Correlation between copy number variations of arm-level result and molecular subtypes
Stomach Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C13F4N36
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/C13F4N36
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 79 arm-level events and 10 molecular subtypes across 331 patients, 170 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 2q gain cnv correlated to 'CN_CNMF'.

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

  • 6p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'MIRSEQ_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 20p gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 1q loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 5p loss cnv correlated to 'CN_CNMF'.

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

  • 6p loss cnv correlated to 'CN_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 7q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

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

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

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

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

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

  • 13q loss cnv correlated to 'CN_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • 17q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

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

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

  • 20p loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

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

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

  • xq loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 170 significant findings detected.

Clinical
Features 		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 Chi-square 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
6p gain 59 (18%) 272 2.15e-09
(1.63e-06) 		6.87e-08
(5.11e-05) 		0.106
(1.00) 		0.266
(1.00) 		0.000219
(0.139) 		7.52e-05
(0.0493) 		1.05e-05
(0.00726) 		0.000206
(0.131) 		0.000116
(0.0753) 		3.8e-06
(0.00271)
16p loss 70 (21%) 261 5.55e-16
(4.35e-13) 		3.48e-06
(0.00248) 		0.812
(1.00) 		0.807
(1.00) 		4.08e-10
(3.12e-07) 		5.3e-07
(0.000388) 		1.71e-06
(0.00124) 		0.000183
(0.117) 		3.1e-06
(0.00222) 		4.86e-06
(0.00343)
19p loss 81 (24%) 250 2.65e-19
(2.09e-16) 		3.11e-12
(2.4e-09) 		0.00996
(1.00) 		0.485
(1.00) 		6.18e-13
(4.8e-10) 		2.22e-12
(1.72e-09) 		5.43e-07
(0.000397) 		2.95e-13
(2.29e-10) 		0.000228
(0.145) 		5.74e-11
(4.41e-08)
5p gain 73 (22%) 258 5.75e-16
(4.5e-13) 		6.2e-06
(0.00435) 		0.275
(1.00) 		0.64
(1.00) 		8.17e-06
(0.0057) 		6.29e-05
(0.0416) 		2.57e-05
(0.0174) 		2.42e-05
(0.0164) 		0.000649
(0.394) 		5.11e-06
(0.0036)
20q gain 209 (63%) 122 3.87e-16
(3.04e-13) 		9.57e-10
(7.29e-07) 		0.044
(1.00) 		0.971
(1.00) 		1.02e-06
(0.000743) 		7.6e-05
(0.0497) 		2.26e-06
(0.00163) 		1.03e-09
(7.87e-07) 		0.0463
(1.00) 		2.37e-09
(1.79e-06)
5q loss 72 (22%) 259 4.36e-12
(3.37e-09) 		4.68e-06
(0.00331) 		0.615
(1.00) 		0.929
(1.00) 		2.34e-07
(0.000172) 		6.63e-06
(0.00464) 		0.0003
(0.188) 		1.15e-06
(0.000836) 		0.000642
(0.391) 		2.99e-08
(2.24e-05)
9p loss 103 (31%) 228 6.89e-18
(5.43e-15) 		1.43e-07
(0.000106) 		0.00104
(0.616) 		0.0388
(1.00) 		1.72e-08
(1.29e-05) 		5.88e-05
(0.039) 		0.000317
(0.199) 		8.3e-06
(0.00579) 		0.229
(1.00) 		4.06e-06
(0.00288)
15q loss 67 (20%) 264 2.99e-07
(0.000219) 		4.6e-05
(0.0307) 		0.00512
(1.00) 		0.0693
(1.00) 		7.74e-05
(0.0505) 		7.52e-05
(0.0493) 		0.000209
(0.133) 		1.25e-05
(0.0086) 		0.00245
(1.00) 		9.84e-05
(0.0641)
16q loss 79 (24%) 252 1.19e-13
(9.24e-11) 		1.83e-07
(0.000135) 		0.0464
(1.00) 		0.564
(1.00) 		6.97e-08
(5.17e-05) 		1.39e-05
(0.00951) 		9.52e-06
(0.0066) 		7.61e-05
(0.0497) 		0.00296
(1.00) 		1.33e-05
(0.00917)
17p loss 115 (35%) 216 2.81e-20
(2.22e-17) 		1.76e-09
(1.34e-06) 		0.463
(1.00) 		0.809
(1.00) 		4.44e-06
(0.00315) 		1.74e-06
(0.00125) 		0.000134
(0.0865) 		1.38e-05
(0.00949) 		0.00278
(1.00) 		4.59e-08
(3.43e-05)
19q loss 62 (19%) 269 1.62e-14
(1.27e-11) 		5.88e-10
(4.49e-07) 		0.0174
(1.00) 		0.1
(1.00) 		1.55e-07
(0.000115) 		2.43e-06
(0.00175) 		3.42e-05
(0.023) 		1.7e-09
(1.29e-06) 		0.000656
(0.398) 		5.02e-08
(3.73e-05)
6q gain 49 (15%) 282 1e-08
(7.55e-06) 		2.01e-05
(0.0137) 		0.123
(1.00) 		0.555
(1.00) 		5.91e-05
(0.0392) 		0.000499
(0.308) 		5.15e-05
(0.0342) 		0.0227
(1.00) 		0.000349
(0.218) 		7.22e-05
(0.0474)
4p loss 122 (37%) 209 4.27e-16
(3.35e-13) 		3.46e-06
(0.00247) 		0.284
(1.00) 		0.56
(1.00) 		0.000349
(0.218) 		0.00113
(0.668) 		1.47e-05
(0.01) 		4.33e-08
(3.24e-05) 		0.00792
(1.00) 		2.22e-06
(0.0016)
3q loss 38 (11%) 293 2.45e-06
(0.00176) 		2.59e-06
(0.00186) 		0.198
(1.00) 		0.292
(1.00) 		7.5e-06
(0.00524) 		4.31e-05
(0.0289) 		4.7e-05
(0.0313) 		0.00126
(0.738) 		0.00584
(1.00) 		0.00447
(1.00)
4q loss 121 (37%) 210 7.16e-18
(5.63e-15) 		1.72e-06
(0.00125) 		0.0709
(1.00) 		0.374
(1.00) 		0.00687
(1.00) 		0.00113
(0.668) 		0.000177
(0.113) 		3.98e-07
(0.000292) 		0.0306
(1.00) 		9.81e-06
(0.0068)
12p loss 45 (14%) 286 5.56e-12
(4.29e-09) 		7.67e-08
(5.68e-05) 		0.249
(1.00) 		0.51
(1.00) 		1.92e-05
(0.0131) 		0.000519
(0.319) 		0.00316
(1.00) 		3.78e-05
(0.0253) 		0.0551
(1.00) 		1.7e-07
(0.000126)
22q loss 101 (31%) 230 1.97e-15
(1.54e-12) 		2.66e-06
(0.00191) 		0.0151
(1.00) 		0.484
(1.00) 		0.000971
(0.578) 		0.00173
(0.996) 		5.75e-06
(0.00403) 		3.89e-08
(2.91e-05) 		0.0342
(1.00) 		1.34e-06
(0.000971)
2p gain 56 (17%) 275 4.72e-06
(0.00334) 		0.018
(1.00) 		0.0484
(1.00) 		0.94
(1.00) 		0.0661
(1.00) 		0.238
(1.00) 		0.000254
(0.16) 		0.00384
(1.00) 		0.00369
(1.00) 		7e-05
(0.0461)
18p gain 62 (19%) 269 6.45e-05
(0.0426) 		3.81e-06
(0.00271) 		0.106
(1.00) 		0.61
(1.00) 		0.0158
(1.00) 		0.076
(1.00) 		0.00574
(1.00) 		0.000133
(0.0859) 		0.0595
(1.00) 		0.00134
(0.783)
20p gain 182 (55%) 149 9.26e-12
(7.14e-09) 		0.000669
(0.405) 		0.0842
(1.00) 		0.704
(1.00) 		0.000777
(0.469) 		0.00863
(1.00) 		0.000438
(0.271) 		5.98e-05
(0.0396) 		0.0168
(1.00) 		0.000142
(0.0915)
21q gain 20 (6%) 311 1.06e-06
(0.000774) 		0.000882
(0.528) 		0.14
(1.00) 		0.666
(1.00) 		0.0101
(1.00) 		0.0656
(1.00) 		0.0175
(1.00) 		0.000153
(0.0988) 		0.119
(1.00) 		3.84e-05
(0.0257)
9q loss 72 (22%) 259 1.36e-08
(1.02e-05) 		0.000868
(0.521) 		0.13
(1.00) 		0.316
(1.00) 		1.31e-05
(0.00903) 		0.00175
(1.00) 		0.00467
(1.00) 		0.00143
(0.828) 		0.0744
(1.00) 		0.000375
(0.233)
14q loss 81 (24%) 250 4.76e-08
(3.55e-05) 		0.00529
(1.00) 		0.559
(1.00) 		0.471
(1.00) 		0.000608
(0.371) 		0.00025
(0.158) 		0.000465
(0.288) 		0.00238
(1.00) 		0.0331
(1.00) 		2.08e-05
(0.0142)
17q loss 54 (16%) 277 8.07e-09
(6.09e-06) 		3.33e-05
(0.0225) 		0.283
(1.00) 		1
(1.00) 		0.00232
(1.00) 		0.000499
(0.308) 		0.000576
(0.353) 		0.0009
(0.538) 		0.0541
(1.00) 		0.000236
(0.15)
21q loss 120 (36%) 211 8.67e-11
(6.65e-08) 		0.000154
(0.0995) 		0.101
(1.00) 		0.28
(1.00) 		0.031
(1.00) 		6.65e-05
(0.0438) 		0.00559
(1.00) 		0.00663
(1.00) 		0.0117
(1.00) 		0.0129
(1.00)
1p gain 37 (11%) 294 8.75e-06
(0.00609) 		0.168
(1.00) 		0.00284
(1.00) 		0.0956
(1.00) 		0.0124
(1.00) 		0.386
(1.00) 		0.0683
(1.00) 		0.2
(1.00) 		0.000384
(0.238) 		0.0827
(1.00)
1q gain 80 (24%) 251 1.52e-10
(1.16e-07) 		0.00317
(1.00) 		0.0274
(1.00) 		0.155
(1.00) 		1.39e-05
(0.00951) 		0.00484
(1.00) 		0.000811
(0.488) 		0.00152
(0.878) 		0.00701
(1.00) 		0.00345
(1.00)
7p gain 145 (44%) 186 1.28e-11
(9.82e-09) 		0.000299
(0.188) 		0.794
(1.00) 		0.907
(1.00) 		0.217
(1.00) 		0.103
(1.00) 		0.273
(1.00) 		0.108
(1.00) 		0.0904
(1.00) 		0.00227
(1.00)
10p gain 80 (24%) 251 4.4e-14
(3.43e-11) 		1.7e-05
(0.0116) 		0.104
(1.00) 		0.429
(1.00) 		0.00075
(0.453) 		0.0199
(1.00) 		0.00798
(1.00) 		0.000548
(0.336) 		0.0849
(1.00) 		0.00209
(1.00)
13q gain 111 (34%) 220 7.58e-11
(5.82e-08) 		0.00212
(1.00) 		0.567
(1.00) 		0.348
(1.00) 		0.0222
(1.00) 		0.796
(1.00) 		0.00133
(0.776) 		0.00251
(1.00) 		0.0117
(1.00) 		0.000223
(0.142)
12q loss 34 (10%) 297 3.85e-09
(2.91e-06) 		1.89e-05
(0.0129) 		0.497
(1.00) 		1
(1.00) 		0.00256
(1.00) 		0.101
(1.00) 		0.2
(1.00) 		0.00117
(0.691) 		0.498
(1.00) 		0.00255
(1.00)
20p loss 16 (5%) 315 0.0193
(1.00) 		0.000113
(0.0734) 		1
(1.00) 		0.525
(1.00) 		0.000249
(0.157) 		0.268
(1.00) 		0.0676
(1.00) 		0.756
(1.00) 		0.726
(1.00) 		0.356
(1.00)
2q gain 49 (15%) 282 0.00016
(0.103) 		0.282
(1.00) 		0.352
(1.00) 		0.555
(1.00) 		0.0134
(1.00) 		0.0813
(1.00) 		0.0155
(1.00) 		0.0372
(1.00) 		0.0222
(1.00) 		0.00709
(1.00)
7q gain 124 (37%) 207 1.18e-10
(9.07e-08) 		0.00205
(1.00) 		0.936
(1.00) 		0.672
(1.00) 		0.573
(1.00) 		0.363
(1.00) 		0.947
(1.00) 		0.795
(1.00) 		0.638
(1.00) 		0.151
(1.00)
8p gain 140 (42%) 191 0.000237
(0.15) 		0.274
(1.00) 		0.488
(1.00) 		0.621
(1.00) 		0.296
(1.00) 		0.106
(1.00) 		0.745
(1.00) 		0.85
(1.00) 		0.041
(1.00) 		0.516
(1.00)
10q gain 55 (17%) 276 1.26e-12
(9.77e-10) 		0.014
(1.00) 		0.128
(1.00) 		0.562
(1.00) 		0.0106
(1.00) 		0.0358
(1.00) 		0.0178
(1.00) 		0.0798
(1.00) 		0.287
(1.00) 		0.0117
(1.00)
11q gain 43 (13%) 288 0.00141
(0.82) 		0.00407
(1.00) 		0.878
(1.00) 		0.608
(1.00) 		0.27
(1.00) 		0.00596
(1.00) 		0.000326
(0.203) 		0.00939
(1.00) 		0.014
(1.00) 		0.00843
(1.00)
1p loss 43 (13%) 288 7.19e-08
(5.33e-05) 		0.00892
(1.00) 		0.0562
(1.00) 		0.586
(1.00) 		0.0353
(1.00) 		0.0592
(1.00) 		0.00657
(1.00) 		0.00341
(1.00) 		0.214
(1.00) 		0.0158
(1.00)
1q loss 20 (6%) 311 3.57e-05
(0.024) 		0.00738
(1.00) 		0.0328
(1.00) 		0.0735
(1.00) 		0.487
(1.00) 		0.0424
(1.00) 		0.354
(1.00) 		0.221
(1.00) 		0.451
(1.00) 		0.155
(1.00)
3p loss 63 (19%) 268 5.14e-06
(0.00362) 		0.000929
(0.554) 		0.331
(1.00) 		0.455
(1.00) 		0.00177
(1.00) 		0.000871
(0.522) 		0.00139
(0.813) 		0.0569
(1.00) 		0.0607
(1.00) 		0.0148
(1.00)
5p loss 42 (13%) 289 1.12e-05
(0.00776) 		0.00131
(0.767) 		0.317
(1.00) 		0.441
(1.00) 		0.000605
(0.37) 		0.00368
(1.00) 		0.0613
(1.00) 		0.0179
(1.00) 		0.0241
(1.00) 		0.00159
(0.921)
6p loss 36 (11%) 295 2.11e-05
(0.0143) 		0.00531
(1.00) 		0.146
(1.00) 		0.256
(1.00) 		0.0248
(1.00) 		0.0408
(1.00) 		0.212
(1.00) 		0.00433
(1.00) 		0.168
(1.00) 		0.00114
(0.674)
6q loss 47 (14%) 284 0.000192
(0.123) 		0.00795
(1.00) 		0.749
(1.00) 		0.752
(1.00) 		0.0308
(1.00) 		0.154
(1.00) 		0.558
(1.00) 		0.032
(1.00) 		0.706
(1.00) 		0.0296
(1.00)
7q loss 21 (6%) 310 2.84e-05
(0.0192) 		0.0332
(1.00) 		0.445
(1.00) 		0.782
(1.00) 		0.00216
(1.00) 		0.0551
(1.00) 		0.0686
(1.00) 		0.0346
(1.00) 		0.00234
(1.00) 		0.0511
(1.00)
8p loss 57 (17%) 274 7.87e-07
(0.000574) 		0.115
(1.00) 		0.388
(1.00) 		0.341
(1.00) 		0.00517
(1.00) 		0.0029
(1.00) 		0.00166
(0.957) 		0.0011
(0.651) 		0.00596
(1.00) 		0.0394
(1.00)
10p loss 38 (11%) 293 9.18e-06
(0.00638) 		0.0431
(1.00) 		0.604
(1.00) 		0.399
(1.00) 		0.0197
(1.00) 		0.0139
(1.00) 		0.0144
(1.00) 		0.0471
(1.00) 		0.144
(1.00) 		0.056
(1.00)
10q loss 44 (13%) 287 4.73e-08
(3.53e-05) 		0.00173
(0.992) 		0.593
(1.00) 		0.54
(1.00) 		0.00107
(0.635) 		0.00941
(1.00) 		0.0587
(1.00) 		0.0229
(1.00) 		0.531
(1.00) 		0.0593
(1.00)
11p loss 47 (14%) 284 3e-06
(0.00214) 		0.000865
(0.52) 		0.0196
(1.00) 		0.705
(1.00) 		0.0635
(1.00) 		0.0191
(1.00) 		0.565
(1.00) 		0.0221
(1.00) 		0.398
(1.00) 		0.0303
(1.00)
13q loss 30 (9%) 301 0.000167
(0.107) 		0.951
(1.00) 		0.676
(1.00) 		0.138
(1.00) 		0.279
(1.00) 		0.539
(1.00) 		0.728
(1.00) 		0.445
(1.00) 		0.315
(1.00) 		0.819
(1.00)
18p loss 92 (28%) 239 4.41e-05
(0.0294) 		0.63
(1.00) 		0.703
(1.00) 		0.131
(1.00) 		0.451
(1.00) 		0.309
(1.00) 		0.0658
(1.00) 		0.478
(1.00) 		0.0498
(1.00) 		0.365
(1.00)
18q loss 116 (35%) 215 2.17e-08
(1.63e-05) 		0.0364
(1.00) 		0.338
(1.00) 		0.366
(1.00) 		0.0125
(1.00) 		0.0242
(1.00) 		0.00255
(1.00) 		0.0138
(1.00) 		0.118
(1.00) 		0.0126
(1.00)
xq loss 41 (12%) 290 5.33e-06
(0.00374) 		0.00714
(1.00) 		0.479
(1.00) 		0.901
(1.00) 		0.037
(1.00) 		0.0122
(1.00) 		0.0488
(1.00) 		0.499
(1.00) 		0.0225
(1.00) 		0.879
(1.00)
3p gain 38 (11%) 293 0.015
(1.00) 		0.132
(1.00) 		0.789
(1.00) 		0.0761
(1.00) 		0.648
(1.00) 		0.437
(1.00) 		0.565
(1.00) 		0.125
(1.00) 		0.42
(1.00) 		0.0455
(1.00)
3q gain 62 (19%) 269 0.0621
(1.00) 		0.252
(1.00) 		0.852
(1.00) 		0.326
(1.00) 		0.193
(1.00) 		0.0628
(1.00) 		0.932
(1.00) 		0.77
(1.00) 		0.755
(1.00) 		0.379
(1.00)
4p gain 12 (4%) 319 0.26
(1.00) 		0.854
(1.00) 		1
(1.00) 		1
(1.00) 		0.517
(1.00) 		0.47
(1.00) 		0.536
(1.00) 		0.367
(1.00) 		0.915
(1.00) 		0.452
(1.00)
4q gain 8 (2%) 323 0.645
(1.00) 		0.848
(1.00) 		0.867
(1.00) 		0.723
(1.00) 		0.158
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.597
(1.00) 		0.785
(1.00) 		0.612
(1.00)
5q gain 29 (9%) 302 0.002
(1.00) 		0.186
(1.00) 		0.644
(1.00) 		0.733
(1.00) 		0.0933
(1.00) 		0.125
(1.00) 		0.0919
(1.00) 		0.118
(1.00) 		0.191
(1.00) 		0.144
(1.00)
8q gain 186 (56%) 145 0.00618
(1.00) 		0.013
(1.00) 		0.712
(1.00) 		0.0715
(1.00) 		0.0256
(1.00) 		0.302
(1.00) 		0.0291
(1.00) 		0.0426
(1.00) 		0.000735
(0.444) 		0.0557
(1.00)
9p gain 42 (13%) 289 0.154
(1.00) 		0.534
(1.00) 		0.551
(1.00) 		0.59
(1.00) 		0.359
(1.00) 		0.415
(1.00) 		0.676
(1.00) 		0.71
(1.00) 		0.808
(1.00) 		0.333
(1.00)
9q gain 52 (16%) 279 0.219
(1.00) 		0.196
(1.00) 		0.32
(1.00) 		0.732
(1.00) 		0.61
(1.00) 		0.493
(1.00) 		0.837
(1.00) 		0.829
(1.00) 		0.875
(1.00) 		0.484
(1.00)
11p gain 35 (11%) 296 0.0409
(1.00) 		0.0133
(1.00) 		0.897
(1.00) 		0.81
(1.00) 		0.248
(1.00) 		0.0072
(1.00) 		0.00148
(0.861) 		0.0331
(1.00) 		0.201
(1.00) 		0.0516
(1.00)
12p gain 66 (20%) 265 0.0129
(1.00) 		0.0953
(1.00) 		0.24
(1.00) 		0.141
(1.00) 		0.154
(1.00) 		0.312
(1.00) 		0.071
(1.00) 		0.79
(1.00) 		0.0109
(1.00) 		0.217
(1.00)
12q gain 58 (18%) 273 0.0389
(1.00) 		0.0268
(1.00) 		0.407
(1.00) 		0.179
(1.00) 		0.958
(1.00) 		0.777
(1.00) 		0.688
(1.00) 		0.745
(1.00) 		0.14
(1.00) 		0.779
(1.00)
14q gain 19 (6%) 312 0.00647
(1.00) 		0.274
(1.00) 		0.933
(1.00) 		0.541
(1.00) 		0.778
(1.00) 		0.93
(1.00) 		0.115
(1.00) 		0.937
(1.00) 		0.202
(1.00) 		0.729
(1.00)
15q gain 26 (8%) 305 0.00166
(0.958) 		0.0536
(1.00) 		0.233
(1.00) 		0.783
(1.00) 		0.0266
(1.00) 		0.066
(1.00) 		0.625
(1.00) 		0.209
(1.00) 		0.569
(1.00) 		0.0275
(1.00)
16p gain 45 (14%) 286 0.145
(1.00) 		0.0548
(1.00) 		0.38
(1.00) 		0.151
(1.00) 		0.0667
(1.00) 		0.343
(1.00) 		0.76
(1.00) 		0.0896
(1.00) 		0.943
(1.00) 		0.495
(1.00)
16q gain 34 (10%) 297 0.276
(1.00) 		0.342
(1.00) 		0.688
(1.00) 		0.146
(1.00) 		0.198
(1.00) 		0.373
(1.00) 		0.707
(1.00) 		0.13
(1.00) 		1
(1.00) 		0.887
(1.00)
17p gain 21 (6%) 310 0.0202
(1.00) 		0.596
(1.00) 		0.727
(1.00) 		0.2
(1.00) 		0.283
(1.00) 		0.734
(1.00) 		0.542
(1.00) 		0.0944
(1.00) 		0.601
(1.00) 		0.791
(1.00)
17q gain 40 (12%) 291 0.0118
(1.00) 		0.283
(1.00) 		0.937
(1.00) 		0.94
(1.00) 		0.473
(1.00) 		0.36
(1.00) 		0.787
(1.00) 		0.805
(1.00) 		0.751
(1.00) 		1
(1.00)
18q gain 43 (13%) 288 0.00368
(1.00) 		0.0024
(1.00) 		0.473
(1.00) 		0.481
(1.00) 		0.325
(1.00) 		0.649
(1.00) 		0.0395
(1.00) 		0.0229
(1.00) 		0.0825
(1.00) 		0.118
(1.00)
19p gain 41 (12%) 290 0.0815
(1.00) 		0.558
(1.00) 		0.382
(1.00) 		0.0574
(1.00) 		0.743
(1.00) 		0.731
(1.00) 		0.806
(1.00) 		0.637
(1.00) 		0.472
(1.00) 		0.746
(1.00)
19q gain 56 (17%) 275 0.0138
(1.00) 		0.192
(1.00) 		0.192
(1.00) 		0.114
(1.00) 		0.0424
(1.00) 		0.122
(1.00) 		0.157
(1.00) 		0.198
(1.00) 		0.285
(1.00) 		0.237
(1.00)
22q gain 26 (8%) 305 0.00976
(1.00) 		0.194
(1.00) 		0.834
(1.00) 		0.392
(1.00) 		0.236
(1.00) 		0.645
(1.00) 		0.456
(1.00) 		0.639
(1.00) 		0.373
(1.00) 		0.575
(1.00)
xq gain 42 (13%) 289 0.000411
(0.255) 		0.0195
(1.00) 		0.46
(1.00) 		0.152
(1.00) 		0.0616
(1.00) 		0.344
(1.00) 		0.0112
(1.00) 		0.451
(1.00) 		0.0623
(1.00) 		0.0362
(1.00)
2p loss 18 (5%) 313 0.00543
(1.00) 		0.0194
(1.00) 		0.52
(1.00) 		0.769
(1.00) 		0.0663
(1.00) 		0.289
(1.00) 		0.128
(1.00) 		0.108
(1.00) 		0.333
(1.00) 		0.538
(1.00)
2q loss 20 (6%) 311 0.00314
(1.00) 		0.00829
(1.00) 		0.852
(1.00) 		0.653
(1.00) 		0.0502
(1.00) 		0.511
(1.00) 		0.0504
(1.00) 		0.0198
(1.00) 		0.227
(1.00) 		0.171
(1.00)
7p loss 11 (3%) 320 0.0061
(1.00) 		0.0978
(1.00) 		0.405
(1.00) 		0.78
(1.00) 		0.000538
(0.33) 		0.139
(1.00) 		0.198
(1.00) 		0.118
(1.00) 		0.0101
(1.00) 		0.0334
(1.00)
8q loss 17 (5%) 314 0.0232
(1.00) 		0.446
(1.00) 		1
(1.00) 		0.679
(1.00) 		0.868
(1.00) 		0.255
(1.00) 		0.315
(1.00) 		0.614
(1.00) 		0.814
(1.00) 		0.47
(1.00)
11q loss 43 (13%) 288 0.00656
(1.00) 		0.107
(1.00) 		0.517
(1.00) 		0.955
(1.00) 		0.714
(1.00) 		0.528
(1.00) 		0.636
(1.00) 		0.221
(1.00) 		0.712
(1.00) 		0.236
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 8.75e-06 (Chi-square test), Q value = 0.0061

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
1P GAIN MUTATED 3 4 7 2 21 0
1P GAIN WILD-TYPE 148 23 48 11 61 3

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

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000384 (Fisher's exact test), Q value = 0.24

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
1P GAIN MUTATED 0 21 6
1P GAIN WILD-TYPE 64 110 73

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 1.52e-10 (Chi-square test), Q value = 1.2e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
1Q GAIN MUTATED 10 12 14 6 37 1
1Q GAIN WILD-TYPE 141 15 41 7 45 2

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1.39e-05 (Chi-square test), Q value = 0.0095

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
1Q GAIN MUTATED 11 7 9 9 30
1Q GAIN WILD-TYPE 54 55 37 28 32

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 4.72e-06 (Chi-square test), Q value = 0.0033

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
2P GAIN MUTATED 8 9 15 1 23 0
2P GAIN WILD-TYPE 143 18 40 12 59 3

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.000254 (Fisher's exact test), Q value = 0.16

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
2P GAIN MUTATED 13 9 33
2P GAIN WILD-TYPE 92 92 82

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.046

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
2P GAIN MUTATED 22 22 5
2P GAIN WILD-TYPE 42 107 76

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00016 (Chi-square test), Q value = 0.1

Table S8.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
2Q GAIN MUTATED 8 8 12 1 20 0
2Q GAIN WILD-TYPE 143 19 43 12 62 3

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 5.75e-16 (Chi-square test), Q value = 4.5e-13

Table S9.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
5P GAIN MUTATED 13 2 9 2 47 0
5P GAIN WILD-TYPE 138 25 46 11 35 3

Figure S9.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 6.2e-06 (Fisher's exact test), Q value = 0.0043

Table S10.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
5P GAIN MUTATED 6 14 4 31
5P GAIN WILD-TYPE 31 66 61 45

Figure S10.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 8.17e-06 (Chi-square test), Q value = 0.0057

Table S11.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
5P GAIN MUTATED 10 5 8 8 28
5P GAIN WILD-TYPE 55 57 38 29 34

Figure S11.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.29e-05 (Fisher's exact test), Q value = 0.042

Table S12.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
5P GAIN MUTATED 26 25 8
5P GAIN WILD-TYPE 43 88 82

Figure S12.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 2.57e-05 (Fisher's exact test), Q value = 0.017

Table S13.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
5P GAIN MUTATED 20 11 42
5P GAIN WILD-TYPE 85 90 73

Figure S13.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.42e-05 (Fisher's exact test), Q value = 0.016

Table S14.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
5P GAIN MUTATED 15 34 24
5P GAIN WILD-TYPE 87 47 114

Figure S14.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.11e-06 (Fisher's exact test), Q value = 0.0036

Table S15.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
5P GAIN MUTATED 28 23 8
5P GAIN WILD-TYPE 36 106 73

Figure S15.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 2.15e-09 (Chi-square test), Q value = 1.6e-06

Table S16.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
6P GAIN MUTATED 6 5 12 2 33 1
6P GAIN WILD-TYPE 145 22 43 11 49 2

Figure S16.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 6.87e-08 (Fisher's exact test), Q value = 5.1e-05

Table S17.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
6P GAIN MUTATED 1 11 2 28
6P GAIN WILD-TYPE 36 69 63 48

Figure S17.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.000219 (Chi-square test), Q value = 0.14

Table S18.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
6P GAIN MUTATED 9 5 6 5 23
6P GAIN WILD-TYPE 56 57 40 32 39

Figure S18.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.52e-05 (Fisher's exact test), Q value = 0.049

Table S19.  Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
6P GAIN MUTATED 23 19 6
6P GAIN WILD-TYPE 46 94 84

Figure S19.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0073

Table S20.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
6P GAIN MUTATED 17 6 35
6P GAIN WILD-TYPE 88 95 80

Figure S20.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000206 (Fisher's exact test), Q value = 0.13

Table S21.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
6P GAIN MUTATED 10 27 21
6P GAIN WILD-TYPE 92 54 117

Figure S21.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000116 (Fisher's exact test), Q value = 0.075

Table S22.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
6P GAIN MUTATED 7 34 4
6P GAIN WILD-TYPE 57 97 75

Figure S22.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.8e-06 (Fisher's exact test), Q value = 0.0027

Table S23.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
6P GAIN MUTATED 22 20 3
6P GAIN WILD-TYPE 42 109 78

Figure S23.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-08 (Chi-square test), Q value = 7.6e-06

Table S24.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
6Q GAIN MUTATED 5 2 10 2 29 1
6Q GAIN WILD-TYPE 146 25 45 11 53 2

Figure S24.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 2.01e-05 (Fisher's exact test), Q value = 0.014

Table S25.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
6Q GAIN MUTATED 1 10 2 22
6Q GAIN WILD-TYPE 36 70 63 54

Figure S25.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 5.91e-05 (Chi-square test), Q value = 0.039

Table S26.  Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
6Q GAIN MUTATED 5 4 5 5 21
6Q GAIN WILD-TYPE 60 58 41 32 41

Figure S26.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 5.15e-05 (Fisher's exact test), Q value = 0.034

Table S27.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
6Q GAIN MUTATED 13 5 30
6Q GAIN WILD-TYPE 92 96 85

Figure S27.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000349 (Fisher's exact test), Q value = 0.22

Table S28.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
6Q GAIN MUTATED 4 29 4
6Q GAIN WILD-TYPE 60 102 75

Figure S28.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.22e-05 (Fisher's exact test), Q value = 0.047

Table S29.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
6Q GAIN MUTATED 17 18 2
6Q GAIN WILD-TYPE 47 111 79

Figure S29.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1.28e-11 (Chi-square test), Q value = 9.8e-09

Table S30.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
7P GAIN MUTATED 37 26 30 6 45 1
7P GAIN WILD-TYPE 114 1 25 7 37 2

Figure S30.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.000299 (Fisher's exact test), Q value = 0.19

Table S31.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
7P GAIN MUTATED 18 41 15 43
7P GAIN WILD-TYPE 19 39 50 33

Figure S31.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1.18e-10 (Chi-square test), Q value = 9.1e-08

Table S32.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
7Q GAIN MUTATED 36 26 27 5 29 1
7Q GAIN WILD-TYPE 115 1 28 8 53 2

Figure S32.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.000237 (Chi-square test), Q value = 0.15

Table S33.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
8P GAIN MUTATED 64 15 17 13 30 1
8P GAIN WILD-TYPE 87 12 38 0 52 2

Figure S33.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 4.4e-14 (Chi-square test), Q value = 3.4e-11

Table S34.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
10P GAIN MUTATED 9 9 32 1 29 0
10P GAIN WILD-TYPE 142 18 23 12 53 3

Figure S34.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.012

Table S35.  Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
10P GAIN MUTATED 3 16 10 34
10P GAIN WILD-TYPE 34 64 55 42

Figure S35.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 1.26e-12 (Chi-square test), Q value = 9.8e-10

Table S36.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
10Q GAIN MUTATED 7 3 28 1 16 0
10Q GAIN WILD-TYPE 144 24 27 12 66 3

Figure S36.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.000326 (Fisher's exact test), Q value = 0.2

Table S37.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
11Q GAIN MUTATED 12 4 25
11Q GAIN WILD-TYPE 93 97 90

Figure S37.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 7.58e-11 (Chi-square test), Q value = 5.8e-08

Table S38.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
13Q GAIN MUTATED 31 21 11 4 44 0
13Q GAIN WILD-TYPE 120 6 44 9 38 3

Figure S38.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000223 (Fisher's exact test), Q value = 0.14

Table S39.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
13Q GAIN MUTATED 35 36 20
13Q GAIN WILD-TYPE 29 93 61

Figure S39.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 6.45e-05 (Chi-square test), Q value = 0.043

Table S40.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
18P GAIN MUTATED 13 4 13 2 29 1
18P GAIN WILD-TYPE 138 23 42 11 53 2

Figure S40.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 3.81e-06 (Fisher's exact test), Q value = 0.0027

Table S41.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
18P GAIN MUTATED 1 10 6 28
18P GAIN WILD-TYPE 36 70 59 48

Figure S41.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000133 (Fisher's exact test), Q value = 0.086

Table S42.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
18P GAIN MUTATED 13 28 17
18P GAIN WILD-TYPE 89 53 121

Figure S42.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 9.26e-12 (Chi-square test), Q value = 7.1e-09

Table S43.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
20P GAIN MUTATED 49 23 40 7 61 2
20P GAIN WILD-TYPE 102 4 15 6 21 1

Figure S43.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.98e-05 (Fisher's exact test), Q value = 0.04

Table S44.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
20P GAIN MUTATED 43 60 72
20P GAIN WILD-TYPE 59 21 66

Figure S44.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000142 (Fisher's exact test), Q value = 0.091

Table S45.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
20P GAIN MUTATED 49 60 39
20P GAIN WILD-TYPE 15 69 42

Figure S45.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 3.87e-16 (Chi-square test), Q value = 3e-13

Table S46.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
20Q GAIN MUTATED 57 25 45 8 72 2
20Q GAIN WILD-TYPE 94 2 10 5 10 1

Figure S46.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 9.57e-10 (Fisher's exact test), Q value = 7.3e-07

Table S47.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
20Q GAIN MUTATED 25 42 28 69
20Q GAIN WILD-TYPE 12 38 37 7

Figure S47.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.02e-06 (Chi-square test), Q value = 0.00074

Table S48.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
20Q GAIN MUTATED 29 31 27 24 56
20Q GAIN WILD-TYPE 36 31 19 13 6

Figure S48.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.6e-05 (Fisher's exact test), Q value = 0.05

Table S49.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
20Q GAIN MUTATED 57 63 47
20Q GAIN WILD-TYPE 12 50 43

Figure S49.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 2.26e-06 (Fisher's exact test), Q value = 0.0016

Table S50.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
20Q GAIN MUTATED 56 53 93
20Q GAIN WILD-TYPE 49 48 22

Figure S50.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.03e-09 (Fisher's exact test), Q value = 7.9e-07

Table S51.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
20Q GAIN MUTATED 49 73 80
20Q GAIN WILD-TYPE 53 8 58

Figure S51.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.37e-09 (Fisher's exact test), Q value = 1.8e-06

Table S52.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
20Q GAIN MUTATED 60 73 41
20Q GAIN WILD-TYPE 4 56 40

Figure S52.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1.06e-06 (Chi-square test), Q value = 0.00077

Table S53.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
21Q GAIN MUTATED 1 1 2 0 16 0
21Q GAIN WILD-TYPE 150 26 53 13 66 3

Figure S53.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.099

Table S54.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
21Q GAIN MUTATED 1 13 6
21Q GAIN WILD-TYPE 101 68 132

Figure S54.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.84e-05 (Fisher's exact test), Q value = 0.026

Table S55.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
21Q GAIN MUTATED 12 7 0
21Q GAIN WILD-TYPE 52 122 81

Figure S55.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 7.19e-08 (Chi-square test), Q value = 5.3e-05

Table S56.  Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
1P LOSS MUTATED 3 5 14 0 19 2
1P LOSS WILD-TYPE 148 22 41 13 63 1

Figure S56.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 3.57e-05 (Chi-square test), Q value = 0.024

Table S57.  Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
1Q LOSS MUTATED 1 0 9 0 9 1
1Q LOSS WILD-TYPE 150 27 46 13 73 2

Figure S57.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 5.14e-06 (Chi-square test), Q value = 0.0036

Table S58.  Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
3P LOSS MUTATED 10 9 16 1 26 1
3P LOSS WILD-TYPE 141 18 39 12 56 2

Figure S58.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 2.45e-06 (Chi-square test), Q value = 0.0018

Table S59.  Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
3Q LOSS MUTATED 2 6 8 1 20 1
3Q LOSS WILD-TYPE 149 21 47 12 62 2

Figure S59.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 2.59e-06 (Fisher's exact test), Q value = 0.0019

Table S60.  Gene #46: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
3Q LOSS MUTATED 1 10 0 20
3Q LOSS WILD-TYPE 36 70 65 56

Figure S60.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 7.5e-06 (Chi-square test), Q value = 0.0052

Table S61.  Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
3Q LOSS MUTATED 2 3 1 6 17
3Q LOSS WILD-TYPE 63 59 45 31 45

Figure S61.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.31e-05 (Fisher's exact test), Q value = 0.029

Table S62.  Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
3Q LOSS MUTATED 18 7 4
3Q LOSS WILD-TYPE 51 106 86

Figure S62.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 4.7e-05 (Fisher's exact test), Q value = 0.031

Table S63.  Gene #46: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
3Q LOSS MUTATED 3 10 25
3Q LOSS WILD-TYPE 102 91 90

Figure S63.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 4.27e-16 (Chi-square test), Q value = 3.3e-13

Table S64.  Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
4P LOSS MUTATED 20 14 37 2 46 3
4P LOSS WILD-TYPE 131 13 18 11 36 0

Figure S64.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 3.46e-06 (Fisher's exact test), Q value = 0.0025

Table S65.  Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
4P LOSS MUTATED 4 25 20 44
4P LOSS WILD-TYPE 33 55 45 32

Figure S65.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.000349 (Chi-square test), Q value = 0.22

Table S66.  Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
4P LOSS MUTATED 11 22 15 11 34
4P LOSS WILD-TYPE 54 40 31 26 28

Figure S66.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.01

Table S67.  Gene #47: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
4P LOSS MUTATED 23 34 60
4P LOSS WILD-TYPE 82 67 55

Figure S67.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.33e-08 (Fisher's exact test), Q value = 3.2e-05

Table S68.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
4P LOSS MUTATED 33 51 33
4P LOSS WILD-TYPE 69 30 105

Figure S68.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.22e-06 (Fisher's exact test), Q value = 0.0016

Table S69.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
4P LOSS MUTATED 40 32 27
4P LOSS WILD-TYPE 24 97 54

Figure S69.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 7.16e-18 (Chi-square test), Q value = 5.6e-15

Table S70.  Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
4Q LOSS MUTATED 19 11 40 2 46 3
4Q LOSS WILD-TYPE 132 16 15 11 36 0

Figure S70.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1.72e-06 (Fisher's exact test), Q value = 0.0012

Table S71.  Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
4Q LOSS MUTATED 4 28 19 45
4Q LOSS WILD-TYPE 33 52 46 31

Figure S71.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.11

Table S72.  Gene #48: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
4Q LOSS MUTATED 25 34 58
4Q LOSS WILD-TYPE 80 67 57

Figure S72.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.98e-07 (Fisher's exact test), Q value = 0.00029

Table S73.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
4Q LOSS MUTATED 31 50 36
4Q LOSS WILD-TYPE 71 31 102

Figure S73.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.81e-06 (Fisher's exact test), Q value = 0.0068

Table S74.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
4Q LOSS MUTATED 40 35 27
4Q LOSS WILD-TYPE 24 94 54

Figure S74.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1.12e-05 (Chi-square test), Q value = 0.0078

Table S75.  Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
5P LOSS MUTATED 3 6 14 2 16 1
5P LOSS WILD-TYPE 148 21 41 11 66 2

Figure S75.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 4.36e-12 (Chi-square test), Q value = 3.4e-09

Table S76.  Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
5Q LOSS MUTATED 5 7 18 4 36 2
5Q LOSS WILD-TYPE 146 20 37 9 46 1

Figure S76.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

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

Table S77.  Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
5Q LOSS MUTATED 3 19 5 31
5Q LOSS WILD-TYPE 34 61 60 45

Figure S77.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 2.34e-07 (Chi-square test), Q value = 0.00017

Table S78.  Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
5Q LOSS MUTATED 11 3 5 7 28
5Q LOSS WILD-TYPE 54 59 41 30 34

Figure S78.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.63e-06 (Fisher's exact test), Q value = 0.0046

Table S79.  Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
5Q LOSS MUTATED 27 20 7
5Q LOSS WILD-TYPE 42 93 83

Figure S79.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.19

Table S80.  Gene #50: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
5Q LOSS MUTATED 19 12 39
5Q LOSS WILD-TYPE 86 89 76

Figure S80.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00084

Table S81.  Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
5Q LOSS MUTATED 10 34 26
5Q LOSS WILD-TYPE 92 47 112

Figure S81.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.99e-08 (Fisher's exact test), Q value = 2.2e-05

Table S82.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
5Q LOSS MUTATED 33 22 9
5Q LOSS WILD-TYPE 31 107 72

Figure S82.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 2.11e-05 (Chi-square test), Q value = 0.014

Table S83.  Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
6P LOSS MUTATED 4 3 14 0 15 0
6P LOSS WILD-TYPE 147 24 41 13 67 3

Figure S83.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 0.000192 (Chi-square test), Q value = 0.12

Table S84.  Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
6Q LOSS MUTATED 10 4 17 0 16 0
6Q LOSS WILD-TYPE 141 23 38 13 66 3

Figure S84.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 2.84e-05 (Chi-square test), Q value = 0.019

Table S85.  Gene #54: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
7Q LOSS MUTATED 0 0 7 1 13 0
7Q LOSS WILD-TYPE 151 27 48 12 69 3

Figure S85.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 7.87e-07 (Chi-square test), Q value = 0.00057

Table S86.  Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
8P LOSS MUTATED 8 6 18 0 24 1
8P LOSS WILD-TYPE 143 21 37 13 58 2

Figure S86.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 6.89e-18 (Chi-square test), Q value = 5.4e-15

Table S87.  Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
9P LOSS MUTATED 13 7 39 4 40 0
9P LOSS WILD-TYPE 138 20 16 9 42 3

Figure S87.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1.43e-07 (Fisher's exact test), Q value = 0.00011

Table S88.  Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
9P LOSS MUTATED 1 22 17 40
9P LOSS WILD-TYPE 36 58 48 36

Figure S88.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1.72e-08 (Chi-square test), Q value = 1.3e-05

Table S89.  Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
9P LOSS MUTATED 6 13 19 9 36
9P LOSS WILD-TYPE 59 49 27 28 26

Figure S89.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.039

Table S90.  Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
9P LOSS MUTATED 36 25 22
9P LOSS WILD-TYPE 33 88 68

Figure S90.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.000317 (Fisher's exact test), Q value = 0.2

Table S91.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
9P LOSS MUTATED 21 27 51
9P LOSS WILD-TYPE 84 74 64

Figure S91.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.3e-06 (Fisher's exact test), Q value = 0.0058

Table S92.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
9P LOSS MUTATED 29 42 28
9P LOSS WILD-TYPE 73 39 110

Figure S92.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.06e-06 (Fisher's exact test), Q value = 0.0029

Table S93.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
9P LOSS MUTATED 37 32 18
9P LOSS WILD-TYPE 27 97 63

Figure S93.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1.36e-08 (Chi-square test), Q value = 1e-05

Table S94.  Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
9Q LOSS MUTATED 11 5 25 3 28 0
9Q LOSS WILD-TYPE 140 22 30 10 54 3

Figure S94.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1.31e-05 (Chi-square test), Q value = 0.009

Table S95.  Gene #58: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
9Q LOSS MUTATED 6 10 13 4 27
9Q LOSS WILD-TYPE 59 52 33 33 35

Figure S95.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S96.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
9Q LOSS MUTATED 26 22 12
9Q LOSS WILD-TYPE 38 107 69

Figure S96.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 9.18e-06 (Chi-square test), Q value = 0.0064

Table S97.  Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
10P LOSS MUTATED 5 2 7 1 22 1
10P LOSS WILD-TYPE 146 25 48 12 60 2

Figure S97.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 4.73e-08 (Chi-square test), Q value = 3.5e-05

Table S98.  Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
10Q LOSS MUTATED 5 5 5 2 27 0
10Q LOSS WILD-TYPE 146 22 50 11 55 3

Figure S98.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 3e-06 (Chi-square test), Q value = 0.0021

Table S99.  Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
11P LOSS MUTATED 7 3 13 0 24 0
11P LOSS WILD-TYPE 144 24 42 13 58 3

Figure S99.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 5.56e-12 (Chi-square test), Q value = 4.3e-09

Table S100.  Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
12P LOSS MUTATED 1 2 10 1 30 1
12P LOSS WILD-TYPE 150 25 45 12 52 2

Figure S100.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 7.67e-08 (Fisher's exact test), Q value = 5.7e-05

Table S101.  Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
12P LOSS MUTATED 0 5 3 25
12P LOSS WILD-TYPE 37 75 62 51

Figure S101.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1.92e-05 (Chi-square test), Q value = 0.013

Table S102.  Gene #63: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
12P LOSS MUTATED 3 4 6 3 20
12P LOSS WILD-TYPE 62 58 40 34 42

Figure S102.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.78e-05 (Fisher's exact test), Q value = 0.025

Table S103.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
12P LOSS MUTATED 8 24 12
12P LOSS WILD-TYPE 94 57 126

Figure S103.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.7e-07 (Fisher's exact test), Q value = 0.00013

Table S104.  Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
12P LOSS MUTATED 22 7 5
12P LOSS WILD-TYPE 42 122 76

Figure S104.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 3.85e-09 (Chi-square test), Q value = 2.9e-06

Table S105.  Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
12Q LOSS MUTATED 0 2 7 1 23 1
12Q LOSS WILD-TYPE 151 25 48 12 59 2

Figure S105.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.013

Table S106.  Gene #64: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
12Q LOSS MUTATED 0 3 4 19
12Q LOSS WILD-TYPE 37 77 61 57

Figure S106.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 0.000167 (Chi-square test), Q value = 0.11

Table S107.  Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
13Q LOSS MUTATED 7 0 14 1 8 0
13Q LOSS WILD-TYPE 144 27 41 12 74 3

Figure S107.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 4.76e-08 (Chi-square test), Q value = 3.5e-05

Table S108.  Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
14Q LOSS MUTATED 16 6 27 1 30 1
14Q LOSS WILD-TYPE 135 21 28 12 52 2

Figure S108.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.16

Table S109.  Gene #66: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
14Q LOSS MUTATED 29 18 17
14Q LOSS WILD-TYPE 40 95 73

Figure S109.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.08e-05 (Fisher's exact test), Q value = 0.014

Table S110.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
14Q LOSS MUTATED 30 22 14
14Q LOSS WILD-TYPE 34 107 67

Figure S110.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 2.99e-07 (Chi-square test), Q value = 0.00022

Table S111.  Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
15Q LOSS MUTATED 9 8 17 2 30 1
15Q LOSS WILD-TYPE 142 19 38 11 52 2

Figure S111.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 4.6e-05 (Fisher's exact test), Q value = 0.031

Table S112.  Gene #67: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
15Q LOSS MUTATED 5 12 5 29
15Q LOSS WILD-TYPE 32 68 60 47

Figure S112.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 7.74e-05 (Chi-square test), Q value = 0.05

Table S113.  Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
15Q LOSS MUTATED 8 4 9 4 23
15Q LOSS WILD-TYPE 57 58 37 33 39

Figure S113.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.52e-05 (Fisher's exact test), Q value = 0.049

Table S114.  Gene #67: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
15Q LOSS MUTATED 23 19 6
15Q LOSS WILD-TYPE 46 94 84

Figure S114.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.000209 (Fisher's exact test), Q value = 0.13

Table S115.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
15Q LOSS MUTATED 14 12 37
15Q LOSS WILD-TYPE 91 89 78

Figure S115.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S116.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
15Q LOSS MUTATED 11 31 21
15Q LOSS WILD-TYPE 91 50 117

Figure S116.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.84e-05 (Fisher's exact test), Q value = 0.064

Table S117.  Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
15Q LOSS MUTATED 25 23 8
15Q LOSS WILD-TYPE 39 106 73

Figure S117.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 5.55e-16 (Chi-square test), Q value = 4.3e-13

Table S118.  Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
16P LOSS MUTATED 8 0 21 0 40 1
16P LOSS WILD-TYPE 143 27 34 13 42 2

Figure S118.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 3.48e-06 (Fisher's exact test), Q value = 0.0025

Table S119.  Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
16P LOSS MUTATED 1 14 7 30
16P LOSS WILD-TYPE 36 66 58 46

Figure S119.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 4.08e-10 (Chi-square test), Q value = 3.1e-07

Table S120.  Gene #68: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
16P LOSS MUTATED 7 5 5 4 31
16P LOSS WILD-TYPE 58 57 41 33 31

Figure S120.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.3e-07 (Fisher's exact test), Q value = 0.00039

Table S121.  Gene #68: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
16P LOSS MUTATED 29 15 8
16P LOSS WILD-TYPE 40 98 82

Figure S121.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1.71e-06 (Fisher's exact test), Q value = 0.0012

Table S122.  Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
16P LOSS MUTATED 12 12 42
16P LOSS WILD-TYPE 93 89 73

Figure S122.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000183 (Fisher's exact test), Q value = 0.12

Table S123.  Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
16P LOSS MUTATED 13 30 23
16P LOSS WILD-TYPE 89 51 115

Figure S123.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.1e-06 (Fisher's exact test), Q value = 0.0022

Table S124.  Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
16P LOSS MUTATED 3 43 11
16P LOSS WILD-TYPE 61 88 68

Figure S124.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.86e-06 (Fisher's exact test), Q value = 0.0034

Table S125.  Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
16P LOSS MUTATED 28 20 9
16P LOSS WILD-TYPE 36 109 72

Figure S125.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1.19e-13 (Chi-square test), Q value = 9.2e-11

Table S126.  Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
16Q LOSS MUTATED 12 1 23 1 41 1
16Q LOSS WILD-TYPE 139 26 32 12 41 2

Figure S126.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1.83e-07 (Fisher's exact test), Q value = 0.00013

Table S127.  Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
16Q LOSS MUTATED 1 13 11 35
16Q LOSS WILD-TYPE 36 67 54 41

Figure S127.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 6.97e-08 (Chi-square test), Q value = 5.2e-05

Table S128.  Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
16Q LOSS MUTATED 6 10 10 5 32
16Q LOSS WILD-TYPE 59 52 36 32 30

Figure S128.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.39e-05 (Fisher's exact test), Q value = 0.0095

Table S129.  Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
16Q LOSS MUTATED 31 18 14
16Q LOSS WILD-TYPE 38 95 76

Figure S129.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 9.52e-06 (Fisher's exact test), Q value = 0.0066

Table S130.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
16Q LOSS MUTATED 14 17 45
16Q LOSS WILD-TYPE 91 84 70

Figure S130.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.61e-05 (Fisher's exact test), Q value = 0.05

Table S131.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
16Q LOSS MUTATED 16 34 26
16Q LOSS WILD-TYPE 86 47 112

Figure S131.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.33e-05 (Fisher's exact test), Q value = 0.0092

Table S132.  Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
16Q LOSS MUTATED 30 22 13
16Q LOSS WILD-TYPE 34 107 68

Figure S132.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 2.81e-20 (Chi-square test), Q value = 2.2e-17

Table S133.  Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
17P LOSS MUTATED 12 17 34 2 47 3
17P LOSS WILD-TYPE 139 10 21 11 35 0

Figure S133.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1.76e-09 (Fisher's exact test), Q value = 1.3e-06

Table S134.  Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
17P LOSS MUTATED 4 28 11 47
17P LOSS WILD-TYPE 33 52 54 29

Figure S134.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 4.44e-06 (Chi-square test), Q value = 0.0032

Table S135.  Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
17P LOSS MUTATED 14 10 18 12 36
17P LOSS WILD-TYPE 51 52 28 25 26

Figure S135.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.74e-06 (Fisher's exact test), Q value = 0.0013

Table S136.  Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
17P LOSS MUTATED 40 32 18
17P LOSS WILD-TYPE 29 81 72

Figure S136.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.087

Table S137.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
17P LOSS MUTATED 33 22 56
17P LOSS WILD-TYPE 72 79 59

Figure S137.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0095

Table S138.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
17P LOSS MUTATED 23 45 43
17P LOSS WILD-TYPE 79 36 95

Figure S138.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.59e-08 (Fisher's exact test), Q value = 3.4e-05

Table S139.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
17P LOSS MUTATED 42 36 18
17P LOSS WILD-TYPE 22 93 63

Figure S139.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 8.07e-09 (Chi-square test), Q value = 6.1e-06

Table S140.  Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
17Q LOSS MUTATED 4 7 18 1 22 2
17Q LOSS WILD-TYPE 147 20 37 12 60 1

Figure S140.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 3.33e-05 (Fisher's exact test), Q value = 0.022

Table S141.  Gene #71: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
17Q LOSS MUTATED 0 12 4 22
17Q LOSS WILD-TYPE 37 68 61 54

Figure S141.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000236 (Fisher's exact test), Q value = 0.15

Table S142.  Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
17Q LOSS MUTATED 21 15 7
17Q LOSS WILD-TYPE 43 114 74

Figure S142.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 4.41e-05 (Chi-square test), Q value = 0.029

Table S143.  Gene #72: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
18P LOSS MUTATED 25 10 26 1 28 2
18P LOSS WILD-TYPE 126 17 29 12 54 1

Figure S143.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 2.17e-08 (Chi-square test), Q value = 1.6e-05

Table S144.  Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
18Q LOSS MUTATED 28 13 29 1 43 2
18Q LOSS WILD-TYPE 123 14 26 12 39 1

Figure S144.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 2.65e-19 (Chi-square test), Q value = 2.1e-16

Table S145.  Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
19P LOSS MUTATED 2 7 21 3 46 2
19P LOSS WILD-TYPE 149 20 34 10 36 1

Figure S145.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 3.11e-12 (Fisher's exact test), Q value = 2.4e-09

Table S146.  Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
19P LOSS MUTATED 3 16 2 40
19P LOSS WILD-TYPE 34 64 63 36

Figure S146.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 6.18e-13 (Chi-square test), Q value = 4.8e-10

Table S147.  Gene #74: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
19P LOSS MUTATED 8 3 8 5 36
19P LOSS WILD-TYPE 57 59 38 32 26

Figure S147.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.22e-12 (Fisher's exact test), Q value = 1.7e-09

Table S148.  Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
19P LOSS MUTATED 37 18 5
19P LOSS WILD-TYPE 32 95 85

Figure S148.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 5.43e-07 (Fisher's exact test), Q value = 4e-04

Table S149.  Gene #74: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
19P LOSS MUTATED 17 13 48
19P LOSS WILD-TYPE 88 88 67

Figure S149.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.95e-13 (Fisher's exact test), Q value = 2.3e-10

Table S150.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
19P LOSS MUTATED 8 45 25
19P LOSS WILD-TYPE 94 36 113

Figure S150.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000228 (Fisher's exact test), Q value = 0.14

Table S151.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 131 79
19P LOSS MUTATED 14 45 8
19P LOSS WILD-TYPE 50 86 71

Figure S151.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.74e-11 (Fisher's exact test), Q value = 4.4e-08

Table S152.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
19P LOSS MUTATED 36 25 6
19P LOSS WILD-TYPE 28 104 75

Figure S152.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1.62e-14 (Chi-square test), Q value = 1.3e-11

Table S153.  Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
19Q LOSS MUTATED 1 5 15 3 36 2
19Q LOSS WILD-TYPE 150 22 40 10 46 1

Figure S153.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 5.88e-10 (Fisher's exact test), Q value = 4.5e-07

Table S154.  Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
19Q LOSS MUTATED 1 10 2 32
19Q LOSS WILD-TYPE 36 70 63 44

Figure S154.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1.55e-07 (Chi-square test), Q value = 0.00011

Table S155.  Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
19Q LOSS MUTATED 5 2 8 5 25
19Q LOSS WILD-TYPE 60 60 38 32 37

Figure S155.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.0017

Table S156.  Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
19Q LOSS MUTATED 24 17 4
19Q LOSS WILD-TYPE 45 96 86

Figure S156.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 3.42e-05 (Fisher's exact test), Q value = 0.023

Table S157.  Gene #75: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
19Q LOSS MUTATED 13 10 37
19Q LOSS WILD-TYPE 92 91 78

Figure S157.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.7e-09 (Fisher's exact test), Q value = 1.3e-06

Table S158.  Gene #75: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
19Q LOSS MUTATED 7 35 18
19Q LOSS WILD-TYPE 95 46 120

Figure S158.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.02e-08 (Fisher's exact test), Q value = 3.7e-05

Table S159.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
19Q LOSS MUTATED 28 18 5
19Q LOSS WILD-TYPE 36 111 76

Figure S159.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.073

Table S160.  Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
20P LOSS MUTATED 0 1 1 12
20P LOSS WILD-TYPE 37 79 64 64

Figure S160.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.000249 (Chi-square test), Q value = 0.16

Table S161.  Gene #76: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 62 46 37 62
20P LOSS MUTATED 0 2 8 0 3
20P LOSS WILD-TYPE 65 60 38 37 59

Figure S161.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 8.67e-11 (Chi-square test), Q value = 6.6e-08

Table S162.  Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
21Q LOSS MUTATED 25 12 36 6 38 3
21Q LOSS WILD-TYPE 126 15 19 7 44 0

Figure S162.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.000154 (Fisher's exact test), Q value = 0.099

Table S163.  Gene #77: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
21Q LOSS MUTATED 3 34 20 35
21Q LOSS WILD-TYPE 34 46 45 41

Figure S163.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.65e-05 (Fisher's exact test), Q value = 0.044

Table S164.  Gene #77: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 113 90
21Q LOSS MUTATED 39 29 26
21Q LOSS WILD-TYPE 30 84 64

Figure S164.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1.97e-15 (Chi-square test), Q value = 1.5e-12

Table S165.  Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
22Q LOSS MUTATED 12 8 34 4 41 2
22Q LOSS WILD-TYPE 139 19 21 9 41 1

Figure S165.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 2.66e-06 (Fisher's exact test), Q value = 0.0019

Table S166.  Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 80 65 76
22Q LOSS MUTATED 2 24 14 38
22Q LOSS WILD-TYPE 35 56 51 38

Figure S166.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 5.75e-06 (Fisher's exact test), Q value = 0.004

Table S167.  Gene #78: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 101 115
22Q LOSS MUTATED 17 27 53
22Q LOSS WILD-TYPE 88 74 62

Figure S167.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.89e-08 (Fisher's exact test), Q value = 2.9e-05

Table S168.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 81 138
22Q LOSS MUTATED 21 46 30
22Q LOSS WILD-TYPE 81 35 108

Figure S168.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.34e-06 (Fisher's exact test), Q value = 0.00097

Table S169.  Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 129 81
22Q LOSS MUTATED 37 29 18
22Q LOSS WILD-TYPE 27 100 63

Figure S169.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 5.33e-06 (Chi-square test), Q value = 0.0037

Table S170.  Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 151 27 55 13 82 3
XQ LOSS MUTATED 3 4 14 1 18 1
XQ LOSS WILD-TYPE 148 23 41 12 64 2

Figure S170.  Get High-res Image Gene #79: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 331

  • Number of significantly arm-level cnvs = 79

  • Number of molecular subtypes = 10

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

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

Fisher's exact test

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

Q value calculation

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[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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