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 45 arm-level results and 10 molecular subtypes across 494 patients, 132 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF'.

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

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

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 11q gain cnv correlated to 'CN_CNMF'.

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

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

  • 13q gain cnv correlated to 'CN_CNMF'.

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

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

  • 16q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 2p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 8q loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

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

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 45 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 132 significant findings detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
7q gain 0 (0%) 475 1.95e-23
(8.15e-21) 		2.06e-05
(0.00732) 		0.805
(1.00) 		0.00206
(0.543) 		7.11e-05
(0.024) 		1.23e-05
(0.00451) 		0.000332
(0.102) 		2.25e-05
(0.00796) 		7.82e-05
(0.0264) 		1.63e-05
(0.00595)
12p gain 0 (0%) 483 1.08e-12
(4.45e-10) 		4.68e-06
(0.00176) 		1
(1.00) 		0.0281
(1.00) 		2.32e-05
(0.0082) 		4.9e-06
(0.00184) 		3.75e-05
(0.0131) 		1.29e-05
(0.00474) 		0.000147
(0.0484) 		9.1e-06
(0.00338)
12q gain 0 (0%) 482 1.34e-12
(5.47e-10) 		1.51e-06
(0.000589) 		1
(1.00) 		0.0281
(1.00) 		7.58e-06
(0.00283) 		1.57e-06
(0.000607) 		1.21e-05
(0.00446) 		3.57e-06
(0.00136) 		5.02e-05
(0.0173) 		2.43e-06
(0.000931)
16p gain 0 (0%) 482 5.86e-14
(2.42e-11) 		1.21e-05
(0.00446) 		0.795
(1.00) 		0.0363
(1.00) 		0.000225
(0.071) 		4.56e-05
(0.0158) 		0.000181
(0.0591) 		4.67e-05
(0.0162) 		0.000388
(0.117) 		2.42e-05
(0.00851)
17p gain 0 (0%) 482 1.99e-09
(8.02e-07) 		1.51e-06
(0.000589) 		0.773
(1.00) 		0.0122
(1.00) 		7.58e-06
(0.00283) 		1.57e-06
(0.000607) 		1.21e-05
(0.00446) 		3.57e-06
(0.00136) 		5.02e-05
(0.0173) 		2.43e-06
(0.000931)
17q gain 0 (0%) 481 3.8e-09
(1.53e-06) 		3.34e-07
(0.000132) 		0.795
(1.00) 		0.0193
(1.00) 		2.22e-06
(0.000855) 		3.35e-07
(0.000132) 		3.86e-06
(0.00145) 		9.76e-07
(0.000383) 		1.69e-05
(0.00617) 		6.38e-07
(0.000251)
2p loss 0 (0%) 486 5.2e-09
(2.08e-06) 		0.000139
(0.0461) 		1
(1.00) 		0.079
(1.00) 		0.000645
(0.189) 		0.000218
(0.0697) 		6.43e-05
(0.022) 		1.99e-05
(0.00709) 		0.000242
(0.0759) 		1.75e-05
(0.00635)
22q loss 0 (0%) 429 4.98e-57
(2.08e-54) 		4.44e-05
(0.0155) 		0.0578
(1.00) 		0.244
(1.00) 		6.84e-11
(2.77e-08) 		8.07e-11
(3.26e-08) 		3.24e-05
(0.0114) 		5.3e-06
(0.00198) 		1.56e-07
(6.17e-05) 		3.09e-06
(0.00118)
5q gain 0 (0%) 480 2.84e-18
(1.17e-15) 		4.86e-05
(0.0168) 		1
(1.00) 		0.0281
(1.00) 		0.000231
(0.0729) 		8.87e-05
(0.0296) 		0.000436
(0.131) 		2.79e-05
(0.00979) 		0.00155
(0.422) 		2.13e-05
(0.00756)
7p gain 0 (0%) 477 1.76e-22
(7.34e-20) 		0.000149
(0.0488) 		0.835
(1.00) 		0.0106
(1.00) 		0.000536
(0.159) 		0.000114
(0.038) 		0.00261
(0.674) 		0.000255
(0.0794) 		0.000527
(0.157) 		0.000184
(0.06)
2q loss 0 (0%) 487 3.94e-09
(1.58e-06) 		0.000343
(0.105) 		0.839
(1.00) 		0.0521
(1.00) 		0.00153
(0.419) 		0.000675
(0.196) 		0.000219
(0.0697) 		7.85e-05
(0.0264) 		0.000758
(0.218) 		7.02e-05
(0.0239)
15q loss 0 (0%) 487 0.000653
(0.19) 		0.000343
(0.105) 		0.457
(1.00) 		0.25
(1.00) 		0.00153
(0.419) 		0.000675
(0.196) 		0.000219
(0.0697) 		7.85e-05
(0.0264) 		0.000758
(0.218) 		7.02e-05
(0.0239)
14q gain 0 (0%) 486 5.2e-09
(2.08e-06) 		0.000139
(0.0461) 		1
(1.00) 		0.25
(1.00) 		0.000645
(0.189) 		0.000218
(0.0697) 		0.00106
(0.303) 		0.000573
(0.17) 		0.00344
(0.864) 		0.000587
(0.173)
16q gain 0 (0%) 484 6.03e-13
(2.48e-10) 		6.6e-05
(0.0225) 		1
(1.00) 		0.126
(1.00) 		0.00181
(0.491) 		0.000415
(0.125) 		0.0014
(0.388) 		0.000637
(0.187) 		0.00278
(0.712) 		0.0005
(0.15)
5p gain 0 (0%) 477 7.68e-20
(3.19e-17) 		0.000366
(0.111) 		0.835
(1.00) 		0.107
(1.00) 		0.00286
(0.729) 		0.000995
(0.285) 		0.00357
(0.893) 		0.000204
(0.066) 		0.00688
(1.00) 		0.000131
(0.0435)
20p gain 0 (0%) 485 1.17e-11
(4.77e-09) 		0.000251
(0.0787) 		1
(1.00) 		0.079
(1.00) 		0.00467
(1.00) 		0.00183
(0.493) 		0.00382
(0.95) 		0.00188
(0.503) 		0.00566
(1.00) 		0.00149
(0.412)
20q gain 0 (0%) 485 1.17e-11
(4.77e-09) 		0.000251
(0.0787) 		1
(1.00) 		0.079
(1.00) 		0.00467
(1.00) 		0.00183
(0.493) 		0.00382
(0.95) 		0.00188
(0.503) 		0.00566
(1.00) 		0.00149
(0.412)
11q loss 0 (0%) 485 3.28e-06
(0.00125) 		0.0106
(1.00) 		0.321
(1.00) 		0.794
(1.00) 		0.0185
(1.00) 		0.017
(1.00) 		0.000352
(0.107) 		0.00336
(0.846) 		0.00122
(0.34) 		0.00275
(0.706)
1q gain 0 (0%) 473 3.68e-06
(0.00139) 		0.0848
(1.00) 		0.00319
(0.808) 		0.0931
(1.00) 		0.0107
(1.00) 		0.00403
(0.99) 		0.233
(1.00) 		0.203
(1.00) 		0.185
(1.00) 		0.0917
(1.00)
4p gain 0 (0%) 490 1.89e-05
(0.00685) 		0.0149
(1.00) 		0.0444
(1.00) 		0.0219
(1.00) 		0.0755
(1.00) 		0.0676
(1.00) 		0.129
(1.00) 		0.0942
(1.00)
4q gain 0 (0%) 490 1.89e-05
(0.00685) 		0.0149
(1.00) 		0.0444
(1.00) 		0.0219
(1.00) 		0.0755
(1.00) 		0.0676
(1.00) 		0.129
(1.00) 		0.0942
(1.00)
11q gain 0 (0%) 490 0.000207
(0.0668) 		0.0149
(1.00) 		0.0444
(1.00) 		0.0219
(1.00) 		0.00833
(1.00) 		0.00467
(1.00) 		0.0227
(1.00) 		0.00439
(1.00)
13q gain 0 (0%) 491 0.0003
(0.0929) 		0.0585
(1.00) 		0.0985
(1.00) 		0.0788
(1.00) 		0.207
(1.00) 		0.355
(1.00) 		0.323
(1.00) 		0.27
(1.00)
19p gain 0 (0%) 490 1.89e-05
(0.00685) 		0.0149
(1.00) 		0.0444
(1.00) 		0.0219
(1.00) 		0.00833
(1.00) 		0.00467
(1.00) 		0.0227
(1.00) 		0.00439
(1.00)
19q gain 0 (0%) 489 1.16e-06
(0.000453) 		0.00581
(1.00) 		0.636
(1.00) 		0.0523
(1.00) 		0.0161
(1.00) 		0.0069
(1.00) 		0.00249
(0.648) 		0.0012
(0.338) 		0.00735
(1.00) 		0.00111
(0.316)
1p loss 0 (0%) 491 0.0003
(0.0929) 		0.582
(1.00) 		0.493
(1.00) 		0.183
(1.00) 		0.207
(1.00) 		0.355
(1.00) 		0.323
(1.00) 		0.27
(1.00)
3q loss 0 (0%) 491 0.0003
(0.0929) 		0.0585
(1.00) 		0.0985
(1.00) 		0.0788
(1.00) 		0.0278
(1.00) 		0.018
(1.00) 		0.0701
(1.00) 		0.0172
(1.00)
8p loss 0 (0%) 490 1.89e-05
(0.00685) 		0.0149
(1.00) 		0.0444
(1.00) 		0.0219
(1.00) 		0.00833
(1.00) 		0.00467
(1.00) 		0.0227
(1.00) 		0.00439
(1.00)
8q loss 0 (0%) 490 1.89e-05
(0.00685) 		0.0149
(1.00) 		0.0444
(1.00) 		0.0219
(1.00) 		0.00833
(1.00) 		0.00467
(1.00) 		0.0227
(1.00) 		0.00439
(1.00)
9p loss 0 (0%) 482 2.13e-11
(8.66e-09) 		0.0712
(1.00) 		0.56
(1.00) 		0.204
(1.00) 		0.0924
(1.00) 		0.134
(1.00) 		0.0506
(1.00) 		0.0401
(1.00) 		0.0792
(1.00) 		0.0276
(1.00)
9q loss 0 (0%) 477 1.59e-13
(6.56e-11) 		0.111
(1.00) 		0.209
(1.00) 		0.00396
(0.977) 		0.182
(1.00) 		0.231
(1.00) 		0.0759
(1.00) 		0.0878
(1.00) 		0.108
(1.00) 		0.0555
(1.00)
10p loss 0 (0%) 488 6.87e-08
(2.73e-05) 		0.0263
(1.00) 		0.0509
(1.00) 		0.0183
(1.00) 		0.00929
(1.00) 		0.00658
(1.00) 		0.0259
(1.00) 		0.00664
(1.00)
10q loss 0 (0%) 489 1.16e-06
(0.000453) 		0.0757
(1.00) 		0.119
(1.00) 		0.0361
(1.00) 		0.0268
(1.00) 		0.0215
(1.00) 		0.0687
(1.00) 		0.0216
(1.00)
11p loss 0 (0%) 487 7.98e-08
(3.17e-05) 		0.00956
(1.00) 		0.495
(1.00) 		1
(1.00) 		0.00712
(1.00) 		0.0174
(1.00) 		0.00316
(0.804) 		0.00196
(0.522) 		0.00954
(1.00) 		0.00199
(0.528)
18p loss 0 (0%) 490 0.000207
(0.0668) 		0.22
(1.00) 		1
(1.00) 		0.284
(1.00) 		0.242
(1.00) 		0.121
(1.00) 		0.115
(1.00) 		0.037
(1.00) 		0.0227
(1.00) 		0.0402
(1.00)
18q loss 0 (0%) 490 0.000207
(0.0668) 		0.22
(1.00) 		1
(1.00) 		0.284
(1.00) 		0.242
(1.00) 		0.121
(1.00) 		0.115
(1.00) 		0.037
(1.00) 		0.0227
(1.00) 		0.0402
(1.00)
21q loss 0 (0%) 488 0.000191
(0.0621) 		0.0973
(1.00) 		0.384
(1.00) 		0.0523
(1.00) 		0.223
(1.00) 		0.226
(1.00) 		0.0684
(1.00) 		0.0841
(1.00) 		0.0892
(1.00) 		0.0459
(1.00)
11p gain 0 (0%) 489 0.00134
(0.373) 		0.00581
(1.00) 		0.0161
(1.00) 		0.0069
(1.00) 		0.00249
(0.648) 		0.0012
(0.338) 		0.00735
(1.00) 		0.00111
(0.316)
18p gain 0 (0%) 491 0.00246
(0.648) 		0.0585
(1.00) 		0.0985
(1.00) 		0.0788
(1.00) 		0.0278
(1.00) 		0.018
(1.00) 		0.0701
(1.00) 		0.0172
(1.00)
18q gain 0 (0%) 491 0.00246
(0.648) 		0.0585
(1.00) 		0.0985
(1.00) 		0.0788
(1.00) 		0.0278
(1.00) 		0.018
(1.00) 		0.0701
(1.00) 		0.0172
(1.00)
21q gain 0 (0%) 491 0.00246
(0.648) 		0.0585
(1.00) 		0.0985
(1.00) 		0.0788
(1.00) 		0.0278
(1.00) 		0.018
(1.00) 		0.0701
(1.00) 		0.0172
(1.00)
6q loss 0 (0%) 491 0.0219
(1.00) 		0.0585
(1.00) 		0.0985
(1.00) 		0.0788
(1.00) 		0.0278
(1.00) 		0.018
(1.00) 		0.0701
(1.00) 		0.0172
(1.00)
13q loss 0 (0%) 483 0.0122
(1.00) 		0.0243
(1.00) 		0.0774
(1.00) 		1
(1.00) 		0.0233
(1.00) 		0.0183
(1.00) 		0.00902
(1.00) 		0.00997
(1.00) 		0.00684
(1.00) 		0.0107
(1.00)
17p loss 0 (0%) 487 0.00118
(0.333) 		0.525
(1.00) 		1
(1.00) 		0.284
(1.00) 		0.786
(1.00) 		0.887
(1.00) 		0.519
(1.00) 		0.493
(1.00) 		0.9
(1.00) 		0.44
(1.00)
19p loss 0 (0%) 490 0.132
(1.00) 		0.0149
(1.00) 		0.278
(1.00) 		0.364
(1.00) 		0.0444
(1.00) 		0.0219
(1.00) 		0.00833
(1.00) 		0.00467
(1.00) 		0.0227
(1.00) 		0.00439
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 3.68e-06 (Fisher's exact test), Q value = 0.0014

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
1Q GAIN CNV 9 11 1
1Q GAIN WILD-TYPE 25 372 76

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

'4p gain' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0068

Table S2.  Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
4P GAIN CNV 4 0 0
4P GAIN WILD-TYPE 30 383 77

Figure S2.  Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0068

Table S3.  Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
4Q GAIN CNV 4 0 0
4Q GAIN WILD-TYPE 30 383 77

Figure S3.  Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 7.68e-20 (Fisher's exact test), Q value = 3.2e-17

Table S4.  Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
5P GAIN CNV 16 1 0
5P GAIN WILD-TYPE 18 382 77

Figure S4.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.000366 (Fisher's exact test), Q value = 0.11

Table S5.  Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
5P GAIN CNV 12 3 2
5P GAIN WILD-TYPE 139 80 258

Figure S5.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.066

Table S6.  Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
5P GAIN CNV 0 11 6
5P GAIN WILD-TYPE 155 119 202

Figure S6.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000131 (Fisher's exact test), Q value = 0.044

Table S7.  Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
5P GAIN CNV 6 11 0
5P GAIN WILD-TYPE 193 117 166

Figure S7.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 2.84e-18 (Fisher's exact test), Q value = 1.2e-15

Table S8.  Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
5Q GAIN CNV 14 0 0
5Q GAIN WILD-TYPE 20 383 77

Figure S8.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 4.86e-05 (Fisher's exact test), Q value = 0.017

Table S9.  Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
5Q GAIN CNV 12 1 1
5Q GAIN WILD-TYPE 139 82 259

Figure S9.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.000231 (Fisher's exact test), Q value = 0.073

Table S10.  Gene #5: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 150 55 114 161
5Q GAIN CNV 12 0 0 2
5Q GAIN WILD-TYPE 138 55 114 159

Figure S10.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.87e-05 (Fisher's exact test), Q value = 0.03

Table S11.  Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
5Q GAIN CNV 12 2 0 0
5Q GAIN WILD-TYPE 120 210 94 42

Figure S11.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.000436 (Fisher's exact test), Q value = 0.13

Table S12.  Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
5Q GAIN CNV 11 1 2
5Q GAIN WILD-TYPE 139 172 168

Figure S12.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.0098

Table S13.  Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
5Q GAIN CNV 0 11 3
5Q GAIN WILD-TYPE 155 119 205

Figure S13.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.13e-05 (Fisher's exact test), Q value = 0.0076

Table S14.  Gene #5: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
5Q GAIN CNV 3 11 0
5Q GAIN WILD-TYPE 196 117 166

Figure S14.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1.76e-22 (Fisher's exact test), Q value = 7.3e-20

Table S15.  Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
7P GAIN CNV 17 0 0
7P GAIN WILD-TYPE 17 383 77

Figure S15.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.000149 (Fisher's exact test), Q value = 0.049

Table S16.  Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
7P GAIN CNV 13 2 2
7P GAIN WILD-TYPE 138 81 258

Figure S16.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.000536 (Fisher's exact test), Q value = 0.16

Table S17.  Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 150 55 114 161
7P GAIN CNV 13 0 1 2
7P GAIN WILD-TYPE 137 55 113 159

Figure S17.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.038

Table S18.  Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
7P GAIN CNV 13 2 1 0
7P GAIN WILD-TYPE 119 210 93 42

Figure S18.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000255 (Fisher's exact test), Q value = 0.079

Table S19.  Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
7P GAIN CNV 1 12 4
7P GAIN WILD-TYPE 154 118 204

Figure S19.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000527 (Fisher's exact test), Q value = 0.16

Table S20.  Gene #6: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
7P GAIN CNV 13 1 3
7P GAIN WILD-TYPE 150 168 158

Figure S20.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.06

Table S21.  Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
7P GAIN CNV 4 12 1
7P GAIN WILD-TYPE 195 116 165

Figure S21.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1.95e-23 (Fisher's exact test), Q value = 8.1e-21

Table S22.  Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
7Q GAIN CNV 18 0 1
7Q GAIN WILD-TYPE 16 383 76

Figure S22.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 2.06e-05 (Fisher's exact test), Q value = 0.0073

Table S23.  Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
7Q GAIN CNV 15 2 2
7Q GAIN WILD-TYPE 136 81 258

Figure S23.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 7.11e-05 (Fisher's exact test), Q value = 0.024

Table S24.  Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 150 55 114 161
7Q GAIN CNV 15 0 1 2
7Q GAIN WILD-TYPE 135 55 113 159

Figure S24.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0045

Table S25.  Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
7Q GAIN CNV 15 2 1 0
7Q GAIN WILD-TYPE 117 210 93 42

Figure S25.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.000332 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
7Q GAIN CNV 14 2 3
7Q GAIN WILD-TYPE 136 171 167

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

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.008

Table S27.  Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
7Q GAIN CNV 1 14 4
7Q GAIN WILD-TYPE 154 116 204

Figure S27.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.82e-05 (Fisher's exact test), Q value = 0.026

Table S28.  Gene #7: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
7Q GAIN CNV 15 1 3
7Q GAIN WILD-TYPE 148 168 158

Figure S28.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.006

Table S29.  Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
7Q GAIN CNV 4 14 1
7Q GAIN WILD-TYPE 195 114 165

Figure S29.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.067

Table S30.  Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
11Q GAIN CNV 3 0 1
11Q GAIN WILD-TYPE 31 383 76

Figure S30.  Get High-res Image Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.08e-12 (Fisher's exact test), Q value = 4.4e-10

Table S31.  Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
12P GAIN CNV 10 0 1
12P GAIN WILD-TYPE 24 383 76

Figure S31.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 4.68e-06 (Fisher's exact test), Q value = 0.0018

Table S32.  Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
12P GAIN CNV 11 0 0
12P GAIN WILD-TYPE 140 83 260

Figure S32.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.0082

Table S33.  Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 150 55 114 161
12P GAIN CNV 11 0 0 0
12P GAIN WILD-TYPE 139 55 114 161

Figure S33.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.9e-06 (Fisher's exact test), Q value = 0.0018

Table S34.  Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
12P GAIN CNV 11 0 0 0
12P GAIN WILD-TYPE 121 212 94 42

Figure S34.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 3.75e-05 (Fisher's exact test), Q value = 0.013

Table S35.  Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
12P GAIN CNV 10 0 1
12P GAIN WILD-TYPE 140 173 169

Figure S35.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.0047

Table S36.  Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
12P GAIN CNV 0 10 1
12P GAIN WILD-TYPE 155 120 207

Figure S36.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000147 (Fisher's exact test), Q value = 0.048

Table S37.  Gene #10: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
12P GAIN CNV 10 0 1
12P GAIN WILD-TYPE 153 169 160

Figure S37.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.1e-06 (Fisher's exact test), Q value = 0.0034

Table S38.  Gene #10: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
12P GAIN CNV 1 10 0
12P GAIN WILD-TYPE 198 118 166

Figure S38.  Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1.34e-12 (Fisher's exact test), Q value = 5.5e-10

Table S39.  Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
12Q GAIN CNV 10 0 2
12Q GAIN WILD-TYPE 24 383 75

Figure S39.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.00059

Table S40.  Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
12Q GAIN CNV 12 0 0
12Q GAIN WILD-TYPE 139 83 260

Figure S40.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 7.58e-06 (Fisher's exact test), Q value = 0.0028

Table S41.  Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 150 55 114 161
12Q GAIN CNV 12 0 0 0
12Q GAIN WILD-TYPE 138 55 114 161

Figure S41.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.57e-06 (Fisher's exact test), Q value = 0.00061

Table S42.  Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
12Q GAIN CNV 12 0 0 0
12Q GAIN WILD-TYPE 120 212 94 42

Figure S42.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0045

Table S43.  Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
12Q GAIN CNV 11 0 1
12Q GAIN WILD-TYPE 139 173 169

Figure S43.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.57e-06 (Fisher's exact test), Q value = 0.0014

Table S44.  Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
12Q GAIN CNV 0 11 1
12Q GAIN WILD-TYPE 155 119 207

Figure S44.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.02e-05 (Fisher's exact test), Q value = 0.017

Table S45.  Gene #11: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
12Q GAIN CNV 11 0 1
12Q GAIN WILD-TYPE 152 169 160

Figure S45.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.00093

Table S46.  Gene #11: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
12Q GAIN CNV 1 11 0
12Q GAIN WILD-TYPE 198 117 166

Figure S46.  Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.093

Table S47.  Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
13Q GAIN CNV 3 0 0
13Q GAIN WILD-TYPE 31 383 77

Figure S47.  Get High-res Image Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 5.2e-09 (Fisher's exact test), Q value = 2.1e-06

Table S48.  Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
14Q GAIN CNV 7 0 1
14Q GAIN WILD-TYPE 27 383 76

Figure S48.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.046

Table S49.  Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
14Q GAIN CNV 8 0 0
14Q GAIN WILD-TYPE 143 83 260

Figure S49.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.000645 (Fisher's exact test), Q value = 0.19

Table S50.  Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 150 55 114 161
14Q GAIN CNV 8 0 0 0
14Q GAIN WILD-TYPE 142 55 114 161

Figure S50.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.07

Table S51.  Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
14Q GAIN CNV 8 0 0 0
14Q GAIN WILD-TYPE 124 212 94 42

Figure S51.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000573 (Fisher's exact test), Q value = 0.17

Table S52.  Gene #13: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
14Q GAIN CNV 0 7 1
14Q GAIN WILD-TYPE 155 123 207

Figure S52.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000587 (Fisher's exact test), Q value = 0.17

Table S53.  Gene #13: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
14Q GAIN CNV 1 7 0
14Q GAIN WILD-TYPE 198 121 166

Figure S53.  Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 5.86e-14 (Fisher's exact test), Q value = 2.4e-11

Table S54.  Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
16P GAIN CNV 11 0 1
16P GAIN WILD-TYPE 23 383 76

Figure S54.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0045

Table S55.  Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
16P GAIN CNV 11 1 0
16P GAIN WILD-TYPE 140 82 260

Figure S55.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000225 (Fisher's exact test), Q value = 0.071

Table S56.  Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 150 55 114 161
16P GAIN CNV 11 0 0 1
16P GAIN WILD-TYPE 139 55 114 160

Figure S56.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.56e-05 (Fisher's exact test), Q value = 0.016

Table S57.  Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
16P GAIN CNV 11 1 0 0
16P GAIN WILD-TYPE 121 211 94 42

Figure S57.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.059

Table S58.  Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
16P GAIN CNV 10 0 2
16P GAIN WILD-TYPE 140 173 168

Figure S58.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.67e-05 (Fisher's exact test), Q value = 0.016

Table S59.  Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
16P GAIN CNV 0 10 2
16P GAIN WILD-TYPE 155 120 206

Figure S59.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000388 (Fisher's exact test), Q value = 0.12

Table S60.  Gene #14: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
16P GAIN CNV 10 0 2
16P GAIN WILD-TYPE 153 169 159

Figure S60.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.0085

Table S61.  Gene #14: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
16P GAIN CNV 2 10 0
16P GAIN WILD-TYPE 197 118 166

Figure S61.  Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 6.03e-13 (Fisher's exact test), Q value = 2.5e-10

Table S62.  Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
16Q GAIN CNV 10 0 0
16Q GAIN WILD-TYPE 24 383 77

Figure S62.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 6.6e-05 (Fisher's exact test), Q value = 0.023

Table S63.  Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
16Q GAIN CNV 9 1 0
16Q GAIN WILD-TYPE 142 82 260

Figure S63.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000415 (Fisher's exact test), Q value = 0.12

Table S64.  Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
16Q GAIN CNV 9 1 0 0
16Q GAIN WILD-TYPE 123 211 94 42

Figure S64.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000637 (Fisher's exact test), Q value = 0.19

Table S65.  Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
16Q GAIN CNV 0 8 2
16Q GAIN WILD-TYPE 155 122 206

Figure S65.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.15

Table S66.  Gene #15: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
16Q GAIN CNV 2 8 0
16Q GAIN WILD-TYPE 197 120 166

Figure S66.  Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1.99e-09 (Fisher's exact test), Q value = 8e-07

Table S67.  Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
17P GAIN CNV 9 2 1
17P GAIN WILD-TYPE 25 381 76

Figure S67.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.00059

Table S68.  Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
17P GAIN CNV 12 0 0
17P GAIN WILD-TYPE 139 83 260

Figure S68.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 7.58e-06 (Fisher's exact test), Q value = 0.0028

Table S69.  Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 150 55 114 161
17P GAIN CNV 12 0 0 0
17P GAIN WILD-TYPE 138 55 114 161

Figure S69.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.57e-06 (Fisher's exact test), Q value = 0.00061

Table S70.  Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
17P GAIN CNV 12 0 0 0
17P GAIN WILD-TYPE 120 212 94 42

Figure S70.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0045

Table S71.  Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
17P GAIN CNV 11 0 1
17P GAIN WILD-TYPE 139 173 169

Figure S71.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.57e-06 (Fisher's exact test), Q value = 0.0014

Table S72.  Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
17P GAIN CNV 0 11 1
17P GAIN WILD-TYPE 155 119 207

Figure S72.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.02e-05 (Fisher's exact test), Q value = 0.017

Table S73.  Gene #16: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
17P GAIN CNV 11 0 1
17P GAIN WILD-TYPE 152 169 160

Figure S73.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.00093

Table S74.  Gene #16: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
17P GAIN CNV 1 11 0
17P GAIN WILD-TYPE 198 117 166

Figure S74.  Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 3.8e-09 (Fisher's exact test), Q value = 1.5e-06

Table S75.  Gene #17: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
17Q GAIN CNV 9 2 2
17Q GAIN WILD-TYPE 25 381 75

Figure S75.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 3.34e-07 (Fisher's exact test), Q value = 0.00013

Table S76.  Gene #17: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
17Q GAIN CNV 13 0 0
17Q GAIN WILD-TYPE 138 83 260

Figure S76.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 2.22e-06 (Fisher's exact test), Q value = 0.00085

Table S77.  Gene #17: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 150 55 114 161
17Q GAIN CNV 13 0 0 0
17Q GAIN WILD-TYPE 137 55 114 161

Figure S77.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.35e-07 (Fisher's exact test), Q value = 0.00013

Table S78.  Gene #17: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
17Q GAIN CNV 13 0 0 0
17Q GAIN WILD-TYPE 119 212 94 42

Figure S78.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 3.86e-06 (Fisher's exact test), Q value = 0.0015

Table S79.  Gene #17: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
17Q GAIN CNV 12 0 1
17Q GAIN WILD-TYPE 138 173 169

Figure S79.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.76e-07 (Fisher's exact test), Q value = 0.00038

Table S80.  Gene #17: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
17Q GAIN CNV 0 12 1
17Q GAIN WILD-TYPE 155 118 207

Figure S80.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.69e-05 (Fisher's exact test), Q value = 0.0062

Table S81.  Gene #17: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
17Q GAIN CNV 12 0 1
17Q GAIN WILD-TYPE 151 169 160

Figure S81.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.38e-07 (Fisher's exact test), Q value = 0.00025

Table S82.  Gene #17: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
17Q GAIN CNV 1 12 0
17Q GAIN WILD-TYPE 198 116 166

Figure S82.  Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0068

Table S83.  Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
19P GAIN CNV 4 0 0
19P GAIN WILD-TYPE 30 383 77

Figure S83.  Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00045

Table S84.  Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
19Q GAIN CNV 5 0 0
19Q GAIN WILD-TYPE 29 383 77

Figure S84.  Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.17e-11 (Fisher's exact test), Q value = 4.8e-09

Table S85.  Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
20P GAIN CNV 9 0 0
20P GAIN WILD-TYPE 25 383 77

Figure S85.  Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000251 (Fisher's exact test), Q value = 0.079

Table S86.  Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
20P GAIN CNV 8 1 0
20P GAIN WILD-TYPE 143 82 260

Figure S86.  Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.17e-11 (Fisher's exact test), Q value = 4.8e-09

Table S87.  Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
20Q GAIN CNV 9 0 0
20Q GAIN WILD-TYPE 25 383 77

Figure S87.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.000251 (Fisher's exact test), Q value = 0.079

Table S88.  Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
20Q GAIN CNV 8 1 0
20Q GAIN WILD-TYPE 143 82 260

Figure S88.  Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.093

Table S89.  Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
1P LOSS CNV 3 0 0
1P LOSS WILD-TYPE 31 383 77

Figure S89.  Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 5.2e-09 (Fisher's exact test), Q value = 2.1e-06

Table S90.  Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
2P LOSS CNV 7 0 1
2P LOSS WILD-TYPE 27 383 76

Figure S90.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.046

Table S91.  Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
2P LOSS CNV 8 0 0
2P LOSS WILD-TYPE 143 83 260

Figure S91.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.000645 (Fisher's exact test), Q value = 0.19

Table S92.  Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 150 55 114 161
2P LOSS CNV 8 0 0 0
2P LOSS WILD-TYPE 142 55 114 161

Figure S92.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.07

Table S93.  Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
2P LOSS CNV 8 0 0 0
2P LOSS WILD-TYPE 124 212 94 42

Figure S93.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.022

Table S94.  Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
2P LOSS CNV 8 0 0
2P LOSS WILD-TYPE 142 173 170

Figure S94.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0071

Table S95.  Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
2P LOSS CNV 0 8 0
2P LOSS WILD-TYPE 155 122 208

Figure S95.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.076

Table S96.  Gene #26: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
2P LOSS CNV 8 0 0
2P LOSS WILD-TYPE 155 169 161

Figure S96.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0063

Table S97.  Gene #26: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
2P LOSS CNV 0 8 0
2P LOSS WILD-TYPE 199 120 166

Figure S97.  Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 3.94e-09 (Fisher's exact test), Q value = 1.6e-06

Table S98.  Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 27 383 77

Figure S98.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.000343 (Fisher's exact test), Q value = 0.1

Table S99.  Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 144 83 260

Figure S99.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000675 (Fisher's exact test), Q value = 0.2

Table S100.  Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
2Q LOSS CNV 7 0 0 0
2Q LOSS WILD-TYPE 125 212 94 42

Figure S100.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.07

Table S101.  Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 143 173 170

Figure S101.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.85e-05 (Fisher's exact test), Q value = 0.026

Table S102.  Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
2Q LOSS CNV 0 7 0
2Q LOSS WILD-TYPE 155 123 208

Figure S102.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000758 (Fisher's exact test), Q value = 0.22

Table S103.  Gene #27: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
2Q LOSS CNV 7 0 0
2Q LOSS WILD-TYPE 156 169 161

Figure S103.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.02e-05 (Fisher's exact test), Q value = 0.024

Table S104.  Gene #27: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
2Q LOSS CNV 0 7 0
2Q LOSS WILD-TYPE 199 121 166

Figure S104.  Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.093

Table S105.  Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
3Q LOSS CNV 3 0 0
3Q LOSS WILD-TYPE 31 383 77

Figure S105.  Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0068

Table S106.  Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
8P LOSS CNV 4 0 0
8P LOSS WILD-TYPE 30 383 77

Figure S106.  Get High-res Image Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0068

Table S107.  Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
8Q LOSS CNV 4 0 0
8Q LOSS WILD-TYPE 30 383 77

Figure S107.  Get High-res Image Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 2.13e-11 (Fisher's exact test), Q value = 8.7e-09

Table S108.  Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
9P LOSS CNV 10 1 1
9P LOSS WILD-TYPE 24 382 76

Figure S108.  Get High-res Image Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.59e-13 (Fisher's exact test), Q value = 6.6e-11

Table S109.  Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
9Q LOSS CNV 13 3 1
9Q LOSS WILD-TYPE 21 380 76

Figure S109.  Get High-res Image Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 6.87e-08 (Fisher's exact test), Q value = 2.7e-05

Table S110.  Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
10P LOSS CNV 6 0 0
10P LOSS WILD-TYPE 28 383 77

Figure S110.  Get High-res Image Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00045

Table S111.  Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
10Q LOSS CNV 5 0 0
10Q LOSS WILD-TYPE 29 383 77

Figure S111.  Get High-res Image Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 7.98e-08 (Fisher's exact test), Q value = 3.2e-05

Table S112.  Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
11P LOSS CNV 6 0 1
11P LOSS WILD-TYPE 28 383 76

Figure S112.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.28e-06 (Fisher's exact test), Q value = 0.0012

Table S113.  Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
11Q LOSS CNV 6 2 1
11Q LOSS WILD-TYPE 28 381 76

Figure S113.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.11

Table S114.  Gene #37: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
11Q LOSS CNV 8 0 1
11Q LOSS WILD-TYPE 142 173 169

Figure S114.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.000653 (Fisher's exact test), Q value = 0.19

Table S115.  Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
15Q LOSS CNV 4 2 1
15Q LOSS WILD-TYPE 30 381 76

Figure S115.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.000343 (Fisher's exact test), Q value = 0.1

Table S116.  Gene #39: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
15Q LOSS CNV 7 0 0
15Q LOSS WILD-TYPE 144 83 260

Figure S116.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000675 (Fisher's exact test), Q value = 0.2

Table S117.  Gene #39: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
15Q LOSS CNV 7 0 0 0
15Q LOSS WILD-TYPE 125 212 94 42

Figure S117.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.07

Table S118.  Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
15Q LOSS CNV 7 0 0
15Q LOSS WILD-TYPE 143 173 170

Figure S118.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.85e-05 (Fisher's exact test), Q value = 0.026

Table S119.  Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
15Q LOSS CNV 0 7 0
15Q LOSS WILD-TYPE 155 123 208

Figure S119.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000758 (Fisher's exact test), Q value = 0.22

Table S120.  Gene #39: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
15Q LOSS CNV 7 0 0
15Q LOSS WILD-TYPE 156 169 161

Figure S120.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.02e-05 (Fisher's exact test), Q value = 0.024

Table S121.  Gene #39: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
15Q LOSS CNV 0 7 0
15Q LOSS WILD-TYPE 199 121 166

Figure S121.  Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.067

Table S122.  Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
18P LOSS CNV 3 0 1
18P LOSS WILD-TYPE 31 383 76

Figure S122.  Get High-res Image Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.067

Table S123.  Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
18Q LOSS CNV 3 0 1
18Q LOSS WILD-TYPE 31 383 76

Figure S123.  Get High-res Image Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.062

Table S124.  Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
21Q LOSS CNV 4 1 1
21Q LOSS WILD-TYPE 30 382 76

Figure S124.  Get High-res Image Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 4.98e-57 (Fisher's exact test), Q value = 2.1e-54

Table S125.  Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 383 77
22Q LOSS CNV 8 0 57
22Q LOSS WILD-TYPE 26 383 20

Figure S125.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 4.44e-05 (Fisher's exact test), Q value = 0.015

Table S126.  Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 83 260
22Q LOSS CNV 36 7 22
22Q LOSS WILD-TYPE 115 76 238

Figure S126.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 6.84e-11 (Fisher's exact test), Q value = 2.8e-08

Table S127.  Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 150 55 114 161
22Q LOSS CNV 35 5 20 1
22Q LOSS WILD-TYPE 115 50 94 160

Figure S127.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.07e-11 (Fisher's exact test), Q value = 3.3e-08

Table S128.  Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 132 212 94 42
22Q LOSS CNV 35 7 18 1
22Q LOSS WILD-TYPE 97 205 76 41

Figure S128.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.011

Table S129.  Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 173 170
22Q LOSS CNV 36 16 13
22Q LOSS WILD-TYPE 114 157 157

Figure S129.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.3e-06 (Fisher's exact test), Q value = 0.002

Table S130.  Gene #45: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 130 208
22Q LOSS CNV 16 34 15
22Q LOSS WILD-TYPE 139 96 193

Figure S130.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.56e-07 (Fisher's exact test), Q value = 6.2e-05

Table S131.  Gene #45: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 169 161
22Q LOSS CNV 42 11 12
22Q LOSS WILD-TYPE 121 158 149

Figure S131.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.09e-06 (Fisher's exact test), Q value = 0.0012

Table S132.  Gene #45: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 199 128 166
22Q LOSS CNV 14 34 17
22Q LOSS WILD-TYPE 185 94 149

Figure S132.  Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Molecular subtypes file = THCA-TP.transferedmergedcluster.txt

  • Number of patients = 494

  • Number of significantly arm-level cnvs = 45

  • Number of molecular subtypes = 10

  • 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

Q value calculation

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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