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 subtypes.

Summary

Testing the association between copy number variation 79 arm-level results and 12 molecular subtypes across 492 patients, 256 significant findings detected with Q value < 0.25.

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

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF'.

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

  • 5p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'CN_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

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

  • 18q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 21q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

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

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 7p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

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

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

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 14q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 18p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 19p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • Xq loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 256 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
15q loss 0 (0%) 411 0.00202
(1.00) 		0.000218
(0.134) 		4.68e-35
(3.99e-32) 		2.97e-13
(2.41e-10) 		0.00259
(1.00) 		0.267
(1.00) 		7.92e-10
(6.15e-07) 		1.07e-10
(8.4e-08) 		5.22e-15
(4.29e-12) 		1.07e-16
(8.88e-14) 		1.05e-06
(0.000747) 		3.04e-08
(2.28e-05)
18p gain 0 (0%) 455 0.379
(1.00) 		0.0902
(1.00) 		4.94e-14
(4.04e-11) 		6.07e-05
(0.0393) 		0.093
(1.00) 		0.429
(1.00) 		3.34e-05
(0.0221) 		7.28e-07
(0.000524) 		4.26e-09
(3.25e-06) 		6.47e-09
(4.92e-06) 		7.18e-05
(0.0463) 		0.000285
(0.174)
4p loss 0 (0%) 426 0.0515
(1.00) 		0.00755
(1.00) 		4.79e-25
(4.05e-22) 		6.03e-11
(4.76e-08) 		0.0339
(1.00) 		0.393
(1.00) 		2.45e-09
(1.88e-06) 		1.29e-07
(9.51e-05) 		1.88e-13
(1.53e-10) 		4.44e-12
(3.58e-09) 		8.45e-05
(0.0542) 		1.78e-06
(0.00126)
4q loss 0 (0%) 428 0.689
(1.00) 		0.272
(1.00) 		1.36e-26
(1.15e-23) 		2.15e-11
(1.71e-08) 		0.131
(1.00) 		0.776
(1.00) 		2.64e-08
(1.99e-05) 		2.45e-08
(1.84e-05) 		1.04e-10
(8.2e-08) 		1.39e-10
(1.09e-07) 		0.000184
(0.114) 		4.68e-06
(0.00325)
8p loss 0 (0%) 439 0.00809
(1.00) 		0.00105
(0.595) 		4.01e-24
(3.39e-21) 		3.7e-11
(2.94e-08) 		0.165
(1.00) 		0.181
(1.00) 		4.84e-12
(3.89e-09) 		6.9e-10
(5.37e-07) 		4.01e-15
(3.3e-12) 		7.17e-17
(5.95e-14) 		9.38e-07
(0.000671) 		1.46e-07
(0.000108)
14q loss 0 (0%) 450 0.00809
(1.00) 		0.00105
(0.595) 		8.94e-17
(7.41e-14) 		1.06e-09
(8.22e-07) 		0.0847
(1.00) 		0.0052
(1.00) 		3.38e-08
(2.52e-05) 		1.95e-07
(0.000143) 		3.34e-09
(2.55e-06) 		9.82e-12
(7.88e-09) 		2.03e-05
(0.0137) 		4.89e-05
(0.0318)
16p loss 0 (0%) 423 0.00809
(1.00) 		0.00105
(0.595) 		2.82e-31
(2.4e-28) 		2.27e-09
(1.74e-06) 		0.193
(1.00) 		0.796
(1.00) 		7.52e-10
(5.84e-07) 		1.47e-09
(1.13e-06) 		1.47e-09
(1.13e-06) 		1.36e-10
(1.07e-07) 		2.56e-05
(0.017) 		1.82e-05
(0.0124)
16q loss 0 (0%) 382 0.00324
(1.00) 		0.000454
(0.271) 		5.94e-40
(5.07e-37) 		2.1e-11
(1.68e-08) 		0.237
(1.00) 		1
(1.00) 		1.01e-11
(8.07e-09) 		2.34e-10
(1.83e-07) 		1.07e-11
(8.55e-09) 		1.9e-11
(1.52e-08) 		5.31e-06
(0.00368) 		6.9e-06
(0.00477)
17p loss 0 (0%) 387 0.00324
(1.00) 		0.000454
(0.271) 		8.66e-53
(7.41e-50) 		7.43e-13
(6.02e-10) 		0.000571
(0.336) 		0.665
(1.00) 		1.6e-20
(1.35e-17) 		2.15e-21
(1.81e-18) 		4.87e-17
(4.05e-14) 		2.92e-15
(2.41e-12) 		2.51e-05
(0.0167) 		2.09e-05
(0.0141)
20q gain 0 (0%) 414 0.0391
(1.00) 		0.00466
(1.00) 		3.62e-24
(3.07e-21) 		8.07e-08
(5.99e-05) 		0.192
(1.00) 		0.58
(1.00) 		1.75e-06
(0.00124) 		0.000621
(0.364) 		1.63e-11
(1.31e-08) 		3.65e-10
(2.84e-07) 		0.000178
(0.111) 		3.45e-05
(0.0228)
5q loss 0 (0%) 447 0.0515
(1.00) 		0.00755
(1.00) 		1.18e-18
(9.85e-16) 		7.92e-09
(6.02e-06) 		0.0481
(1.00) 		0.153
(1.00) 		6.28e-08
(4.68e-05) 		2.96e-08
(2.22e-05) 		2.83e-09
(2.17e-06) 		7.58e-08
(5.63e-05) 		0.0022
(1.00) 		0.000107
(0.0684)
9q loss 0 (0%) 399 0.000567
(0.334) 		4.17e-05
(0.0274) 		1.53e-37
(1.31e-34) 		4.84e-07
(0.000351) 		0.00601
(1.00) 		0.378
(1.00) 		2.56e-13
(2.08e-10) 		2.82e-16
(2.33e-13) 		2.09e-12
(1.69e-09) 		3.83e-10
(2.98e-07) 		0.00586
(1.00) 		0.00454
(1.00)
19p loss 0 (0%) 458 4.63e-12
(3.73e-09) 		9.19e-08
(6.8e-05) 		0.331
(1.00) 		1
(1.00) 		1.84e-05
(0.0125) 		7.84e-06
(0.00541) 		1.01e-05
(0.00697) 		6.41e-07
(0.000462) 		8.18e-06
(0.00564) 		0.00205
(1.00)
3q gain 0 (0%) 442 0.137
(1.00) 		0.272
(1.00) 		3.41e-22
(2.88e-19) 		2.37e-05
(0.0159) 		0.388
(1.00) 		0.301
(1.00) 		1.19e-06
(0.000849) 		5.14e-05
(0.0334) 		2.07e-05
(0.014) 		0.000263
(0.16) 		0.0342
(1.00) 		0.0187
(1.00)
5p gain 0 (0%) 460 0.536
(1.00) 		0.272
(1.00) 		3.01e-09
(2.31e-06) 		0.000138
(0.0869) 		0.0311
(1.00) 		0.712
(1.00) 		3.95e-06
(0.00276) 		0.00042
(0.252) 		1.66e-05
(0.0113) 		5.29e-05
(0.0343) 		0.0011
(0.616) 		7.26e-05
(0.0468)
3p loss 0 (0%) 461 1.34e-14
(1.09e-11) 		0.000129
(0.0814) 		0.000526
(0.311) 		0.028
(1.00) 		1.79e-07
(0.000131) 		8.63e-08
(6.4e-05) 		4.21e-05
(0.0276) 		2.37e-05
(0.0159) 		0.0114
(1.00) 		0.00685
(1.00)
7q loss 0 (0%) 465 4.91e-14
(4.02e-11) 		0.000171
(0.107) 		0.197
(1.00) 		0.0121
(1.00) 		1.32e-07
(9.72e-05) 		1.59e-06
(0.00113) 		1.77e-05
(0.012) 		1.25e-05
(0.00857) 		0.0242
(1.00) 		0.00754
(1.00)
9p loss 0 (0%) 416 0.0129
(1.00) 		0.00193
(1.00) 		2.63e-29
(2.23e-26) 		1.81e-06
(0.00128) 		0.0117
(1.00) 		0.244
(1.00) 		2.12e-12
(1.72e-09) 		7.6e-15
(6.24e-12) 		1.37e-09
(1.06e-06) 		1.19e-08
(9.01e-06) 		0.0266
(1.00) 		0.00914
(1.00)
11p loss 0 (0%) 439 1.44e-21
(1.22e-18) 		8.9e-07
(0.000639) 		0.182
(1.00) 		0.75
(1.00) 		4.46e-08
(3.33e-05) 		2.6e-07
(0.00019) 		1.99e-08
(1.5e-05) 		1.99e-06
(0.0014) 		0.00537
(1.00) 		0.00296
(1.00)
11q loss 0 (0%) 447 1.15e-15
(9.49e-13) 		7.9e-05
(0.0507) 		0.925
(1.00) 		0.713
(1.00) 		0.000397
(0.239) 		8.07e-06
(0.00557) 		2.54e-06
(0.00179) 		0.000184
(0.114) 		0.0184
(1.00) 		0.0242
(1.00)
12p loss 0 (0%) 467 3.86e-11
(3.07e-08) 		0.000161
(0.101) 		0.0577
(1.00) 		1
(1.00) 		3.62e-05
(0.0238) 		0.0057
(1.00) 		9.52e-08
(7.04e-05) 		4.34e-06
(0.00303) 		0.00716
(1.00) 		0.000374
(0.226)
13q loss 0 (0%) 432 0.689
(1.00) 		0.272
(1.00) 		2.43e-18
(2.02e-15) 		0.000107
(0.0679) 		0.161
(1.00) 		0.393
(1.00) 		0.000395
(0.238) 		3.89e-06
(0.00272) 		7.27e-05
(0.0468) 		0.000188
(0.117) 		0.217
(1.00) 		0.0539
(1.00)
17q loss 0 (0%) 424 0.00809
(1.00) 		0.00105
(0.595) 		1.48e-29
(1.26e-26) 		3.37e-05
(0.0222) 		0.0924
(1.00) 		0.612
(1.00) 		4.28e-09
(3.26e-06) 		1.95e-11
(1.55e-08) 		2.71e-07
(0.000198) 		5.5e-07
(0.000398) 		0.0044
(1.00) 		0.00187
(1.00)
18q loss 0 (0%) 443 9.75e-18
(8.11e-15) 		1.92e-06
(0.00135) 		0.725
(1.00) 		1
(1.00) 		3.87e-06
(0.00271) 		5.65e-07
(0.000408) 		3.04e-06
(0.00213) 		2.59e-07
(0.00019) 		0.0139
(1.00) 		0.00317
(1.00)
22q loss 0 (0%) 405 0.00809
(1.00) 		0.00105
(0.595) 		1.41e-36
(1.2e-33) 		3.23e-08
(2.42e-05) 		0.0721
(1.00) 		1
(1.00) 		4.88e-11
(3.86e-08) 		3.29e-14
(2.69e-11) 		9.64e-11
(7.6e-08) 		1.01e-09
(7.84e-07) 		0.0097
(1.00) 		0.00158
(0.876)
19p gain 0 (0%) 461 0.0391
(1.00) 		0.00466
(1.00) 		2.4e-13
(1.96e-10) 		0.00345
(1.00) 		0.528
(1.00) 		0.151
(1.00) 		4.73e-06
(0.00329) 		1.84e-05
(0.0125) 		9.18e-07
(0.000658) 		3.24e-05
(0.0215) 		0.104
(1.00) 		0.116
(1.00)
19q gain 0 (0%) 464 4.28e-13
(3.47e-10) 		0.00143
(0.794) 		0.085
(1.00) 		1
(1.00) 		4.73e-06
(0.00329) 		1.59e-06
(0.00113) 		8.12e-07
(0.000584) 		2.17e-05
(0.0146) 		0.0313
(1.00) 		0.0659
(1.00)
20p gain 0 (0%) 427 0.137
(1.00) 		0.0194
(1.00) 		2.28e-18
(1.9e-15) 		3.25e-05
(0.0216) 		0.291
(1.00) 		1
(1.00) 		9.04e-05
(0.0578) 		0.0119
(1.00) 		1.84e-08
(1.39e-05) 		4.4e-07
(0.000319) 		0.00425
(1.00) 		0.000627
(0.367)
21q loss 0 (0%) 460 0.0391
(1.00) 		0.00466
(1.00) 		6.47e-08
(4.82e-05) 		0.00259
(1.00) 		0.095
(1.00) 		0.75
(1.00) 		0.000148
(0.0933) 		0.00136
(0.762) 		0.00097
(0.553) 		4.43e-05
(0.0289) 		0.00022
(0.135) 		0.000203
(0.126)
1q gain 0 (0%) 354 0.25
(1.00) 		0.29
(1.00) 		3.04e-07
(0.000222) 		0.00646
(1.00) 		0.00123
(0.687) 		0.000715
(0.415) 		3.31e-06
(0.00232) 		9.23e-07
(0.000661) 		3.74e-07
(0.000272) 		0.0178
(1.00) 		0.278
(1.00) 		0.0102
(1.00)
13q gain 0 (0%) 472 9.55e-08
(7.05e-05) 		0.00465
(1.00) 		0.735
(1.00) 		0.367
(1.00) 		7.14e-05
(0.0461) 		0.000462
(0.275) 		3.45e-05
(0.0228) 		4.23e-05
(0.0277) 		0.169
(1.00) 		0.114
(1.00)
21q gain 0 (0%) 467 1.13e-08
(8.61e-06) 		0.0756
(1.00) 		0.237
(1.00) 		0.558
(1.00) 		0.000204
(0.126) 		0.0095
(1.00) 		0.000414
(0.249) 		0.000375
(0.227) 		0.314
(1.00) 		0.119
(1.00)
12q loss 0 (0%) 474 1.23e-09
(9.5e-07) 		9.44e-05
(0.0602) 		0.31
(1.00) 		0.429
(1.00) 		0.00106
(0.595) 		0.0067
(1.00) 		1.25e-06
(0.000891) 		1.67e-06
(0.00118) 		0.00628
(1.00) 		0.000788
(0.453)
19q loss 0 (0%) 464 1.79e-08
(1.35e-05) 		5.03e-05
(0.0327) 		0.734
(1.00) 		0.713
(1.00) 		0.000719
(0.416) 		0.00283
(1.00) 		0.000676
(0.394) 		1.46e-05
(0.01) 		0.000124
(0.0788) 		0.0122
(1.00)
8q gain 0 (0%) 374 0.0336
(1.00) 		0.0339
(1.00) 		1.65e-21
(1.39e-18) 		0.345
(1.00) 		0.00495
(1.00) 		1
(1.00) 		0.00591
(1.00) 		0.000299
(0.182) 		0.0018
(0.996) 		3.27e-05
(0.0216) 		0.0834
(1.00) 		0.00151
(0.841)
5p loss 0 (0%) 465 0.379
(1.00) 		0.0902
(1.00) 		1.16e-10
(9.13e-08) 		0.000323
(0.196) 		0.162
(1.00) 		0.181
(1.00) 		0.000782
(0.451) 		0.000672
(0.392) 		0.000216
(0.133) 		0.00281
(1.00) 		0.149
(1.00) 		0.0611
(1.00)
7p loss 0 (0%) 463 0.137
(1.00) 		0.0194
(1.00) 		9.88e-10
(7.66e-07) 		0.00652
(1.00) 		0.158
(1.00) 		0.201
(1.00) 		0.000162
(0.102) 		2.27e-05
(0.0152) 		0.000783
(0.451) 		0.00338
(1.00) 		0.185
(1.00) 		0.141
(1.00)
10p loss 0 (0%) 469 0.137
(1.00) 		0.0194
(1.00) 		4e-11
(3.17e-08) 		0.000323
(0.196) 		0.474
(1.00) 		0.633
(1.00) 		0.000469
(0.278) 		0.0016
(0.886) 		1.25e-05
(0.00856) 		0.00108
(0.608) 		0.0777
(1.00) 		0.0284
(1.00)
10q loss 0 (0%) 468 2.94e-10
(2.3e-07) 		0.000161
(0.101) 		0.451
(1.00) 		1
(1.00) 		0.000469
(0.278) 		0.0057
(1.00) 		0.000214
(0.132) 		0.00195
(1.00) 		0.123
(1.00) 		0.112
(1.00)
18p loss 0 (0%) 456 3.15e-12
(2.54e-09) 		1.88e-05
(0.0128) 		0.326
(1.00) 		0.746
(1.00) 		0.00066
(0.385) 		0.000172
(0.107) 		0.00472
(1.00) 		0.000594
(0.349) 		0.0533
(1.00) 		0.0214
(1.00)
Xq loss 0 (0%) 474 2.97e-07
(0.000216) 		0.000545
(0.321) 		0.617
(1.00) 		0.633
(1.00) 		0.016
(1.00) 		0.0067
(1.00) 		0.000233
(0.143) 		2.27e-05
(0.0152) 		0.00425
(1.00) 		0.00287
(1.00)
18q gain 0 (0%) 472 0.137
(1.00) 		0.0194
(1.00) 		8.26e-06
(0.00568) 		0.00501
(1.00) 		1
(1.00) 		0.0173
(1.00) 		0.00565
(1.00) 		0.000111
(0.0703) 		0.000436
(0.261) 		0.00137
(0.764) 		0.028
(1.00)
8q loss 0 (0%) 480 2.23e-05
(0.015) 		0.000917
(0.525) 		1
(1.00) 		0.0396
(1.00) 		0.154
(1.00) 		0.000302
(0.183) 		0.000443
(0.265) 		0.00295
(1.00) 		0.0128
(1.00)
2p gain 0 (0%) 441 0.425
(1.00) 		0.481
(1.00) 		5.41e-11
(4.27e-08) 		0.055
(1.00) 		0.177
(1.00) 		0.802
(1.00) 		0.238
(1.00) 		0.434
(1.00) 		0.0184
(1.00) 		0.162
(1.00) 		0.141
(1.00) 		0.0236
(1.00)
2q gain 0 (0%) 452 0.343
(1.00) 		1
(1.00) 		4.83e-11
(3.82e-08) 		0.169
(1.00) 		0.0653
(1.00) 		0.575
(1.00) 		0.3
(1.00) 		0.624
(1.00) 		0.015
(1.00) 		0.117
(1.00) 		0.0819
(1.00) 		0.0313
(1.00)
3p gain 0 (0%) 464 4.15e-19
(3.48e-16) 		0.111
(1.00) 		0.525
(1.00) 		0.652
(1.00) 		0.0149
(1.00) 		0.0429
(1.00) 		0.338
(1.00) 		0.225
(1.00) 		0.404
(1.00) 		0.416
(1.00)
6p gain 0 (0%) 454 0.253
(1.00) 		0.0902
(1.00) 		1.52e-16
(1.26e-13) 		0.0313
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.00665
(1.00) 		0.0075
(1.00) 		0.0121
(1.00) 		0.0302
(1.00) 		0.202
(1.00) 		0.425
(1.00)
6q gain 0 (0%) 462 0.253
(1.00) 		0.0902
(1.00) 		1.58e-13
(1.29e-10) 		0.318
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.00839
(1.00) 		0.00793
(1.00) 		0.168
(1.00) 		0.278
(1.00) 		0.599
(1.00) 		0.708
(1.00)
7p gain 0 (0%) 449 0.935
(1.00) 		0.866
(1.00) 		8.62e-19
(7.22e-16) 		0.0125
(1.00) 		0.733
(1.00) 		0.217
(1.00) 		1
(1.00) 		0.475
(1.00) 		0.244
(1.00) 		0.609
(1.00) 		0.799
(1.00) 		0.481
(1.00)
7q gain 0 (0%) 449 0.855
(1.00) 		1
(1.00) 		2.4e-19
(2.01e-16) 		0.0252
(1.00) 		0.889
(1.00) 		0.0552
(1.00) 		0.385
(1.00) 		0.0331
(1.00) 		0.44
(1.00) 		0.425
(1.00) 		0.909
(1.00) 		0.766
(1.00)
8p gain 0 (0%) 406 0.704
(1.00) 		0.609
(1.00) 		7.48e-18
(6.23e-15) 		0.941
(1.00) 		0.133
(1.00) 		1
(1.00) 		0.474
(1.00) 		0.434
(1.00) 		0.38
(1.00) 		0.0022
(1.00) 		0.416
(1.00) 		0.00575
(1.00)
10q gain 0 (0%) 413 0.00212
(1.00) 		0.0262
(1.00) 		9.34e-05
(0.0597) 		0.145
(1.00) 		0.388
(1.00) 		0.252
(1.00) 		0.0262
(1.00) 		0.256
(1.00) 		0.0128
(1.00) 		0.00257
(1.00) 		0.0446
(1.00) 		0.0217
(1.00)
12p gain 0 (0%) 455 0.64
(1.00) 		1
(1.00) 		4.78e-08
(3.57e-05) 		0.00794
(1.00) 		0.937
(1.00) 		1
(1.00) 		0.0455
(1.00) 		0.0906
(1.00) 		0.0241
(1.00) 		0.0169
(1.00) 		0.127
(1.00) 		0.116
(1.00)
12q gain 0 (0%) 464 0.64
(1.00) 		1
(1.00) 		3.68e-07
(0.000268) 		0.106
(1.00) 		0.901
(1.00) 		1
(1.00) 		0.0811
(1.00) 		0.227
(1.00) 		0.126
(1.00) 		0.311
(1.00) 		0.412
(1.00) 		0.304
(1.00)
14q gain 0 (0%) 472 1
(1.00) 		0.769
(1.00) 		2.16e-05
(0.0146) 		0.214
(1.00) 		0.239
(1.00) 		0.292
(1.00) 		0.401
(1.00) 		0.0737
(1.00) 		0.0486
(1.00) 		0.0281
(1.00) 		0.303
(1.00) 		0.418
(1.00)
17p gain 0 (0%) 485 2.6e-05
(0.0173) 		0.241
(1.00) 		1
(1.00) 		0.316
(1.00) 		0.315
(1.00) 		0.0701
(1.00) 		0.145
(1.00) 		0.855
(1.00) 		0.824
(1.00)
Xq gain 0 (0%) 480 0.000257
(0.157) 		0.321
(1.00) 		0.376
(1.00) 		0.157
(1.00) 		0.447
(1.00) 		0.00871
(1.00) 		0.0888
(1.00) 		0.088
(1.00) 		0.6
(1.00)
1p loss 0 (0%) 479 1.82e-08
(1.38e-05) 		0.000917
(0.525) 		1
(1.00) 		0.0403
(1.00) 		0.0884
(1.00) 		0.0517
(1.00) 		0.00318
(1.00) 		0.17
(1.00) 		0.0522
(1.00)
3q loss 0 (0%) 480 4.31e-05
(0.0281) 		0.0574
(1.00) 		0.024
(1.00) 		0.558
(1.00) 		0.00479
(1.00) 		0.00274
(1.00) 		0.0347
(1.00) 		0.0739
(1.00) 		0.0772
(1.00) 		0.329
(1.00)
6q loss 0 (0%) 480 0.689
(1.00) 		0.272
(1.00) 		0.000236
(0.145) 		0.0349
(1.00) 		0.858
(1.00) 		0.558
(1.00) 		0.016
(1.00) 		0.0384
(1.00) 		0.133
(1.00) 		0.0103
(1.00) 		0.136
(1.00) 		0.219
(1.00)
20p loss 0 (0%) 477 0.000122
(0.0775) 		0.106
(1.00) 		0.243
(1.00) 		0.633
(1.00) 		0.0368
(1.00) 		0.0465
(1.00) 		0.00635
(1.00) 		0.0702
(1.00) 		0.241
(1.00) 		0.148
(1.00)
1p gain 0 (0%) 471 0.467
(1.00) 		0.491
(1.00) 		0.035
(1.00) 		0.661
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.182
(1.00) 		0.29
(1.00) 		0.00743
(1.00) 		0.0758
(1.00) 		0.166
(1.00) 		0.143
(1.00)
4p gain 0 (0%) 486 0.0039
(1.00) 		0.123
(1.00) 		0.14
(1.00) 		0.0396
(1.00) 		0.154
(1.00) 		0.0229
(1.00) 		0.0281
(1.00) 		0.425
(1.00) 		0.442
(1.00)
5q gain 0 (0%) 483 0.00286
(1.00) 		0.423
(1.00) 		1
(1.00) 		0.0679
(1.00) 		0.286
(1.00) 		0.052
(1.00) 		0.203
(1.00) 		0.151
(1.00) 		0.0719
(1.00)
9p gain 0 (0%) 478 0.0484
(1.00) 		0.0841
(1.00) 		1
(1.00) 		0.822
(1.00) 		0.0787
(1.00) 		0.0699
(1.00) 		0.0294
(1.00) 		0.124
(1.00) 		0.0684
(1.00)
9q gain 0 (0%) 488 0.352
(1.00) 		0.361
(1.00) 		0.781
(1.00) 		0.361
(1.00) 		0.387
(1.00) 		0.127
(1.00) 		0.425
(1.00) 		0.0728
(1.00)
10p gain 0 (0%) 405 0.00714
(1.00) 		0.0476
(1.00) 		0.0007
(0.406) 		0.171
(1.00) 		0.284
(1.00) 		0.136
(1.00) 		0.0155
(1.00) 		0.255
(1.00) 		0.0639
(1.00) 		0.0178
(1.00) 		0.0535
(1.00) 		0.027
(1.00)
11p gain 0 (0%) 484 0.137
(1.00) 		0.272
(1.00) 		0.0099
(1.00) 		0.036
(1.00) 		0.109
(1.00) 		1
(1.00) 		0.157
(1.00) 		0.447
(1.00) 		0.13
(1.00) 		0.238
(1.00) 		0.821
(1.00) 		0.784
(1.00)
11q gain 0 (0%) 484 0.0111
(1.00) 		0.374
(1.00) 		0.109
(1.00) 		0.299
(1.00) 		0.194
(1.00) 		0.396
(1.00) 		0.242
(1.00) 		0.361
(1.00) 		1
(1.00) 		1
(1.00)
15q gain 0 (0%) 486 0.00416
(1.00) 		0.846
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.699
(1.00) 		0.884
(1.00) 		1
(1.00) 		0.36
(1.00) 		0.208
(1.00)
16p gain 0 (0%) 480 0.000794
(0.456) 		0.0309
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.0679
(1.00) 		0.0787
(1.00) 		0.0831
(1.00) 		0.336
(1.00) 		0.586
(1.00) 		0.329
(1.00)
16q gain 0 (0%) 488 0.046
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.785
(1.00) 		1
(1.00)
17q gain 0 (0%) 479 0.000727
(0.42) 		0.00345
(1.00) 		0.0531
(1.00) 		1
(1.00) 		0.0276
(1.00) 		0.284
(1.00) 		0.00887
(1.00) 		0.011
(1.00) 		0.14
(1.00) 		0.0854
(1.00)
22q gain 0 (0%) 483 0.00473
(1.00) 		0.000524
(0.31) 		0.376
(1.00) 		0.115
(1.00) 		0.361
(1.00) 		0.00132
(0.739) 		0.00259
(1.00) 		0.0536
(1.00) 		0.0391
(1.00)
1q loss 0 (0%) 488 0.0365
(1.00) 		0.0562
(1.00) 		0.115
(1.00) 		0.361
(1.00) 		0.0991
(1.00) 		0.127
(1.00) 		0.425
(1.00) 		0.442
(1.00)
2p loss 0 (0%) 486 0.019
(1.00) 		0.517
(1.00) 		0.14
(1.00) 		0.157
(1.00) 		0.0878
(1.00) 		0.773
(1.00) 		0.199
(1.00) 		0.855
(1.00) 		0.161
(1.00)
2q loss 0 (0%) 484 0.00637
(1.00) 		0.197
(1.00) 		0.14
(1.00) 		0.157
(1.00) 		0.0878
(1.00) 		0.493
(1.00) 		0.192
(1.00) 		0.685
(1.00) 		0.277
(1.00)
6p loss 0 (0%) 482 0.689
(1.00) 		0.272
(1.00) 		0.000862
(0.494) 		0.0945
(1.00) 		0.858
(1.00) 		0.558
(1.00) 		0.194
(1.00) 		0.249
(1.00) 		0.172
(1.00) 		0.0171
(1.00) 		0.279
(1.00) 		0.548
(1.00)
20q loss 0 (0%) 485 0.0106
(1.00) 		0.0526
(1.00) 		0.528
(1.00) 		0.391
(1.00) 		0.474
(1.00) 		0.164
(1.00) 		0.078
(1.00) 		0.127
(1.00) 		0.171
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 3.04e-07 (Chi-square test), Q value = 0.00022

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
1Q GAIN CNV 85 18 21 8 6
1Q GAIN WILD-TYPE 205 22 118 9 0

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 3.31e-06 (Fisher's exact test), Q value = 0.0023

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
1Q GAIN CNV 24 26 51
1Q GAIN WILD-TYPE 118 81 62

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.23e-07 (Fisher's exact test), Q value = 0.00066

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
1Q GAIN CNV 26 24 31 20
1Q GAIN WILD-TYPE 39 68 34 120

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 3.74e-07 (Fisher's exact test), Q value = 0.00027

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
1Q GAIN CNV 41 35 62
1Q GAIN WILD-TYPE 166 109 70

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

'2p gain' versus 'CN_CNMF'

P value = 5.41e-11 (Chi-square test), Q value = 4.3e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
2P GAIN CNV 9 14 22 5 1
2P GAIN WILD-TYPE 281 26 117 12 5

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

'2q gain' versus 'CN_CNMF'

P value = 4.83e-11 (Chi-square test), Q value = 3.8e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
2Q GAIN CNV 6 13 16 4 1
2Q GAIN WILD-TYPE 284 27 123 13 5

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

'3p gain' versus 'CN_CNMF'

P value = 4.15e-19 (Chi-square test), Q value = 3.5e-16

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
3P GAIN CNV 1 4 13 9 1
3P GAIN WILD-TYPE 289 36 126 8 5

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

'3q gain' versus 'CN_CNMF'

P value = 3.41e-22 (Chi-square test), Q value = 2.9e-19

Table S8.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
3Q GAIN CNV 2 5 31 11 1
3Q GAIN WILD-TYPE 288 35 108 6 5

Figure S8.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 2.37e-05 (Fisher's exact test), Q value = 0.016

Table S9.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
3Q GAIN CNV 29 6 6
3Q GAIN WILD-TYPE 114 78 144

Figure S9.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00085

Table S10.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
3Q GAIN CNV 26 6 1
3Q GAIN WILD-TYPE 116 101 112

Figure S10.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.14e-05 (Fisher's exact test), Q value = 0.033

Table S11.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
3Q GAIN CNV 0 3 7 23
3Q GAIN WILD-TYPE 65 89 58 117

Figure S11.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 2.07e-05 (Fisher's exact test), Q value = 0.014

Table S12.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
3Q GAIN CNV 37 7 6
3Q GAIN WILD-TYPE 170 137 126

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000263 (Fisher's exact test), Q value = 0.16

Table S13.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
3Q GAIN CNV 9 5 4 32
3Q GAIN WILD-TYPE 184 74 23 152

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 3.01e-09 (Chi-square test), Q value = 2.3e-06

Table S14.  Gene #8: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
5P GAIN CNV 3 2 25 1 1
5P GAIN WILD-TYPE 287 38 114 16 5

Figure S14.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.000138 (Fisher's exact test), Q value = 0.087

Table S15.  Gene #8: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
5P GAIN CNV 20 3 3
5P GAIN WILD-TYPE 123 81 147

Figure S15.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 3.95e-06 (Fisher's exact test), Q value = 0.0028

Table S16.  Gene #8: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
5P GAIN CNV 19 0 3
5P GAIN WILD-TYPE 123 107 110

Figure S16.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.011

Table S17.  Gene #8: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
5P GAIN CNV 25 1 5
5P GAIN WILD-TYPE 182 143 127

Figure S17.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.29e-05 (Fisher's exact test), Q value = 0.034

Table S18.  Gene #8: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
5P GAIN CNV 3 3 1 24
5P GAIN WILD-TYPE 190 76 26 160

Figure S18.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.26e-05 (Fisher's exact test), Q value = 0.047

Table S19.  Gene #8: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
5P GAIN CNV 0 22 3
5P GAIN WILD-TYPE 117 175 42

Figure S19.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1.52e-16 (Chi-square test), Q value = 1.3e-13

Table S20.  Gene #10: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
6P GAIN CNV 1 3 25 8 1
6P GAIN WILD-TYPE 289 37 114 9 5

Figure S20.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 1.58e-13 (Chi-square test), Q value = 1.3e-10

Table S21.  Gene #11: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
6Q GAIN CNV 1 3 18 7 1
6Q GAIN WILD-TYPE 289 37 121 10 5

Figure S21.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 8.62e-19 (Chi-square test), Q value = 7.2e-16

Table S22.  Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
7P GAIN CNV 5 17 14 6 1
7P GAIN WILD-TYPE 285 23 125 11 5

Figure S22.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2.4e-19 (Chi-square test), Q value = 2e-16

Table S23.  Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
7Q GAIN CNV 8 17 10 7 1
7Q GAIN WILD-TYPE 282 23 129 10 5

Figure S23.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 7.48e-18 (Chi-square test), Q value = 6.2e-15

Table S24.  Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
8P GAIN CNV 28 16 25 15 2
8P GAIN WILD-TYPE 262 24 114 2 4

Figure S24.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1.65e-21 (Chi-square test), Q value = 1.4e-18

Table S25.  Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
8Q GAIN CNV 29 19 51 16 3
8Q GAIN WILD-TYPE 261 21 88 1 3

Figure S25.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000299 (Fisher's exact test), Q value = 0.18

Table S26.  Gene #15: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
8Q GAIN CNV 10 12 9 47
8Q GAIN WILD-TYPE 55 80 56 93

Figure S26.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.27e-05 (Fisher's exact test), Q value = 0.022

Table S27.  Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
8Q GAIN CNV 28 17 13 57
8Q GAIN WILD-TYPE 165 62 14 127

Figure S27.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 9.34e-05 (Chi-square test), Q value = 0.06

Table S28.  Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
10Q GAIN CNV 44 12 13 7 3
10Q GAIN WILD-TYPE 246 28 126 10 3

Figure S28.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 4.78e-08 (Chi-square test), Q value = 3.6e-05

Table S29.  Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
12P GAIN CNV 7 7 19 1 3
12P GAIN WILD-TYPE 283 33 120 16 3

Figure S29.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 3.68e-07 (Chi-square test), Q value = 0.00027

Table S30.  Gene #23: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
12Q GAIN CNV 7 6 11 1 3
12Q GAIN WILD-TYPE 283 34 128 16 3

Figure S30.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 9.55e-08 (Chi-square test), Q value = 7e-05

Table S31.  Gene #24: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
13Q GAIN CNV 1 0 17 1 1
13Q GAIN WILD-TYPE 289 40 122 16 5

Figure S31.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 7.14e-05 (Fisher's exact test), Q value = 0.046

Table S32.  Gene #24: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
13Q GAIN CNV 13 1 0
13Q GAIN WILD-TYPE 129 106 113

Figure S32.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 3.45e-05 (Fisher's exact test), Q value = 0.023

Table S33.  Gene #24: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
13Q GAIN CNV 18 2 0
13Q GAIN WILD-TYPE 189 142 132

Figure S33.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.23e-05 (Fisher's exact test), Q value = 0.028

Table S34.  Gene #24: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
13Q GAIN CNV 2 0 0 18
13Q GAIN WILD-TYPE 191 79 27 166

Figure S34.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 2.16e-05 (Chi-square test), Q value = 0.015

Table S35.  Gene #25: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
14Q GAIN CNV 2 2 13 3 0
14Q GAIN WILD-TYPE 288 38 126 14 6

Figure S35.  Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 2.6e-05 (Chi-square test), Q value = 0.017

Table S36.  Gene #29: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
17P GAIN CNV 1 0 3 2 1
17P GAIN WILD-TYPE 289 40 136 15 5

Figure S36.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 4.94e-14 (Chi-square test), Q value = 4e-11

Table S37.  Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
18P GAIN CNV 2 2 32 1 0
18P GAIN WILD-TYPE 288 38 107 16 6

Figure S37.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 6.07e-05 (Fisher's exact test), Q value = 0.039

Table S38.  Gene #31: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
18P GAIN CNV 20 8 2
18P GAIN WILD-TYPE 123 76 148

Figure S38.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.022

Table S39.  Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
18P GAIN CNV 18 2 1
18P GAIN WILD-TYPE 124 105 112

Figure S39.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.28e-07 (Fisher's exact test), Q value = 0.00052

Table S40.  Gene #31: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
18P GAIN CNV 0 1 0 20
18P GAIN WILD-TYPE 65 91 65 120

Figure S40.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 4.26e-09 (Fisher's exact test), Q value = 3.2e-06

Table S41.  Gene #31: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
18P GAIN CNV 33 1 3
18P GAIN WILD-TYPE 174 143 129

Figure S41.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.47e-09 (Fisher's exact test), Q value = 4.9e-06

Table S42.  Gene #31: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
18P GAIN CNV 2 3 0 32
18P GAIN WILD-TYPE 191 76 27 152

Figure S42.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.18e-05 (Fisher's exact test), Q value = 0.046

Table S43.  Gene #31: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
18P GAIN CNV 24 1 6
18P GAIN WILD-TYPE 145 115 68

Figure S43.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000285 (Fisher's exact test), Q value = 0.17

Table S44.  Gene #31: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
18P GAIN CNV 2 27 2
18P GAIN WILD-TYPE 115 170 43

Figure S44.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 8.26e-06 (Chi-square test), Q value = 0.0057

Table S45.  Gene #32: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
18Q GAIN CNV 2 1 16 1 0
18Q GAIN WILD-TYPE 288 39 123 16 6

Figure S45.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.07

Table S46.  Gene #32: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
18Q GAIN CNV 17 0 3
18Q GAIN WILD-TYPE 190 144 129

Figure S46.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 2.4e-13 (Chi-square test), Q value = 2e-10

Table S47.  Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
19P GAIN CNV 0 1 27 3 0
19P GAIN WILD-TYPE 290 39 112 14 6

Figure S47.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 4.73e-06 (Fisher's exact test), Q value = 0.0033

Table S48.  Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
19P GAIN CNV 16 1 0
19P GAIN WILD-TYPE 126 106 113

Figure S48.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.84e-05 (Fisher's exact test), Q value = 0.013

Table S49.  Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
19P GAIN CNV 0 0 1 16
19P GAIN WILD-TYPE 65 92 64 124

Figure S49.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 9.18e-07 (Fisher's exact test), Q value = 0.00066

Table S50.  Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
19P GAIN CNV 27 3 1
19P GAIN WILD-TYPE 180 141 131

Figure S50.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.021

Table S51.  Gene #33: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
19P GAIN CNV 4 1 2 24
19P GAIN WILD-TYPE 189 78 25 160

Figure S51.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 4.28e-13 (Chi-square test), Q value = 3.5e-10

Table S52.  Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
19Q GAIN CNV 0 0 25 3 0
19Q GAIN WILD-TYPE 290 40 114 14 6

Figure S52.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 4.73e-06 (Fisher's exact test), Q value = 0.0033

Table S53.  Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
19Q GAIN CNV 16 1 0
19Q GAIN WILD-TYPE 126 106 113

Figure S53.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.59e-06 (Fisher's exact test), Q value = 0.0011

Table S54.  Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
19Q GAIN CNV 0 0 0 17
19Q GAIN WILD-TYPE 65 92 65 123

Figure S54.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 8.12e-07 (Fisher's exact test), Q value = 0.00058

Table S55.  Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
19Q GAIN CNV 25 2 1
19Q GAIN WILD-TYPE 182 142 131

Figure S55.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.015

Table S56.  Gene #34: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
19Q GAIN CNV 3 1 1 23
19Q GAIN WILD-TYPE 190 78 26 161

Figure S56.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 2.28e-18 (Chi-square test), Q value = 1.9e-15

Table S57.  Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
20P GAIN CNV 4 13 43 3 2
20P GAIN WILD-TYPE 286 27 96 14 4

Figure S57.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 3.25e-05 (Fisher's exact test), Q value = 0.022

Table S58.  Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
20P GAIN CNV 37 9 11
20P GAIN WILD-TYPE 106 75 139

Figure S58.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 9.04e-05 (Fisher's exact test), Q value = 0.058

Table S59.  Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
20P GAIN CNV 27 5 5
20P GAIN WILD-TYPE 115 102 108

Figure S59.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1.84e-08 (Fisher's exact test), Q value = 1.4e-05

Table S60.  Gene #35: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
20P GAIN CNV 50 7 8
20P GAIN WILD-TYPE 157 137 124

Figure S60.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.4e-07 (Fisher's exact test), Q value = 0.00032

Table S61.  Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
20P GAIN CNV 11 10 0 44
20P GAIN WILD-TYPE 182 69 27 140

Figure S61.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 3.62e-24 (Chi-square test), Q value = 3.1e-21

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
20Q GAIN CNV 4 15 54 3 2
20Q GAIN WILD-TYPE 286 25 85 14 4

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

'20q gain' versus 'METHLYATION_CNMF'

P value = 8.07e-08 (Fisher's exact test), Q value = 6e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
20Q GAIN CNV 47 10 12
20Q GAIN WILD-TYPE 96 74 138

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

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.75e-06 (Fisher's exact test), Q value = 0.0012

Table S64.  Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
20Q GAIN CNV 32 5 5
20Q GAIN WILD-TYPE 110 102 108

Figure S64.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1.63e-11 (Fisher's exact test), Q value = 1.3e-08

Table S65.  Gene #36: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
20Q GAIN CNV 61 8 8
20Q GAIN WILD-TYPE 146 136 124

Figure S65.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.65e-10 (Fisher's exact test), Q value = 2.8e-07

Table S66.  Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
20Q GAIN CNV 12 10 0 55
20Q GAIN WILD-TYPE 181 69 27 129

Figure S66.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000178 (Fisher's exact test), Q value = 0.11

Table S67.  Gene #36: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
20Q GAIN CNV 45 9 13
20Q GAIN WILD-TYPE 124 107 61

Figure S67.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.45e-05 (Fisher's exact test), Q value = 0.023

Table S68.  Gene #36: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
20Q GAIN CNV 8 52 7
20Q GAIN WILD-TYPE 109 145 38

Figure S68.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1.13e-08 (Chi-square test), Q value = 8.6e-06

Table S69.  Gene #37: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
21Q GAIN CNV 1 2 21 1 0
21Q GAIN WILD-TYPE 289 38 118 16 6

Figure S69.  Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.13

Table S70.  Gene #37: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
21Q GAIN CNV 12 1 0
21Q GAIN WILD-TYPE 130 106 113

Figure S70.  Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.000414 (Fisher's exact test), Q value = 0.25

Table S71.  Gene #37: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
21Q GAIN CNV 20 4 1
21Q GAIN WILD-TYPE 187 140 131

Figure S71.  Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000375 (Fisher's exact test), Q value = 0.23

Table S72.  Gene #37: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
21Q GAIN CNV 4 1 0 20
21Q GAIN WILD-TYPE 189 78 27 164

Figure S72.  Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Xq gain' versus 'CN_CNMF'

P value = 0.000257 (Chi-square test), Q value = 0.16

Table S73.  Gene #39: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
XQ GAIN CNV 0 1 10 1 0
XQ GAIN WILD-TYPE 290 39 129 16 6

Figure S73.  Get High-res Image Gene #39: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1.82e-08 (Chi-square test), Q value = 1.4e-05

Table S74.  Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
1P LOSS CNV 0 4 7 0 2
1P LOSS WILD-TYPE 290 36 132 17 4

Figure S74.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1.34e-14 (Chi-square test), Q value = 1.1e-11

Table S75.  Gene #44: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
3P LOSS CNV 0 2 29 0 0
3P LOSS WILD-TYPE 290 38 110 17 6

Figure S75.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.000129 (Fisher's exact test), Q value = 0.081

Table S76.  Gene #44: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
3P LOSS CNV 19 6 2
3P LOSS WILD-TYPE 124 78 148

Figure S76.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1.79e-07 (Fisher's exact test), Q value = 0.00013

Table S77.  Gene #44: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
3P LOSS CNV 19 1 0
3P LOSS WILD-TYPE 123 106 113

Figure S77.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.63e-08 (Fisher's exact test), Q value = 6.4e-05

Table S78.  Gene #44: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
3P LOSS CNV 0 0 0 20
3P LOSS WILD-TYPE 65 92 65 120

Figure S78.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 4.21e-05 (Fisher's exact test), Q value = 0.028

Table S79.  Gene #44: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
3P LOSS CNV 24 2 3
3P LOSS WILD-TYPE 183 142 129

Figure S79.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.37e-05 (Fisher's exact test), Q value = 0.016

Table S80.  Gene #44: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
3P LOSS CNV 2 3 1 23
3P LOSS WILD-TYPE 191 76 26 161

Figure S80.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 4.31e-05 (Chi-square test), Q value = 0.028

Table S81.  Gene #45: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
3Q LOSS CNV 0 1 11 0 0
3Q LOSS WILD-TYPE 290 39 128 17 6

Figure S81.  Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 4.79e-25 (Chi-square test), Q value = 4.1e-22

Table S82.  Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
4P LOSS CNV 2 8 54 1 1
4P LOSS WILD-TYPE 288 32 85 16 5

Figure S82.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 6.03e-11 (Fisher's exact test), Q value = 4.8e-08

Table S83.  Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
4P LOSS CNV 41 15 3
4P LOSS WILD-TYPE 102 69 147

Figure S83.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 2.45e-09 (Fisher's exact test), Q value = 1.9e-06

Table S84.  Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
4P LOSS CNV 30 1 3
4P LOSS WILD-TYPE 112 106 110

Figure S84.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.29e-07 (Fisher's exact test), Q value = 9.5e-05

Table S85.  Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
4P LOSS CNV 2 1 2 29
4P LOSS WILD-TYPE 63 91 63 111

Figure S85.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1.88e-13 (Fisher's exact test), Q value = 1.5e-10

Table S86.  Gene #46: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
4P LOSS CNV 55 4 5
4P LOSS WILD-TYPE 152 140 127

Figure S86.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.44e-12 (Fisher's exact test), Q value = 3.6e-09

Table S87.  Gene #46: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
4P LOSS CNV 4 7 4 49
4P LOSS WILD-TYPE 189 72 23 135

Figure S87.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.45e-05 (Fisher's exact test), Q value = 0.054

Table S88.  Gene #46: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
4P LOSS CNV 39 6 14
4P LOSS WILD-TYPE 130 110 60

Figure S88.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.78e-06 (Fisher's exact test), Q value = 0.0013

Table S89.  Gene #46: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
4P LOSS CNV 5 49 5
4P LOSS WILD-TYPE 112 148 40

Figure S89.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1.36e-26 (Chi-square test), Q value = 1.2e-23

Table S90.  Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
4Q LOSS CNV 1 8 54 0 1
4Q LOSS WILD-TYPE 289 32 85 17 5

Figure S90.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 2.15e-11 (Fisher's exact test), Q value = 1.7e-08

Table S91.  Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
4Q LOSS CNV 39 16 2
4Q LOSS WILD-TYPE 104 68 148

Figure S91.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 2.64e-08 (Fisher's exact test), Q value = 2e-05

Table S92.  Gene #47: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
4Q LOSS CNV 27 0 5
4Q LOSS WILD-TYPE 115 107 108

Figure S92.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.45e-08 (Fisher's exact test), Q value = 1.8e-05

Table S93.  Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
4Q LOSS CNV 2 0 2 28
4Q LOSS WILD-TYPE 63 92 63 112

Figure S93.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.04e-10 (Fisher's exact test), Q value = 8.2e-08

Table S94.  Gene #47: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
4Q LOSS CNV 51 6 5
4Q LOSS WILD-TYPE 156 138 127

Figure S94.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.39e-10 (Fisher's exact test), Q value = 1.1e-07

Table S95.  Gene #47: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
4Q LOSS CNV 5 6 5 46
4Q LOSS WILD-TYPE 188 73 22 138

Figure S95.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S96.  Gene #47: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
4Q LOSS CNV 37 6 14
4Q LOSS WILD-TYPE 132 110 60

Figure S96.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.68e-06 (Fisher's exact test), Q value = 0.0033

Table S97.  Gene #47: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
4Q LOSS CNV 5 47 5
4Q LOSS WILD-TYPE 112 150 40

Figure S97.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1.16e-10 (Chi-square test), Q value = 9.1e-08

Table S98.  Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
5P LOSS CNV 0 8 19 0 0
5P LOSS WILD-TYPE 290 32 120 17 6

Figure S98.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.000323 (Fisher's exact test), Q value = 0.2

Table S99.  Gene #48: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
5P LOSS CNV 15 4 1
5P LOSS WILD-TYPE 128 80 149

Figure S99.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.000216 (Fisher's exact test), Q value = 0.13

Table S100.  Gene #48: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
5P LOSS CNV 22 3 2
5P LOSS WILD-TYPE 185 141 130

Figure S100.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1.18e-18 (Chi-square test), Q value = 9.9e-16

Table S101.  Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
5Q LOSS CNV 0 7 38 0 0
5Q LOSS WILD-TYPE 290 33 101 17 6

Figure S101.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 7.92e-09 (Fisher's exact test), Q value = 6e-06

Table S102.  Gene #49: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
5Q LOSS CNV 29 6 1
5Q LOSS WILD-TYPE 114 78 149

Figure S102.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 6.28e-08 (Fisher's exact test), Q value = 4.7e-05

Table S103.  Gene #49: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
5Q LOSS CNV 25 1 2
5Q LOSS WILD-TYPE 117 106 111

Figure S103.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.96e-08 (Fisher's exact test), Q value = 2.2e-05

Table S104.  Gene #49: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
5Q LOSS CNV 0 0 3 25
5Q LOSS WILD-TYPE 65 92 62 115

Figure S104.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 2.83e-09 (Fisher's exact test), Q value = 2.2e-06

Table S105.  Gene #49: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
5Q LOSS CNV 38 4 2
5Q LOSS WILD-TYPE 169 140 130

Figure S105.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.58e-08 (Fisher's exact test), Q value = 5.6e-05

Table S106.  Gene #49: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
5Q LOSS CNV 4 4 1 35
5Q LOSS WILD-TYPE 189 75 26 149

Figure S106.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.068

Table S107.  Gene #49: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
5Q LOSS CNV 3 30 1
5Q LOSS WILD-TYPE 114 167 44

Figure S107.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.000236 (Chi-square test), Q value = 0.14

Table S108.  Gene #51: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
6Q LOSS CNV 0 3 9 0 0
6Q LOSS WILD-TYPE 290 37 130 17 6

Figure S108.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 9.88e-10 (Chi-square test), Q value = 7.7e-07

Table S109.  Gene #52: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
7P LOSS CNV 3 1 24 0 1
7P LOSS WILD-TYPE 287 39 115 17 5

Figure S109.  Get High-res Image Gene #52: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.1

Table S110.  Gene #52: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
7P LOSS CNV 18 2 2
7P LOSS WILD-TYPE 124 105 111

Figure S110.  Get High-res Image Gene #52: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.015

Table S111.  Gene #52: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
7P LOSS CNV 2 0 1 19
7P LOSS WILD-TYPE 63 92 64 121

Figure S111.  Get High-res Image Gene #52: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 4.91e-14 (Chi-square test), Q value = 4e-11

Table S112.  Gene #53: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
7Q LOSS CNV 0 0 26 0 1
7Q LOSS WILD-TYPE 290 40 113 17 5

Figure S112.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.11

Table S113.  Gene #53: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
7Q LOSS CNV 16 6 1
7Q LOSS WILD-TYPE 127 78 149

Figure S113.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 1.32e-07 (Fisher's exact test), Q value = 9.7e-05

Table S114.  Gene #53: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
7Q LOSS CNV 17 0 0
7Q LOSS WILD-TYPE 125 107 113

Figure S114.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.59e-06 (Fisher's exact test), Q value = 0.0011

Table S115.  Gene #53: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
7Q LOSS CNV 0 0 0 17
7Q LOSS WILD-TYPE 65 92 65 123

Figure S115.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 1.77e-05 (Fisher's exact test), Q value = 0.012

Table S116.  Gene #53: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
7Q LOSS CNV 23 3 1
7Q LOSS WILD-TYPE 184 141 131

Figure S116.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.0086

Table S117.  Gene #53: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
7Q LOSS CNV 3 1 0 23
7Q LOSS WILD-TYPE 190 78 27 161

Figure S117.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 4.01e-24 (Chi-square test), Q value = 3.4e-21

Table S118.  Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
8P LOSS CNV 2 1 48 2 0
8P LOSS WILD-TYPE 288 39 91 15 6

Figure S118.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 3.7e-11 (Fisher's exact test), Q value = 2.9e-08

Table S119.  Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
8P LOSS CNV 36 9 1
8P LOSS WILD-TYPE 107 75 149

Figure S119.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 4.84e-12 (Fisher's exact test), Q value = 3.9e-09

Table S120.  Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
8P LOSS CNV 30 0 1
8P LOSS WILD-TYPE 112 107 112

Figure S120.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.9e-10 (Fisher's exact test), Q value = 5.4e-07

Table S121.  Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
8P LOSS CNV 1 0 1 29
8P LOSS WILD-TYPE 64 92 64 111

Figure S121.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 4.01e-15 (Fisher's exact test), Q value = 3.3e-12

Table S122.  Gene #54: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
8P LOSS CNV 47 1 2
8P LOSS WILD-TYPE 160 143 130

Figure S122.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.17e-17 (Fisher's exact test), Q value = 6e-14

Table S123.  Gene #54: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
8P LOSS CNV 1 2 0 47
8P LOSS WILD-TYPE 192 77 27 137

Figure S123.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.38e-07 (Fisher's exact test), Q value = 0.00067

Table S124.  Gene #54: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
8P LOSS CNV 31 1 12
8P LOSS WILD-TYPE 138 115 62

Figure S124.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.46e-07 (Fisher's exact test), Q value = 0.00011

Table S125.  Gene #54: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
8P LOSS CNV 1 39 4
8P LOSS WILD-TYPE 116 158 41

Figure S125.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 2.23e-05 (Chi-square test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
8Q LOSS CNV 0 0 11 1 0
8Q LOSS WILD-TYPE 290 40 128 16 6

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

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.000302 (Fisher's exact test), Q value = 0.18

Table S127.  Gene #55: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
8Q LOSS CNV 11 0 0
8Q LOSS WILD-TYPE 196 144 132

Figure S127.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 2.63e-29 (Chi-square test), Q value = 2.2e-26

Table S128.  Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
9P LOSS CNV 2 11 61 2 0
9P LOSS WILD-TYPE 288 29 78 15 6

Figure S128.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1.81e-06 (Fisher's exact test), Q value = 0.0013

Table S129.  Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
9P LOSS CNV 36 19 8
9P LOSS WILD-TYPE 107 65 142

Figure S129.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 2.12e-12 (Fisher's exact test), Q value = 1.7e-09

Table S130.  Gene #56: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
9P LOSS CNV 41 3 3
9P LOSS WILD-TYPE 101 104 110

Figure S130.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.6e-15 (Fisher's exact test), Q value = 6.2e-12

Table S131.  Gene #56: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
9P LOSS CNV 0 1 3 43
9P LOSS WILD-TYPE 65 91 62 97

Figure S131.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1.37e-09 (Fisher's exact test), Q value = 1.1e-06

Table S132.  Gene #56: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
9P LOSS CNV 55 15 4
9P LOSS WILD-TYPE 152 129 128

Figure S132.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.19e-08 (Fisher's exact test), Q value = 9e-06

Table S133.  Gene #56: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
9P LOSS CNV 14 4 4 52
9P LOSS WILD-TYPE 179 75 23 132

Figure S133.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.027

Table S134.  Gene #57: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
9Q LOSS CNV 0 0 7
9Q LOSS WILD-TYPE 19 19 8

Figure S134.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1.53e-37 (Chi-square test), Q value = 1.3e-34

Table S135.  Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
9Q LOSS CNV 3 13 75 1 1
9Q LOSS WILD-TYPE 287 27 64 16 5

Figure S135.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 4.84e-07 (Fisher's exact test), Q value = 0.00035

Table S136.  Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
9Q LOSS CNV 46 21 12
9Q LOSS WILD-TYPE 97 63 138

Figure S136.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 2.56e-13 (Fisher's exact test), Q value = 2.1e-10

Table S137.  Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
9Q LOSS CNV 48 4 5
9Q LOSS WILD-TYPE 94 103 108

Figure S137.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.82e-16 (Fisher's exact test), Q value = 2.3e-13

Table S138.  Gene #57: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
9Q LOSS CNV 0 2 5 50
9Q LOSS WILD-TYPE 65 90 60 90

Figure S138.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 2.09e-12 (Fisher's exact test), Q value = 1.7e-09

Table S139.  Gene #57: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
9Q LOSS CNV 69 16 6
9Q LOSS WILD-TYPE 138 128 126

Figure S139.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.83e-10 (Fisher's exact test), Q value = 3e-07

Table S140.  Gene #57: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
9Q LOSS CNV 15 8 6 62
9Q LOSS WILD-TYPE 178 71 21 122

Figure S140.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 4e-11 (Chi-square test), Q value = 3.2e-08

Table S141.  Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
10P LOSS CNV 0 1 22 0 0
10P LOSS WILD-TYPE 290 39 117 17 6

Figure S141.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.000323 (Fisher's exact test), Q value = 0.2

Table S142.  Gene #58: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
10P LOSS CNV 15 4 1
10P LOSS WILD-TYPE 128 80 149

Figure S142.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.0086

Table S143.  Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
10P LOSS CNV 20 1 1
10P LOSS WILD-TYPE 187 143 131

Figure S143.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 2.94e-10 (Chi-square test), Q value = 2.3e-07

Table S144.  Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
10Q LOSS CNV 1 1 22 0 0
10Q LOSS WILD-TYPE 289 39 117 17 6

Figure S144.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.1

Table S145.  Gene #59: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
10Q LOSS CNV 16 5 1
10Q LOSS WILD-TYPE 127 79 149

Figure S145.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.13

Table S146.  Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
10Q LOSS CNV 20 2 2
10Q LOSS WILD-TYPE 187 142 130

Figure S146.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1.44e-21 (Chi-square test), Q value = 1.2e-18

Table S147.  Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
11P LOSS CNV 1 4 45 1 2
11P LOSS WILD-TYPE 289 36 94 16 4

Figure S147.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 8.9e-07 (Fisher's exact test), Q value = 0.00064

Table S148.  Gene #60: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
11P LOSS CNV 30 14 4
11P LOSS WILD-TYPE 113 70 146

Figure S148.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 4.46e-08 (Fisher's exact test), Q value = 3.3e-05

Table S149.  Gene #60: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
11P LOSS CNV 24 0 3
11P LOSS WILD-TYPE 118 107 110

Figure S149.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.6e-07 (Fisher's exact test), Q value = 0.00019

Table S150.  Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
11P LOSS CNV 1 0 2 24
11P LOSS WILD-TYPE 64 92 63 116

Figure S150.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1.99e-08 (Fisher's exact test), Q value = 1.5e-05

Table S151.  Gene #60: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
11P LOSS CNV 42 7 3
11P LOSS WILD-TYPE 165 137 129

Figure S151.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-06 (Fisher's exact test), Q value = 0.0014

Table S152.  Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
11P LOSS CNV 7 5 3 37
11P LOSS WILD-TYPE 186 74 24 147

Figure S152.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1.15e-15 (Chi-square test), Q value = 9.5e-13

Table S153.  Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
11Q LOSS CNV 1 6 35 1 2
11Q LOSS WILD-TYPE 289 34 104 16 4

Figure S153.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 7.9e-05 (Fisher's exact test), Q value = 0.051

Table S154.  Gene #61: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
11Q LOSS CNV 26 12 5
11Q LOSS WILD-TYPE 117 72 145

Figure S154.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.000397 (Fisher's exact test), Q value = 0.24

Table S155.  Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
11Q LOSS CNV 17 2 2
11Q LOSS WILD-TYPE 125 105 111

Figure S155.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.07e-06 (Fisher's exact test), Q value = 0.0056

Table S156.  Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
11Q LOSS CNV 1 0 1 19
11Q LOSS WILD-TYPE 64 92 64 121

Figure S156.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 2.54e-06 (Fisher's exact test), Q value = 0.0018

Table S157.  Gene #61: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
11Q LOSS CNV 35 7 3
11Q LOSS WILD-TYPE 172 137 129

Figure S157.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S158.  Gene #61: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
11Q LOSS CNV 8 4 2 31
11Q LOSS WILD-TYPE 185 75 25 153

Figure S158.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 3.86e-11 (Chi-square test), Q value = 3.1e-08

Table S159.  Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
12P LOSS CNV 0 2 23 0 0
12P LOSS WILD-TYPE 290 38 116 17 6

Figure S159.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.1

Table S160.  Gene #62: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
12P LOSS CNV 16 5 1
12P LOSS WILD-TYPE 127 79 149

Figure S160.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 3.62e-05 (Fisher's exact test), Q value = 0.024

Table S161.  Gene #62: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
12P LOSS CNV 12 0 0
12P LOSS WILD-TYPE 130 107 113

Figure S161.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 9.52e-08 (Fisher's exact test), Q value = 7e-05

Table S162.  Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
12P LOSS CNV 23 1 0
12P LOSS WILD-TYPE 184 143 132

Figure S162.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.34e-06 (Fisher's exact test), Q value = 0.003

Table S163.  Gene #62: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
12P LOSS CNV 1 1 1 21
12P LOSS WILD-TYPE 192 78 26 163

Figure S163.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000374 (Fisher's exact test), Q value = 0.23

Table S164.  Gene #62: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
12P LOSS CNV 1 20 0
12P LOSS WILD-TYPE 116 177 45

Figure S164.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1.23e-09 (Chi-square test), Q value = 9.5e-07

Table S165.  Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
12Q LOSS CNV 0 0 18 0 0
12Q LOSS WILD-TYPE 290 40 121 17 6

Figure S165.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 9.44e-05 (Fisher's exact test), Q value = 0.06

Table S166.  Gene #63: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
12Q LOSS CNV 13 3 0
12Q LOSS WILD-TYPE 130 81 150

Figure S166.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00089

Table S167.  Gene #63: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
12Q LOSS CNV 17 0 0
12Q LOSS WILD-TYPE 190 144 132

Figure S167.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.67e-06 (Fisher's exact test), Q value = 0.0012

Table S168.  Gene #63: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
12Q LOSS CNV 0 0 0 17
12Q LOSS WILD-TYPE 193 79 27 167

Figure S168.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 2.43e-18 (Chi-square test), Q value = 2e-15

Table S169.  Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
13Q LOSS CNV 5 15 39 0 1
13Q LOSS WILD-TYPE 285 25 100 17 5

Figure S169.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.068

Table S170.  Gene #64: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
13Q LOSS CNV 31 14 8
13Q LOSS WILD-TYPE 112 70 142

Figure S170.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.000395 (Fisher's exact test), Q value = 0.24

Table S171.  Gene #64: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
13Q LOSS CNV 23 3 6
13Q LOSS WILD-TYPE 119 104 107

Figure S171.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.89e-06 (Fisher's exact test), Q value = 0.0027

Table S172.  Gene #64: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
13Q LOSS CNV 3 1 2 26
13Q LOSS WILD-TYPE 62 91 63 114

Figure S172.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 7.27e-05 (Fisher's exact test), Q value = 0.047

Table S173.  Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
13Q LOSS CNV 41 10 8
13Q LOSS WILD-TYPE 166 134 124

Figure S173.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000188 (Fisher's exact test), Q value = 0.12

Table S174.  Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
13Q LOSS CNV 11 7 6 35
13Q LOSS WILD-TYPE 182 72 21 149

Figure S174.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 8.94e-17 (Chi-square test), Q value = 7.4e-14

Table S175.  Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
14Q LOSS CNV 0 4 35 1 2
14Q LOSS WILD-TYPE 290 36 104 16 4

Figure S175.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1.06e-09 (Fisher's exact test), Q value = 8.2e-07

Table S176.  Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
14Q LOSS CNV 27 5 0
14Q LOSS WILD-TYPE 116 79 150

Figure S176.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 3.38e-08 (Fisher's exact test), Q value = 2.5e-05

Table S177.  Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
14Q LOSS CNV 23 0 2
14Q LOSS WILD-TYPE 119 107 111

Figure S177.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.95e-07 (Fisher's exact test), Q value = 0.00014

Table S178.  Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
14Q LOSS CNV 1 0 1 23
14Q LOSS WILD-TYPE 64 92 64 117

Figure S178.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 3.34e-09 (Fisher's exact test), Q value = 2.6e-06

Table S179.  Gene #65: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
14Q LOSS CNV 35 1 4
14Q LOSS WILD-TYPE 172 143 128

Figure S179.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.82e-12 (Fisher's exact test), Q value = 7.9e-09

Table S180.  Gene #65: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
14Q LOSS CNV 0 4 1 35
14Q LOSS WILD-TYPE 193 75 26 149

Figure S180.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.03e-05 (Fisher's exact test), Q value = 0.014

Table S181.  Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
14Q LOSS CNV 26 1 5
14Q LOSS WILD-TYPE 143 115 69

Figure S181.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.89e-05 (Fisher's exact test), Q value = 0.032

Table S182.  Gene #65: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
14Q LOSS CNV 1 28 3
14Q LOSS WILD-TYPE 116 169 42

Figure S182.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.13

Table S183.  Gene #66: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
15Q LOSS CNV 0 0 6
15Q LOSS WILD-TYPE 19 19 9

Figure S183.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 4.68e-35 (Chi-square test), Q value = 4e-32

Table S184.  Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
15Q LOSS CNV 1 10 67 0 3
15Q LOSS WILD-TYPE 289 30 72 17 3

Figure S184.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 2.97e-13 (Fisher's exact test), Q value = 2.4e-10

Table S185.  Gene #66: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
15Q LOSS CNV 50 17 4
15Q LOSS WILD-TYPE 93 67 146

Figure S185.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 7.92e-10 (Fisher's exact test), Q value = 6.1e-07

Table S186.  Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
15Q LOSS CNV 36 2 5
15Q LOSS WILD-TYPE 106 105 108

Figure S186.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-10 (Fisher's exact test), Q value = 8.4e-08

Table S187.  Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
15Q LOSS CNV 1 1 4 37
15Q LOSS WILD-TYPE 64 91 61 103

Figure S187.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 5.22e-15 (Fisher's exact test), Q value = 4.3e-12

Table S188.  Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
15Q LOSS CNV 66 7 6
15Q LOSS WILD-TYPE 141 137 126

Figure S188.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.07e-16 (Fisher's exact test), Q value = 8.9e-14

Table S189.  Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
15Q LOSS CNV 4 8 6 61
15Q LOSS WILD-TYPE 189 71 21 123

Figure S189.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00075

Table S190.  Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
15Q LOSS CNV 48 6 16
15Q LOSS WILD-TYPE 121 110 58

Figure S190.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.04e-08 (Fisher's exact test), Q value = 2.3e-05

Table S191.  Gene #66: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
15Q LOSS CNV 5 58 7
15Q LOSS WILD-TYPE 112 139 38

Figure S191.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 2.82e-31 (Chi-square test), Q value = 2.4e-28

Table S192.  Gene #67: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
16P LOSS CNV 2 6 61 0 0
16P LOSS WILD-TYPE 288 34 78 17 6

Figure S192.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 2.27e-09 (Fisher's exact test), Q value = 1.7e-06

Table S193.  Gene #67: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
16P LOSS CNV 38 17 4
16P LOSS WILD-TYPE 105 67 146

Figure S193.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 7.52e-10 (Fisher's exact test), Q value = 5.8e-07

Table S194.  Gene #67: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
16P LOSS CNV 35 2 4
16P LOSS WILD-TYPE 107 105 109

Figure S194.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.47e-09 (Fisher's exact test), Q value = 1.1e-06

Table S195.  Gene #67: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
16P LOSS CNV 3 1 2 35
16P LOSS WILD-TYPE 62 91 63 105

Figure S195.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1.47e-09 (Fisher's exact test), Q value = 1.1e-06

Table S196.  Gene #67: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
16P LOSS CNV 52 6 8
16P LOSS WILD-TYPE 155 138 124

Figure S196.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.36e-10 (Fisher's exact test), Q value = 1.1e-07

Table S197.  Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
16P LOSS CNV 6 7 4 49
16P LOSS WILD-TYPE 187 72 23 135

Figure S197.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.56e-05 (Fisher's exact test), Q value = 0.017

Table S198.  Gene #67: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
16P LOSS CNV 38 5 15
16P LOSS WILD-TYPE 131 111 59

Figure S198.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.82e-05 (Fisher's exact test), Q value = 0.012

Table S199.  Gene #67: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
16P LOSS CNV 6 47 5
16P LOSS WILD-TYPE 111 150 40

Figure S199.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 5.94e-40 (Chi-square test), Q value = 5.1e-37

Table S200.  Gene #68: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
16Q LOSS CNV 13 10 87 0 0
16Q LOSS WILD-TYPE 277 30 52 17 6

Figure S200.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 2.1e-11 (Fisher's exact test), Q value = 1.7e-08

Table S201.  Gene #68: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
16Q LOSS CNV 58 25 11
16Q LOSS WILD-TYPE 85 59 139

Figure S201.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1.01e-11 (Fisher's exact test), Q value = 8.1e-09

Table S202.  Gene #68: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
16Q LOSS CNV 54 6 11
16Q LOSS WILD-TYPE 88 101 102

Figure S202.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.34e-10 (Fisher's exact test), Q value = 1.8e-07

Table S203.  Gene #68: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
16Q LOSS CNV 9 4 6 52
16Q LOSS WILD-TYPE 56 88 59 88

Figure S203.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1.07e-11 (Fisher's exact test), Q value = 8.6e-09

Table S204.  Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
16Q LOSS CNV 77 12 17
16Q LOSS WILD-TYPE 130 132 115

Figure S204.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.9e-11 (Fisher's exact test), Q value = 1.5e-08

Table S205.  Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
16Q LOSS CNV 18 11 5 72
16Q LOSS WILD-TYPE 175 68 22 112

Figure S205.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.31e-06 (Fisher's exact test), Q value = 0.0037

Table S206.  Gene #68: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
16Q LOSS CNV 59 12 21
16Q LOSS WILD-TYPE 110 104 53

Figure S206.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.9e-06 (Fisher's exact test), Q value = 0.0048

Table S207.  Gene #68: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
16Q LOSS CNV 13 69 10
16Q LOSS WILD-TYPE 104 128 35

Figure S207.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 8.66e-53 (Chi-square test), Q value = 7.4e-50

Table S208.  Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
17P LOSS CNV 3 9 93 0 0
17P LOSS WILD-TYPE 287 31 46 17 6

Figure S208.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 7.43e-13 (Fisher's exact test), Q value = 6e-10

Table S209.  Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
17P LOSS CNV 61 18 10
17P LOSS WILD-TYPE 82 66 140

Figure S209.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1.6e-20 (Fisher's exact test), Q value = 1.3e-17

Table S210.  Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
17P LOSS CNV 58 2 4
17P LOSS WILD-TYPE 84 105 109

Figure S210.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.15e-21 (Fisher's exact test), Q value = 1.8e-18

Table S211.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
17P LOSS CNV 1 0 5 58
17P LOSS WILD-TYPE 64 92 60 82

Figure S211.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 4.87e-17 (Fisher's exact test), Q value = 4e-14

Table S212.  Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
17P LOSS CNV 81 15 6
17P LOSS WILD-TYPE 126 129 126

Figure S212.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.92e-15 (Fisher's exact test), Q value = 2.4e-12

Table S213.  Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
17P LOSS CNV 15 7 5 75
17P LOSS WILD-TYPE 178 72 22 109

Figure S213.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.51e-05 (Fisher's exact test), Q value = 0.017

Table S214.  Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
17P LOSS CNV 56 12 19
17P LOSS WILD-TYPE 113 104 55

Figure S214.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.09e-05 (Fisher's exact test), Q value = 0.014

Table S215.  Gene #69: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
17P LOSS CNV 12 64 11
17P LOSS WILD-TYPE 105 133 34

Figure S215.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1.48e-29 (Chi-square test), Q value = 1.3e-26

Table S216.  Gene #70: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
17Q LOSS CNV 1 9 58 0 0
17Q LOSS WILD-TYPE 289 31 81 17 6

Figure S216.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.022

Table S217.  Gene #70: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
17Q LOSS CNV 35 14 9
17Q LOSS WILD-TYPE 108 70 141

Figure S217.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 4.28e-09 (Fisher's exact test), Q value = 3.3e-06

Table S218.  Gene #70: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
17Q LOSS CNV 33 2 4
17Q LOSS WILD-TYPE 109 105 109

Figure S218.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.95e-11 (Fisher's exact test), Q value = 1.6e-08

Table S219.  Gene #70: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
17Q LOSS CNV 1 0 3 35
17Q LOSS WILD-TYPE 64 92 62 105

Figure S219.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 2.71e-07 (Fisher's exact test), Q value = 2e-04

Table S220.  Gene #70: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
17Q LOSS CNV 48 11 6
17Q LOSS WILD-TYPE 159 133 126

Figure S220.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.5e-07 (Fisher's exact test), Q value = 4e-04

Table S221.  Gene #70: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
17Q LOSS CNV 11 5 5 44
17Q LOSS WILD-TYPE 182 74 22 140

Figure S221.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 3.15e-12 (Chi-square test), Q value = 2.5e-09

Table S222.  Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
18P LOSS CNV 1 9 25 0 1
18P LOSS WILD-TYPE 289 31 114 17 5

Figure S222.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.013

Table S223.  Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
18P LOSS CNV 22 6 2
18P LOSS WILD-TYPE 121 78 148

Figure S223.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000172 (Fisher's exact test), Q value = 0.11

Table S224.  Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
18P LOSS CNV 1 0 4 17
18P LOSS WILD-TYPE 64 92 61 123

Figure S224.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 9.75e-18 (Chi-square test), Q value = 8.1e-15

Table S225.  Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
18Q LOSS CNV 1 9 38 0 1
18Q LOSS WILD-TYPE 289 31 101 17 5

Figure S225.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1.92e-06 (Fisher's exact test), Q value = 0.0014

Table S226.  Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
18Q LOSS CNV 30 10 4
18Q LOSS WILD-TYPE 113 74 146

Figure S226.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 3.87e-06 (Fisher's exact test), Q value = 0.0027

Table S227.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
18Q LOSS CNV 23 1 4
18Q LOSS WILD-TYPE 119 106 109

Figure S227.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.65e-07 (Fisher's exact test), Q value = 0.00041

Table S228.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
18Q LOSS CNV 1 0 3 24
18Q LOSS WILD-TYPE 64 92 62 116

Figure S228.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 3.04e-06 (Fisher's exact test), Q value = 0.0021

Table S229.  Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
18Q LOSS CNV 37 5 6
18Q LOSS WILD-TYPE 170 139 126

Figure S229.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.59e-07 (Fisher's exact test), Q value = 0.00019

Table S230.  Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
18Q LOSS CNV 4 6 6 32
18Q LOSS WILD-TYPE 189 73 21 152

Figure S230.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 4.63e-12 (Chi-square test), Q value = 3.7e-09

Table S231.  Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
19P LOSS CNV 0 7 26 1 0
19P LOSS WILD-TYPE 290 33 113 16 6

Figure S231.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 9.19e-08 (Fisher's exact test), Q value = 6.8e-05

Table S232.  Gene #73: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
19P LOSS CNV 25 4 1
19P LOSS WILD-TYPE 118 80 149

Figure S232.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1.84e-05 (Fisher's exact test), Q value = 0.013

Table S233.  Gene #73: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
19P LOSS CNV 16 0 2
19P LOSS WILD-TYPE 126 107 111

Figure S233.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.84e-06 (Fisher's exact test), Q value = 0.0054

Table S234.  Gene #73: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
19P LOSS CNV 1 0 0 17
19P LOSS WILD-TYPE 64 92 65 123

Figure S234.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.007

Table S235.  Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
19P LOSS CNV 27 2 4
19P LOSS WILD-TYPE 180 142 128

Figure S235.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.41e-07 (Fisher's exact test), Q value = 0.00046

Table S236.  Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
19P LOSS CNV 1 4 3 25
19P LOSS WILD-TYPE 192 75 24 159

Figure S236.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.18e-06 (Fisher's exact test), Q value = 0.0056

Table S237.  Gene #73: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
19P LOSS CNV 26 1 3
19P LOSS WILD-TYPE 143 115 71

Figure S237.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 1.79e-08 (Chi-square test), Q value = 1.4e-05

Table S238.  Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
19Q LOSS CNV 1 6 20 1 0
19Q LOSS WILD-TYPE 289 34 119 16 6

Figure S238.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 5.03e-05 (Fisher's exact test), Q value = 0.033

Table S239.  Gene #74: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
19Q LOSS CNV 18 5 1
19Q LOSS WILD-TYPE 125 79 149

Figure S239.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.01

Table S240.  Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
19Q LOSS CNV 1 3 3 20
19Q LOSS WILD-TYPE 192 76 24 164

Figure S240.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000124 (Fisher's exact test), Q value = 0.079

Table S241.  Gene #74: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
19Q LOSS CNV 21 1 2
19Q LOSS WILD-TYPE 148 115 72

Figure S241.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 0.000122 (Chi-square test), Q value = 0.078

Table S242.  Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
20P LOSS CNV 1 2 12 0 0
20P LOSS WILD-TYPE 289 38 127 17 6

Figure S242.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 6.47e-08 (Chi-square test), Q value = 4.8e-05

Table S243.  Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
21Q LOSS CNV 3 4 23 1 1
21Q LOSS WILD-TYPE 287 36 116 16 5

Figure S243.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.093

Table S244.  Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
21Q LOSS CNV 15 0 3
21Q LOSS WILD-TYPE 127 107 110

Figure S244.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.43e-05 (Fisher's exact test), Q value = 0.029

Table S245.  Gene #77: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
21Q LOSS CNV 2 7 0 21
21Q LOSS WILD-TYPE 191 72 27 163

Figure S245.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.14

Table S246.  Gene #77: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 116 74
21Q LOSS CNV 21 1 3
21Q LOSS WILD-TYPE 148 115 71

Figure S246.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000203 (Fisher's exact test), Q value = 0.13

Table S247.  Gene #77: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 117 197 45
21Q LOSS CNV 1 23 1
21Q LOSS WILD-TYPE 116 174 44

Figure S247.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1.41e-36 (Chi-square test), Q value = 1.2e-33

Table S248.  Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
22Q LOSS CNV 1 13 71 1 1
22Q LOSS WILD-TYPE 289 27 68 16 5

Figure S248.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 3.23e-08 (Fisher's exact test), Q value = 2.4e-05

Table S249.  Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 84 150
22Q LOSS CNV 46 22 10
22Q LOSS WILD-TYPE 97 62 140

Figure S249.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 4.88e-11 (Fisher's exact test), Q value = 3.9e-08

Table S250.  Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
22Q LOSS CNV 41 3 5
22Q LOSS WILD-TYPE 101 104 108

Figure S250.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.29e-14 (Fisher's exact test), Q value = 2.7e-11

Table S251.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
22Q LOSS CNV 1 1 3 44
22Q LOSS WILD-TYPE 64 91 62 96

Figure S251.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 9.64e-11 (Fisher's exact test), Q value = 7.6e-08

Table S252.  Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
22Q LOSS CNV 64 14 7
22Q LOSS WILD-TYPE 143 130 125

Figure S252.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.01e-09 (Fisher's exact test), Q value = 7.8e-07

Table S253.  Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
22Q LOSS CNV 13 8 6 58
22Q LOSS WILD-TYPE 180 71 21 126

Figure S253.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Xq loss' versus 'CN_CNMF'

P value = 2.97e-07 (Chi-square test), Q value = 0.00022

Table S254.  Gene #79: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
XQ LOSS CNV 0 1 16 1 0
XQ LOSS WILD-TYPE 290 39 123 16 6

Figure S254.  Get High-res Image Gene #79: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'Xq loss' versus 'MIRSEQ_CNMF'

P value = 0.000233 (Fisher's exact test), Q value = 0.14

Table S255.  Gene #79: 'Xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
XQ LOSS CNV 16 1 1
XQ LOSS WILD-TYPE 191 143 131

Figure S255.  Get High-res Image Gene #79: 'Xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.015

Table S256.  Gene #79: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
XQ LOSS CNV 0 1 1 16
XQ LOSS WILD-TYPE 193 78 26 168

Figure S256.  Get High-res Image Gene #79: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Molecular subtypes file = UCEC-TP.transferedmergedcluster.txt

  • Number of patients = 492

  • Number of significantly arm-level cnvs = 79

  • 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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