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 32 peak regions and 12 molecular subtypes across 504 patients, 133 significant findings detected with Q value < 0.25.

Amp Peak 1(1q24.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
Amp Peak 2(1q32.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
Amp Peak 3(3q26.32) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 5(5q35.1) cnvs correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 6(7q36.3) cnvs correlated to 'CN_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CNMF'.
Amp Peak 7(8q24.22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 1(1p36.23) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 2(1p31.1) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 3(1q43) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 4(2q37.3) cnvs correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 5(3p25.3) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 6(3p21.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 7(3p12.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 8(3p12.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 9(3q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 10(3q21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 11(4q34.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 12(6q26) cnvs correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 13(6q26) cnvs correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 14(8p23.2) cnvs correlated to 'CN_CNMF'.
Del Peak 15(9p23) 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 16(9p21.3) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 17(10q23.31) cnvs correlated to 'CN_CNMF'.
Del Peak 18(13q13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Del Peak 19(14q31.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 32 regions and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 133 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	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 16(9p21 3)	0 (0%)	350	0.00125 (0.307)	0.000168 (0.0456)	7.82e-49 (2.98e-46)	6.57e-20 (2.44e-17)	5.23e-08 (1.75e-05)	0.000469 (0.122)	2.08e-23 (7.76e-21)	1.15e-27 (4.31e-25)	4.52e-16 (1.65e-13)	2.26e-07 (7.35e-05)	1.7e-09 (5.83e-07)	8.33e-07 (0.000267)
Del Peak 1(1p36 23)	0 (0%)	406	0.000181 (0.0488)	0.000139 (0.0381)	2.6e-12 (9.14e-10)	0.0348 (1.00)	2.28e-05 (0.00678)	0.000147 (0.0402)	0.000118 (0.0327)	0.000449 (0.117)	6.83e-07 (0.00022)	6.69e-09 (2.27e-06)	0.00824 (1.00)	0.000562 (0.144)
Del Peak 5(3p25 3)	0 (0%)	63	1.55e-07 (5.11e-05)	1.19e-08 (4.03e-06)	7.78e-31 (2.93e-28)	0.000223 (0.0589)	3.42e-05 (0.01)	0.0317 (1.00)	2.88e-12 (1.01e-09)	7.52e-16 (2.73e-13)	3.19e-05 (0.00939)	1.34e-14 (4.8e-12)	0.0269 (1.00)	0.00031 (0.0812)
Del Peak 6(3p21 32)	0 (0%)	60	1.55e-07 (5.11e-05)	1.19e-08 (4.03e-06)	2.81e-33 (1.06e-30)	0.00063 (0.159)	5.46e-05 (0.0157)	0.0234 (1.00)	1.15e-13 (4.1e-11)	3.21e-16 (1.17e-13)	1.01e-06 (0.000322)	2.54e-15 (9.15e-13)	0.00282 (0.662)	2.11e-05 (0.0063)
Del Peak 15(9p23)	0 (0%)	357	0.00362 (0.823)	0.000587 (0.15)	9.66e-51 (3.69e-48)	1.34e-19 (4.94e-17)	1.41e-07 (4.67e-05)	0.002 (0.475)	3.59e-23 (1.34e-20)	9.21e-24 (3.46e-21)	1.07e-15 (3.88e-13)	3.08e-05 (0.00908)	1.16e-09 (3.98e-07)	7.85e-07 (0.000252)
Del Peak 19(14q31 1)	0 (0%)	282	5.92e-05 (0.0169)	0.000113 (0.0316)	1.15e-17 (4.22e-15)	5.98e-07 (0.000194)	2.35e-14 (8.41e-12)	1.88e-07 (6.16e-05)	6.67e-20 (2.47e-17)	6.4e-15 (2.3e-12)	5.25e-11 (1.82e-08)	0.536 (1.00)	0.000185 (0.0497)	0.00765 (1.00)
Amp Peak 7(8q24 22)	0 (0%)	429	0.226 (1.00)	0.325 (1.00)	3.33e-21 (1.24e-18)	2.16e-06 (0.000677)	3.77e-06 (0.00116)	0.00425 (0.937)	2.78e-12 (9.77e-10)	2.89e-11 (1.01e-08)	3.18e-09 (1.08e-06)	5.88e-05 (0.0168)	6.69e-07 (0.000216)	0.000235 (0.0618)
Del Peak 18(13q13 3)	0 (0%)	428	0.0144 (1.00)	0.0174 (1.00)	3.56e-09 (1.21e-06)	0.000101 (0.0286)	2e-06 (0.000627)	0.14 (1.00)	1.24e-06 (0.000392)	9.39e-08 (3.12e-05)	2.38e-06 (0.000743)	1.59e-06 (5e-04)	0.0292 (1.00)	2.14e-05 (0.00639)
Amp Peak 3(3q26 32)	0 (0%)	422	0.0484 (1.00)	0.0491 (1.00)	2.14e-12 (7.56e-10)	1.86e-05 (0.00558)	0.0035 (0.802)	1.06e-05 (0.00321)	1.41e-06 (0.000447)	9.53e-08 (3.15e-05)	5.45e-08 (1.81e-05)	0.000979 (0.245)	0.0017 (0.409)	0.171 (1.00)
Del Peak 12(6q26)	0 (0%)	359	0.015 (1.00)	0.00669 (1.00)	1.88e-17 (6.9e-15)	0.0894 (1.00)	6.38e-05 (0.0181)	0.004 (0.892)	0.000478 (0.123)	0.0191 (1.00)	4.89e-08 (1.64e-05)	0.0157 (1.00)	0.000508 (0.13)	5.18e-05 (0.015)
Del Peak 13(6q26)	0 (0%)	359	0.015 (1.00)	0.00669 (1.00)	1.88e-17 (6.9e-15)	0.0894 (1.00)	3.06e-05 (0.00905)	0.00542 (1.00)	0.000159 (0.0433)	0.0191 (1.00)	1.35e-08 (4.54e-06)	0.0403 (1.00)	0.000126 (0.0348)	5.18e-05 (0.015)
Del Peak 2(1p31 1)	0 (0%)	432	0.00167 (0.404)	0.000606 (0.153)	2.11e-09 (7.2e-07)	0.0318 (1.00)	4e-05 (0.0116)	0.00807 (1.00)	0.0596 (1.00)	0.00727 (1.00)	0.000111 (0.0312)	2.92e-06 (0.000904)	0.0894 (1.00)	0.00374 (0.843)
Amp Peak 2(1q32 1)	0 (0%)	444	0.41 (1.00)	0.411 (1.00)	3.01e-15 (1.08e-12)	0.164 (1.00)	0.265 (1.00)	0.123 (1.00)	7.94e-06 (0.00243)	0.000588 (0.15)	8.39e-06 (0.00256)	0.175 (1.00)	0.0253 (1.00)	0.0468 (1.00)
Del Peak 7(3p12 3)	0 (0%)	184	0.0035 (0.802)	0.00103 (0.257)	6.2e-37 (2.36e-34)	0.0459 (1.00)	0.485 (1.00)	0.446 (1.00)	8.39e-05 (0.0238)	2.57e-06 (8e-04)	0.0595 (1.00)	0.000183 (0.0491)	0.0192 (1.00)	0.0409 (1.00)
Del Peak 11(4q34 3)	0 (0%)	428	0.314 (1.00)	0.27 (1.00)	3.4e-12 (1.19e-09)	0.000139 (0.0382)	0.00312 (0.721)	0.134 (1.00)	0.000344 (0.0898)	1.18e-05 (0.00355)	0.246 (1.00)	0.0168 (1.00)	0.00944 (1.00)	0.0467 (1.00)
Amp Peak 1(1q24 1)	0 (0%)	443	0.259 (1.00)	0.245 (1.00)	6.12e-13 (2.17e-10)	0.342 (1.00)	0.258 (1.00)	0.388 (1.00)	3.88e-05 (0.0113)	0.00128 (0.314)	9.74e-06 (0.00295)	0.417 (1.00)	0.0509 (1.00)	0.0928 (1.00)
Amp Peak 6(7q36 3)	0 (0%)	338	0.667 (1.00)	0.753 (1.00)	9.1e-14 (3.24e-11)	0.0325 (1.00)	0.000192 (0.051)	0.0175 (1.00)	0.00013 (0.0358)	0.00373 (0.843)	0.0275 (1.00)	0.12 (1.00)	0.00581 (1.00)	0.0228 (1.00)
Del Peak 4(2q37 3)	0 (0%)	454	0.00156 (0.379)	0.00299 (0.696)	0.86 (1.00)	0.825 (1.00)	0.199 (1.00)	0.413 (1.00)	0.000109 (0.0306)	0.00019 (0.0507)	0.0445 (1.00)	8.72e-06 (0.00265)	0.479 (1.00)	0.00179 (0.429)
Amp Peak 5(5q35 1)	0 (0%)	188	0.0174 (1.00)	0.00717 (1.00)	0.00541 (1.00)	0.928 (1.00)	0.0151 (1.00)	0.00332 (0.764)	0.0134 (1.00)	0.000701 (0.176)	0.411 (1.00)	6.65e-06 (0.00205)	0.948 (1.00)	0.287 (1.00)
Del Peak 3(1q43)	0 (0%)	466	0.0107 (1.00)	0.0133 (1.00)	7.08e-06 (0.00217)	0.64 (1.00)	0.00409 (0.908)	0.0108 (1.00)	0.00846 (1.00)	0.00476 (1.00)	0.409 (1.00)	9.26e-07 (0.000295)	0.685 (1.00)	0.657 (1.00)
Del Peak 8(3p12 2)	0 (0%)	212	0.0404 (1.00)	0.0199 (1.00)	2.6e-32 (9.81e-30)	0.439 (1.00)	0.422 (1.00)	0.358 (1.00)	0.00398 (0.892)	0.000211 (0.0559)	0.335 (1.00)	0.00742 (1.00)	0.0116 (1.00)	0.0323 (1.00)
Del Peak 9(3q11 2)	0 (0%)	350	0.183 (1.00)	0.121 (1.00)	1.15e-09 (3.97e-07)	0.578 (1.00)	0.861 (1.00)	0.135 (1.00)	0.523 (1.00)	0.106 (1.00)	0.701 (1.00)	0.0601 (1.00)	0.169 (1.00)	0.0251 (1.00)
Del Peak 10(3q21 3)	0 (0%)	399	0.538 (1.00)	0.462 (1.00)	3.67e-05 (0.0107)	0.67 (1.00)	0.471 (1.00)	0.0773 (1.00)	0.342 (1.00)	0.0962 (1.00)	0.968 (1.00)	0.14 (1.00)	0.253 (1.00)	0.132 (1.00)
Del Peak 14(8p23 2)	0 (0%)	356	0.502 (1.00)	0.626 (1.00)	2.67e-07 (8.67e-05)	0.0539 (1.00)	0.00424 (0.937)	0.156 (1.00)	0.00256 (0.604)	0.00869 (1.00)	0.00111 (0.274)	0.0143 (1.00)	0.0104 (1.00)	0.0248 (1.00)
Del Peak 17(10q23 31)	0 (0%)	414	0.441 (1.00)	0.554 (1.00)	6.49e-10 (2.24e-07)	0.00103 (0.257)	0.911 (1.00)	0.0717 (1.00)	0.0578 (1.00)	0.0344 (1.00)	0.0231 (1.00)	0.0238 (1.00)	0.201 (1.00)	0.0354 (1.00)
Amp Peak 4(4q32 1)	0 (0%)	490			0.476 (1.00)	0.337 (1.00)	0.693 (1.00)	0.516 (1.00)	0.0813 (1.00)	0.466 (1.00)	0.0071 (1.00)	0.055 (1.00)	0.0532 (1.00)	1 (1.00)
Amp Peak 8(10p14)	0 (0%)	488	0.189 (1.00)	0.207 (1.00)	0.00126 (0.309)	0.171 (1.00)	0.548 (1.00)	0.054 (1.00)	0.0321 (1.00)	0.00295 (0.691)	0.134 (1.00)	0.118 (1.00)	0.873 (1.00)	0.881 (1.00)
Amp Peak 9(17q24 3)	0 (0%)	467	0.0692 (1.00)	0.0988 (1.00)	0.00197 (0.469)	0.212 (1.00)	0.243 (1.00)	0.0371 (1.00)	0.197 (1.00)	0.0204 (1.00)	0.128 (1.00)	0.0476 (1.00)	0.00642 (1.00)	0.0234 (1.00)
Amp Peak 10(Xp22 2)	0 (0%)	468	1 (1.00)	1 (1.00)	0.00311 (0.721)	0.09 (1.00)	0.00598 (1.00)	0.0129 (1.00)	0.1 (1.00)	0.166 (1.00)	0.0221 (1.00)	0.618 (1.00)	0.0784 (1.00)	0.439 (1.00)
Amp Peak 11(Xp11 4)	0 (0%)	467	0.843 (1.00)	0.842 (1.00)	0.00177 (0.426)	0.0298 (1.00)	0.00732 (1.00)	0.00446 (0.976)	0.0321 (1.00)	0.0469 (1.00)	0.0221 (1.00)	0.373 (1.00)	0.0784 (1.00)	0.439 (1.00)
Amp Peak 12(Xq11 2)	0 (0%)	471	0.172 (1.00)	0.182 (1.00)	0.0473 (1.00)	0.154 (1.00)	0.105 (1.00)	0.0545 (1.00)	0.104 (1.00)	0.391 (1.00)	0.0745 (1.00)	0.166 (1.00)	0.156 (1.00)	0.412 (1.00)
Amp Peak 13(Xq28)	0 (0%)	465	0.49 (1.00)	0.591 (1.00)	0.18 (1.00)	0.648 (1.00)	0.0552 (1.00)	0.0292 (1.00)	0.0807 (1.00)	0.119 (1.00)	0.258 (1.00)	0.153 (1.00)	0.034 (1.00)	0.0442 (1.00)

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

P value = 6.12e-13 (Fisher's exact test), Q value = 2.2e-10

Table S1. Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
AMP PEAK 1(1Q24.1) CNV	46	12	3
AMP PEAK 1(1Q24.1) WILD-TYPE	118	204	121

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 3.88e-05 (Fisher's exact test), Q value = 0.011

Table S2. Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
AMP PEAK 1(1Q24.1) CNV	18	36	3
AMP PEAK 1(1Q24.1) WILD-TYPE	179	143	94

Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 1(1q24.1)' versus 'MIRSEQ_CNMF'

P value = 9.74e-06 (Fisher's exact test), Q value = 0.003

Table S3. Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
AMP PEAK 1(1Q24.1) CNV	4	18	36
AMP PEAK 1(1Q24.1) WILD-TYPE	111	173	133

Figure S3. Get High-res Image Gene #1: 'Amp Peak 1(1q24.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

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

P value = 3.01e-15 (Fisher's exact test), Q value = 1.1e-12

Table S4. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
AMP PEAK 2(1Q32.1) CNV	48	9	3
AMP PEAK 2(1Q32.1) WILD-TYPE	116	207	121

Figure S4. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 7.94e-06 (Fisher's exact test), Q value = 0.0024

Table S5. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
AMP PEAK 2(1Q32.1) CNV	18	36	2
AMP PEAK 2(1Q32.1) WILD-TYPE	179	143	95

Figure S5. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

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

P value = 0.000588 (Fisher's exact test), Q value = 0.15

Table S6. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
AMP PEAK 2(1Q32.1) CNV	1	22	33
AMP PEAK 2(1Q32.1) WILD-TYPE	68	192	157

Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

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

P value = 8.39e-06 (Fisher's exact test), Q value = 0.0026

Table S7. Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
AMP PEAK 2(1Q32.1) CNV	4	17	36
AMP PEAK 2(1Q32.1) WILD-TYPE	111	174	133

Figure S7. Get High-res Image Gene #2: 'Amp Peak 2(1q32.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 3(3q26.32)' versus 'CN_CNMF'

P value = 2.14e-12 (Fisher's exact test), Q value = 7.6e-10

Table S8. Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
AMP PEAK 3(3Q26.32) CNV	54	11	17
AMP PEAK 3(3Q26.32) WILD-TYPE	110	205	107

Figure S8. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 3(3q26.32)' versus 'METHLYATION_CNMF'

P value = 1.86e-05 (Fisher's exact test), Q value = 0.0056

Table S9. Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	119	71
AMP PEAK 3(3Q26.32) CNV	26	6	15
AMP PEAK 3(3Q26.32) WILD-TYPE	73	113	56

Figure S9. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 3(3q26.32)' versus 'RPPA_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0032

Table S10. Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	152	109
AMP PEAK 3(3Q26.32) CNV	17	24	34
AMP PEAK 3(3Q26.32) WILD-TYPE	169	128	75

Figure S10. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 3(3q26.32)' versus 'MRNASEQ_CNMF'

P value = 1.41e-06 (Fisher's exact test), Q value = 0.00045

Table S11. Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
AMP PEAK 3(3Q26.32) CNV	18	51	11
AMP PEAK 3(3Q26.32) WILD-TYPE	179	128	86

Figure S11. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 3(3q26.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.53e-08 (Fisher's exact test), Q value = 3.2e-05

Table S12. Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
AMP PEAK 3(3Q26.32) CNV	7	18	55
AMP PEAK 3(3Q26.32) WILD-TYPE	62	196	135

Figure S12. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 3(3q26.32)' versus 'MIRSEQ_CNMF'

P value = 5.45e-08 (Fisher's exact test), Q value = 1.8e-05

Table S13. Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
AMP PEAK 3(3Q26.32) CNV	12	15	50
AMP PEAK 3(3Q26.32) WILD-TYPE	103	176	119

Figure S13. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 3(3q26.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000979 (Fisher's exact test), Q value = 0.24

Table S14. Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
AMP PEAK 3(3Q26.32) CNV	9	37	31
AMP PEAK 3(3Q26.32) WILD-TYPE	26	123	249

Figure S14. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 5(5q35.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000701 (Fisher's exact test), Q value = 0.18

Table S15. Gene #5: 'Amp Peak 5(5q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
AMP PEAK 5(5Q35.1) CNV	30	148	122
AMP PEAK 5(5Q35.1) WILD-TYPE	39	66	68

Figure S15. Get High-res Image Gene #5: 'Amp Peak 5(5q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 5(5q35.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.65e-06 (Fisher's exact test), Q value = 0.002

Table S16. Gene #5: 'Amp Peak 5(5q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
AMP PEAK 5(5Q35.1) CNV	9	101	192
AMP PEAK 5(5Q35.1) WILD-TYPE	26	59	88

Figure S16. Get High-res Image Gene #5: 'Amp Peak 5(5q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 6(7q36.3)' versus 'CN_CNMF'

P value = 9.1e-14 (Fisher's exact test), Q value = 3.2e-11

Table S17. Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
AMP PEAK 6(7Q36.3) CNV	86	34	46
AMP PEAK 6(7Q36.3) WILD-TYPE	78	182	78

Figure S17. Get High-res Image Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(7q36.3)' versus 'RPPA_CNMF'

P value = 0.000192 (Chi-square test), Q value = 0.051

Table S18. Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
AMP PEAK 6(7Q36.3) CNV	21	23	32	32	10	30
AMP PEAK 6(7Q36.3) WILD-TYPE	79	65	52	43	33	27

Figure S18. Get High-res Image Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 6(7q36.3)' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.036

Table S19. Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
AMP PEAK 6(7Q36.3) CNV	48	80	29
AMP PEAK 6(7Q36.3) WILD-TYPE	149	99	68

Figure S19. Get High-res Image Gene #6: 'Amp Peak 6(7q36.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 7(8q24.22)' versus 'CN_CNMF'

P value = 3.33e-21 (Fisher's exact test), Q value = 1.2e-18

Table S20. Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
AMP PEAK 7(8Q24.22) CNV	57	2	16
AMP PEAK 7(8Q24.22) WILD-TYPE	107	214	108

Figure S20. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(8q24.22)' versus 'METHLYATION_CNMF'

P value = 2.16e-06 (Fisher's exact test), Q value = 0.00068

Table S21. Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	119	71
AMP PEAK 7(8Q24.22) CNV	30	6	13
AMP PEAK 7(8Q24.22) WILD-TYPE	69	113	58

Figure S21. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 7(8q24.22)' versus 'RPPA_CNMF'

P value = 3.77e-06 (Chi-square test), Q value = 0.0012

Table S22. Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
AMP PEAK 7(8Q24.22) CNV	6	14	14	12	1	21
AMP PEAK 7(8Q24.22) WILD-TYPE	94	74	70	63	42	36

Figure S22. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Amp Peak 7(8q24.22)' versus 'MRNASEQ_CNMF'

P value = 2.78e-12 (Fisher's exact test), Q value = 9.8e-10

Table S23. Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
AMP PEAK 7(8Q24.22) CNV	8	53	8
AMP PEAK 7(8Q24.22) WILD-TYPE	189	126	89

Figure S23. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 7(8q24.22)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.89e-11 (Fisher's exact test), Q value = 1e-08

Table S24. Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
AMP PEAK 7(8Q24.22) CNV	3	12	54
AMP PEAK 7(8Q24.22) WILD-TYPE	66	202	136

Figure S24. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 7(8q24.22)' versus 'MIRSEQ_CNMF'

P value = 3.18e-09 (Fisher's exact test), Q value = 1.1e-06

Table S25. Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
AMP PEAK 7(8Q24.22) CNV	13	10	48
AMP PEAK 7(8Q24.22) WILD-TYPE	102	181	121

Figure S25. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Amp Peak 7(8q24.22)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.017

Table S26. Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
AMP PEAK 7(8Q24.22) CNV	5	40	26
AMP PEAK 7(8Q24.22) WILD-TYPE	30	120	254

Figure S26. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 7(8q24.22)' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.69e-07 (Fisher's exact test), Q value = 0.00022

Table S27. Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	74
AMP PEAK 7(8Q24.22) CNV	2	4	23
AMP PEAK 7(8Q24.22) WILD-TYPE	48	85	51

Figure S27. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Amp Peak 7(8q24.22)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000235 (Fisher's exact test), Q value = 0.062

Table S28. Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	92	64
AMP PEAK 7(8Q24.22) CNV	16	4	9
AMP PEAK 7(8Q24.22) WILD-TYPE	41	88	55

Figure S28. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 1(1p36.23)' versus 'MRNA_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.049

Table S29. Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 1(1P36.23) CNV	2	8	8
DEL PEAK 1(1P36.23) WILD-TYPE	31	16	5

Figure S29. Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.23)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000139 (Fisher's exact test), Q value = 0.038

Table S30. Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
DEL PEAK 1(1P36.23) CNV	9	2	7
DEL PEAK 1(1P36.23) WILD-TYPE	5	30	17

Figure S30. Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 1(1p36.23)' versus 'CN_CNMF'

P value = 2.6e-12 (Fisher's exact test), Q value = 9.1e-10

Table S31. Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 1(1P36.23) CNV	52	12	34
DEL PEAK 1(1P36.23) WILD-TYPE	112	204	90

Figure S31. Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.23)' versus 'RPPA_CNMF'

P value = 2.28e-05 (Chi-square test), Q value = 0.0068

Table S32. Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
DEL PEAK 1(1P36.23) CNV	8	10	22	24	5	18
DEL PEAK 1(1P36.23) WILD-TYPE	92	78	62	51	38	39

Figure S32. Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 1(1p36.23)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000147 (Fisher's exact test), Q value = 0.04

Table S33. Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	152	109
DEL PEAK 1(1P36.23) CNV	20	35	32
DEL PEAK 1(1P36.23) WILD-TYPE	166	117	77

Figure S33. Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 1(1p36.23)' versus 'MRNASEQ_CNMF'

P value = 0.000118 (Fisher's exact test), Q value = 0.033

Table S34. Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 1(1P36.23) CNV	24	53	17
DEL PEAK 1(1P36.23) WILD-TYPE	173	126	80

Figure S34. Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 1(1p36.23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000449 (Fisher's exact test), Q value = 0.12

Table S35. Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 1(1P36.23) CNV	18	26	50
DEL PEAK 1(1P36.23) WILD-TYPE	51	188	140

Figure S35. Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.23)' versus 'MIRSEQ_CNMF'

P value = 6.83e-07 (Fisher's exact test), Q value = 0.00022

Table S36. Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
DEL PEAK 1(1P36.23) CNV	22	20	56
DEL PEAK 1(1P36.23) WILD-TYPE	93	171	113

Figure S36. Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 1(1p36.23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.69e-09 (Fisher's exact test), Q value = 2.3e-06

Table S37. Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
DEL PEAK 1(1P36.23) CNV	20	42	36
DEL PEAK 1(1P36.23) WILD-TYPE	15	118	244

Figure S37. Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 1(1p36.23)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000562 (Fisher's exact test), Q value = 0.14

Table S38. Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	92	64
DEL PEAK 1(1P36.23) CNV	20	9	16
DEL PEAK 1(1P36.23) WILD-TYPE	37	83	48

Figure S38. Get High-res Image Gene #14: 'Del Peak 1(1p36.23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 2(1p31.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000606 (Fisher's exact test), Q value = 0.15

Table S39. Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
DEL PEAK 2(1P31.1) CNV	8	2	4
DEL PEAK 2(1P31.1) WILD-TYPE	6	30	20

Figure S39. Get High-res Image Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 2(1p31.1)' versus 'CN_CNMF'

P value = 2.11e-09 (Fisher's exact test), Q value = 7.2e-07

Table S40. Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 2(1P31.1) CNV	38	8	26
DEL PEAK 2(1P31.1) WILD-TYPE	126	208	98

Figure S40. Get High-res Image Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 2(1p31.1)' versus 'RPPA_CNMF'

P value = 4e-05 (Chi-square test), Q value = 0.012

Table S41. Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
DEL PEAK 2(1P31.1) CNV	9	4	12	21	4	15
DEL PEAK 2(1P31.1) WILD-TYPE	91	84	72	54	39	42

Figure S41. Get High-res Image Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 2(1p31.1)' versus 'MIRSEQ_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.031

Table S42. Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
DEL PEAK 2(1P31.1) CNV	12	18	42
DEL PEAK 2(1P31.1) WILD-TYPE	103	173	127

Figure S42. Get High-res Image Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 2(1p31.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.92e-06 (Fisher's exact test), Q value = 9e-04

Table S43. Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
DEL PEAK 2(1P31.1) CNV	17	22	33
DEL PEAK 2(1P31.1) WILD-TYPE	18	138	247

Figure S43. Get High-res Image Gene #15: 'Del Peak 2(1p31.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 3(1q43)' versus 'CN_CNMF'

P value = 7.08e-06 (Fisher's exact test), Q value = 0.0022

Table S44. Gene #16: 'Del Peak 3(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 3(1Q43) CNV	12	5	21
DEL PEAK 3(1Q43) WILD-TYPE	152	211	103

Figure S44. Get High-res Image Gene #16: 'Del Peak 3(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(1q43)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.26e-07 (Fisher's exact test), Q value = 3e-04

Table S45. Gene #16: 'Del Peak 3(1q43)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
DEL PEAK 3(1Q43) CNV	13	9	16
DEL PEAK 3(1Q43) WILD-TYPE	22	151	264

Figure S45. Get High-res Image Gene #16: 'Del Peak 3(1q43)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(2q37.3)' versus 'MRNASEQ_CNMF'

P value = 0.000109 (Fisher's exact test), Q value = 0.031

Table S46. Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 4(2Q37.3) CNV	7	19	18
DEL PEAK 4(2Q37.3) WILD-TYPE	190	160	79

Figure S46. Get High-res Image Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 4(2q37.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.051

Table S47. Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 4(2Q37.3) CNV	12	8	24
DEL PEAK 4(2Q37.3) WILD-TYPE	57	206	166

Figure S47. Get High-res Image Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 4(2q37.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.72e-06 (Fisher's exact test), Q value = 0.0027

Table S48. Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
DEL PEAK 4(2Q37.3) CNV	12	18	16
DEL PEAK 4(2Q37.3) WILD-TYPE	23	142	264

Figure S48. Get High-res Image Gene #17: 'Del Peak 4(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(3p25.3)' versus 'MRNA_CNMF'

P value = 1.55e-07 (Fisher's exact test), Q value = 5.1e-05

Table S49. Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 5(3P25.3) CNV	32	22	3
DEL PEAK 5(3P25.3) WILD-TYPE	1	2	10

Figure S49. Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 5(3p25.3)' versus 'MRNA_CHIERARCHICAL'

P value = 1.19e-08 (Fisher's exact test), Q value = 4e-06

Table S50. Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
DEL PEAK 5(3P25.3) CNV	3	31	23
DEL PEAK 5(3P25.3) WILD-TYPE	11	1	1

Figure S50. Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 5(3p25.3)' versus 'CN_CNMF'

P value = 7.78e-31 (Fisher's exact test), Q value = 2.9e-28

Table S51. Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 5(3P25.3) CNV	158	214	69
DEL PEAK 5(3P25.3) WILD-TYPE	6	2	55

Figure S51. Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 5(3p25.3)' versus 'METHLYATION_CNMF'

P value = 0.000223 (Fisher's exact test), Q value = 0.059

Table S52. Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	119	71
DEL PEAK 5(3P25.3) CNV	94	109	53
DEL PEAK 5(3P25.3) WILD-TYPE	5	10	18

Figure S52. Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 5(3p25.3)' versus 'RPPA_CNMF'

P value = 3.42e-05 (Chi-square test), Q value = 0.01

Table S53. Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
DEL PEAK 5(3P25.3) CNV	99	74	75	56	40	52
DEL PEAK 5(3P25.3) WILD-TYPE	1	14	9	19	3	5

Figure S53. Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 5(3p25.3)' versus 'MRNASEQ_CNMF'

P value = 2.88e-12 (Fisher's exact test), Q value = 1e-09

Table S54. Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 5(3P25.3) CNV	190	160	63
DEL PEAK 5(3P25.3) WILD-TYPE	7	19	34

Figure S54. Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 5(3p25.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.52e-16 (Fisher's exact test), Q value = 2.7e-13

Table S55. Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 5(3P25.3) CNV	37	206	170
DEL PEAK 5(3P25.3) WILD-TYPE	32	8	20

Figure S55. Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 5(3p25.3)' versus 'MIRSEQ_CNMF'

P value = 3.19e-05 (Fisher's exact test), Q value = 0.0094

Table S56. Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
DEL PEAK 5(3P25.3) CNV	96	182	137
DEL PEAK 5(3P25.3) WILD-TYPE	19	9	32

Figure S56. Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 5(3p25.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.34e-14 (Fisher's exact test), Q value = 4.8e-12

Table S57. Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
DEL PEAK 5(3P25.3) CNV	15	133	267
DEL PEAK 5(3P25.3) WILD-TYPE	20	27	13

Figure S57. Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(3p25.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.081

Table S58. Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	92	64
DEL PEAK 5(3P25.3) CNV	49	88	47
DEL PEAK 5(3P25.3) WILD-TYPE	8	4	17

Figure S58. Get High-res Image Gene #18: 'Del Peak 5(3p25.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 6(3p21.32)' versus 'MRNA_CNMF'

P value = 1.55e-07 (Fisher's exact test), Q value = 5.1e-05

Table S59. Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 6(3P21.32) CNV	32	22	3
DEL PEAK 6(3P21.32) WILD-TYPE	1	2	10

Figure S59. Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 6(3p21.32)' versus 'MRNA_CHIERARCHICAL'

P value = 1.19e-08 (Fisher's exact test), Q value = 4e-06

Table S60. Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
DEL PEAK 6(3P21.32) CNV	3	31	23
DEL PEAK 6(3P21.32) WILD-TYPE	11	1	1

Figure S60. Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 6(3p21.32)' versus 'CN_CNMF'

P value = 2.81e-33 (Fisher's exact test), Q value = 1.1e-30

Table S61. Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 6(3P21.32) CNV	160	215	69
DEL PEAK 6(3P21.32) WILD-TYPE	4	1	55

Figure S61. Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(3p21.32)' versus 'METHLYATION_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.16

Table S62. Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	119	71
DEL PEAK 6(3P21.32) CNV	94	109	54
DEL PEAK 6(3P21.32) WILD-TYPE	5	10	17

Figure S62. Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 6(3p21.32)' versus 'RPPA_CNMF'

P value = 5.46e-05 (Chi-square test), Q value = 0.016

Table S63. Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
DEL PEAK 6(3P21.32) CNV	99	73	75	58	40	54
DEL PEAK 6(3P21.32) WILD-TYPE	1	15	9	17	3	3

Figure S63. Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 6(3p21.32)' versus 'MRNASEQ_CNMF'

P value = 1.15e-13 (Fisher's exact test), Q value = 4.1e-11

Table S64. Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 6(3P21.32) CNV	192	161	63
DEL PEAK 6(3P21.32) WILD-TYPE	5	18	34

Figure S64. Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 6(3p21.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.21e-16 (Fisher's exact test), Q value = 1.2e-13

Table S65. Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 6(3P21.32) CNV	38	208	170
DEL PEAK 6(3P21.32) WILD-TYPE	31	6	20

Figure S65. Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(3p21.32)' versus 'MIRSEQ_CNMF'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00032

Table S66. Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
DEL PEAK 6(3P21.32) CNV	94	185	139
DEL PEAK 6(3P21.32) WILD-TYPE	21	6	30

Figure S66. Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 6(3p21.32)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.54e-15 (Fisher's exact test), Q value = 9.2e-13

Table S67. Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
DEL PEAK 6(3P21.32) CNV	16	132	270
DEL PEAK 6(3P21.32) WILD-TYPE	19	28	10

Figure S67. Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(3p21.32)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.11e-05 (Fisher's exact test), Q value = 0.0063

Table S68. Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	92	64
DEL PEAK 6(3P21.32) CNV	51	89	46
DEL PEAK 6(3P21.32) WILD-TYPE	6	3	18

Figure S68. Get High-res Image Gene #19: 'Del Peak 6(3p21.32)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 7(3p12.3)' versus 'CN_CNMF'

P value = 6.2e-37 (Fisher's exact test), Q value = 2.4e-34

Table S69. Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 7(3P12.3) CNV	145	153	22
DEL PEAK 7(3P12.3) WILD-TYPE	19	63	102

Figure S69. Get High-res Image Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 7(3p12.3)' versus 'MRNASEQ_CNMF'

P value = 8.39e-05 (Fisher's exact test), Q value = 0.024

Table S70. Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 7(3P12.3) CNV	133	121	42
DEL PEAK 7(3P12.3) WILD-TYPE	64	58	55

Figure S70. Get High-res Image Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 7(3p12.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.57e-06 (Fisher's exact test), Q value = 8e-04

Table S71. Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 7(3P12.3) CNV	24	143	129
DEL PEAK 7(3P12.3) WILD-TYPE	45	71	61

Figure S71. Get High-res Image Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(3p12.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000183 (Fisher's exact test), Q value = 0.049

Table S72. Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
DEL PEAK 7(3P12.3) CNV	12	95	193
DEL PEAK 7(3P12.3) WILD-TYPE	23	65	87

Figure S72. Get High-res Image Gene #20: 'Del Peak 7(3p12.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 8(3p12.2)' versus 'CN_CNMF'

P value = 2.6e-32 (Fisher's exact test), Q value = 9.8e-30

Table S73. Gene #21: 'Del Peak 8(3p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 8(3P12.2) CNV	136	137	19
DEL PEAK 8(3P12.2) WILD-TYPE	28	79	105

Figure S73. Get High-res Image Gene #21: 'Del Peak 8(3p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 8(3p12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000211 (Fisher's exact test), Q value = 0.056

Table S74. Gene #21: 'Del Peak 8(3p12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 8(3P12.2) CNV	24	125	120
DEL PEAK 8(3P12.2) WILD-TYPE	45	89	70

Figure S74. Get High-res Image Gene #21: 'Del Peak 8(3p12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 9(3q11.2)' versus 'CN_CNMF'

P value = 1.15e-09 (Fisher's exact test), Q value = 4e-07

Table S75. Gene #22: 'Del Peak 9(3q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 9(3Q11.2) CNV	72	69	13
DEL PEAK 9(3Q11.2) WILD-TYPE	92	147	111

Figure S75. Get High-res Image Gene #22: 'Del Peak 9(3q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(3q21.3)' versus 'CN_CNMF'

P value = 3.67e-05 (Fisher's exact test), Q value = 0.011

Table S76. Gene #23: 'Del Peak 10(3q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 10(3Q21.3) CNV	52	40	13
DEL PEAK 10(3Q21.3) WILD-TYPE	112	176	111

Figure S76. Get High-res Image Gene #23: 'Del Peak 10(3q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q34.3)' versus 'CN_CNMF'

P value = 3.4e-12 (Fisher's exact test), Q value = 1.2e-09

Table S77. Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 11(4Q34.3) CNV	49	8	19
DEL PEAK 11(4Q34.3) WILD-TYPE	115	208	105

Figure S77. Get High-res Image Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q34.3)' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.038

Table S78. Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	119	71
DEL PEAK 11(4Q34.3) CNV	30	10	12
DEL PEAK 11(4Q34.3) WILD-TYPE	69	109	59

Figure S78. Get High-res Image Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(4q34.3)' versus 'MRNASEQ_CNMF'

P value = 0.000344 (Fisher's exact test), Q value = 0.09

Table S79. Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 11(4Q34.3) CNV	24	41	6
DEL PEAK 11(4Q34.3) WILD-TYPE	173	138	91

Figure S79. Get High-res Image Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 11(4q34.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0035

Table S80. Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 11(4Q34.3) CNV	2	24	45
DEL PEAK 11(4Q34.3) WILD-TYPE	67	190	145

Figure S80. Get High-res Image Gene #24: 'Del Peak 11(4q34.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 12(6q26)' versus 'CN_CNMF'

P value = 1.88e-17 (Fisher's exact test), Q value = 6.9e-15

Table S81. Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 12(6Q26) CNV	89	30	26
DEL PEAK 12(6Q26) WILD-TYPE	75	186	98

Figure S81. Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 12(6q26)' versus 'RPPA_CNMF'

P value = 6.38e-05 (Chi-square test), Q value = 0.018

Table S82. Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
DEL PEAK 12(6Q26) CNV	32	10	29	22	8	27
DEL PEAK 12(6Q26) WILD-TYPE	68	78	55	53	35	30

Figure S82. Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 12(6q26)' versus 'MRNASEQ_CNMF'

P value = 0.000478 (Fisher's exact test), Q value = 0.12

Table S83. Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 12(6Q26) CNV	48	68	17
DEL PEAK 12(6Q26) WILD-TYPE	149	111	80

Figure S83. Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(6q26)' versus 'MIRSEQ_CNMF'

P value = 4.89e-08 (Fisher's exact test), Q value = 1.6e-05

Table S84. Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
DEL PEAK 12(6Q26) CNV	22	39	77
DEL PEAK 12(6Q26) WILD-TYPE	93	152	92

Figure S84. Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 12(6q26)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.13

Table S85. Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	74
DEL PEAK 12(6Q26) CNV	9	19	34
DEL PEAK 12(6Q26) WILD-TYPE	41	70	40

Figure S85. Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(6q26)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.18e-05 (Fisher's exact test), Q value = 0.015

Table S86. Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	92	64
DEL PEAK 12(6Q26) CNV	30	18	14
DEL PEAK 12(6Q26) WILD-TYPE	27	74	50

Figure S86. Get High-res Image Gene #25: 'Del Peak 12(6q26)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 13(6q26)' versus 'CN_CNMF'

P value = 1.88e-17 (Fisher's exact test), Q value = 6.9e-15

Table S87. Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 13(6Q26) CNV	89	30	26
DEL PEAK 13(6Q26) WILD-TYPE	75	186	98

Figure S87. Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(6q26)' versus 'RPPA_CNMF'

P value = 3.06e-05 (Chi-square test), Q value = 0.009

Table S88. Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
DEL PEAK 13(6Q26) CNV	31	10	29	22	8	28
DEL PEAK 13(6Q26) WILD-TYPE	69	78	55	53	35	29

Figure S88. Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 13(6q26)' versus 'MRNASEQ_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.043

Table S89. Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 13(6Q26) CNV	48	69	16
DEL PEAK 13(6Q26) WILD-TYPE	149	110	81

Figure S89. Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 13(6q26)' versus 'MIRSEQ_CNMF'

P value = 1.35e-08 (Fisher's exact test), Q value = 4.5e-06

Table S90. Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
DEL PEAK 13(6Q26) CNV	21	39	78
DEL PEAK 13(6Q26) WILD-TYPE	94	152	91

Figure S90. Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 13(6q26)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.035

Table S91. Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	74
DEL PEAK 13(6Q26) CNV	8	19	35
DEL PEAK 13(6Q26) WILD-TYPE	42	70	39

Figure S91. Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 13(6q26)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.18e-05 (Fisher's exact test), Q value = 0.015

Table S92. Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	92	64
DEL PEAK 13(6Q26) CNV	30	18	14
DEL PEAK 13(6Q26) WILD-TYPE	27	74	50

Figure S92. Get High-res Image Gene #26: 'Del Peak 13(6q26)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 14(8p23.2)' versus 'CN_CNMF'

P value = 2.67e-07 (Fisher's exact test), Q value = 8.7e-05

Table S93. Gene #27: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 14(8P23.2) CNV	73	40	35
DEL PEAK 14(8P23.2) WILD-TYPE	91	176	89

Figure S93. Get High-res Image Gene #27: 'Del Peak 14(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(9p23)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000587 (Fisher's exact test), Q value = 0.15

Table S94. Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
DEL PEAK 15(9P23) CNV	1	4	13
DEL PEAK 15(9P23) WILD-TYPE	13	28	11

Figure S94. Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 15(9p23)' versus 'CN_CNMF'

P value = 9.66e-51 (Fisher's exact test), Q value = 3.7e-48

Table S95. Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 15(9P23) CNV	112	3	32
DEL PEAK 15(9P23) WILD-TYPE	52	213	92

Figure S95. Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(9p23)' versus 'METHLYATION_CNMF'

P value = 1.34e-19 (Fisher's exact test), Q value = 4.9e-17

Table S96. Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	119	71
DEL PEAK 15(9P23) CNV	60	6	24
DEL PEAK 15(9P23) WILD-TYPE	39	113	47

Figure S96. Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 15(9p23)' versus 'RPPA_CNMF'

P value = 1.41e-07 (Chi-square test), Q value = 4.7e-05

Table S97. Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
DEL PEAK 15(9P23) CNV	17	23	32	18	10	35
DEL PEAK 15(9P23) WILD-TYPE	83	65	52	57	33	22

Figure S97. Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 15(9p23)' versus 'MRNASEQ_CNMF'

P value = 3.59e-23 (Fisher's exact test), Q value = 1.3e-20

Table S98. Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 15(9P23) CNV	24	101	13
DEL PEAK 15(9P23) WILD-TYPE	173	78	84

Figure S98. Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 15(9p23)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.21e-24 (Fisher's exact test), Q value = 3.5e-21

Table S99. Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 15(9P23) CNV	9	24	105
DEL PEAK 15(9P23) WILD-TYPE	60	190	85

Figure S99. Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 15(9p23)' versus 'MIRSEQ_CNMF'

P value = 1.07e-15 (Fisher's exact test), Q value = 3.9e-13

Table S100. Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
DEL PEAK 15(9P23) CNV	26	25	88
DEL PEAK 15(9P23) WILD-TYPE	89	166	81

Figure S100. Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 15(9p23)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.08e-05 (Fisher's exact test), Q value = 0.0091

Table S101. Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
DEL PEAK 15(9P23) CNV	10	68	61
DEL PEAK 15(9P23) WILD-TYPE	25	92	219

Figure S101. Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 15(9p23)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.16e-09 (Fisher's exact test), Q value = 4e-07

Table S102. Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	74
DEL PEAK 15(9P23) CNV	12	11	43
DEL PEAK 15(9P23) WILD-TYPE	38	78	31

Figure S102. Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 15(9p23)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.85e-07 (Fisher's exact test), Q value = 0.00025

Table S103. Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	92	64
DEL PEAK 15(9P23) CNV	33	15	18
DEL PEAK 15(9P23) WILD-TYPE	24	77	46

Figure S103. Get High-res Image Gene #28: 'Del Peak 15(9p23)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.046

Table S104. Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
DEL PEAK 16(9P21.3) CNV	1	4	14
DEL PEAK 16(9P21.3) WILD-TYPE	13	28	10

Figure S104. Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'CN_CNMF'

P value = 7.82e-49 (Fisher's exact test), Q value = 3e-46

Table S105. Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 16(9P21.3) CNV	115	6	33
DEL PEAK 16(9P21.3) WILD-TYPE	49	210	91

Figure S105. Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 16(9p21.3)' versus 'METHLYATION_CNMF'

P value = 6.57e-20 (Fisher's exact test), Q value = 2.4e-17

Table S106. Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	119	71
DEL PEAK 16(9P21.3) CNV	60	6	27
DEL PEAK 16(9P21.3) WILD-TYPE	39	113	44

Figure S106. Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 16(9p21.3)' versus 'RPPA_CNMF'

P value = 5.23e-08 (Chi-square test), Q value = 1.7e-05

Table S107. Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
DEL PEAK 16(9P21.3) CNV	18	26	32	19	10	37
DEL PEAK 16(9P21.3) WILD-TYPE	82	62	52	56	33	20

Figure S107. Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 16(9p21.3)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000469 (Fisher's exact test), Q value = 0.12

Table S108. Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	152	109
DEL PEAK 16(9P21.3) CNV	42	52	48
DEL PEAK 16(9P21.3) WILD-TYPE	144	100	61

Figure S108. Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 2.08e-23 (Fisher's exact test), Q value = 7.8e-21

Table S109. Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 16(9P21.3) CNV	26	105	15
DEL PEAK 16(9P21.3) WILD-TYPE	171	74	82

Figure S109. Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 16(9p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.15e-27 (Fisher's exact test), Q value = 4.3e-25

Table S110. Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 16(9P21.3) CNV	8	25	113
DEL PEAK 16(9P21.3) WILD-TYPE	61	189	77

Figure S110. Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_CNMF'

P value = 4.52e-16 (Fisher's exact test), Q value = 1.6e-13

Table S111. Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
DEL PEAK 16(9P21.3) CNV	29	26	91
DEL PEAK 16(9P21.3) WILD-TYPE	86	165	78

Figure S111. Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.26e-07 (Fisher's exact test), Q value = 7.4e-05

Table S112. Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
DEL PEAK 16(9P21.3) CNV	11	75	60
DEL PEAK 16(9P21.3) WILD-TYPE	24	85	220

Figure S112. Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.7e-09 (Fisher's exact test), Q value = 5.8e-07

Table S113. Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	74
DEL PEAK 16(9P21.3) CNV	13	11	43
DEL PEAK 16(9P21.3) WILD-TYPE	37	78	31

Figure S113. Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'Del Peak 16(9p21.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.33e-07 (Fisher's exact test), Q value = 0.00027

Table S114. Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	92	64
DEL PEAK 16(9P21.3) CNV	33	15	19
DEL PEAK 16(9P21.3) WILD-TYPE	24	77	45

Figure S114. Get High-res Image Gene #29: 'Del Peak 16(9p21.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 17(10q23.31)' versus 'CN_CNMF'

P value = 6.49e-10 (Fisher's exact test), Q value = 2.2e-07

Table S115. Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 17(10Q23.31) CNV	49	13	28
DEL PEAK 17(10Q23.31) WILD-TYPE	115	203	96

Figure S115. Get High-res Image Gene #30: 'Del Peak 17(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(13q13.3)' versus 'CN_CNMF'

P value = 3.56e-09 (Fisher's exact test), Q value = 1.2e-06

Table S116. Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 18(13Q13.3) CNV	43	10	23
DEL PEAK 18(13Q13.3) WILD-TYPE	121	206	101

Figure S116. Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(13q13.3)' versus 'METHLYATION_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.029

Table S117. Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	119	71
DEL PEAK 18(13Q13.3) CNV	18	7	20
DEL PEAK 18(13Q13.3) WILD-TYPE	81	112	51

Figure S117. Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 18(13q13.3)' versus 'RPPA_CNMF'

P value = 2e-06 (Chi-square test), Q value = 0.00063

Table S118. Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
DEL PEAK 18(13Q13.3) CNV	2	12	14	13	7	21
DEL PEAK 18(13Q13.3) WILD-TYPE	98	76	70	62	36	36

Figure S118. Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 18(13q13.3)' versus 'MRNASEQ_CNMF'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.00039

Table S119. Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 18(13Q13.3) CNV	15	48	11
DEL PEAK 18(13Q13.3) WILD-TYPE	182	131	86

Figure S119. Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 18(13q13.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.39e-08 (Fisher's exact test), Q value = 3.1e-05

Table S120. Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 18(13Q13.3) CNV	9	14	51
DEL PEAK 18(13Q13.3) WILD-TYPE	60	200	139

Figure S120. Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(13q13.3)' versus 'MIRSEQ_CNMF'

P value = 2.38e-06 (Fisher's exact test), Q value = 0.00074

Table S121. Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
DEL PEAK 18(13Q13.3) CNV	15	14	45
DEL PEAK 18(13Q13.3) WILD-TYPE	100	177	124

Figure S121. Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 18(13q13.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.59e-06 (Fisher's exact test), Q value = 5e-04

Table S122. Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	160	280
DEL PEAK 18(13Q13.3) CNV	13	36	25
DEL PEAK 18(13Q13.3) WILD-TYPE	22	124	255

Figure S122. Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 18(13q13.3)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.0064

Table S123. Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	92	64
DEL PEAK 18(13Q13.3) CNV	21	6	10
DEL PEAK 18(13Q13.3) WILD-TYPE	36	86	54

Figure S123. Get High-res Image Gene #31: 'Del Peak 18(13q13.3)' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'Del Peak 19(14q31.1)' versus 'MRNA_CNMF'

P value = 5.92e-05 (Fisher's exact test), Q value = 0.017

Table S124. Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	24	13
DEL PEAK 19(14Q31.1) CNV	10	19	2
DEL PEAK 19(14Q31.1) WILD-TYPE	23	5	11

Figure S124. Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 19(14q31.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000113 (Fisher's exact test), Q value = 0.032

Table S125. Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	32	24
DEL PEAK 19(14Q31.1) CNV	3	9	19
DEL PEAK 19(14Q31.1) WILD-TYPE	11	23	5

Figure S125. Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 19(14q31.1)' versus 'CN_CNMF'

P value = 1.15e-17 (Fisher's exact test), Q value = 4.2e-15

Table S126. Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	216	124
DEL PEAK 19(14Q31.1) CNV	117	59	46
DEL PEAK 19(14Q31.1) WILD-TYPE	47	157	78

Figure S126. Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(14q31.1)' versus 'METHLYATION_CNMF'

P value = 5.98e-07 (Fisher's exact test), Q value = 0.00019

Table S127. Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	99	119	71
DEL PEAK 19(14Q31.1) CNV	60	31	36
DEL PEAK 19(14Q31.1) WILD-TYPE	39	88	35

Figure S127. Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(14q31.1)' versus 'RPPA_CNMF'

P value = 2.35e-14 (Chi-square test), Q value = 8.4e-12

Table S128. Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	100	88	84	75	43	57
DEL PEAK 19(14Q31.1) CNV	30	30	64	23	13	41
DEL PEAK 19(14Q31.1) WILD-TYPE	70	58	20	52	30	16

Figure S128. Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #5: 'RPPA_CNMF'

'Del Peak 19(14q31.1)' versus 'RPPA_CHIERARCHICAL'

P value = 1.88e-07 (Fisher's exact test), Q value = 6.2e-05

Table S129. Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	152	109
DEL PEAK 19(14Q31.1) CNV	57	92	52
DEL PEAK 19(14Q31.1) WILD-TYPE	129	60	57

Figure S129. Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(14q31.1)' versus 'MRNASEQ_CNMF'

P value = 6.67e-20 (Fisher's exact test), Q value = 2.5e-17

Table S130. Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	197	179	97
DEL PEAK 19(14Q31.1) CNV	68	126	17
DEL PEAK 19(14Q31.1) WILD-TYPE	129	53	80

Figure S130. Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 19(14q31.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.4e-15 (Fisher's exact test), Q value = 2.3e-12

Table S131. Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	69	214	190
DEL PEAK 19(14Q31.1) CNV	11	76	124
DEL PEAK 19(14Q31.1) WILD-TYPE	58	138	66

Figure S131. Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(14q31.1)' versus 'MIRSEQ_CNMF'

P value = 5.25e-11 (Fisher's exact test), Q value = 1.8e-08

Table S132. Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	115	191	169
DEL PEAK 19(14Q31.1) CNV	37	64	111
DEL PEAK 19(14Q31.1) WILD-TYPE	78	127	58

Figure S132. Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Del Peak 19(14q31.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000185 (Fisher's exact test), Q value = 0.05

Table S133. Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	50	89	74
DEL PEAK 19(14Q31.1) CNV	18	31	48
DEL PEAK 19(14Q31.1) WILD-TYPE	32	58	26

Figure S133. Get High-res Image Gene #32: 'Del Peak 19(14q31.1)' versus Molecular Subtype #11: 'MIRSEQ_MATURE_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 = KIRC-TP.transferedmergedcluster.txt
Number of patients = 504
Number of copy number variation regions = 32
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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