45	51	49	106

Figure S40. Get High-res Image Gene #19: 'Amp Peak 19(Xp22.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(Xp11.22)' versus 'CN_CNMF'

P value = 1.84e-09 (Fisher's exact test), Q value = 9.6e-07

Table S41. Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
AMP PEAK 20(XP11.22) CNV	19	4	13	2
AMP PEAK 20(XP11.22) WILD-TYPE	33	53	41	104

Figure S41. Get High-res Image Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(Xp11.22)' versus 'METHLYATION_CNMF'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.00076

Table S42. Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
AMP PEAK 20(XP11.22) CNV	32	4	1	1
AMP PEAK 20(XP11.22) WILD-TYPE	90	38	65	33

Figure S42. Get High-res Image Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 20(Xp11.22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000355 (Fisher's exact test), Q value = 0.16

Table S43. Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	141	92
AMP PEAK 20(XP11.22) CNV	1	31	6
AMP PEAK 20(XP11.22) WILD-TYPE	35	110	86

Figure S43. Get High-res Image Gene #20: 'Amp Peak 20(Xp11.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'MRNA_CNMF'

P value = 0.000549 (Fisher's exact test), Q value = 0.24

Table S44. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	9	10	8
DEL PEAK 1(1P36.31) CNV	0	8	2
DEL PEAK 1(1P36.31) WILD-TYPE	9	2	6

Figure S44. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNA_CHIERARCHICAL'

P value = 5.86e-05 (Fisher's exact test), Q value = 0.027

Table S45. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	6	10	4
DEL PEAK 1(1P36.31) CNV	7	2	0	1
DEL PEAK 1(1P36.31) WILD-TYPE	0	4	10	3

Figure S45. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'CN_CNMF'

P value = 8.49e-14 (Fisher's exact test), Q value = 4.5e-11

Table S46. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 1(1P36.31) CNV	5	9	15	67
DEL PEAK 1(1P36.31) WILD-TYPE	47	48	39	39

Figure S46. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.31)' versus 'METHLYATION_CNMF'

P value = 4.92e-43 (Fisher's exact test), Q value = 2.7e-40

Table S47. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
DEL PEAK 1(1P36.31) CNV	8	9	66	9
DEL PEAK 1(1P36.31) WILD-TYPE	114	33	0	25

Figure S47. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNASEQ_CNMF'

P value = 7.9e-06 (Fisher's exact test), Q value = 0.0038

Table S48. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	78	97
DEL PEAK 1(1P36.31) CNV	16	34	46
DEL PEAK 1(1P36.31) WILD-TYPE	78	44	51

Figure S48. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.23e-23 (Fisher's exact test), Q value = 1.8e-20

Table S49. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	141	92
DEL PEAK 1(1P36.31) CNV	36	21	39
DEL PEAK 1(1P36.31) WILD-TYPE	0	120	53

Figure S49. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_CNMF'

P value = 8.86e-06 (Chi-square test), Q value = 0.0043

Table S50. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	48	89	16	53
DEL PEAK 1(1P36.31) CNV	11	10	40	12	23
DEL PEAK 1(1P36.31) WILD-TYPE	51	38	49	4	30

Figure S50. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000303 (Fisher's exact test), Q value = 0.13

Table S51. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	145	109
DEL PEAK 1(1P36.31) CNV	2	40	54
DEL PEAK 1(1P36.31) WILD-TYPE	12	105	55

Figure S51. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.15e-08 (Chi-square test), Q value = 5.9e-06

Table S52. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	44	48	35	71	27	31	4	8
DEL PEAK 1(1P36.31) CNV	2	14	8	33	21	14	0	4
DEL PEAK 1(1P36.31) WILD-TYPE	42	34	27	38	6	17	4	4

Figure S52. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 1(1p36.31)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.048

Table S53. Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	105	121
DEL PEAK 1(1P36.31) CNV	9	27	60
DEL PEAK 1(1P36.31) WILD-TYPE	33	78	61

Figure S53. Get High-res Image Gene #21: 'Del Peak 1(1p36.31)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000173 (Fisher's exact test), Q value = 0.078

Table S54. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	6	10	4
DEL PEAK 2(1P32.3) CNV	7	2	1	0
DEL PEAK 2(1P32.3) WILD-TYPE	0	4	9	4

Figure S54. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'CN_CNMF'

P value = 2.21e-17 (Fisher's exact test), Q value = 1.2e-14

Table S55. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 2(1P32.3) CNV	4	5	12	67
DEL PEAK 2(1P32.3) WILD-TYPE	48	52	42	39

Figure S55. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p32.3)' versus 'METHLYATION_CNMF'

P value = 2.3e-48 (Fisher's exact test), Q value = 1.3e-45

Table S56. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
DEL PEAK 2(1P32.3) CNV	4	6	66	9
DEL PEAK 2(1P32.3) WILD-TYPE	118	36	0	25

Figure S56. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 2(1p32.3)' versus 'RPPA_CNMF'

P value = 0.000477 (Fisher's exact test), Q value = 0.21

Table S57. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 2(1P32.3) CNV	8	16	28	35
DEL PEAK 2(1P32.3) WILD-TYPE	44	46	40	39

Figure S57. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 2(1p32.3)' versus 'MRNASEQ_CNMF'

P value = 2.73e-09 (Fisher's exact test), Q value = 1.4e-06

Table S58. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	78	97
DEL PEAK 2(1P32.3) CNV	9	34	45
DEL PEAK 2(1P32.3) WILD-TYPE	85	44	52

Figure S58. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p32.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.06e-27 (Fisher's exact test), Q value = 1.7e-24

Table S59. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	141	92
DEL PEAK 2(1P32.3) CNV	36	14	38
DEL PEAK 2(1P32.3) WILD-TYPE	0	127	54

Figure S59. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_CNMF'

P value = 5.78e-08 (Chi-square test), Q value = 2.9e-05

Table S60. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	48	89	16	53
DEL PEAK 2(1P32.3) CNV	11	4	40	12	21
DEL PEAK 2(1P32.3) WILD-TYPE	51	44	49	4	32

Figure S60. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.2e-05 (Fisher's exact test), Q value = 0.015

Table S61. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	145	109
DEL PEAK 2(1P32.3) CNV	1	35	52
DEL PEAK 2(1P32.3) WILD-TYPE	13	110	57

Figure S61. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.54e-09 (Chi-square test), Q value = 8.1e-07

Table S62. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	44	48	35	71	27	31	4	8
DEL PEAK 2(1P32.3) CNV	2	9	8	32	21	12	0	4
DEL PEAK 2(1P32.3) WILD-TYPE	42	39	27	39	6	19	4	4

Figure S62. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 2(1p32.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00054

Table S63. Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	105	121
DEL PEAK 2(1P32.3) CNV	5	24	59
DEL PEAK 2(1P32.3) WILD-TYPE	37	81	62

Figure S63. Get High-res Image Gene #22: 'Del Peak 2(1p32.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 1.97e-06 (Fisher's exact test), Q value = 0.00097

Table S64. Gene #24: 'Del Peak 4(2p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 4(2P25.3) CNV	9	2	12	1
DEL PEAK 4(2P25.3) WILD-TYPE	43	55	42	105

Figure S64. Get High-res Image Gene #24: 'Del Peak 4(2p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 9.7e-07 (Fisher's exact test), Q value = 0.00048

Table S65. Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 5(2Q37.1) CNV	14	9	9	1
DEL PEAK 5(2Q37.1) WILD-TYPE	38	48	45	105

Figure S65. Get High-res Image Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0092

Table S66. Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
DEL PEAK 5(2Q37.1) CNV	28	2	1	2
DEL PEAK 5(2Q37.1) WILD-TYPE	94	40	65	32

Figure S66. Get High-res Image Gene #25: 'Del Peak 5(2q37.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(2q37.3)' versus 'CN_CNMF'

P value = 6.07e-06 (Fisher's exact test), Q value = 0.003

Table S67. Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 6(2Q37.3) CNV	15	10	12	3
DEL PEAK 6(2Q37.3) WILD-TYPE	37	47	42	103

Figure S67. Get High-res Image Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(2q37.3)' versus 'METHLYATION_CNMF'

P value = 1.8e-07 (Fisher's exact test), Q value = 9.1e-05

Table S68. Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
DEL PEAK 6(2Q37.3) CNV	35	1	2	2
DEL PEAK 6(2Q37.3) WILD-TYPE	87	41	64	32

Figure S68. Get High-res Image Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(2q37.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.052

Table S69. Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	105	121
DEL PEAK 6(2Q37.3) CNV	3	28	9
DEL PEAK 6(2Q37.3) WILD-TYPE	39	77	112

Figure S69. Get High-res Image Gene #26: 'Del Peak 6(2q37.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 7(3p21.1)' versus 'CN_CNMF'

P value = 5.04e-07 (Fisher's exact test), Q value = 0.00025

Table S70. Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 7(3P21.1) CNV	8	4	15	1
DEL PEAK 7(3P21.1) WILD-TYPE	44	53	39	105

Figure S70. Get High-res Image Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(3p21.1)' versus 'RPPA_CNMF'

P value = 0.000478 (Fisher's exact test), Q value = 0.21

Table S71. Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 7(3P21.1) CNV	4	16	3	4
DEL PEAK 7(3P21.1) WILD-TYPE	48	46	65	70

Figure S71. Get High-res Image Gene #27: 'Del Peak 7(3p21.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 8(4q35.2)' versus 'CN_CNMF'

P value = 9.34e-09 (Fisher's exact test), Q value = 4.8e-06

Table S72. Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 8(4Q35.2) CNV	16	4	32	24
DEL PEAK 8(4Q35.2) WILD-TYPE	36	53	22	82

Figure S72. Get High-res Image Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(4q35.2)' versus 'METHLYATION_CNMF'

P value = 9.66e-07 (Fisher's exact test), Q value = 0.00048

Table S73. Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
DEL PEAK 8(4Q35.2) CNV	43	2	28	3
DEL PEAK 8(4Q35.2) WILD-TYPE	79	40	38	31

Figure S73. Get High-res Image Gene #28: 'Del Peak 8(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 9(5q35.2)' versus 'CN_CNMF'

P value = 4.08e-09 (Fisher's exact test), Q value = 2.1e-06

Table S74. Gene #29: 'Del Peak 9(5q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 9(5Q35.2) CNV	13	1	17	3
DEL PEAK 9(5Q35.2) WILD-TYPE	39	56	37	103

Figure S74. Get High-res Image Gene #29: 'Del Peak 9(5q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(6q24.3)' versus 'CN_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.061

Table S75. Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 11(6Q24.3) CNV	6	12	19	8
DEL PEAK 11(6Q24.3) WILD-TYPE	46	45	35	98

Figure S75. Get High-res Image Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(6q24.3)' versus 'MIRSEQ_CNMF'

P value = 0.000171 (Chi-square test), Q value = 0.078

Table S76. Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	48	89	16	53
DEL PEAK 11(6Q24.3) CNV	22	7	12	1	3
DEL PEAK 11(6Q24.3) WILD-TYPE	40	41	77	15	50

Figure S76. Get High-res Image Gene #31: 'Del Peak 11(6q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(9p21.3)' versus 'CN_CNMF'

P value = 3.04e-11 (Fisher's exact test), Q value = 1.6e-08

Table S77. Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 12(9P21.3) CNV	13	38	30	18
DEL PEAK 12(9P21.3) WILD-TYPE	39	19	24	88

Figure S77. Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(9p21.3)' versus 'METHLYATION_CNMF'

P value = 2.66e-08 (Fisher's exact test), Q value = 1.4e-05

Table S78. Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
DEL PEAK 12(9P21.3) CNV	49	30	13	5
DEL PEAK 12(9P21.3) WILD-TYPE	73	12	53	29

Figure S78. Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 12(9p21.3)' versus 'RPPA_CNMF'

P value = 8.67e-06 (Fisher's exact test), Q value = 0.0042

Table S79. Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 12(9P21.3) CNV	11	38	26	18
DEL PEAK 12(9P21.3) WILD-TYPE	41	24	42	56

Figure S79. Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 12(9p21.3)' versus 'RPPA_CHIERARCHICAL'

P value = 9.22e-05 (Fisher's exact test), Q value = 0.043

Table S80. Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	129	119
DEL PEAK 12(9P21.3) CNV	2	63	28
DEL PEAK 12(9P21.3) WILD-TYPE	6	66	91

Figure S80. Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 12(9p21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000199 (Fisher's exact test), Q value = 0.09

Table S81. Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	105	121
DEL PEAK 12(9P21.3) CNV	27	38	34
DEL PEAK 12(9P21.3) WILD-TYPE	15	67	87

Figure S81. Get High-res Image Gene #32: 'Del Peak 12(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'CN_CNMF'

P value = 6.21e-19 (Fisher's exact test), Q value = 3.3e-16

Table S82. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 13(10Q26.3) CNV	14	38	25	4
DEL PEAK 13(10Q26.3) WILD-TYPE	38	19	29	102

Figure S82. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(10q26.3)' versus 'METHLYATION_CNMF'

P value = 1.3e-20 (Fisher's exact test), Q value = 7e-18

Table S83. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
DEL PEAK 13(10Q26.3) CNV	36	37	3	4
DEL PEAK 13(10Q26.3) WILD-TYPE	86	5	63	30

Figure S83. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 13(10q26.3)' versus 'RPPA_CNMF'

P value = 1.56e-07 (Fisher's exact test), Q value = 7.9e-05

Table S84. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 13(10Q26.3) CNV	13	36	13	11
DEL PEAK 13(10Q26.3) WILD-TYPE	39	26	55	63

Figure S84. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 13(10q26.3)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000214 (Fisher's exact test), Q value = 0.097

Table S85. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	129	119
DEL PEAK 13(10Q26.3) CNV	2	51	20
DEL PEAK 13(10Q26.3) WILD-TYPE	6	78	99

Figure S85. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'MRNASEQ_CNMF'

P value = 2.13e-08 (Fisher's exact test), Q value = 1.1e-05

Table S86. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	78	97
DEL PEAK 13(10Q26.3) CNV	50	14	17
DEL PEAK 13(10Q26.3) WILD-TYPE	44	64	80

Figure S86. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(10q26.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.92e-09 (Fisher's exact test), Q value = 1.5e-06

Table S87. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	141	92
DEL PEAK 13(10Q26.3) CNV	1	64	16
DEL PEAK 13(10Q26.3) WILD-TYPE	35	77	76

Figure S87. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.98e-06 (Fisher's exact test), Q value = 0.0029

Table S88. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	145	109
DEL PEAK 13(10Q26.3) CNV	10	53	18
DEL PEAK 13(10Q26.3) WILD-TYPE	4	92	91

Figure S88. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 13(10q26.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.5e-09 (Chi-square test), Q value = 2.3e-06

Table S89. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	44	48	35	71	27	31	4	8
DEL PEAK 13(10Q26.3) CNV	9	33	5	13	5	12	3	1
DEL PEAK 13(10Q26.3) WILD-TYPE	35	15	30	58	22	19	1	7

Figure S89. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 13(10q26.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.26e-11 (Fisher's exact test), Q value = 6.7e-09

Table S90. Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	105	121
DEL PEAK 13(10Q26.3) CNV	32	29	20
DEL PEAK 13(10Q26.3) WILD-TYPE	10	76	101

Figure S90. Get High-res Image Gene #33: 'Del Peak 13(10q26.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(11p15.5)' versus 'CN_CNMF'

P value = 1.88e-09 (Fisher's exact test), Q value = 9.8e-07

Table S91. Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 14(11P15.5) CNV	23	8	20	6
DEL PEAK 14(11P15.5) WILD-TYPE	29	49	34	100

Figure S91. Get High-res Image Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(11p15.5)' versus 'METHLYATION_CNMF'

P value = 2.11e-10 (Fisher's exact test), Q value = 1.1e-07

Table S92. Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
DEL PEAK 14(11P15.5) CNV	46	6	0	5
DEL PEAK 14(11P15.5) WILD-TYPE	76	36	66	29

Figure S92. Get High-res Image Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 14(11p15.5)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.62e-05 (Fisher's exact test), Q value = 0.012

Table S93. Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	141	92
DEL PEAK 14(11P15.5) CNV	0	42	15
DEL PEAK 14(11P15.5) WILD-TYPE	36	99	77

Figure S93. Get High-res Image Gene #34: 'Del Peak 14(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(11q25)' versus 'CN_CNMF'

P value = 0.000243 (Fisher's exact test), Q value = 0.11

Table S94. Gene #35: 'Del Peak 15(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 15(11Q25) CNV	6	4	10	1
DEL PEAK 15(11Q25) WILD-TYPE	46	53	44	105

Figure S94. Get High-res Image Gene #35: 'Del Peak 15(11q25)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(12q12)' versus 'CN_CNMF'

P value = 5.28e-06 (Fisher's exact test), Q value = 0.0026

Table S95. Gene #36: 'Del Peak 16(12q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 16(12Q12) CNV	18	4	8	5
DEL PEAK 16(12Q12) WILD-TYPE	34	53	46	101

Figure S95. Get High-res Image Gene #36: 'Del Peak 16(12q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 17(13q14.2)' versus 'CN_CNMF'

P value = 3.93e-30 (Fisher's exact test), Q value = 2.2e-27

Table S96. Gene #37: 'Del Peak 17(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 17(13Q14.2) CNV	19	8	47	3
DEL PEAK 17(13Q14.2) WILD-TYPE	33	49	7	103

Figure S96. Get High-res Image Gene #37: 'Del Peak 17(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(13q21.2)' versus 'CN_CNMF'

P value = 1.52e-29 (Fisher's exact test), Q value = 8.3e-27

Table S97. Gene #38: 'Del Peak 18(13q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 18(13Q21.2) CNV	20	10	47	3
DEL PEAK 18(13Q21.2) WILD-TYPE	32	47	7	103

Figure S97. Get High-res Image Gene #38: 'Del Peak 18(13q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(13q22.1)' versus 'CN_CNMF'

P value = 2.75e-25 (Fisher's exact test), Q value = 1.5e-22

Table S98. Gene #39: 'Del Peak 19(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 19(13Q22.1) CNV	18	9	45	5
DEL PEAK 19(13Q22.1) WILD-TYPE	34	48	9	101

Figure S98. Get High-res Image Gene #39: 'Del Peak 19(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 20(13q34)' versus 'CN_CNMF'

P value = 5.37e-17 (Fisher's exact test), Q value = 2.9e-14

Table S99. Gene #40: 'Del Peak 20(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 20(13Q34) CNV	15	6	33	3
DEL PEAK 20(13Q34) WILD-TYPE	37	51	21	103

Figure S99. Get High-res Image Gene #40: 'Del Peak 20(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(14q24.3)' versus 'CN_CNMF'

P value = 5.54e-05 (Fisher's exact test), Q value = 0.026

Table S100. Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 21(14Q24.3) CNV	7	14	25	15
DEL PEAK 21(14Q24.3) WILD-TYPE	45	43	29	91

Figure S100. Get High-res Image Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 21(14q24.3)' versus 'MIRSEQ_CNMF'

P value = 0.000514 (Chi-square test), Q value = 0.22

Table S101. Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	48	89	16	53
DEL PEAK 21(14Q24.3) CNV	27	8	15	3	8
DEL PEAK 21(14Q24.3) WILD-TYPE	35	40	74	13	45

Figure S101. Get High-res Image Gene #41: 'Del Peak 21(14q24.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(19q13.42)' versus 'CN_CNMF'

P value = 1.55e-15 (Fisher's exact test), Q value = 8.3e-13

Table S102. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 25(19Q13.42) CNV	13	9	39	75
DEL PEAK 25(19Q13.42) WILD-TYPE	39	48	15	31

Figure S102. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(19q13.42)' versus 'METHLYATION_CNMF'

P value = 9.49e-28 (Fisher's exact test), Q value = 5.2e-25

Table S103. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
DEL PEAK 25(19Q13.42) CNV	53	4	66	10
DEL PEAK 25(19Q13.42) WILD-TYPE	69	38	0	24

Figure S103. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 25(19q13.42)' versus 'MRNASEQ_CNMF'

P value = 7.99e-07 (Fisher's exact test), Q value = 4e-04

Table S104. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	78	97
DEL PEAK 25(19Q13.42) CNV	27	50	59
DEL PEAK 25(19Q13.42) WILD-TYPE	67	28	38

Figure S104. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 25(19q13.42)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.06e-15 (Fisher's exact test), Q value = 4.8e-12

Table S105. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	141	92
DEL PEAK 25(19Q13.42) CNV	36	47	53
DEL PEAK 25(19Q13.42) WILD-TYPE	0	94	39

Figure S105. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_CNMF'

P value = 8.24e-05 (Chi-square test), Q value = 0.038

Table S106. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	48	89	16	53
DEL PEAK 25(19Q13.42) CNV	27	14	51	15	29
DEL PEAK 25(19Q13.42) WILD-TYPE	35	34	38	1	24

Figure S106. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000298 (Fisher's exact test), Q value = 0.13

Table S107. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	145	109
DEL PEAK 25(19Q13.42) CNV	1	69	66
DEL PEAK 25(19Q13.42) WILD-TYPE	13	76	43

Figure S107. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.28e-05 (Chi-square test), Q value = 0.011

Table S108. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	44	48	35	71	27	31	4	8
DEL PEAK 25(19Q13.42) CNV	16	13	20	41	24	17	1	4
DEL PEAK 25(19Q13.42) WILD-TYPE	28	35	15	30	3	14	3	4

Figure S108. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 25(19q13.42)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.19e-08 (Fisher's exact test), Q value = 2.6e-05

Table S109. Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	105	121
DEL PEAK 25(19Q13.42) CNV	5	57	74
DEL PEAK 25(19Q13.42) WILD-TYPE	37	48	47

Figure S109. Get High-res Image Gene #45: 'Del Peak 25(19q13.42)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 26(22q13.31)' versus 'CN_CNMF'

P value = 1.41e-09 (Fisher's exact test), Q value = 7.4e-07

Table S110. Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 26(22Q13.31) CNV	11	14	15	0
DEL PEAK 26(22Q13.31) WILD-TYPE	41	43	39	106

Figure S110. Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(22q13.31)' versus 'METHLYATION_CNMF'

P value = 2.85e-06 (Fisher's exact test), Q value = 0.0014

Table S111. Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	42	66	34
DEL PEAK 26(22Q13.31) CNV	23	13	0	3
DEL PEAK 26(22Q13.31) WILD-TYPE	99	29	66	31

Figure S111. Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 26(22q13.31)' versus 'RPPA_CNMF'

P value = 6.75e-05 (Fisher's exact test), Q value = 0.031

Table S112. Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	62	68	74
DEL PEAK 26(22Q13.31) CNV	4	22	8	6
DEL PEAK 26(22Q13.31) WILD-TYPE	48	40	60	68

Figure S112. Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 26(22q13.31)' versus 'MRNASEQ_CNMF'

P value = 6.92e-06 (Fisher's exact test), Q value = 0.0034

Table S113. Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	78	97
DEL PEAK 26(22Q13.31) CNV	28	5	7
DEL PEAK 26(22Q13.31) WILD-TYPE	66	73	90

Figure S113. Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 26(22q13.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.77e-05 (Fisher's exact test), Q value = 0.018

Table S114. Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	141	92
DEL PEAK 26(22Q13.31) CNV	0	33	7
DEL PEAK 26(22Q13.31) WILD-TYPE	36	108	85

Figure S114. Get High-res Image Gene #46: 'Del Peak 26(22q13.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 27(Xp22.2)' versus 'CN_CNMF'

P value = 6.73e-09 (Fisher's exact test), Q value = 3.5e-06

Table S115. Gene #47: 'Del Peak 27(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 27(XP22.2) CNV	14	5	28	11
DEL PEAK 27(XP22.2) WILD-TYPE	38	52	26	95

Figure S115. Get High-res Image Gene #47: 'Del Peak 27(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(Xq21.1)' versus 'CN_CNMF'

P value = 5.92e-05 (Fisher's exact test), Q value = 0.028

Table S116. Gene #48: 'Del Peak 28(Xq21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	52	57	54	106
DEL PEAK 28(XQ21.1) CNV	6	3	18	8
DEL PEAK 28(XQ21.1) WILD-TYPE	46	54	36	98

Figure S116. Get High-res Image Gene #48: 'Del Peak 28(Xq21.1)' 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 = LGG-TP.transferedmergedcluster.txt
Number of patients = 269
Number of copy number variation regions = 48
Number of molecular subtypes = 12
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

[4] GISTIC_version2

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