Correlation between copy number variations of arm-level result and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1222SFG
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1222SFG
Overview
Introduction

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

Summary

Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 493 patients, 177 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

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

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 4p gain cnv correlated to 'CN_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 6q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 8p gain cnv correlated to 'CN_CNMF'.

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

  • 10p gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 14q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

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

  • 5p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • 6q loss cnv correlated to 'METHLYATION_CNMF'.

  • 7p loss cnv correlated to 'CN_CNMF'.

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

  • 8q loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'CN_CNMF'.

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

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

  • 16p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 17p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

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

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 177 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
8q gain 235 (48%) 258 0.024
(1.00) 		0.0244
(1.00) 		2.34e-20
(2.22e-17) 		1.34e-05
(0.0114) 		0.287
(1.00) 		0.0396
(1.00) 		9.18e-08
(8.35e-05) 		1.93e-05
(0.016) 		4.24e-06
(0.00369) 		2.41e-05
(0.0199) 		0.000199
(0.155) 		1.13e-05
(0.00962)
12p gain 131 (27%) 362 0.221
(1.00) 		0.0501
(1.00) 		1.06e-06
(0.000936) 		0.0509
(1.00) 		0.0166
(1.00) 		0.0205
(1.00) 		4.46e-09
(4.13e-06) 		4.3e-11
(4.02e-08) 		1.46e-05
(0.0124) 		1.81e-05
(0.0151) 		6.62e-08
(6.03e-05) 		4.9e-08
(4.48e-05)
12q gain 126 (26%) 367 0.221
(1.00) 		0.103
(1.00) 		3.78e-08
(3.47e-05) 		0.0168
(1.00) 		0.17
(1.00) 		0.0399
(1.00) 		1.14e-11
(1.07e-08) 		5.74e-12
(5.39e-09) 		1.19e-05
(0.0101) 		3.13e-06
(0.00273) 		2.22e-07
(0.000201) 		6.19e-07
(0.000554)
20p gain 164 (33%) 329 0.0815
(1.00) 		0.191
(1.00) 		6.66e-05
(0.0535) 		0.00644
(1.00) 		0.421
(1.00) 		0.265
(1.00) 		0.000214
(0.166) 		6.56e-06
(0.00566) 		2.82e-05
(0.0231) 		5.4e-06
(0.00468) 		0.000189
(0.148) 		2.77e-05
(0.0227)
20q gain 189 (38%) 304 0.01
(1.00) 		0.0239
(1.00) 		1.64e-07
(0.000149) 		0.00114
(0.822) 		0.228
(1.00) 		0.0314
(1.00) 		4.47e-06
(0.00389) 		3.34e-07
(3e-04) 		2.04e-06
(0.00179) 		6.85e-07
(0.000612) 		1.77e-05
(0.0148) 		1.69e-05
(0.0141)
4q loss 132 (27%) 361 0.00043
(0.327) 		0.000811
(0.597) 		2.35e-06
(0.00206) 		0.00336
(1.00) 		0.278
(1.00) 		0.0476
(1.00) 		9.39e-08
(8.52e-05) 		7.54e-13
(7.1e-10) 		1.77e-06
(0.00156) 		2.31e-07
(0.000209) 		0.000287
(0.222) 		0.000289
(0.223)
5q loss 137 (28%) 356 0.0641
(1.00) 		0.0411
(1.00) 		2.49e-09
(2.31e-06) 		0.000644
(0.479) 		0.00117
(0.84) 		0.00554
(1.00) 		1.55e-06
(0.00137) 		1.44e-08
(1.32e-05) 		9.39e-07
(0.000832) 		2.65e-06
(0.00232) 		6.96e-06
(0.006) 		4.6e-07
(0.000413)
19p loss 235 (48%) 258 0.815
(1.00) 		1
(1.00) 		5.34e-08
(4.87e-05) 		1.2e-10
(1.12e-07) 		0.335
(1.00) 		0.522
(1.00) 		7.15e-07
(0.000637) 		2.35e-07
(0.000212) 		2.5e-05
(0.0206) 		3.18e-07
(0.000286) 		0.0062
(1.00) 		1.63e-05
(0.0136)
22q loss 212 (43%) 281 0.126
(1.00) 		0.118
(1.00) 		1.06e-09
(9.86e-07) 		2.8e-05
(0.0229) 		0.798
(1.00) 		0.0688
(1.00) 		8.98e-08
(8.17e-05) 		5.38e-07
(0.000482) 		0.000205
(0.159) 		9.04e-07
(0.000803) 		0.000337
(0.259) 		3.35e-05
(0.0273)
2p gain 148 (30%) 345 0.301
(1.00) 		0.119
(1.00) 		3.86e-08
(3.53e-05) 		0.000614
(0.46) 		0.444
(1.00) 		0.358
(1.00) 		8.92e-05
(0.0709) 		5.18e-06
(0.0045) 		1.1e-06
(0.000974) 		7.36e-06
(0.00634) 		0.00204
(1.00) 		6.12e-05
(0.0493)
7p gain 251 (51%) 242 0.856
(1.00) 		0.535
(1.00) 		1.34e-20
(1.27e-17) 		0.00272
(1.00) 		0.000443
(0.336) 		0.000542
(0.408) 		2.78e-11
(2.61e-08) 		1.01e-11
(9.45e-09) 		4.23e-06
(0.00369) 		0.000908
(0.666) 		0.00032
(0.247) 		1.66e-05
(0.0139)
11q gain 112 (23%) 381 0.01
(1.00) 		0.02
(1.00) 		2.8e-08
(2.57e-05) 		0.0742
(1.00) 		0.261
(1.00) 		0.343
(1.00) 		0.00412
(1.00) 		0.000194
(0.151) 		5.15e-05
(0.0416) 		8.66e-05
(0.0691) 		0.000317
(0.245) 		0.0037
(1.00)
4p loss 116 (24%) 377 0.186
(1.00) 		0.145
(1.00) 		4.45e-05
(0.036) 		0.212
(1.00) 		0.195
(1.00) 		0.218
(1.00) 		8.76e-05
(0.0697) 		8.23e-08
(7.49e-05) 		7.71e-06
(0.00663) 		3.55e-06
(0.0031) 		0.00593
(1.00) 		0.000356
(0.273)
16q loss 137 (28%) 356 0.551
(1.00) 		0.707
(1.00) 		9.14e-06
(0.00784) 		0.000321
(0.247) 		0.0738
(1.00) 		0.219
(1.00) 		1.69e-07
(0.000153) 		3.53e-07
(0.000317) 		0.00667
(1.00) 		0.0313
(1.00) 		0.00133
(0.948) 		3.36e-05
(0.0273)
19q loss 153 (31%) 340 0.344
(1.00) 		0.475
(1.00) 		1.47e-07
(0.000133) 		8.18e-07
(0.000727) 		0.272
(1.00) 		0.22
(1.00) 		0.000103
(0.0816) 		0.000177
(0.138) 		0.000677
(0.503) 		7.8e-05
(0.0623) 		0.026
(1.00) 		0.000359
(0.275)
14q gain 120 (24%) 373 0.803
(1.00) 		0.722
(1.00) 		9.11e-09
(8.4e-06) 		0.0156
(1.00) 		0.229
(1.00) 		0.127
(1.00) 		7.43e-05
(0.0595) 		0.00356
(1.00) 		3.2e-05
(0.0261) 		2.67e-05
(0.0219) 		0.00078
(0.577) 		0.0147
(1.00)
17q gain 186 (38%) 307 0.305
(1.00) 		0.312
(1.00) 		1.72e-08
(1.58e-05) 		0.000909
(0.666) 		0.624
(1.00) 		0.172
(1.00) 		4.29e-05
(0.0348) 		6.2e-06
(0.00536) 		8.91e-06
(0.00765) 		0.000367
(0.28) 		0.0606
(1.00) 		0.000637
(0.475)
18q gain 66 (13%) 427 0.595
(1.00) 		0.14
(1.00) 		0.000139
(0.109) 		1.61e-06
(0.00142) 		0.0217
(1.00) 		0.0172
(1.00) 		1.81e-05
(0.0151) 		2.6e-05
(0.0214) 		0.0109
(1.00) 		0.00079
(0.583) 		0.0027
(1.00) 		0.00174
(1.00)
13q loss 243 (49%) 250 0.105
(1.00) 		0.268
(1.00) 		2.62e-17
(2.47e-14) 		0.157
(1.00) 		0.000538
(0.405) 		2.79e-06
(0.00244) 		3.09e-07
(0.000278) 		5.43e-06
(0.0047) 		0.0137
(1.00) 		0.0103
(1.00) 		0.0428
(1.00) 		0.162
(1.00)
15q loss 233 (47%) 260 0.101
(1.00) 		0.176
(1.00) 		7.26e-07
(0.000646) 		0.0201
(1.00) 		0.127
(1.00) 		0.0735
(1.00) 		5.61e-13
(5.28e-10) 		1.49e-06
(0.00132) 		1.59e-05
(0.0134) 		0.00199
(1.00) 		0.0177
(1.00) 		0.00295
(1.00)
21q loss 157 (32%) 336 0.184
(1.00) 		0.191
(1.00) 		7.21e-07
(0.000642) 		0.0415
(1.00) 		0.0315
(1.00) 		0.00316
(1.00) 		2.26e-10
(2.1e-07) 		5.86e-09
(5.41e-06) 		0.000425
(0.323) 		1.37e-06
(0.00121) 		0.00698
(1.00) 		0.000996
(0.726)
7q gain 207 (42%) 286 0.482
(1.00) 		0.388
(1.00) 		9.72e-11
(9.07e-08) 		0.0349
(1.00) 		0.133
(1.00) 		0.221
(1.00) 		5.7e-09
(5.27e-06) 		1.21e-08
(1.12e-05) 		0.0026
(1.00) 		0.00371
(1.00) 		0.0117
(1.00) 		0.00158
(1.00)
10p gain 105 (21%) 388 0.236
(1.00) 		0.308
(1.00) 		0.000641
(0.478) 		1.26e-05
(0.0107) 		0.018
(1.00) 		0.00405
(1.00) 		7.64e-05
(0.0611) 		1.52e-05
(0.0128) 		0.00913
(1.00) 		0.0013
(0.927) 		0.0384
(1.00) 		0.00439
(1.00)
18p gain 91 (18%) 402 0.876
(1.00) 		0.751
(1.00) 		3.35e-05
(0.0273) 		2.4e-05
(0.0199) 		0.256
(1.00) 		0.65
(1.00) 		0.0203
(1.00) 		0.00466
(1.00) 		0.0151
(1.00) 		0.00092
(0.673) 		0.00571
(1.00) 		2.67e-05
(0.0219)
1p loss 79 (16%) 414 0.0797
(1.00) 		0.14
(1.00) 		1.88e-05
(0.0157) 		0.000138
(0.109) 		0.908
(1.00) 		0.108
(1.00) 		9.66e-05
(0.0766) 		0.00102
(0.743) 		0.521
(1.00) 		0.0491
(1.00) 		0.456
(1.00) 		0.224
(1.00)
3p loss 205 (42%) 288 0.343
(1.00) 		0.117
(1.00) 		2.02e-05
(0.0167) 		4.81e-06
(0.00418) 		0.253
(1.00) 		0.323
(1.00) 		0.0311
(1.00) 		5.31e-06
(0.00461) 		0.0219
(1.00) 		0.35
(1.00) 		0.123
(1.00) 		0.11
(1.00)
8p loss 191 (39%) 302 0.132
(1.00) 		0.0285
(1.00) 		8.73e-19
(8.25e-16) 		0.241
(1.00) 		0.0496
(1.00) 		0.00995
(1.00) 		0.000101
(0.0797) 		3.94e-05
(0.0319) 		0.00258
(1.00) 		0.0326
(1.00) 		0.00566
(1.00) 		0.0014
(0.994)
9q loss 238 (48%) 255 0.499
(1.00) 		1
(1.00) 		2.4e-05
(0.0199) 		0.00361
(1.00) 		0.418
(1.00) 		0.029
(1.00) 		0.139
(1.00) 		9.29e-06
(0.00795) 		0.00642
(1.00) 		0.0025
(1.00) 		0.0259
(1.00) 		0.000173
(0.135)
16p loss 108 (22%) 385 0.453
(1.00) 		0.411
(1.00) 		9.33e-06
(0.00797) 		0.000558
(0.419) 		0.232
(1.00) 		0.517
(1.00) 		4.71e-05
(0.0381) 		1.42e-05
(0.0121) 		0.00845
(1.00) 		0.0364
(1.00) 		0.00783
(1.00) 		0.0024
(1.00)
18q loss 207 (42%) 286 0.519
(1.00) 		0.668
(1.00) 		3.76e-10
(3.49e-07) 		0.819
(1.00) 		0.00357
(1.00) 		0.000269
(0.209) 		0.000277
(0.215) 		0.00598
(1.00) 		0.0253
(1.00) 		1
(1.00) 		0.687
(1.00) 		0.772
(1.00)
3q gain 86 (17%) 407 0.0797
(1.00) 		0.14
(1.00) 		0.00142
(1.00) 		0.146
(1.00) 		0.0265
(1.00) 		0.106
(1.00) 		3.11e-05
(0.0254) 		1.52e-05
(0.0128) 		0.0156
(1.00) 		0.0323
(1.00) 		0.00949
(1.00) 		0.0233
(1.00)
6p gain 141 (29%) 352 0.354
(1.00) 		0.0645
(1.00) 		1.59e-05
(0.0134) 		1.94e-06
(0.00171) 		0.0296
(1.00) 		0.742
(1.00) 		0.0965
(1.00) 		0.578
(1.00) 		0.0267
(1.00) 		0.00801
(1.00) 		0.0667
(1.00) 		0.00237
(1.00)
17p gain 83 (17%) 410 0.453
(1.00) 		0.411
(1.00) 		6.17e-05
(0.0496) 		0.0911
(1.00) 		0.831
(1.00) 		0.0817
(1.00) 		0.00996
(1.00) 		0.00287
(1.00) 		1.05e-05
(0.00893) 		0.00111
(0.807) 		0.227
(1.00) 		0.0588
(1.00)
10p loss 108 (22%) 385 0.816
(1.00) 		0.416
(1.00) 		7.13e-07
(0.000636) 		0.184
(1.00) 		0.0394
(1.00) 		0.0123
(1.00) 		7.29e-05
(0.0584) 		0.0269
(1.00) 		0.00376
(1.00) 		0.0508
(1.00) 		0.00188
(1.00) 		0.0359
(1.00)
11p loss 108 (22%) 385 0.144
(1.00) 		0.0799
(1.00) 		7.93e-05
(0.0633) 		0.0147
(1.00) 		0.0356
(1.00) 		0.283
(1.00) 		0.00383
(1.00) 		1.64e-05
(0.0137) 		0.0265
(1.00) 		0.0158
(1.00) 		0.027
(1.00) 		0.0197
(1.00)
17p loss 206 (42%) 287 0.549
(1.00) 		0.59
(1.00) 		2.17e-11
(2.03e-08) 		0.00013
(0.102) 		0.132
(1.00) 		0.00627
(1.00) 		0.000942
(0.688) 		0.000625
(0.468) 		0.5
(1.00) 		0.478
(1.00) 		0.606
(1.00) 		0.303
(1.00)
1p gain 133 (27%) 360 0.388
(1.00) 		1
(1.00) 		1.26e-08
(1.16e-05) 		0.312
(1.00) 		0.0729
(1.00) 		0.00459
(1.00) 		0.117
(1.00) 		0.00259
(1.00) 		0.073
(1.00) 		0.987
(1.00) 		0.313
(1.00) 		0.654
(1.00)
2q gain 135 (27%) 358 0.126
(1.00) 		0.302
(1.00) 		7.89e-06
(0.00678) 		0.0013
(0.926) 		0.694
(1.00) 		0.749
(1.00) 		0.0765
(1.00) 		0.000987
(0.72) 		0.00178
(1.00) 		0.00147
(1.00) 		0.0281
(1.00) 		0.000597
(0.448)
4p gain 80 (16%) 413 0.876
(1.00) 		0.869
(1.00) 		1.24e-05
(0.0105) 		0.035
(1.00) 		0.301
(1.00) 		0.0908
(1.00) 		0.0446
(1.00) 		0.0148
(1.00) 		0.088
(1.00) 		0.173
(1.00) 		0.434
(1.00) 		0.284
(1.00)
5p gain 267 (54%) 226 0.798
(1.00) 		0.59
(1.00) 		6.75e-11
(6.31e-08) 		0.777
(1.00) 		0.16
(1.00) 		0.571
(1.00) 		0.0236
(1.00) 		0.0322
(1.00) 		0.0446
(1.00) 		0.116
(1.00) 		0.0911
(1.00) 		0.0375
(1.00)
6q gain 60 (12%) 433 1
(1.00) 		1
(1.00) 		0.0131
(1.00) 		0.00679
(1.00) 		0.164
(1.00) 		0.944
(1.00) 		0.201
(1.00) 		0.137
(1.00) 		0.00203
(1.00) 		0.000105
(0.0831) 		0.282
(1.00) 		0.00191
(1.00)
8p gain 123 (25%) 370 0.151
(1.00) 		0.176
(1.00) 		2.15e-10
(2e-07) 		0.0533
(1.00) 		0.436
(1.00) 		0.376
(1.00) 		0.00126
(0.906) 		0.00674
(1.00) 		0.455
(1.00) 		0.35
(1.00) 		0.842
(1.00) 		0.784
(1.00)
11p gain 92 (19%) 401 0.00952
(1.00) 		0.00906
(1.00) 		1.62e-05
(0.0136) 		0.607
(1.00) 		0.545
(1.00) 		0.468
(1.00) 		0.188
(1.00) 		0.0161
(1.00) 		0.000441
(0.335) 		0.000533
(0.403) 		0.000523
(0.395) 		0.00109
(0.789)
15q gain 35 (7%) 458 0.192
(1.00) 		0.157
(1.00) 		0.384
(1.00) 		0.343
(1.00) 		0.561
(1.00) 		0.326
(1.00) 		6.84e-09
(6.31e-06) 		0.000513
(0.388) 		0.773
(1.00) 		0.806
(1.00) 		0.194
(1.00) 		0.691
(1.00)
21q gain 94 (19%) 399 0.538
(1.00) 		0.466
(1.00) 		5.78e-05
(0.0466) 		0.984
(1.00) 		0.331
(1.00) 		0.0638
(1.00) 		0.0276
(1.00) 		0.13
(1.00) 		0.335
(1.00) 		0.657
(1.00) 		0.639
(1.00) 		0.734
(1.00)
5p loss 40 (8%) 453 0.595
(1.00) 		0.453
(1.00) 		0.676
(1.00) 		0.0182
(1.00) 		0.388
(1.00) 		0.287
(1.00) 		0.0289
(1.00) 		2.91e-05
(0.0238) 		0.0711
(1.00) 		0.0641
(1.00) 		0.0169
(1.00) 		0.00112
(0.813)
6q loss 208 (42%) 285 0.247
(1.00) 		0.32
(1.00) 		0.0299
(1.00) 		8.96e-05
(0.0711) 		0.813
(1.00) 		0.538
(1.00) 		0.0809
(1.00) 		0.0899
(1.00) 		0.338
(1.00) 		0.0423
(1.00) 		0.726
(1.00) 		0.101
(1.00)
7p loss 33 (7%) 460 1
(1.00) 		1
(1.00) 		1.61e-05
(0.0135) 		0.0367
(1.00) 		0.33
(1.00) 		0.713
(1.00) 		0.00529
(1.00) 		0.0184
(1.00) 		0.279
(1.00) 		0.366
(1.00) 		0.867
(1.00) 		0.23
(1.00)
8q loss 54 (11%) 439 0.000278
(0.215) 		0.53
(1.00) 		0.293
(1.00) 		0.375
(1.00) 		0.153
(1.00) 		0.133
(1.00) 		0.213
(1.00) 		0.739
(1.00) 		0.412
(1.00) 		0.651
(1.00)
9p loss 254 (52%) 239 0.0516
(1.00) 		0.465
(1.00) 		0.00182
(1.00) 		0.0411
(1.00) 		0.215
(1.00) 		0.0638
(1.00) 		0.00122
(0.877) 		0.000154
(0.121) 		0.0628
(1.00) 		0.0632
(1.00) 		0.352
(1.00) 		0.0889
(1.00)
10q loss 128 (26%) 365 0.816
(1.00) 		0.416
(1.00) 		1.95e-05
(0.0161) 		0.0642
(1.00) 		0.0543
(1.00) 		0.0131
(1.00) 		0.00135
(0.962) 		0.0662
(1.00) 		0.00521
(1.00) 		0.00683
(1.00) 		0.00129
(0.924) 		0.000852
(0.626)
12q loss 93 (19%) 400 0.554
(1.00) 		0.418
(1.00) 		1.52e-05
(0.0128) 		0.0817
(1.00) 		0.0947
(1.00) 		0.0175
(1.00) 		0.00126
(0.902) 		0.0105
(1.00) 		0.202
(1.00) 		0.107
(1.00) 		0.555
(1.00) 		0.361
(1.00)
17q loss 55 (11%) 438 0.294
(1.00) 		0.546
(1.00) 		0.000114
(0.0899) 		0.0486
(1.00) 		0.0109
(1.00) 		0.00762
(1.00) 		0.129
(1.00) 		0.123
(1.00) 		0.422
(1.00) 		0.16
(1.00) 		0.0822
(1.00) 		0.782
(1.00)
18p loss 169 (34%) 324 0.438
(1.00) 		0.631
(1.00) 		1.31e-05
(0.0112) 		0.75
(1.00) 		0.0371
(1.00) 		0.00211
(1.00) 		0.022
(1.00) 		0.00467
(1.00) 		0.0288
(1.00) 		0.694
(1.00) 		0.144
(1.00) 		0.79
(1.00)
1q gain 297 (60%) 196 0.121
(1.00) 		1
(1.00) 		0.00169
(1.00) 		0.00125
(0.897) 		0.000756
(0.56) 		0.0208
(1.00) 		0.128
(1.00) 		0.918
(1.00) 		0.518
(1.00) 		0.145
(1.00) 		0.0149
(1.00) 		0.126
(1.00)
3p gain 40 (8%) 453 0.0036
(1.00) 		0.0137
(1.00) 		0.108
(1.00) 		0.137
(1.00) 		0.000403
(0.307) 		0.00112
(0.813) 		0.063
(1.00) 		0.181
(1.00) 		0.163
(1.00) 		0.0564
(1.00)
4q gain 46 (9%) 447 0.329
(1.00) 		0.505
(1.00) 		0.0108
(1.00) 		0.901
(1.00) 		0.399
(1.00) 		0.392
(1.00) 		0.00442
(1.00) 		0.0284
(1.00) 		0.0166
(1.00) 		0.237
(1.00) 		0.16
(1.00) 		0.289
(1.00)
5q gain 124 (25%) 369 0.195
(1.00) 		0.453
(1.00) 		0.00558
(1.00) 		0.549
(1.00) 		0.0283
(1.00) 		0.365
(1.00) 		0.00585
(1.00) 		0.0774
(1.00) 		0.146
(1.00) 		0.0135
(1.00) 		0.0362
(1.00) 		0.0592
(1.00)
9p gain 42 (9%) 451 0.0143
(1.00) 		0.104
(1.00) 		0.449
(1.00) 		0.45
(1.00) 		0.000998
(0.727) 		0.619
(1.00) 		0.205
(1.00) 		0.648
(1.00) 		0.204
(1.00) 		0.211
(1.00)
9q gain 30 (6%) 463 0.252
(1.00) 		0.297
(1.00) 		0.572
(1.00) 		0.566
(1.00) 		0.0783
(1.00) 		0.782
(1.00) 		0.494
(1.00) 		0.724
(1.00) 		0.442
(1.00) 		0.255
(1.00)
10q gain 76 (15%) 417 0.0378
(1.00) 		0.00149
(1.00) 		0.286
(1.00) 		0.0902
(1.00) 		0.000334
(0.257) 		0.0169
(1.00) 		0.372
(1.00) 		0.0827
(1.00) 		0.214
(1.00) 		0.679
(1.00)
13q gain 43 (9%) 450 0.414
(1.00) 		0.466
(1.00) 		0.736
(1.00) 		0.00258
(1.00) 		0.0486
(1.00) 		0.0577
(1.00) 		0.0513
(1.00) 		0.0854
(1.00) 		0.978
(1.00) 		0.866
(1.00) 		0.81
(1.00) 		0.805
(1.00)
16p gain 127 (26%) 366 0.532
(1.00) 		0.235
(1.00) 		0.00312
(1.00) 		1
(1.00) 		0.298
(1.00) 		0.15
(1.00) 		0.178
(1.00) 		0.189
(1.00) 		0.00996
(1.00) 		0.00868
(1.00) 		0.0489
(1.00) 		0.444
(1.00)
16q gain 94 (19%) 399 0.437
(1.00) 		0.27
(1.00) 		0.00256
(1.00) 		0.939
(1.00) 		0.0693
(1.00) 		0.0729
(1.00) 		0.426
(1.00) 		0.783
(1.00) 		0.00198
(1.00) 		0.00214
(1.00) 		0.0209
(1.00) 		0.775
(1.00)
19p gain 32 (6%) 461 0.192
(1.00) 		0.0514
(1.00) 		0.188
(1.00) 		0.318
(1.00) 		1
(1.00) 		0.791
(1.00) 		0.987
(1.00) 		0.617
(1.00) 		0.44
(1.00) 		0.63
(1.00) 		0.0219
(1.00) 		0.266
(1.00)
19q gain 71 (14%) 422 0.0502
(1.00) 		0.0514
(1.00) 		0.00296
(1.00) 		0.00659
(1.00) 		0.946
(1.00) 		0.695
(1.00) 		0.168
(1.00) 		0.0138
(1.00) 		0.382
(1.00) 		0.041
(1.00) 		0.0721
(1.00) 		0.0499
(1.00)
22q gain 61 (12%) 432 0.108
(1.00) 		0.132
(1.00) 		0.00348
(1.00) 		0.785
(1.00) 		0.215
(1.00) 		0.191
(1.00) 		0.163
(1.00) 		0.0546
(1.00) 		0.6
(1.00) 		0.758
(1.00) 		0.462
(1.00) 		0.509
(1.00)
xq gain 68 (14%) 425 0.658
(1.00) 		0.505
(1.00) 		0.00071
(0.526) 		0.26
(1.00) 		0.274
(1.00) 		0.116
(1.00) 		0.0346
(1.00) 		0.336
(1.00) 		0.114
(1.00) 		0.318
(1.00) 		0.221
(1.00) 		0.474
(1.00)
1q loss 28 (6%) 465 0.179
(1.00) 		0.00395
(1.00) 		0.179
(1.00) 		0.463
(1.00) 		0.0696
(1.00) 		0.0121
(1.00) 		0.694
(1.00) 		0.363
(1.00) 		0.294
(1.00) 		0.0763
(1.00)
2p loss 24 (5%) 469 0.75
(1.00) 		0.591
(1.00) 		0.123
(1.00) 		0.19
(1.00) 		0.611
(1.00) 		1
(1.00) 		0.978
(1.00) 		0.771
(1.00) 		0.0865
(1.00) 		0.133
(1.00) 		0.0686
(1.00) 		0.491
(1.00)
2q loss 23 (5%) 470 0.00167
(1.00) 		0.00388
(1.00) 		0.426
(1.00) 		1
(1.00) 		0.268
(1.00) 		0.475
(1.00) 		0.32
(1.00) 		0.144
(1.00) 		0.453
(1.00) 		0.26
(1.00)
3q loss 140 (28%) 353 0.552
(1.00) 		0.191
(1.00) 		0.0146
(1.00) 		0.000546
(0.41) 		0.916
(1.00) 		0.845
(1.00) 		0.0647
(1.00) 		0.168
(1.00) 		0.674
(1.00) 		0.923
(1.00) 		0.845
(1.00) 		0.647
(1.00)
6p loss 101 (20%) 392 0.0126
(1.00) 		0.00838
(1.00) 		0.0538
(1.00) 		0.388
(1.00) 		0.528
(1.00) 		0.58
(1.00) 		0.187
(1.00) 		0.292
(1.00) 		0.538
(1.00) 		0.252
(1.00) 		0.506
(1.00) 		0.403
(1.00)
7q loss 39 (8%) 454 0.803
(1.00) 		0.176
(1.00) 		0.00708
(1.00) 		0.291
(1.00) 		0.91
(1.00) 		0.463
(1.00) 		0.0859
(1.00) 		0.291
(1.00) 		0.355
(1.00) 		0.349
(1.00) 		0.269
(1.00) 		0.46
(1.00)
11q loss 88 (18%) 405 0.841
(1.00) 		0.411
(1.00) 		0.007
(1.00) 		0.0108
(1.00) 		0.00359
(1.00) 		0.513
(1.00) 		0.00146
(1.00) 		0.000378
(0.288) 		0.0559
(1.00) 		0.026
(1.00) 		0.0285
(1.00) 		0.0273
(1.00)
12p loss 106 (22%) 387 0.63
(1.00) 		0.77
(1.00) 		0.00573
(1.00) 		0.357
(1.00) 		0.0473
(1.00) 		0.0982
(1.00) 		0.0065
(1.00) 		0.0576
(1.00) 		0.264
(1.00) 		0.329
(1.00) 		0.607
(1.00) 		0.521
(1.00)
14q loss 111 (23%) 382 0.929
(1.00) 		0.466
(1.00) 		0.061
(1.00) 		0.363
(1.00) 		0.171
(1.00) 		0.0602
(1.00) 		0.0217
(1.00) 		0.00162
(1.00) 		0.074
(1.00) 		0.0345
(1.00) 		0.000756
(0.56) 		0.0361
(1.00)
20p loss 114 (23%) 379 0.333
(1.00) 		0.631
(1.00) 		0.00036
(0.275) 		0.00384
(1.00) 		0.000631
(0.471) 		0.00272
(1.00) 		0.016
(1.00) 		0.0494
(1.00) 		0.965
(1.00) 		0.95
(1.00) 		0.126
(1.00) 		0.839
(1.00)
20q loss 67 (14%) 426 0.513
(1.00) 		0.882
(1.00) 		0.408
(1.00) 		0.614
(1.00) 		0.262
(1.00) 		0.894
(1.00) 		0.625
(1.00) 		0.979
(1.00) 		0.599
(1.00) 		0.896
(1.00) 		0.132
(1.00) 		0.933
(1.00)
xq loss 64 (13%) 429 0.276
(1.00) 		0.0398
(1.00) 		0.000824
(0.607) 		0.00294
(1.00) 		0.455
(1.00) 		0.363
(1.00) 		0.44
(1.00) 		0.221
(1.00) 		0.346
(1.00) 		0.252
(1.00) 		0.506
(1.00) 		0.338
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 1.26e-08 (Fisher's exact test), Q value = 1.2e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
1P GAIN MUTATED 79 35 19
1P GAIN WILD-TYPE 107 181 72

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

'2p gain' versus 'CN_CNMF'

P value = 3.86e-08 (Fisher's exact test), Q value = 3.5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
2P GAIN MUTATED 74 36 38
2P GAIN WILD-TYPE 112 180 53

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 8.92e-05 (Chi-square test), Q value = 0.071

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
2P GAIN MUTATED 40 18 25 49 16
2P GAIN WILD-TYPE 98 94 51 57 38

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.18e-06 (Fisher's exact test), Q value = 0.0045

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
2P GAIN MUTATED 34 44 70
2P GAIN WILD-TYPE 85 167 86

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1.1e-06 (Fisher's exact test), Q value = 0.00097

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
2P GAIN MUTATED 37 96 14
2P GAIN WILD-TYPE 142 135 64

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.36e-06 (Fisher's exact test), Q value = 0.0063

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
2P GAIN MUTATED 6 98 43
2P GAIN WILD-TYPE 45 151 145

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.12e-05 (Fisher's exact test), Q value = 0.049

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
2P GAIN MUTATED 10 75 38
2P GAIN WILD-TYPE 39 113 150

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 7.89e-06 (Fisher's exact test), Q value = 0.0068

Table S8.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
2Q GAIN MUTATED 60 37 38
2Q GAIN WILD-TYPE 126 179 53

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 3.11e-05 (Chi-square test), Q value = 0.025

Table S9.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
3Q GAIN MUTATED 34 2 16 23 10
3Q GAIN WILD-TYPE 104 110 60 83 44

Figure S9.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.013

Table S10.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
3Q GAIN MUTATED 29 18 38
3Q GAIN WILD-TYPE 90 193 118

Figure S10.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.011

Table S11.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
4P GAIN MUTATED 48 18 14
4P GAIN WILD-TYPE 138 198 77

Figure S11.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 6.75e-11 (Fisher's exact test), Q value = 6.3e-08

Table S12.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
5P GAIN MUTATED 135 84 48
5P GAIN WILD-TYPE 51 132 43

Figure S12.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.013

Table S13.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
6P GAIN MUTATED 62 40 39
6P GAIN WILD-TYPE 124 176 52

Figure S13.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1.94e-06 (Fisher's exact test), Q value = 0.0017

Table S14.  Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
6P GAIN MUTATED 56 44 21
6P GAIN WILD-TYPE 85 96 129

Figure S14.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000105 (Fisher's exact test), Q value = 0.083

Table S15.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
6Q GAIN MUTATED 6 44 9
6Q GAIN WILD-TYPE 45 205 179

Figure S15.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1.34e-20 (Fisher's exact test), Q value = 1.3e-17

Table S16.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
7P GAIN MUTATED 145 72 34
7P GAIN WILD-TYPE 41 144 57

Figure S16.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 2.78e-11 (Chi-square test), Q value = 2.6e-08

Table S17.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
7P GAIN MUTATED 103 32 38 47 27
7P GAIN WILD-TYPE 35 80 38 59 27

Figure S17.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.01e-11 (Fisher's exact test), Q value = 9.5e-09

Table S18.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
7P GAIN MUTATED 92 79 76
7P GAIN WILD-TYPE 27 132 80

Figure S18.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 4.23e-06 (Fisher's exact test), Q value = 0.0037

Table S19.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
7P GAIN MUTATED 66 130 52
7P GAIN WILD-TYPE 113 101 26

Figure S19.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.25

Table S20.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
7P GAIN MUTATED 59 106 49
7P GAIN WILD-TYPE 96 86 29

Figure S20.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.014

Table S21.  Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
7P GAIN MUTATED 34 108 72
7P GAIN WILD-TYPE 15 80 116

Figure S21.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 9.72e-11 (Fisher's exact test), Q value = 9.1e-08

Table S22.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
7Q GAIN MUTATED 114 63 30
7Q GAIN WILD-TYPE 72 153 61

Figure S22.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 5.7e-09 (Chi-square test), Q value = 5.3e-06

Table S23.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
7Q GAIN MUTATED 87 27 33 34 22
7Q GAIN WILD-TYPE 51 85 43 72 32

Figure S23.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.21e-08 (Fisher's exact test), Q value = 1.1e-05

Table S24.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
7Q GAIN MUTATED 77 65 61
7Q GAIN WILD-TYPE 42 146 95

Figure S24.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 2.15e-10 (Fisher's exact test), Q value = 2e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
8P GAIN MUTATED 33 41 49
8P GAIN WILD-TYPE 153 175 42

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

'8q gain' versus 'CN_CNMF'

P value = 2.34e-20 (Fisher's exact test), Q value = 2.2e-17

Table S26.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
8Q GAIN MUTATED 92 64 79
8Q GAIN WILD-TYPE 94 152 12

Figure S26.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1.34e-05 (Fisher's exact test), Q value = 0.011

Table S27.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
8Q GAIN MUTATED 82 76 49
8Q GAIN WILD-TYPE 59 64 101

Figure S27.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 9.18e-08 (Chi-square test), Q value = 8.3e-05

Table S28.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
8Q GAIN MUTATED 68 33 32 74 21
8Q GAIN WILD-TYPE 70 79 44 32 33

Figure S28.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.016

Table S29.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
8Q GAIN MUTATED 60 75 93
8Q GAIN WILD-TYPE 59 136 63

Figure S29.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 4.24e-06 (Fisher's exact test), Q value = 0.0037

Table S30.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
8Q GAIN MUTATED 60 134 39
8Q GAIN WILD-TYPE 119 97 39

Figure S30.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.41e-05 (Fisher's exact test), Q value = 0.02

Table S31.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
8Q GAIN MUTATED 21 144 68
8Q GAIN WILD-TYPE 30 105 120

Figure S31.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.16

Table S32.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
8Q GAIN MUTATED 56 112 37
8Q GAIN WILD-TYPE 99 80 41

Figure S32.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0096

Table S33.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
8Q GAIN MUTATED 23 114 68
8Q GAIN WILD-TYPE 26 74 120

Figure S33.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.011

Table S34.  Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
10P GAIN MUTATED 38 41 14
10P GAIN WILD-TYPE 103 99 136

Figure S34.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 7.64e-05 (Chi-square test), Q value = 0.061

Table S35.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
10P GAIN MUTATED 27 10 20 37 9
10P GAIN WILD-TYPE 111 102 56 69 45

Figure S35.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.013

Table S36.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
10P GAIN MUTATED 21 29 53
10P GAIN WILD-TYPE 98 182 103

Figure S36.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1.62e-05 (Fisher's exact test), Q value = 0.014

Table S37.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
11P GAIN MUTATED 45 21 26
11P GAIN WILD-TYPE 141 195 65

Figure S37.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 2.8e-08 (Fisher's exact test), Q value = 2.6e-05

Table S38.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
11Q GAIN MUTATED 63 23 26
11Q GAIN WILD-TYPE 123 193 65

Figure S38.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000194 (Fisher's exact test), Q value = 0.15

Table S39.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
11Q GAIN MUTATED 35 30 47
11Q GAIN WILD-TYPE 84 181 109

Figure S39.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 5.15e-05 (Fisher's exact test), Q value = 0.042

Table S40.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
11Q GAIN MUTATED 21 65 23
11Q GAIN WILD-TYPE 158 166 55

Figure S40.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.66e-05 (Fisher's exact test), Q value = 0.069

Table S41.  Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
11Q GAIN MUTATED 18 67 24
11Q GAIN WILD-TYPE 33 182 164

Figure S41.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000317 (Fisher's exact test), Q value = 0.24

Table S42.  Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
11Q GAIN MUTATED 19 51 25
11Q GAIN WILD-TYPE 136 141 53

Figure S42.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00094

Table S43.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
12P GAIN MUTATED 50 38 43
12P GAIN WILD-TYPE 136 178 48

Figure S43.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 4.46e-09 (Chi-square test), Q value = 4.1e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
12P GAIN MUTATED 40 5 30 42 12
12P GAIN WILD-TYPE 98 107 46 64 42

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

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.3e-11 (Fisher's exact test), Q value = 4e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
12P GAIN MUTATED 30 28 71
12P GAIN WILD-TYPE 89 183 85

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

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
12P GAIN MUTATED 28 83 18
12P GAIN WILD-TYPE 151 148 60

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

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.81e-05 (Fisher's exact test), Q value = 0.015

Table S47.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
12P GAIN MUTATED 11 88 30
12P GAIN WILD-TYPE 40 161 158

Figure S47.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.62e-08 (Fisher's exact test), Q value = 6e-05

Table S48.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
12P GAIN MUTATED 18 73 23
12P GAIN WILD-TYPE 137 119 55

Figure S48.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.9e-08 (Fisher's exact test), Q value = 4.5e-05

Table S49.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
12P GAIN MUTATED 13 75 26
12P GAIN WILD-TYPE 36 113 162

Figure S49.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 3.78e-08 (Fisher's exact test), Q value = 3.5e-05

Table S50.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
12Q GAIN MUTATED 41 39 46
12Q GAIN WILD-TYPE 145 177 45

Figure S50.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1.14e-11 (Chi-square test), Q value = 1.1e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
12Q GAIN MUTATED 31 6 29 49 9
12Q GAIN WILD-TYPE 107 106 47 57 45

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

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.74e-12 (Fisher's exact test), Q value = 5.4e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
12Q GAIN MUTATED 27 26 71
12Q GAIN WILD-TYPE 92 185 85

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

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.01

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
12Q GAIN MUTATED 27 81 16
12Q GAIN WILD-TYPE 152 150 62

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

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.13e-06 (Fisher's exact test), Q value = 0.0027

Table S54.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
12Q GAIN MUTATED 12 86 26
12Q GAIN WILD-TYPE 39 163 162

Figure S54.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.22e-07 (Fisher's exact test), Q value = 2e-04

Table S55.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
12Q GAIN MUTATED 17 68 24
12Q GAIN WILD-TYPE 138 124 54

Figure S55.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6.19e-07 (Fisher's exact test), Q value = 0.00055

Table S56.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
12Q GAIN MUTATED 16 68 25
12Q GAIN WILD-TYPE 33 120 163

Figure S56.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 9.11e-09 (Fisher's exact test), Q value = 8.4e-06

Table S57.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
14Q GAIN MUTATED 47 30 43
14Q GAIN WILD-TYPE 139 186 48

Figure S57.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 7.43e-05 (Chi-square test), Q value = 0.059

Table S58.  Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
14Q GAIN MUTATED 37 19 9 42 11
14Q GAIN WILD-TYPE 101 93 67 64 43

Figure S58.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 3.2e-05 (Fisher's exact test), Q value = 0.026

Table S59.  Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
14Q GAIN MUTATED 23 69 25
14Q GAIN WILD-TYPE 156 162 53

Figure S59.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.67e-05 (Fisher's exact test), Q value = 0.022

Table S60.  Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
14Q GAIN MUTATED 18 74 25
14Q GAIN WILD-TYPE 33 175 163

Figure S60.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 6.84e-09 (Chi-square test), Q value = 6.3e-06

Table S61.  Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
15Q GAIN MUTATED 3 5 19 6 2
15Q GAIN WILD-TYPE 135 107 57 100 52

Figure S61.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 6.17e-05 (Fisher's exact test), Q value = 0.05

Table S62.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
17P GAIN MUTATED 28 25 30
17P GAIN WILD-TYPE 158 191 61

Figure S62.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0089

Table S63.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
17P GAIN MUTATED 16 58 7
17P GAIN WILD-TYPE 163 173 71

Figure S63.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1.72e-08 (Fisher's exact test), Q value = 1.6e-05

Table S64.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
17Q GAIN MUTATED 91 50 45
17Q GAIN WILD-TYPE 95 166 46

Figure S64.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 4.29e-05 (Chi-square test), Q value = 0.035

Table S65.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
17Q GAIN MUTATED 72 28 20 44 18
17Q GAIN WILD-TYPE 66 84 56 62 36

Figure S65.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.2e-06 (Fisher's exact test), Q value = 0.0054

Table S66.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
17Q GAIN MUTATED 62 55 65
17Q GAIN WILD-TYPE 57 156 91

Figure S66.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 8.91e-06 (Fisher's exact test), Q value = 0.0076

Table S67.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
17Q GAIN MUTATED 46 112 26
17Q GAIN WILD-TYPE 133 119 52

Figure S67.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 3.35e-05 (Fisher's exact test), Q value = 0.027

Table S68.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
18P GAIN MUTATED 47 21 23
18P GAIN WILD-TYPE 139 195 68

Figure S68.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 2.4e-05 (Fisher's exact test), Q value = 0.02

Table S69.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
18P GAIN MUTATED 40 27 12
18P GAIN WILD-TYPE 101 113 138

Figure S69.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.67e-05 (Fisher's exact test), Q value = 0.022

Table S70.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
18P GAIN MUTATED 7 53 19
18P GAIN WILD-TYPE 42 135 169

Figure S70.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.11

Table S71.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
18Q GAIN MUTATED 29 15 22
18Q GAIN WILD-TYPE 157 201 69

Figure S71.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1.61e-06 (Fisher's exact test), Q value = 0.0014

Table S72.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
18Q GAIN MUTATED 34 16 6
18Q GAIN WILD-TYPE 107 124 144

Figure S72.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1.81e-05 (Chi-square test), Q value = 0.015

Table S73.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
18Q GAIN MUTATED 14 8 9 30 4
18Q GAIN WILD-TYPE 124 104 67 76 50

Figure S73.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.6e-05 (Fisher's exact test), Q value = 0.021

Table S74.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
18Q GAIN MUTATED 13 15 37
18Q GAIN WILD-TYPE 106 196 119

Figure S74.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 6.66e-05 (Fisher's exact test), Q value = 0.053

Table S75.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
20P GAIN MUTATED 62 55 47
20P GAIN WILD-TYPE 124 161 44

Figure S75.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.000214 (Chi-square test), Q value = 0.17

Table S76.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
20P GAIN MUTATED 45 27 24 53 11
20P GAIN WILD-TYPE 93 85 52 53 43

Figure S76.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.56e-06 (Fisher's exact test), Q value = 0.0057

Table S77.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
20P GAIN MUTATED 43 46 71
20P GAIN WILD-TYPE 76 165 85

Figure S77.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.023

Table S78.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
20P GAIN MUTATED 37 92 33
20P GAIN WILD-TYPE 142 139 45

Figure S78.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.4e-06 (Fisher's exact test), Q value = 0.0047

Table S79.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
20P GAIN MUTATED 21 103 38
20P GAIN WILD-TYPE 30 146 150

Figure S79.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.15

Table S80.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
20P GAIN MUTATED 33 75 34
20P GAIN WILD-TYPE 122 117 44

Figure S80.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.77e-05 (Fisher's exact test), Q value = 0.023

Table S81.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
20P GAIN MUTATED 21 80 41
20P GAIN WILD-TYPE 28 108 147

Figure S81.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1.64e-07 (Fisher's exact test), Q value = 0.00015

Table S82.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
20Q GAIN MUTATED 80 56 53
20Q GAIN WILD-TYPE 106 160 38

Figure S82.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 4.47e-06 (Chi-square test), Q value = 0.0039

Table S83.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
20Q GAIN MUTATED 59 24 27 59 16
20Q GAIN WILD-TYPE 79 88 49 47 38

Figure S83.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.34e-07 (Fisher's exact test), Q value = 3e-04

Table S84.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
20Q GAIN MUTATED 54 52 79
20Q GAIN WILD-TYPE 65 159 77

Figure S84.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 2.04e-06 (Fisher's exact test), Q value = 0.0018

Table S85.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
20Q GAIN MUTATED 42 109 34
20Q GAIN WILD-TYPE 137 122 44

Figure S85.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.85e-07 (Fisher's exact test), Q value = 0.00061

Table S86.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
20Q GAIN MUTATED 23 118 44
20Q GAIN WILD-TYPE 28 131 144

Figure S86.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.77e-05 (Fisher's exact test), Q value = 0.015

Table S87.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
20Q GAIN MUTATED 38 92 35
20Q GAIN WILD-TYPE 117 100 43

Figure S87.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.69e-05 (Fisher's exact test), Q value = 0.014

Table S88.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
20Q GAIN MUTATED 22 93 50
20Q GAIN WILD-TYPE 27 95 138

Figure S88.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 5.78e-05 (Fisher's exact test), Q value = 0.047

Table S89.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
21Q GAIN MUTATED 54 31 9
21Q GAIN WILD-TYPE 132 185 82

Figure S89.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.016

Table S90.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
1P LOSS MUTATED 17 33 29
1P LOSS WILD-TYPE 169 183 62

Figure S90.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.000138 (Fisher's exact test), Q value = 0.11

Table S91.  Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
1P LOSS MUTATED 34 22 10
1P LOSS WILD-TYPE 107 118 140

Figure S91.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 9.66e-05 (Chi-square test), Q value = 0.077

Table S92.  Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
1P LOSS MUTATED 19 10 14 30 2
1P LOSS WILD-TYPE 119 102 62 76 52

Figure S92.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.017

Table S93.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
3P LOSS MUTATED 83 68 54
3P LOSS WILD-TYPE 103 148 37

Figure S93.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 4.81e-06 (Fisher's exact test), Q value = 0.0042

Table S94.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
3P LOSS MUTATED 82 48 48
3P LOSS WILD-TYPE 59 92 102

Figure S94.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.31e-06 (Fisher's exact test), Q value = 0.0046

Table S95.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
3P LOSS MUTATED 44 69 90
3P LOSS WILD-TYPE 75 142 66

Figure S95.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 4.45e-05 (Fisher's exact test), Q value = 0.036

Table S96.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
4P LOSS MUTATED 50 32 34
4P LOSS WILD-TYPE 136 184 57

Figure S96.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 8.76e-05 (Chi-square test), Q value = 0.07

Table S97.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
4P LOSS MUTATED 30 12 22 40 11
4P LOSS WILD-TYPE 108 100 54 66 43

Figure S97.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.23e-08 (Fisher's exact test), Q value = 7.5e-05

Table S98.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
4P LOSS MUTATED 23 30 62
4P LOSS WILD-TYPE 96 181 94

Figure S98.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 7.71e-06 (Fisher's exact test), Q value = 0.0066

Table S99.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
4P LOSS MUTATED 23 76 16
4P LOSS WILD-TYPE 156 155 62

Figure S99.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.55e-06 (Fisher's exact test), Q value = 0.0031

Table S100.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
4P LOSS MUTATED 6 82 27
4P LOSS WILD-TYPE 45 167 161

Figure S100.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 2.35e-06 (Fisher's exact test), Q value = 0.0021

Table S101.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
4Q LOSS MUTATED 56 36 40
4Q LOSS WILD-TYPE 130 180 51

Figure S101.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 9.39e-08 (Chi-square test), Q value = 8.5e-05

Table S102.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
4Q LOSS MUTATED 33 12 25 49 11
4Q LOSS WILD-TYPE 105 100 51 57 43

Figure S102.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.54e-13 (Fisher's exact test), Q value = 7.1e-10

Table S103.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
4Q LOSS MUTATED 24 30 76
4Q LOSS WILD-TYPE 95 181 80

Figure S103.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.77e-06 (Fisher's exact test), Q value = 0.0016

Table S104.  Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
4Q LOSS MUTATED 26 85 20
4Q LOSS WILD-TYPE 153 146 58

Figure S104.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.31e-07 (Fisher's exact test), Q value = 0.00021

Table S105.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
4Q LOSS MUTATED 11 93 27
4Q LOSS WILD-TYPE 40 156 161

Figure S105.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000287 (Fisher's exact test), Q value = 0.22

Table S106.  Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
4Q LOSS MUTATED 26 68 17
4Q LOSS WILD-TYPE 129 124 61

Figure S106.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000289 (Fisher's exact test), Q value = 0.22

Table S107.  Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
4Q LOSS MUTATED 11 67 33
4Q LOSS WILD-TYPE 38 121 155

Figure S107.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.91e-05 (Fisher's exact test), Q value = 0.024

Table S108.  Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
5P LOSS MUTATED 8 6 25
5P LOSS WILD-TYPE 111 205 131

Figure S108.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 2.49e-09 (Fisher's exact test), Q value = 2.3e-06

Table S109.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
5Q LOSS MUTATED 69 30 38
5Q LOSS WILD-TYPE 117 186 53

Figure S109.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1.55e-06 (Chi-square test), Q value = 0.0014

Table S110.  Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
5Q LOSS MUTATED 47 12 22 44 9
5Q LOSS WILD-TYPE 91 100 54 62 45

Figure S110.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.44e-08 (Fisher's exact test), Q value = 1.3e-05

Table S111.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
5Q LOSS MUTATED 37 31 66
5Q LOSS WILD-TYPE 82 180 90

Figure S111.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 9.39e-07 (Fisher's exact test), Q value = 0.00083

Table S112.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
5Q LOSS MUTATED 27 88 20
5Q LOSS WILD-TYPE 152 143 58

Figure S112.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.65e-06 (Fisher's exact test), Q value = 0.0023

Table S113.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
5Q LOSS MUTATED 12 93 30
5Q LOSS WILD-TYPE 39 156 158

Figure S113.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.96e-06 (Fisher's exact test), Q value = 0.006

Table S114.  Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 192 78
5Q LOSS MUTATED 25 75 18
5Q LOSS WILD-TYPE 130 117 60

Figure S114.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.6e-07 (Fisher's exact test), Q value = 0.00041

Table S115.  Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
5Q LOSS MUTATED 9 77 32
5Q LOSS WILD-TYPE 40 111 156

Figure S115.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 8.96e-05 (Fisher's exact test), Q value = 0.071

Table S116.  Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
6Q LOSS MUTATED 65 75 44
6Q LOSS WILD-TYPE 76 65 106

Figure S116.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 1.61e-05 (Fisher's exact test), Q value = 0.014

Table S117.  Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
7P LOSS MUTATED 5 11 17
7P LOSS WILD-TYPE 181 205 74

Figure S117.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 8.73e-19 (Fisher's exact test), Q value = 8.2e-16

Table S118.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
8P LOSS MUTATED 119 45 27
8P LOSS WILD-TYPE 67 171 64

Figure S118.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.000101 (Chi-square test), Q value = 0.08

Table S119.  Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
8P LOSS MUTATED 76 36 23 41 14
8P LOSS WILD-TYPE 62 76 53 65 40

Figure S119.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.94e-05 (Fisher's exact test), Q value = 0.032

Table S120.  Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
8P LOSS MUTATED 67 66 57
8P LOSS WILD-TYPE 52 145 99

Figure S120.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.000278 (Fisher's exact test), Q value = 0.22

Table S121.  Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
8Q LOSS MUTATED 34 16 4
8Q LOSS WILD-TYPE 152 200 87

Figure S121.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000154 (Fisher's exact test), Q value = 0.12

Table S122.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
9P LOSS MUTATED 53 96 102
9P LOSS WILD-TYPE 66 115 54

Figure S122.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 2.4e-05 (Fisher's exact test), Q value = 0.02

Table S123.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
9Q LOSS MUTATED 101 80 57
9Q LOSS WILD-TYPE 85 136 34

Figure S123.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.29e-06 (Fisher's exact test), Q value = 0.0079

Table S124.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
9Q LOSS MUTATED 53 83 100
9Q LOSS WILD-TYPE 66 128 56

Figure S124.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000173 (Fisher's exact test), Q value = 0.14

Table S125.  Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
9Q LOSS MUTATED 22 109 69
9Q LOSS WILD-TYPE 27 79 119

Figure S125.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 7.13e-07 (Fisher's exact test), Q value = 0.00064

Table S126.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
10P LOSS MUTATED 64 27 17
10P LOSS WILD-TYPE 122 189 74

Figure S126.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 7.29e-05 (Chi-square test), Q value = 0.058

Table S127.  Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
10P LOSS MUTATED 46 18 5 23 15
10P LOSS WILD-TYPE 92 94 71 83 39

Figure S127.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.95e-05 (Fisher's exact test), Q value = 0.016

Table S128.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
10Q LOSS MUTATED 69 36 23
10Q LOSS WILD-TYPE 117 180 68

Figure S128.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 7.93e-05 (Fisher's exact test), Q value = 0.063

Table S129.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
11P LOSS MUTATED 53 28 27
11P LOSS WILD-TYPE 133 188 64

Figure S129.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.014

Table S130.  Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
11P LOSS MUTATED 31 25 48
11P LOSS WILD-TYPE 88 186 108

Figure S130.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.013

Table S131.  Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
12Q LOSS MUTATED 54 32 7
12Q LOSS WILD-TYPE 132 184 84

Figure S131.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 2.62e-17 (Fisher's exact test), Q value = 2.5e-14

Table S132.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
13Q LOSS MUTATED 122 59 62
13Q LOSS WILD-TYPE 64 157 29

Figure S132.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2.79e-06 (Fisher's exact test), Q value = 0.0024

Table S133.  Gene #65: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 70 59
13Q LOSS MUTATED 64 16 31
13Q LOSS WILD-TYPE 42 54 28

Figure S133.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 3.09e-07 (Chi-square test), Q value = 0.00028

Table S134.  Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
13Q LOSS MUTATED 87 40 24 66 24
13Q LOSS WILD-TYPE 51 72 52 40 30

Figure S134.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.43e-06 (Fisher's exact test), Q value = 0.0047

Table S135.  Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
13Q LOSS MUTATED 76 79 86
13Q LOSS WILD-TYPE 43 132 70

Figure S135.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 7.26e-07 (Fisher's exact test), Q value = 0.00065

Table S136.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
15Q LOSS MUTATED 107 73 53
15Q LOSS WILD-TYPE 79 143 38

Figure S136.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 5.61e-13 (Chi-square test), Q value = 5.3e-10

Table S137.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
15Q LOSS MUTATED 92 36 13 61 26
15Q LOSS WILD-TYPE 46 76 63 45 28

Figure S137.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.0013

Table S138.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
15Q LOSS MUTATED 79 78 71
15Q LOSS WILD-TYPE 40 133 85

Figure S138.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.013

Table S139.  Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
15Q LOSS MUTATED 60 126 45
15Q LOSS WILD-TYPE 119 105 33

Figure S139.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 9.33e-06 (Fisher's exact test), Q value = 0.008

Table S140.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
16P LOSS MUTATED 49 27 32
16P LOSS WILD-TYPE 137 189 59

Figure S140.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 4.71e-05 (Chi-square test), Q value = 0.038

Table S141.  Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
16P LOSS MUTATED 42 10 14 34 8
16P LOSS WILD-TYPE 96 102 62 72 46

Figure S141.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.012

Table S142.  Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
16P LOSS MUTATED 37 26 45
16P LOSS WILD-TYPE 82 185 111

Figure S142.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 9.14e-06 (Fisher's exact test), Q value = 0.0078

Table S143.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
16Q LOSS MUTATED 64 37 36
16Q LOSS WILD-TYPE 122 179 55

Figure S143.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.000321 (Fisher's exact test), Q value = 0.25

Table S144.  Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
16Q LOSS MUTATED 45 49 24
16Q LOSS WILD-TYPE 96 91 126

Figure S144.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1.69e-07 (Chi-square test), Q value = 0.00015

Table S145.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
16Q LOSS MUTATED 59 15 16 39 8
16Q LOSS WILD-TYPE 79 97 60 67 46

Figure S145.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.53e-07 (Fisher's exact test), Q value = 0.00032

Table S146.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
16Q LOSS MUTATED 52 35 50
16Q LOSS WILD-TYPE 67 176 106

Figure S146.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.36e-05 (Fisher's exact test), Q value = 0.027

Table S147.  Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
16Q LOSS MUTATED 10 72 34
16Q LOSS WILD-TYPE 39 116 154

Figure S147.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 2.17e-11 (Fisher's exact test), Q value = 2e-08

Table S148.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
17P LOSS MUTATED 111 55 40
17P LOSS WILD-TYPE 75 161 51

Figure S148.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S149.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
17P LOSS MUTATED 56 77 46
17P LOSS WILD-TYPE 85 63 104

Figure S149.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.000114 (Fisher's exact test), Q value = 0.09

Table S150.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
17Q LOSS MUTATED 30 10 15
17Q LOSS WILD-TYPE 156 206 76

Figure S150.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 1.31e-05 (Fisher's exact test), Q value = 0.011

Table S151.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
18P LOSS MUTATED 88 55 26
18P LOSS WILD-TYPE 98 161 65

Figure S151.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 3.76e-10 (Fisher's exact test), Q value = 3.5e-07

Table S152.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
18Q LOSS MUTATED 113 68 26
18Q LOSS WILD-TYPE 73 148 65

Figure S152.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.000269 (Fisher's exact test), Q value = 0.21

Table S153.  Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 106 70 59
18Q LOSS MUTATED 63 20 26
18Q LOSS WILD-TYPE 43 50 33

Figure S153.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.000277 (Chi-square test), Q value = 0.22

Table S154.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
18Q LOSS MUTATED 79 39 33 33 20
18Q LOSS WILD-TYPE 59 73 43 73 34

Figure S154.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 5.34e-08 (Fisher's exact test), Q value = 4.9e-05

Table S155.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
19P LOSS MUTATED 99 74 62
19P LOSS WILD-TYPE 87 142 29

Figure S155.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1.2e-10 (Fisher's exact test), Q value = 1.1e-07

Table S156.  Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
19P LOSS MUTATED 96 60 44
19P LOSS WILD-TYPE 45 80 106

Figure S156.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 7.15e-07 (Chi-square test), Q value = 0.00064

Table S157.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
19P LOSS MUTATED 63 39 42 73 17
19P LOSS WILD-TYPE 75 73 34 33 37

Figure S157.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.35e-07 (Fisher's exact test), Q value = 0.00021

Table S158.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
19P LOSS MUTATED 55 77 102
19P LOSS WILD-TYPE 64 134 54

Figure S158.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 2.5e-05 (Fisher's exact test), Q value = 0.021

Table S159.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
19P LOSS MUTATED 65 134 31
19P LOSS WILD-TYPE 114 97 47

Figure S159.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.18e-07 (Fisher's exact test), Q value = 0.00029

Table S160.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
19P LOSS MUTATED 15 147 68
19P LOSS WILD-TYPE 36 102 120

Figure S160.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.014

Table S161.  Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
19P LOSS MUTATED 18 112 69
19P LOSS WILD-TYPE 31 76 119

Figure S161.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1.47e-07 (Fisher's exact test), Q value = 0.00013

Table S162.  Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
19Q LOSS MUTATED 76 39 38
19Q LOSS WILD-TYPE 110 177 53

Figure S162.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 8.18e-07 (Fisher's exact test), Q value = 0.00073

Table S163.  Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
19Q LOSS MUTATED 60 47 23
19Q LOSS WILD-TYPE 81 93 127

Figure S163.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.000103 (Chi-square test), Q value = 0.082

Table S164.  Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
19Q LOSS MUTATED 48 23 22 50 10
19Q LOSS WILD-TYPE 90 89 54 56 44

Figure S164.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000177 (Fisher's exact test), Q value = 0.14

Table S165.  Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
19Q LOSS MUTATED 43 46 64
19Q LOSS WILD-TYPE 76 165 92

Figure S165.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.8e-05 (Fisher's exact test), Q value = 0.062

Table S166.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
19Q LOSS MUTATED 12 98 39
19Q LOSS WILD-TYPE 39 151 149

Figure S166.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 7.21e-07 (Fisher's exact test), Q value = 0.00064

Table S167.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
21Q LOSS MUTATED 50 56 51
21Q LOSS WILD-TYPE 136 160 40

Figure S167.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 2.26e-10 (Chi-square test), Q value = 2.1e-07

Table S168.  Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
21Q LOSS MUTATED 40 14 30 58 11
21Q LOSS WILD-TYPE 98 98 46 48 43

Figure S168.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.86e-09 (Fisher's exact test), Q value = 5.4e-06

Table S169.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
21Q LOSS MUTATED 33 42 78
21Q LOSS WILD-TYPE 86 169 78

Figure S169.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.37e-06 (Fisher's exact test), Q value = 0.0012

Table S170.  Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
21Q LOSS MUTATED 9 105 40
21Q LOSS WILD-TYPE 42 144 148

Figure S170.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1.06e-09 (Fisher's exact test), Q value = 9.9e-07

Table S171.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 186 216 91
22Q LOSS MUTATED 94 60 58
22Q LOSS WILD-TYPE 92 156 33

Figure S171.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 2.8e-05 (Fisher's exact test), Q value = 0.023

Table S172.  Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 140 150
22Q LOSS MUTATED 70 74 43
22Q LOSS WILD-TYPE 71 66 107

Figure S172.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 8.98e-08 (Chi-square test), Q value = 8.2e-05

Table S173.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 138 112 76 106 54
22Q LOSS MUTATED 70 30 34 63 11
22Q LOSS WILD-TYPE 68 82 42 43 43

Figure S173.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.38e-07 (Fisher's exact test), Q value = 0.00048

Table S174.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 211 156
22Q LOSS MUTATED 59 62 87
22Q LOSS WILD-TYPE 60 149 69

Figure S174.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.000205 (Fisher's exact test), Q value = 0.16

Table S175.  Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 231 78
22Q LOSS MUTATED 56 119 33
22Q LOSS WILD-TYPE 123 112 45

Figure S175.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.04e-07 (Fisher's exact test), Q value = 8e-04

Table S176.  Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 249 188
22Q LOSS MUTATED 12 134 62
22Q LOSS WILD-TYPE 39 115 126

Figure S176.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.35e-05 (Fisher's exact test), Q value = 0.027

Table S177.  Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 188 188
22Q LOSS MUTATED 16 104 63
22Q LOSS WILD-TYPE 33 84 125

Figure S177.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 493

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Chi-square test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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