Correlation between copy number variations of arm-level result and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 514 patients, 200 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 4p gain cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MRNASEQ_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 10p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 14q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • xq loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 200 significant findings detected.

Clinical
Features 		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 Chi-square test
14q loss 214 (42%) 300 3.12e-05
(0.0228) 		4.31e-05
(0.0314) 		6.37e-18
(5.58e-15) 		6.21e-08
(5.01e-05) 		1.01e-13
(8.72e-11) 		1.28e-07
(0.000102) 		1.97e-21
(1.73e-18) 		7.89e-16
(6.88e-13) 		2.41e-11
(2.03e-08) 		0.165
(1.00) 		8.25e-07
(0.000642) 		2.9e-05
(0.0213)
2p loss 14 (3%) 500 3.58e-05
(0.0261) 		6.3e-05
(0.0454) 		1.38e-06
(0.00107) 		0.668
(1.00) 		4.58e-05
(0.0334) 		2.35e-06
(0.00181) 		2.39e-07
(0.00019) 		4.73e-09
(3.88e-06) 		8.4e-05
(0.0602) 		4.5e-12
(3.82e-09) 		0.0741
(1.00) 		1.64e-13
(1.41e-10)
2q loss 14 (3%) 500 0.000249
(0.173) 		0.000389
(0.267) 		1.38e-06
(0.00107) 		1
(1.00) 		0.000316
(0.219) 		2.35e-06
(0.00181) 		2.39e-07
(0.00019) 		6.39e-08
(5.15e-05) 		2.32e-05
(0.0172) 		2.53e-10
(2.1e-07) 		0.0741
(1.00) 		1.64e-13
(1.41e-10)
20p gain 111 (22%) 403 0.116
(1.00) 		0.163
(1.00) 		7.57e-22
(6.67e-19) 		5.62e-05
(0.0408) 		1.07e-07
(8.58e-05) 		0.00174
(1.00) 		1.15e-12
(9.78e-10) 		2.16e-12
(1.84e-09) 		3.32e-10
(2.76e-07) 		0.000241
(0.169) 		6.18e-07
(0.000484) 		0.0316
(1.00)
20q gain 114 (22%) 400 0.0457
(1.00) 		0.0675
(1.00) 		2.82e-23
(2.49e-20) 		5.62e-05
(0.0408) 		6.76e-09
(5.51e-06) 		0.000896
(0.586) 		2.62e-14
(2.27e-11) 		1.9e-13
(1.62e-10) 		3.55e-11
(2.98e-08) 		0.000154
(0.109) 		2.7e-07
(0.000214) 		0.0197
(1.00)
6p loss 99 (19%) 415 0.0113
(1.00) 		0.00282
(1.00) 		8.48e-16
(7.38e-13) 		0.000723
(0.48) 		3.74e-06
(0.00285) 		0.000258
(0.18) 		3.05e-08
(2.47e-05) 		5.76e-07
(0.000452) 		7.99e-11
(6.68e-08) 		0.000278
(0.193) 		4.38e-07
(0.000345) 		0.00961
(1.00)
9p loss 146 (28%) 368 0.00417
(1.00) 		0.000533
(0.36) 		2.06e-47
(1.83e-44) 		1.76e-19
(1.54e-16) 		4.89e-06
(0.00372) 		0.000935
(0.608) 		2.12e-22
(1.87e-19) 		1.18e-25
(1.04e-22) 		2.97e-15
(2.57e-12) 		3.49e-05
(0.0255) 		1.04e-10
(8.66e-08) 		0.00242
(1.00)
9q loss 147 (29%) 367 0.0101
(1.00) 		0.00143
(0.917) 		3.06e-46
(2.71e-43) 		1.8e-18
(1.58e-15) 		1.06e-06
(0.000824) 		0.00159
(1.00) 		6.79e-23
(5.99e-20) 		3.26e-25
(2.89e-22) 		1.29e-16
(1.13e-13) 		0.000159
(0.112) 		4.55e-10
(3.76e-07) 		0.00043
(0.293)
18p loss 91 (18%) 423 0.0574
(1.00) 		0.135
(1.00) 		1.36e-13
(1.17e-10) 		2.68e-07
(0.000212) 		3.07e-08
(2.48e-05) 		0.00183
(1.00) 		7.08e-19
(6.22e-16) 		1.89e-15
(1.64e-12) 		3.61e-11
(3.03e-08) 		1.7e-05
(0.0127) 		4.42e-07
(0.000348) 		0.00862
(1.00)
18q loss 93 (18%) 421 0.0468
(1.00) 		0.0649
(1.00) 		2.29e-13
(1.96e-10) 		1.97e-06
(0.00152) 		1.99e-07
(0.000158) 		0.0067
(1.00) 		6.42e-18
(5.61e-15) 		4.1e-15
(3.55e-12) 		1.11e-10
(9.2e-08) 		1.4e-05
(0.0105) 		1.68e-07
(0.000134) 		0.00233
(1.00)
3q gain 60 (12%) 454 0.0122
(1.00) 		0.0188
(1.00) 		2.99e-11
(2.52e-08) 		0.0111
(1.00) 		0.000564
(0.38) 		5.97e-07
(0.000468) 		1.3e-05
(0.00979) 		1.87e-06
(0.00144) 		1.45e-08
(1.18e-05) 		4.11e-06
(0.00313) 		0.000181
(0.128) 		0.111
(1.00)
8q gain 59 (11%) 455 0.226
(1.00) 		0.325
(1.00) 		9.3e-19
(8.15e-16) 		6.54e-06
(0.00496) 		5.21e-05
(0.0379) 		0.0213
(1.00) 		8.36e-12
(7.08e-09) 		1.2e-09
(9.88e-07) 		6.49e-11
(5.44e-08) 		0.0024
(1.00) 		6.51e-07
(0.000508) 		0.00255
(1.00)
12p gain 120 (23%) 394 0.0129
(1.00) 		0.0142
(1.00) 		9.53e-14
(8.24e-11) 		0.000174
(0.123) 		1.34e-12
(1.14e-09) 		0.00103
(0.67) 		1.91e-11
(1.61e-08) 		2.37e-12
(2.01e-09) 		1.1e-10
(9.16e-08) 		0.0236
(1.00) 		7.35e-08
(5.91e-05) 		0.00598
(1.00)
12q gain 120 (23%) 394 0.0129
(1.00) 		0.0142
(1.00) 		1.74e-13
(1.49e-10) 		0.000118
(0.0845) 		1.87e-13
(1.6e-10) 		0.000431
(0.293) 		6.4e-11
(5.36e-08) 		2.37e-12
(2.01e-09) 		3.2e-11
(2.69e-08) 		0.0518
(1.00) 		7.35e-08
(5.91e-05) 		0.00598
(1.00)
17p loss 45 (9%) 469 0.000135
(0.0961) 		0.000271
(0.188) 		5.35e-09
(4.38e-06) 		0.14
(1.00) 		0.00511
(1.00) 		0.00163
(1.00) 		1.61e-06
(0.00124) 		1.4e-07
(0.000112) 		9.59e-08
(7.69e-05) 		1.69e-06
(0.00131) 		0.0335
(1.00) 		0.0199
(1.00)
3p loss 370 (72%) 144 0.00349
(1.00) 		0.000663
(0.443) 		4.72e-24
(4.18e-21) 		0.0207
(1.00) 		0.0197
(1.00) 		0.00482
(1.00) 		1.72e-08
(1.39e-05) 		3.36e-10
(2.78e-07) 		0.0164
(1.00) 		2.81e-05
(0.0207) 		0.128
(1.00) 		5.27e-06
(0.004)
6q loss 126 (25%) 388 0.0475
(1.00) 		0.0212
(1.00) 		6.58e-15
(5.69e-12) 		0.0434
(1.00) 		2.57e-05
(0.019) 		0.00327
(1.00) 		0.000134
(0.0952) 		0.00497
(1.00) 		3.86e-07
(0.000304) 		0.0233
(1.00) 		0.000132
(0.0938) 		0.0801
(1.00)
13q loss 69 (13%) 445 0.00304
(1.00) 		0.00455
(1.00) 		9.33e-11
(7.79e-08) 		0.000737
(0.489) 		7.66e-06
(0.00579) 		0.00307
(1.00) 		4.1e-06
(0.00312) 		3.54e-07
(0.00028) 		3.23e-06
(0.00247) 		0.00194
(1.00) 		0.05
(1.00) 		0.00844
(1.00)
17q loss 28 (5%) 486 0.000618
(0.414) 		0.000912
(0.595) 		2.42e-06
(0.00186) 		0.585
(1.00) 		0.157
(1.00) 		0.0237
(1.00) 		0.000386
(0.265) 		5.87e-05
(0.0424) 		1.14e-05
(0.00863) 		9.14e-07
(0.000711) 		0.16
(1.00) 		1.81e-05
(0.0135)
8p gain 31 (6%) 483 6.29e-09
(5.13e-06) 		0.000964
(0.627) 		0.0096
(1.00) 		0.202
(1.00) 		1.91e-05
(0.0142) 		0.000329
(0.227) 		6.98e-06
(0.00529) 		0.00582
(1.00) 		0.0052
(1.00) 		0.0485
(1.00)
22q loss 39 (8%) 475 0.0101
(1.00) 		0.0155
(1.00) 		5.85e-09
(4.78e-06) 		0.00695
(1.00) 		0.00423
(1.00) 		0.0358
(1.00) 		6.24e-07
(0.000488) 		2.84e-06
(0.00218) 		1.18e-05
(0.00885) 		0.127
(1.00) 		0.000656
(0.439) 		0.498
(1.00)
1q gain 51 (10%) 463 0.41
(1.00) 		0.411
(1.00) 		1.74e-15
(1.51e-12) 		0.0369
(1.00) 		0.0875
(1.00) 		0.0312
(1.00) 		1.85e-05
(0.0137) 		0.000364
(0.251) 		2.16e-05
(0.016) 		0.954
(1.00) 		0.0308
(1.00) 		0.013
(1.00)
7p gain 168 (33%) 346 0.416
(1.00) 		0.577
(1.00) 		9.53e-14
(8.24e-11) 		0.00627
(1.00) 		1.61e-05
(0.012) 		0.00178
(1.00) 		0.000127
(0.0908) 		0.00181
(1.00) 		0.00635
(1.00) 		0.648
(1.00) 		0.0377
(1.00) 		0.261
(1.00)
7q gain 169 (33%) 345 0.416
(1.00) 		0.577
(1.00) 		1.24e-13
(1.06e-10) 		0.0156
(1.00) 		2.78e-05
(0.0205) 		0.000692
(0.461) 		0.000144
(0.102) 		0.00159
(1.00) 		0.00797
(1.00) 		0.429
(1.00) 		0.052
(1.00) 		0.0375
(1.00)
19q gain 57 (11%) 457 0.102
(1.00) 		0.149
(1.00) 		2.36e-11
(1.99e-08) 		0.000287
(0.199) 		0.00102
(0.662) 		0.00619
(1.00) 		0.00197
(1.00) 		0.000775
(0.512) 		2.97e-05
(0.0218) 		0.00333
(1.00) 		0.00805
(1.00) 		0.828
(1.00)
1p loss 56 (11%) 458 0.00128
(0.822) 		0.000389
(0.267) 		1.1e-09
(9.04e-07) 		0.469
(1.00) 		0.000492
(0.333) 		0.178
(1.00) 		0.137
(1.00) 		0.00262
(1.00) 		0.0346
(1.00) 		1.97e-08
(1.6e-05) 		0.394
(1.00) 		0.000248
(0.173)
1q loss 36 (7%) 478 0.0107
(1.00) 		0.0133
(1.00) 		5.03e-10
(4.16e-07) 		0.289
(1.00) 		0.0102
(1.00) 		0.0695
(1.00) 		0.00416
(1.00) 		0.000678
(0.452) 		0.0421
(1.00) 		2.54e-08
(2.05e-05) 		0.488
(1.00) 		1.41e-05
(0.0106)
15q loss 35 (7%) 479 0.118
(1.00) 		0.127
(1.00) 		2.59e-10
(2.15e-07) 		0.00787
(1.00) 		0.042
(1.00) 		0.414
(1.00) 		3.2e-06
(0.00245) 		8.15e-07
(0.000636) 		0.00231
(1.00) 		0.078
(1.00) 		0.00231
(1.00) 		0.421
(1.00)
3p gain 20 (4%) 494 0.0536
(1.00) 		0.0623
(1.00) 		0.00038
(0.262) 		0.585
(1.00) 		0.0444
(1.00) 		0.00059
(0.396) 		0.00506
(1.00) 		0.00213
(1.00) 		6.13e-05
(0.0443) 		0.0002
(0.141) 		0.00202
(1.00) 		0.0628
(1.00)
4p gain 13 (3%) 501 0.0668
(1.00) 		0.377
(1.00) 		0.253
(1.00) 		0.00175
(1.00) 		0.000418
(0.285) 		0.0692
(1.00) 		0.000208
(0.146) 		0.0226
(1.00) 		0.0484
(1.00) 		6.88e-05
(0.0495)
4q gain 13 (3%) 501 0.273
(1.00) 		0.449
(1.00) 		0.253
(1.00) 		0.0201
(1.00) 		0.000418
(0.285) 		0.144
(1.00) 		0.000208
(0.146) 		0.0226
(1.00) 		0.0484
(1.00) 		6.88e-05
(0.0495)
19p gain 51 (10%) 463 0.226
(1.00) 		0.325
(1.00) 		1.98e-09
(1.63e-06) 		0.00252
(1.00) 		0.00936
(1.00) 		0.0521
(1.00) 		0.00467
(1.00) 		0.00277
(1.00) 		0.000192
(0.135) 		0.00885
(1.00) 		0.0261
(1.00) 		0.942
(1.00)
4q loss 65 (13%) 449 0.387
(1.00) 		0.346
(1.00) 		1.04e-11
(8.77e-09) 		0.000529
(0.358) 		0.051
(1.00) 		0.199
(1.00) 		0.00077
(0.509) 		9.78e-06
(0.00739) 		0.382
(1.00) 		0.141
(1.00) 		0.0406
(1.00) 		0.293
(1.00)
xq loss 46 (9%) 468 0.0238
(1.00) 		0.00917
(1.00) 		1.97e-05
(0.0146) 		0.0222
(1.00) 		0.143
(1.00) 		0.00382
(1.00) 		0.0553
(1.00) 		0.00419
(1.00) 		0.0158
(1.00) 		1.43e-05
(0.0107) 		0.027
(1.00) 		0.0167
(1.00)
1p gain 23 (4%) 491 1
(1.00) 		1
(1.00) 		1.3e-07
(0.000104) 		0.00164
(1.00) 		0.00137
(0.878) 		0.00617
(1.00) 		0.0111
(1.00) 		0.00197
(1.00) 		0.000572
(0.385) 		0.261
(1.00) 		0.025
(1.00) 		0.0244
(1.00)
2p gain 76 (15%) 438 0.561
(1.00) 		0.4
(1.00) 		2.53e-09
(2.08e-06) 		0.201
(1.00) 		0.0118
(1.00) 		0.871
(1.00) 		0.165
(1.00) 		0.0351
(1.00) 		0.644
(1.00) 		0.0928
(1.00) 		0.0682
(1.00) 		0.0922
(1.00)
2q gain 77 (15%) 437 0.561
(1.00) 		0.4
(1.00) 		2.14e-07
(0.00017) 		0.3
(1.00) 		0.0115
(1.00) 		0.934
(1.00) 		0.156
(1.00) 		0.0354
(1.00) 		0.712
(1.00) 		0.0928
(1.00) 		0.15
(1.00) 		0.0689
(1.00)
5p gain 190 (37%) 324 0.835
(1.00) 		0.778
(1.00) 		0.000101
(0.0719) 		0.172
(1.00) 		0.0843
(1.00) 		0.113
(1.00) 		0.0128
(1.00) 		0.00077
(0.509) 		0.109
(1.00) 		0.807
(1.00) 		0.128
(1.00) 		0.54
(1.00)
10p gain 17 (3%) 497 0.000929
(0.606) 		0.113
(1.00) 		0.276
(1.00) 		0.472
(1.00) 		0.00084
(0.551) 		0.00018
(0.127) 		0.075
(1.00) 		0.433
(1.00) 		0.466
(1.00) 		0.138
(1.00)
11p gain 31 (6%) 483 0.232
(1.00) 		0.252
(1.00) 		1.42e-05
(0.0106) 		0.308
(1.00) 		0.195
(1.00) 		0.246
(1.00) 		0.29
(1.00) 		0.182
(1.00) 		0.313
(1.00) 		0.0275
(1.00) 		0.205
(1.00) 		0.33
(1.00)
11q gain 29 (6%) 485 0.341
(1.00) 		0.539
(1.00) 		0.000276
(0.191) 		0.188
(1.00) 		0.423
(1.00) 		0.513
(1.00) 		0.549
(1.00) 		0.483
(1.00) 		0.593
(1.00) 		0.0218
(1.00) 		0.523
(1.00) 		0.243
(1.00)
17p gain 25 (5%) 489 0.0186
(1.00) 		0.0349
(1.00) 		2.84e-05
(0.0209) 		0.727
(1.00) 		0.329
(1.00) 		0.0734
(1.00) 		0.237
(1.00) 		0.0589
(1.00) 		0.296
(1.00) 		0.0555
(1.00) 		0.291
(1.00) 		0.134
(1.00)
17q gain 31 (6%) 483 0.0692
(1.00) 		0.0988
(1.00) 		8.05e-05
(0.0578) 		0.394
(1.00) 		0.493
(1.00) 		0.0761
(1.00) 		0.134
(1.00) 		0.0171
(1.00) 		0.182
(1.00) 		0.0319
(1.00) 		0.112
(1.00) 		0.0667
(1.00)
21q gain 50 (10%) 464 0.269
(1.00) 		0.28
(1.00) 		3.43e-06
(0.00262) 		0.00867
(1.00) 		0.0011
(0.711) 		0.509
(1.00) 		0.000705
(0.469) 		0.00189
(1.00) 		0.00908
(1.00) 		1
(1.00) 		0.0574
(1.00) 		0.141
(1.00)
22q gain 40 (8%) 474 0.327
(1.00) 		0.0289
(1.00) 		5.78e-05
(0.0418) 		0.679
(1.00) 		0.378
(1.00) 		0.581
(1.00) 		0.11
(1.00) 		0.148
(1.00) 		0.0737
(1.00) 		0.228
(1.00) 		0.0156
(1.00) 		0.168
(1.00)
4p loss 71 (14%) 443 0.531
(1.00) 		0.389
(1.00) 		3.04e-09
(2.49e-06) 		0.00136
(0.872) 		0.0845
(1.00) 		0.336
(1.00) 		0.00183
(1.00) 		0.00166
(1.00) 		0.847
(1.00) 		0.312
(1.00) 		0.0743
(1.00) 		0.375
(1.00)
8p loss 136 (26%) 378 0.354
(1.00) 		0.426
(1.00) 		8.21e-05
(0.0589) 		0.216
(1.00) 		0.185
(1.00) 		0.291
(1.00) 		0.0692
(1.00) 		0.0661
(1.00) 		0.0835
(1.00) 		0.0542
(1.00) 		0.15
(1.00) 		0.324
(1.00)
10p loss 66 (13%) 448 0.173
(1.00) 		0.239
(1.00) 		4.96e-09
(4.06e-06) 		0.0553
(1.00) 		0.742
(1.00) 		0.267
(1.00) 		0.175
(1.00) 		0.316
(1.00) 		0.067
(1.00) 		0.027
(1.00) 		0.0906
(1.00) 		0.084
(1.00)
10q loss 87 (17%) 427 0.315
(1.00) 		0.36
(1.00) 		2.12e-08
(1.72e-05) 		0.00715
(1.00) 		0.99
(1.00) 		0.149
(1.00) 		0.11
(1.00) 		0.186
(1.00) 		0.109
(1.00) 		0.128
(1.00) 		0.138
(1.00) 		0.0214
(1.00)
11p loss 18 (4%) 496 3.4e-05
(0.0249) 		0.0473
(1.00) 		0.14
(1.00) 		0.553
(1.00) 		0.15
(1.00) 		0.0662
(1.00) 		0.181
(1.00) 		0.0476
(1.00) 		0.0644
(1.00) 		0.114
(1.00)
11q loss 23 (4%) 491 0.189
(1.00) 		0.207
(1.00) 		5.91e-07
(0.000464) 		0.0143
(1.00) 		0.101
(1.00) 		0.418
(1.00) 		0.0126
(1.00) 		0.00391
(1.00) 		0.0282
(1.00) 		0.113
(1.00) 		0.0285
(1.00) 		0.227
(1.00)
21q loss 55 (11%) 459 0.026
(1.00) 		0.0306
(1.00) 		9.25e-09
(7.53e-06) 		0.0241
(1.00) 		0.0277
(1.00) 		0.00788
(1.00) 		0.00573
(1.00) 		0.00135
(0.864) 		0.0099
(1.00) 		0.000849
(0.556) 		0.213
(1.00) 		0.017
(1.00)
5q gain 204 (40%) 310 0.292
(1.00) 		0.212
(1.00) 		0.00723
(1.00) 		0.389
(1.00) 		0.398
(1.00) 		0.103
(1.00) 		0.0731
(1.00) 		0.00459
(1.00) 		0.566
(1.00) 		0.367
(1.00) 		0.22
(1.00) 		0.417
(1.00)
6p gain 11 (2%) 503 0.202
(1.00) 		0.34
(1.00) 		0.0672
(1.00) 		0.587
(1.00) 		0.794
(1.00) 		0.846
(1.00) 		0.796
(1.00) 		1
(1.00) 		0.845
(1.00) 		0.257
(1.00)
6q gain 9 (2%) 505 0.0926
(1.00) 		0.569
(1.00) 		0.0168
(1.00) 		0.766
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.779
(1.00) 		1
(1.00) 		0.447
(1.00)
9p gain 13 (3%) 501 0.0106
(1.00) 		0.902
(1.00) 		0.806
(1.00) 		0.716
(1.00) 		0.238
(1.00) 		0.409
(1.00) 		0.938
(1.00) 		0.0166
(1.00) 		0.727
(1.00) 		0.529
(1.00)
9q gain 12 (2%) 502 0.000806
(0.53) 		0.835
(1.00) 		0.568
(1.00) 		0.291
(1.00) 		0.251
(1.00) 		0.555
(1.00) 		0.806
(1.00) 		0.0289
(1.00) 		1
(1.00) 		0.737
(1.00)
10q gain 12 (2%) 502 0.00117
(0.756) 		0.0822
(1.00) 		0.0673
(1.00) 		0.546
(1.00) 		0.0142
(1.00) 		0.00751
(1.00) 		0.0765
(1.00) 		0.348
(1.00) 		0.373
(1.00) 		0.27
(1.00)
13q gain 22 (4%) 492 0.249
(1.00) 		0.0104
(1.00) 		0.648
(1.00) 		0.569
(1.00) 		0.0747
(1.00) 		0.512
(1.00) 		0.432
(1.00) 		0.712
(1.00) 		0.931
(1.00) 		0.178
(1.00)
14q gain 16 (3%) 498 0.769
(1.00) 		0.783
(1.00) 		0.00127
(0.82) 		0.328
(1.00) 		0.0121
(1.00) 		0.007
(1.00) 		0.0196
(1.00) 		0.0492
(1.00) 		0.00987
(1.00) 		0.00525
(1.00) 		0.373
(1.00) 		0.0139
(1.00)
15q gain 26 (5%) 488 1
(1.00) 		1
(1.00) 		0.00106
(0.683) 		0.599
(1.00) 		0.452
(1.00) 		0.15
(1.00) 		0.63
(1.00) 		0.856
(1.00) 		0.673
(1.00) 		0.284
(1.00) 		0.489
(1.00) 		0.369
(1.00)
16p gain 107 (21%) 407 0.282
(1.00) 		0.337
(1.00) 		0.000827
(0.543) 		0.399
(1.00) 		0.00147
(0.936) 		0.0498
(1.00) 		0.0139
(1.00) 		0.00524
(1.00) 		0.0686
(1.00) 		0.687
(1.00) 		0.123
(1.00) 		0.275
(1.00)
16q gain 99 (19%) 415 0.233
(1.00) 		0.218
(1.00) 		0.000439
(0.297) 		0.227
(1.00) 		0.0023
(1.00) 		0.0635
(1.00) 		0.0122
(1.00) 		0.0242
(1.00) 		0.0243
(1.00) 		0.517
(1.00) 		0.0301
(1.00) 		0.316
(1.00)
18p gain 25 (5%) 489 0.312
(1.00) 		0.252
(1.00) 		0.081
(1.00) 		0.405
(1.00) 		0.832
(1.00) 		0.191
(1.00) 		0.0761
(1.00) 		0.936
(1.00) 		0.687
(1.00) 		0.642
(1.00) 		0.691
(1.00) 		0.177
(1.00)
18q gain 25 (5%) 489 0.312
(1.00) 		0.252
(1.00) 		0.117
(1.00) 		0.413
(1.00) 		0.733
(1.00) 		0.51
(1.00) 		0.0761
(1.00) 		0.936
(1.00) 		0.859
(1.00) 		0.642
(1.00) 		0.691
(1.00) 		0.177
(1.00)
xq gain 30 (6%) 484 0.389
(1.00) 		0.328
(1.00) 		0.204
(1.00) 		0.705
(1.00) 		0.0217
(1.00) 		0.0119
(1.00) 		0.179
(1.00) 		0.317
(1.00) 		0.437
(1.00) 		0.909
(1.00) 		0.294
(1.00) 		0.191
(1.00)
3q loss 102 (20%) 412 0.72
(1.00) 		0.718
(1.00) 		0.000407
(0.278) 		0.359
(1.00) 		0.173
(1.00) 		0.0845
(1.00) 		0.187
(1.00) 		0.29
(1.00) 		0.906
(1.00) 		0.167
(1.00) 		0.185
(1.00) 		0.342
(1.00)
5p loss 7 (1%) 507 0.0228
(1.00) 		0.291
(1.00) 		0.657
(1.00) 		0.287
(1.00) 		0.0266
(1.00) 		0.0209
(1.00) 		0.0285
(1.00) 		0.0354
(1.00)
5q loss 6 (1%) 508 0.0489
(1.00) 		0.534
(1.00) 		0.471
(1.00) 		0.626
(1.00) 		0.0453
(1.00) 		0.0475
(1.00) 		0.0602
(1.00) 		0.00533
(1.00)
7p loss 3 (1%) 511 0.181
(1.00) 		0.0581
(1.00) 		0.128
(1.00) 		0.0556
(1.00) 		0.289
(1.00) 		0.0581
(1.00) 		0.65
(1.00)
7q loss 4 (1%) 510 0.0915
(1.00) 		0.363
(1.00) 		0.098
(1.00) 		1
(1.00) 		0.0491
(1.00) 		0.0615
(1.00) 		0.0335
(1.00) 		0.519
(1.00) 		0.0581
(1.00) 		0.65
(1.00)
8q loss 67 (13%) 447 0.647
(1.00) 		0.747
(1.00) 		0.133
(1.00) 		0.106
(1.00) 		0.289
(1.00) 		0.486
(1.00) 		0.707
(1.00) 		0.594
(1.00) 		0.589
(1.00) 		0.334
(1.00) 		0.237
(1.00) 		0.515
(1.00)
12p loss 3 (1%) 511 0.344
(1.00) 		0.437
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.448
(1.00)
12q loss 4 (1%) 510 0.577
(1.00) 		0.525
(1.00) 		0.185
(1.00) 		1
(1.00) 		1
(1.00) 		0.213
(1.00) 		0.756
(1.00)
16p loss 10 (2%) 504 0.275
(1.00) 		0.631
(1.00) 		0.036
(1.00) 		0.837
(1.00) 		0.293
(1.00) 		0.045
(1.00) 		0.269
(1.00) 		0.125
(1.00) 		0.373
(1.00) 		0.546
(1.00)
16q loss 15 (3%) 499 0.0602
(1.00) 		0.344
(1.00) 		0.0576
(1.00) 		0.595
(1.00) 		0.199
(1.00) 		0.00593
(1.00) 		0.103
(1.00) 		0.0341
(1.00) 		0.71
(1.00) 		0.715
(1.00)
19p loss 11 (2%) 503 0.000426
(0.29) 		0.0604
(1.00) 		0.00059
(0.396) 		0.000788
(0.519) 		0.165
(1.00) 		0.0176
(1.00) 		0.269
(1.00) 		0.178
(1.00) 		0.115
(1.00) 		0.00827
(1.00)
19q loss 4 (1%) 510 0.0134
(1.00) 		0.89
(1.00) 		0.168
(1.00) 		0.352
(1.00) 		0.388
(1.00) 		0.83
(1.00) 		1
(1.00)
20p loss 8 (2%) 506 0.223
(1.00) 		1
(1.00) 		0.0582
(1.00) 		1
(1.00) 		0.0907
(1.00) 		0.445
(1.00) 		0.0155
(1.00) 		0.0811
(1.00)
20q loss 3 (1%) 511 0.181
(1.00) 		0.0581
(1.00) 		0.763
(1.00) 		0.0556
(1.00) 		0.00883
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 1.3e-07 (Fisher's exact test), Q value = 1e-04

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
1P GAIN MUTATED 20 2 1
1P GAIN WILD-TYPE 142 221 128

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 1.74e-15 (Fisher's exact test), Q value = 1.5e-12

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
1Q GAIN MUTATED 43 6 2
1Q GAIN WILD-TYPE 119 217 127

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.014

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
1Q GAIN MUTATED 15 2 32
1Q GAIN WILD-TYPE 200 106 155

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.016

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
1Q GAIN MUTATED 3 14 32
1Q GAIN WILD-TYPE 107 195 145

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 2.53e-09 (Fisher's exact test), Q value = 2.1e-06

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
2P GAIN MUTATED 47 13 16
2P GAIN WILD-TYPE 115 210 113

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 2.14e-07 (Fisher's exact test), Q value = 0.00017

Table S6.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
2Q GAIN MUTATED 45 16 16
2Q GAIN WILD-TYPE 117 207 113

Figure S6.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 6.13e-05 (Fisher's exact test), Q value = 0.044

Table S7.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
3P GAIN MUTATED 3 1 16
3P GAIN WILD-TYPE 107 208 161

Figure S7.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.14

Table S8.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
3P GAIN MUTATED 7 4 9
3P GAIN WILD-TYPE 36 265 175

Figure S8.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 2.99e-11 (Fisher's exact test), Q value = 2.5e-08

Table S9.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
3Q GAIN MUTATED 40 5 15
3Q GAIN WILD-TYPE 122 218 114

Figure S9.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 5.97e-07 (Fisher's exact test), Q value = 0.00047

Table S10.  Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
3Q GAIN MUTATED 9 16 29
3Q GAIN WILD-TYPE 177 136 80

Figure S10.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0098

Table S11.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
3Q GAIN MUTATED 11 11 38
3Q GAIN WILD-TYPE 204 97 149

Figure S11.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.87e-06 (Fisher's exact test), Q value = 0.0014

Table S12.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
3Q GAIN MUTATED 10 41 9
3Q GAIN WILD-TYPE 216 164 70

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1.45e-08 (Fisher's exact test), Q value = 1.2e-05

Table S13.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
3Q GAIN MUTATED 8 9 42
3Q GAIN WILD-TYPE 102 200 135

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.11e-06 (Fisher's exact test), Q value = 0.0031

Table S14.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
3Q GAIN MUTATED 14 17 28
3Q GAIN WILD-TYPE 29 252 156

Figure S14.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.13

Table S15.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
3Q GAIN MUTATED 2 7 22
3Q GAIN WILD-TYPE 48 92 65

Figure S15.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.000208 (Fisher's exact test), Q value = 0.15

Table S16.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
4P GAIN MUTATED 2 0 11
4P GAIN WILD-TYPE 108 209 166

Figure S16.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.88e-05 (Chi-square test), Q value = 0.05

Table S17.  Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
4P GAIN MUTATED 2 1 0 1 0
4P GAIN WILD-TYPE 9 53 79 10 81

Figure S17.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.000208 (Fisher's exact test), Q value = 0.15

Table S18.  Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
4Q GAIN MUTATED 2 0 11
4Q GAIN WILD-TYPE 108 209 166

Figure S18.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.88e-05 (Chi-square test), Q value = 0.05

Table S19.  Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
4Q GAIN MUTATED 2 1 0 1 0
4Q GAIN WILD-TYPE 9 53 79 10 81

Figure S19.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.072

Table S20.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
5P GAIN MUTATED 81 64 45
5P GAIN WILD-TYPE 81 159 84

Figure S20.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 9.53e-14 (Fisher's exact test), Q value = 8.2e-11

Table S21.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
7P GAIN MUTATED 84 35 49
7P GAIN WILD-TYPE 78 188 80

Figure S21.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 1.61e-05 (Chi-square test), Q value = 0.012

Table S22.  Gene #13: '7p gain' 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
7P GAIN MUTATED 21 19 34 34 11 30
7P GAIN WILD-TYPE 79 69 50 41 32 27

Figure S22.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.091

Table S23.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
7P GAIN MUTATED 52 32 82
7P GAIN WILD-TYPE 163 76 105

Figure S23.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1.24e-13 (Fisher's exact test), Q value = 1.1e-10

Table S24.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
7Q GAIN MUTATED 83 35 51
7Q GAIN WILD-TYPE 79 188 78

Figure S24.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 2.78e-05 (Chi-square test), Q value = 0.021

Table S25.  Gene #14: '7q gain' 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
7Q GAIN MUTATED 21 21 34 34 10 30
7Q GAIN WILD-TYPE 79 67 50 41 33 27

Figure S25.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.000144 (Fisher's exact test), Q value = 0.1

Table S26.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
7Q GAIN MUTATED 52 33 82
7Q GAIN WILD-TYPE 163 75 105

Figure S26.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 6.29e-09 (Fisher's exact test), Q value = 5.1e-06

Table S27.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
8P GAIN MUTATED 22 0 9
8P GAIN WILD-TYPE 140 223 120

Figure S27.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.014

Table S28.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
8P GAIN MUTATED 3 5 23
8P GAIN WILD-TYPE 212 103 164

Figure S28.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000329 (Fisher's exact test), Q value = 0.23

Table S29.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
8P GAIN MUTATED 5 23 3
8P GAIN WILD-TYPE 221 182 76

Figure S29.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.0053

Table S30.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
8P GAIN MUTATED 3 4 24
8P GAIN WILD-TYPE 107 205 153

Figure S30.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 9.3e-19 (Fisher's exact test), Q value = 8.2e-16

Table S31.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
8Q GAIN MUTATED 45 0 14
8Q GAIN WILD-TYPE 117 223 115

Figure S31.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 6.54e-06 (Fisher's exact test), Q value = 0.005

Table S32.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
8Q GAIN MUTATED 24 3 9
8Q GAIN WILD-TYPE 76 111 67

Figure S32.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 5.21e-05 (Chi-square test), Q value = 0.038

Table S33.  Gene #16: '8q gain' 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
8Q GAIN MUTATED 4 9 15 8 1 16
8Q GAIN WILD-TYPE 96 79 69 67 42 41

Figure S33.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 8.36e-12 (Fisher's exact test), Q value = 7.1e-09

Table S34.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
8Q GAIN MUTATED 6 6 46
8Q GAIN WILD-TYPE 209 102 141

Figure S34.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.2e-09 (Fisher's exact test), Q value = 9.9e-07

Table S35.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
8Q GAIN MUTATED 9 46 3
8Q GAIN WILD-TYPE 217 159 76

Figure S35.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 6.49e-11 (Fisher's exact test), Q value = 5.4e-08

Table S36.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
8Q GAIN MUTATED 6 7 44
8Q GAIN WILD-TYPE 104 202 133

Figure S36.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.51e-07 (Fisher's exact test), Q value = 0.00051

Table S37.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
8Q GAIN MUTATED 1 2 21
8Q GAIN WILD-TYPE 49 97 66

Figure S37.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.13

Table S38.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
10P GAIN MUTATED 1 15 1
10P GAIN WILD-TYPE 225 190 78

Figure S38.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.011

Table S39.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
11P GAIN MUTATED 16 2 13
11P GAIN WILD-TYPE 146 221 116

Figure S39.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.000276 (Fisher's exact test), Q value = 0.19

Table S40.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
11Q GAIN MUTATED 13 3 13
11Q GAIN WILD-TYPE 149 220 116

Figure S40.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 9.53e-14 (Fisher's exact test), Q value = 8.2e-11

Table S41.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
12P GAIN MUTATED 67 19 34
12P GAIN WILD-TYPE 95 204 95

Figure S41.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.000174 (Fisher's exact test), Q value = 0.12

Table S42.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
12P GAIN MUTATED 37 15 22
12P GAIN WILD-TYPE 63 99 54

Figure S42.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 1.34e-12 (Chi-square test), Q value = 1.1e-09

Table S43.  Gene #23: '12p gain' 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
12P GAIN MUTATED 4 17 31 14 6 31
12P GAIN WILD-TYPE 96 71 53 61 37 26

Figure S43.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.91e-11 (Fisher's exact test), Q value = 1.6e-08

Table S44.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
12P GAIN MUTATED 25 18 76
12P GAIN WILD-TYPE 190 90 111

Figure S44.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.37e-12 (Fisher's exact test), Q value = 2e-09

Table S45.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
12P GAIN MUTATED 25 82 12
12P GAIN WILD-TYPE 201 123 67

Figure S45.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1.1e-10 (Fisher's exact test), Q value = 9.2e-08

Table S46.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
12P GAIN MUTATED 19 26 73
12P GAIN WILD-TYPE 91 183 104

Figure S46.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.35e-08 (Fisher's exact test), Q value = 5.9e-05

Table S47.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
12P GAIN MUTATED 9 7 36
12P GAIN WILD-TYPE 41 92 51

Figure S47.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1.74e-13 (Fisher's exact test), Q value = 1.5e-10

Table S48.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
12Q GAIN MUTATED 66 19 35
12Q GAIN WILD-TYPE 96 204 94

Figure S48.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.000118 (Fisher's exact test), Q value = 0.084

Table S49.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
12Q GAIN MUTATED 38 15 21
12Q GAIN WILD-TYPE 62 99 55

Figure S49.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 1.87e-13 (Chi-square test), Q value = 1.6e-10

Table S50.  Gene #24: '12q gain' 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
12Q GAIN MUTATED 4 16 31 14 6 32
12Q GAIN WILD-TYPE 96 72 53 61 37 25

Figure S50.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 6.4e-11 (Fisher's exact test), Q value = 5.4e-08

Table S51.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
12Q GAIN MUTATED 25 19 75
12Q GAIN WILD-TYPE 190 89 112

Figure S51.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.37e-12 (Fisher's exact test), Q value = 2e-09

Table S52.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
12Q GAIN MUTATED 25 82 12
12Q GAIN WILD-TYPE 201 123 67

Figure S52.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 3.2e-11 (Fisher's exact test), Q value = 2.7e-08

Table S53.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
12Q GAIN MUTATED 18 26 74
12Q GAIN WILD-TYPE 92 183 103

Figure S53.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.35e-08 (Fisher's exact test), Q value = 5.9e-05

Table S54.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
12Q GAIN MUTATED 9 7 36
12Q GAIN WILD-TYPE 41 92 51

Figure S54.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 2.84e-05 (Fisher's exact test), Q value = 0.021

Table S55.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
17P GAIN MUTATED 14 1 10
17P GAIN WILD-TYPE 148 222 119

Figure S55.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 8.05e-05 (Fisher's exact test), Q value = 0.058

Table S56.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
17Q GAIN MUTATED 18 3 10
17Q GAIN WILD-TYPE 144 220 119

Figure S56.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1.98e-09 (Fisher's exact test), Q value = 1.6e-06

Table S57.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
19P GAIN MUTATED 29 3 19
19P GAIN WILD-TYPE 133 220 110

Figure S57.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.13

Table S58.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
19P GAIN MUTATED 9 10 31
19P GAIN WILD-TYPE 101 199 146

Figure S58.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 2.36e-11 (Fisher's exact test), Q value = 2e-08

Table S59.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
19Q GAIN MUTATED 35 3 19
19Q GAIN WILD-TYPE 127 220 110

Figure S59.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.000287 (Fisher's exact test), Q value = 0.2

Table S60.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
19Q GAIN MUTATED 24 7 6
19Q GAIN WILD-TYPE 76 107 70

Figure S60.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 2.97e-05 (Fisher's exact test), Q value = 0.022

Table S61.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
19Q GAIN MUTATED 9 11 35
19Q GAIN WILD-TYPE 101 198 142

Figure S61.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 7.57e-22 (Fisher's exact test), Q value = 6.7e-19

Table S62.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
20P GAIN MUTATED 65 7 39
20P GAIN WILD-TYPE 97 216 90

Figure S62.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 5.62e-05 (Fisher's exact test), Q value = 0.041

Table S63.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
20P GAIN MUTATED 34 11 18
20P GAIN WILD-TYPE 66 103 58

Figure S63.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 1.07e-07 (Chi-square test), Q value = 8.6e-05

Table S64.  Gene #36: '20p gain' 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
20P GAIN MUTATED 7 21 19 18 5 28
20P GAIN WILD-TYPE 93 67 65 57 38 29

Figure S64.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1.15e-12 (Fisher's exact test), Q value = 9.8e-10

Table S65.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
20P GAIN MUTATED 19 19 73
20P GAIN WILD-TYPE 196 89 114

Figure S65.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.16e-12 (Fisher's exact test), Q value = 1.8e-09

Table S66.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
20P GAIN MUTATED 22 78 11
20P GAIN WILD-TYPE 204 127 68

Figure S66.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 3.32e-10 (Fisher's exact test), Q value = 2.8e-07

Table S67.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
20P GAIN MUTATED 24 20 66
20P GAIN WILD-TYPE 86 189 111

Figure S67.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000241 (Fisher's exact test), Q value = 0.17

Table S68.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
20P GAIN MUTATED 13 41 56
20P GAIN WILD-TYPE 30 228 128

Figure S68.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.18e-07 (Fisher's exact test), Q value = 0.00048

Table S69.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
20P GAIN MUTATED 9 6 32
20P GAIN WILD-TYPE 41 93 55

Figure S69.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 2.82e-23 (Fisher's exact test), Q value = 2.5e-20

Table S70.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
20Q GAIN MUTATED 69 7 38
20Q GAIN WILD-TYPE 93 216 91

Figure S70.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 5.62e-05 (Fisher's exact test), Q value = 0.041

Table S71.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
20Q GAIN MUTATED 34 11 18
20Q GAIN WILD-TYPE 66 103 58

Figure S71.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 6.76e-09 (Chi-square test), Q value = 5.5e-06

Table S72.  Gene #37: '20q gain' 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
20Q GAIN MUTATED 7 20 21 18 5 30
20Q GAIN WILD-TYPE 93 68 63 57 38 27

Figure S72.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 2.62e-14 (Fisher's exact test), Q value = 2.3e-11

Table S73.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
20Q GAIN MUTATED 19 18 77
20Q GAIN WILD-TYPE 196 90 110

Figure S73.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.9e-13 (Fisher's exact test), Q value = 1.6e-10

Table S74.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
20Q GAIN MUTATED 22 81 11
20Q GAIN WILD-TYPE 204 124 68

Figure S74.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 3.55e-11 (Fisher's exact test), Q value = 3e-08

Table S75.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
20Q GAIN MUTATED 24 20 69
20Q GAIN WILD-TYPE 86 189 108

Figure S75.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000154 (Fisher's exact test), Q value = 0.11

Table S76.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
20Q GAIN MUTATED 13 42 58
20Q GAIN WILD-TYPE 30 227 126

Figure S76.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.7e-07 (Fisher's exact test), Q value = 0.00021

Table S77.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
20Q GAIN MUTATED 9 6 33
20Q GAIN WILD-TYPE 41 93 54

Figure S77.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 3.43e-06 (Fisher's exact test), Q value = 0.0026

Table S78.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
21Q GAIN MUTATED 32 10 8
21Q GAIN WILD-TYPE 130 213 121

Figure S78.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 5.78e-05 (Fisher's exact test), Q value = 0.042

Table S79.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
22Q GAIN MUTATED 21 5 14
22Q GAIN WILD-TYPE 141 218 115

Figure S79.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1.1e-09 (Fisher's exact test), Q value = 9e-07

Table S80.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
1P LOSS MUTATED 26 4 26
1P LOSS WILD-TYPE 136 219 103

Figure S80.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.97e-08 (Fisher's exact test), Q value = 1.6e-05

Table S81.  Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
1P LOSS MUTATED 19 21 16
1P LOSS WILD-TYPE 24 248 168

Figure S81.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000248 (Chi-square test), Q value = 0.17

Table S82.  Gene #41: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
1P LOSS MUTATED 5 5 11 1 2
1P LOSS WILD-TYPE 6 49 68 10 79

Figure S82.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 5.03e-10 (Fisher's exact test), Q value = 4.2e-07

Table S83.  Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
1Q LOSS MUTATED 11 1 24
1Q LOSS WILD-TYPE 151 222 105

Figure S83.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.54e-08 (Fisher's exact test), Q value = 2.1e-05

Table S84.  Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
1Q LOSS MUTATED 15 10 11
1Q LOSS WILD-TYPE 28 259 173

Figure S84.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.41e-05 (Chi-square test), Q value = 0.011

Table S85.  Gene #42: '1q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
1Q LOSS MUTATED 5 5 4 1 2
1Q LOSS WILD-TYPE 6 49 75 10 79

Figure S85.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 3.58e-05 (Fisher's exact test), Q value = 0.026

Table S86.  Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
2P LOSS MUTATED 0 1 6
2P LOSS WILD-TYPE 33 23 7

Figure S86.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6.3e-05 (Fisher's exact test), Q value = 0.045

Table S87.  Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
2P LOSS MUTATED 6 0 1
2P LOSS WILD-TYPE 8 32 23

Figure S87.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.0011

Table S88.  Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
2P LOSS MUTATED 2 0 12
2P LOSS WILD-TYPE 160 223 117

Figure S88.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 4.58e-05 (Chi-square test), Q value = 0.033

Table S89.  Gene #43: '2p loss' 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
2P LOSS MUTATED 0 0 0 7 0 2
2P LOSS WILD-TYPE 100 88 84 68 43 55

Figure S89.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2.35e-06 (Fisher's exact test), Q value = 0.0018

Table S90.  Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
2P LOSS MUTATED 0 0 9
2P LOSS WILD-TYPE 186 152 100

Figure S90.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 2.39e-07 (Fisher's exact test), Q value = 0.00019

Table S91.  Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
2P LOSS MUTATED 0 12 2
2P LOSS WILD-TYPE 215 96 185

Figure S91.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.73e-09 (Fisher's exact test), Q value = 3.9e-06

Table S92.  Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
2P LOSS MUTATED 0 2 12
2P LOSS WILD-TYPE 226 203 67

Figure S92.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 8.4e-05 (Fisher's exact test), Q value = 0.06

Table S93.  Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
2P LOSS MUTATED 2 0 12
2P LOSS WILD-TYPE 108 209 165

Figure S93.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.5e-12 (Fisher's exact test), Q value = 3.8e-09

Table S94.  Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
2P LOSS MUTATED 12 1 1
2P LOSS WILD-TYPE 31 268 183

Figure S94.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.64e-13 (Chi-square test), Q value = 1.4e-10

Table S95.  Gene #43: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
2P LOSS MUTATED 4 1 0 0 0
2P LOSS WILD-TYPE 7 53 79 11 81

Figure S95.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.17

Table S96.  Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
2Q LOSS MUTATED 0 1 5
2Q LOSS WILD-TYPE 33 23 8

Figure S96.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.0011

Table S97.  Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
2Q LOSS MUTATED 2 0 12
2Q LOSS WILD-TYPE 160 223 117

Figure S97.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.000316 (Chi-square test), Q value = 0.22

Table S98.  Gene #44: '2q loss' 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
2Q LOSS MUTATED 0 0 0 6 0 3
2Q LOSS WILD-TYPE 100 88 84 69 43 54

Figure S98.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2.35e-06 (Fisher's exact test), Q value = 0.0018

Table S99.  Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
2Q LOSS MUTATED 0 0 9
2Q LOSS WILD-TYPE 186 152 100

Figure S99.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 2.39e-07 (Fisher's exact test), Q value = 0.00019

Table S100.  Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
2Q LOSS MUTATED 0 12 2
2Q LOSS WILD-TYPE 215 96 185

Figure S100.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.39e-08 (Fisher's exact test), Q value = 5.1e-05

Table S101.  Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
2Q LOSS MUTATED 0 3 11
2Q LOSS WILD-TYPE 226 202 68

Figure S101.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.017

Table S102.  Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
2Q LOSS MUTATED 1 0 13
2Q LOSS WILD-TYPE 109 209 164

Figure S102.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.53e-10 (Fisher's exact test), Q value = 2.1e-07

Table S103.  Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
2Q LOSS MUTATED 11 2 1
2Q LOSS WILD-TYPE 32 267 183

Figure S103.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.64e-13 (Chi-square test), Q value = 1.4e-10

Table S104.  Gene #44: '2q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
2Q LOSS MUTATED 4 1 0 0 0
2Q LOSS WILD-TYPE 7 53 79 11 81

Figure S104.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 4.72e-24 (Fisher's exact test), Q value = 4.2e-21

Table S105.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
3P LOSS MUTATED 142 182 46
3P LOSS WILD-TYPE 20 41 83

Figure S105.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1.72e-08 (Fisher's exact test), Q value = 1.4e-05

Table S106.  Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
3P LOSS MUTATED 177 54 136
3P LOSS WILD-TYPE 38 54 51

Figure S106.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.36e-10 (Fisher's exact test), Q value = 2.8e-07

Table S107.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
3P LOSS MUTATED 182 153 32
3P LOSS WILD-TYPE 44 52 47

Figure S107.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.021

Table S108.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
3P LOSS MUTATED 20 212 124
3P LOSS WILD-TYPE 23 57 60

Figure S108.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.27e-06 (Chi-square test), Q value = 0.004

Table S109.  Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
3P LOSS MUTATED 1 33 64 9 63
3P LOSS WILD-TYPE 10 21 15 2 18

Figure S109.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 3.04e-09 (Fisher's exact test), Q value = 2.5e-06

Table S110.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
4P LOSS MUTATED 43 10 18
4P LOSS WILD-TYPE 119 213 111

Figure S110.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1.04e-11 (Fisher's exact test), Q value = 8.8e-09

Table S111.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
4Q LOSS MUTATED 43 6 16
4Q LOSS WILD-TYPE 119 217 113

Figure S111.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.78e-06 (Fisher's exact test), Q value = 0.0074

Table S112.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
4Q LOSS MUTATED 23 41 1
4Q LOSS WILD-TYPE 203 164 78

Figure S112.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 8.48e-16 (Fisher's exact test), Q value = 7.4e-13

Table S113.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
6P LOSS MUTATED 59 10 30
6P LOSS WILD-TYPE 103 213 99

Figure S113.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 3.74e-06 (Chi-square test), Q value = 0.0029

Table S114.  Gene #51: '6p loss' 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
6P LOSS MUTATED 17 7 17 18 4 25
6P LOSS WILD-TYPE 83 81 67 57 39 32

Figure S114.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.000258 (Fisher's exact test), Q value = 0.18

Table S115.  Gene #51: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
6P LOSS MUTATED 22 32 34
6P LOSS WILD-TYPE 164 120 75

Figure S115.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 3.05e-08 (Fisher's exact test), Q value = 2.5e-05

Table S116.  Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
6P LOSS MUTATED 20 16 60
6P LOSS WILD-TYPE 195 92 127

Figure S116.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.76e-07 (Fisher's exact test), Q value = 0.00045

Table S117.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
6P LOSS MUTATED 22 61 13
6P LOSS WILD-TYPE 204 144 66

Figure S117.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 7.99e-11 (Fisher's exact test), Q value = 6.7e-08

Table S118.  Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
6P LOSS MUTATED 13 19 63
6P LOSS WILD-TYPE 97 190 114

Figure S118.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000278 (Fisher's exact test), Q value = 0.19

Table S119.  Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
6P LOSS MUTATED 16 36 43
6P LOSS WILD-TYPE 27 233 141

Figure S119.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.38e-07 (Fisher's exact test), Q value = 0.00035

Table S120.  Gene #51: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
6P LOSS MUTATED 6 5 30
6P LOSS WILD-TYPE 44 94 57

Figure S120.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 6.58e-15 (Fisher's exact test), Q value = 5.7e-12

Table S121.  Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
6Q LOSS MUTATED 74 22 30
6Q LOSS WILD-TYPE 88 201 99

Figure S121.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 2.57e-05 (Chi-square test), Q value = 0.019

Table S122.  Gene #52: '6q loss' 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
6Q LOSS MUTATED 28 8 24 19 6 26
6Q LOSS WILD-TYPE 72 80 60 56 37 31

Figure S122.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.095

Table S123.  Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
6Q LOSS MUTATED 40 18 65
6Q LOSS WILD-TYPE 175 90 122

Figure S123.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 3.86e-07 (Fisher's exact test), Q value = 3e-04

Table S124.  Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
6Q LOSS MUTATED 18 35 69
6Q LOSS WILD-TYPE 92 174 108

Figure S124.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.094

Table S125.  Gene #52: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
6Q LOSS MUTATED 9 14 35
6Q LOSS WILD-TYPE 41 85 52

Figure S125.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 8.21e-05 (Fisher's exact test), Q value = 0.059

Table S126.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
8P LOSS MUTATED 63 43 30
8P LOSS WILD-TYPE 99 180 99

Figure S126.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 2.06e-47 (Fisher's exact test), Q value = 1.8e-44

Table S127.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
9P LOSS MUTATED 109 5 32
9P LOSS WILD-TYPE 53 218 97

Figure S127.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1.76e-19 (Fisher's exact test), Q value = 1.5e-16

Table S128.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
9P LOSS MUTATED 60 5 24
9P LOSS WILD-TYPE 40 109 52

Figure S128.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 4.89e-06 (Chi-square test), Q value = 0.0037

Table S129.  Gene #57: '9p loss' 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
9P LOSS MUTATED 18 24 31 18 10 33
9P LOSS WILD-TYPE 82 64 53 57 33 24

Figure S129.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 2.12e-22 (Fisher's exact test), Q value = 1.9e-19

Table S130.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
9P LOSS MUTATED 26 16 102
9P LOSS WILD-TYPE 189 92 85

Figure S130.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-25 (Fisher's exact test), Q value = 1e-22

Table S131.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
9P LOSS MUTATED 24 111 9
9P LOSS WILD-TYPE 202 94 70

Figure S131.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 2.97e-15 (Fisher's exact test), Q value = 2.6e-12

Table S132.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
9P LOSS MUTATED 27 26 88
9P LOSS WILD-TYPE 83 183 89

Figure S132.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.49e-05 (Fisher's exact test), Q value = 0.026

Table S133.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
9P LOSS MUTATED 15 54 72
9P LOSS WILD-TYPE 28 215 112

Figure S133.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.04e-10 (Fisher's exact test), Q value = 8.7e-08

Table S134.  Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
9P LOSS MUTATED 14 8 45
9P LOSS WILD-TYPE 36 91 42

Figure S134.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 3.06e-46 (Fisher's exact test), Q value = 2.7e-43

Table S135.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
9Q LOSS MUTATED 109 6 32
9Q LOSS WILD-TYPE 53 217 97

Figure S135.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.8e-18 (Fisher's exact test), Q value = 1.6e-15

Table S136.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
9Q LOSS MUTATED 58 5 25
9Q LOSS WILD-TYPE 42 109 51

Figure S136.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 1.06e-06 (Chi-square test), Q value = 0.00082

Table S137.  Gene #58: '9q loss' 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
9Q LOSS MUTATED 17 24 34 18 10 33
9Q LOSS WILD-TYPE 83 64 50 57 33 24

Figure S137.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 6.79e-23 (Fisher's exact test), Q value = 6e-20

Table S138.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
9Q LOSS MUTATED 26 16 103
9Q LOSS WILD-TYPE 189 92 84

Figure S138.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.26e-25 (Fisher's exact test), Q value = 2.9e-22

Table S139.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
9Q LOSS MUTATED 24 111 10
9Q LOSS WILD-TYPE 202 94 69

Figure S139.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1.29e-16 (Fisher's exact test), Q value = 1.1e-13

Table S140.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
9Q LOSS MUTATED 26 25 90
9Q LOSS WILD-TYPE 84 184 87

Figure S140.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000159 (Fisher's exact test), Q value = 0.11

Table S141.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
9Q LOSS MUTATED 14 56 71
9Q LOSS WILD-TYPE 29 213 113

Figure S141.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.55e-10 (Fisher's exact test), Q value = 3.8e-07

Table S142.  Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
9Q LOSS MUTATED 14 9 45
9Q LOSS WILD-TYPE 36 90 42

Figure S142.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 4.96e-09 (Fisher's exact test), Q value = 4.1e-06

Table S143.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
10P LOSS MUTATED 32 7 27
10P LOSS WILD-TYPE 130 216 102

Figure S143.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 2.12e-08 (Fisher's exact test), Q value = 1.7e-05

Table S144.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
10Q LOSS MUTATED 43 14 30
10Q LOSS WILD-TYPE 119 209 99

Figure S144.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 3.4e-05 (Fisher's exact test), Q value = 0.025

Table S145.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
11P LOSS MUTATED 12 0 6
11P LOSS WILD-TYPE 150 223 123

Figure S145.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 5.91e-07 (Fisher's exact test), Q value = 0.00046

Table S146.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
11Q LOSS MUTATED 17 0 6
11Q LOSS WILD-TYPE 145 223 123

Figure S146.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 9.33e-11 (Fisher's exact test), Q value = 7.8e-08

Table S147.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
13Q LOSS MUTATED 37 6 26
13Q LOSS WILD-TYPE 125 217 103

Figure S147.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 7.66e-06 (Chi-square test), Q value = 0.0058

Table S148.  Gene #65: '13q loss' 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
13Q LOSS MUTATED 3 10 14 13 3 19
13Q LOSS WILD-TYPE 97 78 70 62 40 38

Figure S148.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 4.1e-06 (Fisher's exact test), Q value = 0.0031

Table S149.  Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
13Q LOSS MUTATED 13 13 43
13Q LOSS WILD-TYPE 202 95 144

Figure S149.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.54e-07 (Fisher's exact test), Q value = 0.00028

Table S150.  Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
13Q LOSS MUTATED 12 47 10
13Q LOSS WILD-TYPE 214 158 69

Figure S150.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 3.23e-06 (Fisher's exact test), Q value = 0.0025

Table S151.  Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
13Q LOSS MUTATED 12 13 42
13Q LOSS WILD-TYPE 98 196 135

Figure S151.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 3.12e-05 (Fisher's exact test), Q value = 0.023

Table S152.  Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
14Q LOSS MUTATED 9 19 2
14Q LOSS WILD-TYPE 24 5 11

Figure S152.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.031

Table S153.  Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
14Q LOSS MUTATED 3 8 19
14Q LOSS WILD-TYPE 11 24 5

Figure S153.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 6.37e-18 (Fisher's exact test), Q value = 5.6e-15

Table S154.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
14Q LOSS MUTATED 112 55 47
14Q LOSS WILD-TYPE 50 168 82

Figure S154.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 6.21e-08 (Fisher's exact test), Q value = 5e-05

Table S155.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
14Q LOSS MUTATED 58 24 36
14Q LOSS WILD-TYPE 42 90 40

Figure S155.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 1.01e-13 (Chi-square test), Q value = 8.7e-11

Table S156.  Gene #66: '14q loss' 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
14Q LOSS MUTATED 27 28 62 23 13 39
14Q LOSS WILD-TYPE 73 60 22 52 30 18

Figure S156.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1.28e-07 (Fisher's exact test), Q value = 1e-04

Table S157.  Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 152 109
14Q LOSS MUTATED 53 89 50
14Q LOSS WILD-TYPE 133 63 59

Figure S157.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1.97e-21 (Fisher's exact test), Q value = 1.7e-18

Table S158.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
14Q LOSS MUTATED 68 16 126
14Q LOSS WILD-TYPE 147 92 61

Figure S158.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.89e-16 (Fisher's exact test), Q value = 6.9e-13

Table S159.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
14Q LOSS MUTATED 71 127 12
14Q LOSS WILD-TYPE 155 78 67

Figure S159.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 2.41e-11 (Fisher's exact test), Q value = 2e-08

Table S160.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
14Q LOSS MUTATED 35 62 111
14Q LOSS WILD-TYPE 75 147 66

Figure S160.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.25e-07 (Fisher's exact test), Q value = 0.00064

Table S161.  Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
14Q LOSS MUTATED 16 29 57
14Q LOSS WILD-TYPE 34 70 30

Figure S161.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.9e-05 (Chi-square test), Q value = 0.021

Table S162.  Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
14Q LOSS MUTATED 1 22 51 3 25
14Q LOSS WILD-TYPE 10 32 28 8 56

Figure S162.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 2.59e-10 (Fisher's exact test), Q value = 2.1e-07

Table S163.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
15Q LOSS MUTATED 28 1 6
15Q LOSS WILD-TYPE 134 222 123

Figure S163.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 3.2e-06 (Fisher's exact test), Q value = 0.0025

Table S164.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
15Q LOSS MUTATED 6 2 27
15Q LOSS WILD-TYPE 209 106 160

Figure S164.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.15e-07 (Fisher's exact test), Q value = 0.00064

Table S165.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
15Q LOSS MUTATED 5 29 1
15Q LOSS WILD-TYPE 221 176 78

Figure S165.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.096

Table S166.  Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
17P LOSS MUTATED 0 5 6
17P LOSS WILD-TYPE 33 19 7

Figure S166.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000271 (Fisher's exact test), Q value = 0.19

Table S167.  Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 32 24
17P LOSS MUTATED 6 0 5
17P LOSS WILD-TYPE 8 32 19

Figure S167.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 5.35e-09 (Fisher's exact test), Q value = 4.4e-06

Table S168.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
17P LOSS MUTATED 25 2 18
17P LOSS WILD-TYPE 137 221 111

Figure S168.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1.61e-06 (Fisher's exact test), Q value = 0.0012

Table S169.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
17P LOSS MUTATED 4 15 26
17P LOSS WILD-TYPE 211 93 161

Figure S169.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.4e-07 (Fisher's exact test), Q value = 0.00011

Table S170.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
17P LOSS MUTATED 4 26 15
17P LOSS WILD-TYPE 222 179 64

Figure S170.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 9.59e-08 (Fisher's exact test), Q value = 7.7e-05

Table S171.  Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
17P LOSS MUTATED 9 4 32
17P LOSS WILD-TYPE 101 205 145

Figure S171.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.69e-06 (Fisher's exact test), Q value = 0.0013

Table S172.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
17P LOSS MUTATED 14 13 18
17P LOSS WILD-TYPE 29 256 166

Figure S172.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 2.42e-06 (Fisher's exact test), Q value = 0.0019

Table S173.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
17Q LOSS MUTATED 12 1 15
17Q LOSS WILD-TYPE 150 222 114

Figure S173.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.87e-05 (Fisher's exact test), Q value = 0.042

Table S174.  Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
17Q LOSS MUTATED 3 14 11
17Q LOSS WILD-TYPE 223 191 68

Figure S174.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0086

Table S175.  Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
17Q LOSS MUTATED 5 2 21
17Q LOSS WILD-TYPE 105 207 156

Figure S175.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.14e-07 (Fisher's exact test), Q value = 0.00071

Table S176.  Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
17Q LOSS MUTATED 12 8 8
17Q LOSS WILD-TYPE 31 261 176

Figure S176.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.81e-05 (Chi-square test), Q value = 0.014

Table S177.  Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 54 79 11 81
17Q LOSS MUTATED 4 1 2 0 4
17Q LOSS WILD-TYPE 7 53 77 11 77

Figure S177.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1.36e-13 (Fisher's exact test), Q value = 1.2e-10

Table S178.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
18P LOSS MUTATED 56 11 24
18P LOSS WILD-TYPE 106 212 105

Figure S178.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 2.68e-07 (Fisher's exact test), Q value = 0.00021

Table S179.  Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
18P LOSS MUTATED 28 5 22
18P LOSS WILD-TYPE 72 109 54

Figure S179.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 3.07e-08 (Chi-square test), Q value = 2.5e-05

Table S180.  Gene #72: '18p loss' 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
18P LOSS MUTATED 5 14 23 15 2 24
18P LOSS WILD-TYPE 95 74 61 60 41 33

Figure S180.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 7.08e-19 (Fisher's exact test), Q value = 6.2e-16

Table S181.  Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
18P LOSS MUTATED 10 9 71
18P LOSS WILD-TYPE 205 99 116

Figure S181.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-15 (Fisher's exact test), Q value = 1.6e-12

Table S182.  Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
18P LOSS MUTATED 11 70 9
18P LOSS WILD-TYPE 215 135 70

Figure S182.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 3.61e-11 (Fisher's exact test), Q value = 3e-08

Table S183.  Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
18P LOSS MUTATED 22 12 57
18P LOSS WILD-TYPE 88 197 120

Figure S183.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.013

Table S184.  Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
18P LOSS MUTATED 14 30 47
18P LOSS WILD-TYPE 29 239 137

Figure S184.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.42e-07 (Fisher's exact test), Q value = 0.00035

Table S185.  Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
18P LOSS MUTATED 9 4 29
18P LOSS WILD-TYPE 41 95 58

Figure S185.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 2.29e-13 (Fisher's exact test), Q value = 2e-10

Table S186.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
18Q LOSS MUTATED 57 12 24
18Q LOSS WILD-TYPE 105 211 105

Figure S186.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1.97e-06 (Fisher's exact test), Q value = 0.0015

Table S187.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 114 76
18Q LOSS MUTATED 27 6 22
18Q LOSS WILD-TYPE 73 108 54

Figure S187.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 1.99e-07 (Chi-square test), Q value = 0.00016

Table S188.  Gene #73: '18q loss' 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
18Q LOSS MUTATED 5 14 23 16 4 24
18Q LOSS WILD-TYPE 95 74 61 59 39 33

Figure S188.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 6.42e-18 (Fisher's exact test), Q value = 5.6e-15

Table S189.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
18Q LOSS MUTATED 11 10 71
18Q LOSS WILD-TYPE 204 98 116

Figure S189.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.1e-15 (Fisher's exact test), Q value = 3.6e-12

Table S190.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
18Q LOSS MUTATED 11 70 11
18Q LOSS WILD-TYPE 215 135 68

Figure S190.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1.11e-10 (Fisher's exact test), Q value = 9.2e-08

Table S191.  Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
18Q LOSS MUTATED 23 13 57
18Q LOSS WILD-TYPE 87 196 120

Figure S191.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.4e-05 (Fisher's exact test), Q value = 0.011

Table S192.  Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
18Q LOSS MUTATED 15 31 47
18Q LOSS WILD-TYPE 28 238 137

Figure S192.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.68e-07 (Fisher's exact test), Q value = 0.00013

Table S193.  Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 99 87
18Q LOSS MUTATED 8 4 30
18Q LOSS WILD-TYPE 42 95 57

Figure S193.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 9.25e-09 (Fisher's exact test), Q value = 7.5e-06

Table S194.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
21Q LOSS MUTATED 23 5 27
21Q LOSS WILD-TYPE 139 218 102

Figure S194.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 5.85e-09 (Fisher's exact test), Q value = 4.8e-06

Table S195.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
22Q LOSS MUTATED 24 1 14
22Q LOSS WILD-TYPE 138 222 115

Figure S195.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 6.24e-07 (Fisher's exact test), Q value = 0.00049

Table S196.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
22Q LOSS MUTATED 5 4 30
22Q LOSS WILD-TYPE 210 104 157

Figure S196.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0022

Table S197.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 226 205 79
22Q LOSS MUTATED 4 29 6
22Q LOSS WILD-TYPE 222 176 73

Figure S197.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0089

Table S198.  Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 209 177
22Q LOSS MUTATED 3 8 28
22Q LOSS WILD-TYPE 107 201 149

Figure S198.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.015

Table S199.  Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 162 223 129
XQ LOSS MUTATED 27 7 12
XQ LOSS WILD-TYPE 135 216 117

Figure S199.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.011

Table S200.  Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 269 184
XQ LOSS MUTATED 14 18 13
XQ LOSS WILD-TYPE 29 251 171

Figure S200.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtypes file = KIRC-TP.transferedmergedcluster.txt

  • Number of patients = 514

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, 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)
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