Correlation between copy number variation genes (focal events) and molecular subtypes
Colorectal Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C14B2ZP2
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 variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C14B2ZP2
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 40 focal events and 12 molecular subtypes across 589 patients, 139 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 1q cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 2p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 2q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 3p cnv correlated to 'CN_CNMF'.

  • 3q cnv correlated to 'CN_CNMF'.

  • 4p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 4q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 5p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 5q cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 6p cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 6q cnv correlated to 'CN_CNMF'.

  • 7p cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 7q cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 9p cnv correlated to 'CN_CNMF'.

  • 10p cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 10q cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 11p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 11q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 13q cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 14q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • 17p cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 18p cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 18q cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 19p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 19q cnv correlated to 'CN_CNMF'.

  • 20p cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 20q cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 22q cnv correlated to 'MRNA_CNMF',  'CN_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • xq 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 40 focal 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, 139 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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
20q 451 (77%) 138 3.3e-14
(1.51e-11) 		5.11e-13
(2.31e-10) 		6.98e-34
(3.31e-31) 		1.02e-16
(4.73e-14) 		0.0212
(1.00) 		0.00568
(1.00) 		1.45e-17
(6.82e-15) 		6.24e-14
(2.85e-11) 		0.0259
(1.00) 		0.173
(1.00) 		6.05e-12
(2.73e-09) 		0.000705
(0.242)
17p 358 (61%) 231 8.21e-07
(0.000336) 		8.06e-06
(0.00317) 		6.29e-27
(2.98e-24) 		7.3e-09
(3.18e-06) 		0.0834
(1.00) 		0.056
(1.00) 		3.09e-09
(1.35e-06) 		5.08e-09
(2.22e-06) 		0.0022
(0.705) 		0.0126
(1.00) 		3.32e-08
(1.42e-05) 		0.0683
(1.00)
18p 392 (67%) 197 1.01e-10
(4.51e-08) 		1.79e-08
(7.67e-06) 		2.06e-37
(9.83e-35) 		2.97e-16
(1.38e-13) 		0.0215
(1.00) 		0.0209
(1.00) 		1.64e-18
(7.74e-16) 		1.58e-13
(7.14e-11) 		0.00628
(1.00) 		0.131
(1.00) 		1.06e-13
(4.82e-11) 		0.0021
(0.678)
18q 407 (69%) 182 1.2e-09
(5.32e-07) 		4.13e-08
(1.76e-05) 		1.27e-38
(6.08e-36) 		2.79e-15
(1.28e-12) 		0.0845
(1.00) 		0.0871
(1.00) 		6.06e-16
(2.8e-13) 		1.19e-13
(5.39e-11) 		0.00136
(0.445) 		0.0822
(1.00) 		3.37e-11
(1.51e-08) 		0.00308
(0.959)
20p 399 (68%) 190 2.27e-07
(9.53e-05) 		3.83e-09
(1.67e-06) 		9.46e-17
(4.41e-14) 		1.35e-08
(5.8e-06) 		0.00823
(1.00) 		0.107
(1.00) 		1.24e-08
(5.37e-06) 		4.86e-07
(0.000201) 		0.46
(1.00) 		0.757
(1.00) 		9.96e-06
(0.0039) 		0.163
(1.00)
7p 336 (57%) 253 0.000881
(0.296) 		0.000549
(0.193) 		2.79e-21
(1.32e-18) 		6.44e-06
(0.00256) 		0.013
(1.00) 		0.0275
(1.00) 		2.88e-08
(1.23e-05) 		1.89e-09
(8.32e-07) 		0.00542
(1.00) 		0.00753
(1.00) 		4.5e-06
(0.0018) 		0.483
(1.00)
7q 302 (51%) 287 0.000268
(0.0966) 		0.00232
(0.736) 		4.55e-14
(2.08e-11) 		0.000307
(0.11) 		0.144
(1.00) 		0.121
(1.00) 		5.79e-07
(0.000239) 		4.59e-07
(0.000191) 		0.012
(1.00) 		0.0733
(1.00) 		2.52e-05
(0.00975) 		0.261
(1.00)
13q 374 (63%) 215 9.09e-06
(0.00356) 		0.00197
(0.635) 		1.59e-34
(7.56e-32) 		2.23e-09
(9.79e-07) 		0.188
(1.00) 		0.196
(1.00) 		4.9e-08
(2.08e-05) 		8.63e-09
(3.74e-06) 		0.00108
(0.361) 		0.288
(1.00) 		5.94e-10
(2.64e-07) 		0.00463
(1.00)
4p 202 (34%) 387 0.0249
(1.00) 		0.059
(1.00) 		2.05e-15
(9.42e-13) 		0.000106
(0.0393) 		0.35
(1.00) 		0.507
(1.00) 		1.4e-05
(0.00545) 		5.45e-06
(0.00217) 		0.0422
(1.00) 		0.0918
(1.00) 		1.78e-05
(0.00691) 		0.0968
(1.00)
4q 197 (33%) 392 0.0103
(1.00) 		0.0508
(1.00) 		2.1e-17
(9.85e-15) 		3.64e-06
(0.00147) 		0.505
(1.00) 		0.261
(1.00) 		3.4e-05
(0.0129) 		4.98e-06
(0.00199) 		0.146
(1.00) 		0.029
(1.00) 		0.000139
(0.0507) 		0.0152
(1.00)
8p 369 (63%) 220 0.00864
(1.00) 		0.000859
(0.29) 		1.79e-44
(8.59e-42) 		0.000134
(0.0492) 		0.0248
(1.00) 		0.0777
(1.00) 		7.38e-07
(0.000303) 		1.2e-06
(0.000488) 		0.0507
(1.00) 		0.101
(1.00) 		9.09e-05
(0.034) 		0.168
(1.00)
14q 235 (40%) 354 0.00221
(0.707) 		0.00491
(1.00) 		3.26e-25
(1.54e-22) 		2.06e-05
(0.00798) 		0.00564
(1.00) 		0.174
(1.00) 		4.5e-11
(2.01e-08) 		3.04e-05
(0.0116) 		0.0815
(1.00) 		0.769
(1.00) 		2.82e-08
(1.21e-05) 		0.114
(1.00)
15q 231 (39%) 358 0.000556
(0.194) 		0.00365
(1.00) 		8.29e-18
(3.89e-15) 		0.00392
(1.00) 		0.0798
(1.00) 		0.514
(1.00) 		1.7e-05
(0.0066) 		3.68e-07
(0.000154) 		0.807
(1.00) 		0.805
(1.00) 		4.75e-06
(0.0019) 		0.103
(1.00)
10p 140 (24%) 449 0.358
(1.00) 		0.452
(1.00) 		4.8e-07
(0.000199) 		0.1
(1.00) 		0.358
(1.00) 		0.158
(1.00) 		0.000281
(0.101) 		0.000184
(0.067) 		0.0795
(1.00) 		0.0293
(1.00) 		0.000311
(0.111) 		0.00118
(0.389)
10q 128 (22%) 461 0.0505
(1.00) 		0.364
(1.00) 		5.93e-11
(2.65e-08) 		0.0998
(1.00) 		0.103
(1.00) 		0.671
(1.00) 		0.000553
(0.194) 		0.000109
(0.0404) 		0.46
(1.00) 		0.267
(1.00) 		0.000123
(0.0453) 		0.000804
(0.273)
11p 153 (26%) 436 0.103
(1.00) 		0.34
(1.00) 		1e-08
(4.33e-06) 		6.95e-06
(0.00275) 		0.26
(1.00) 		0.78
(1.00) 		0.00542
(1.00) 		3.84e-05
(0.0146) 		0.568
(1.00) 		0.425
(1.00) 		0.000311
(0.111) 		0.561
(1.00)
11q 162 (28%) 427 0.021
(1.00) 		0.123
(1.00) 		1.63e-09
(7.2e-07) 		8.81e-07
(0.000359) 		0.319
(1.00) 		0.829
(1.00) 		0.00274
(0.86) 		9.47e-05
(0.0353) 		0.418
(1.00) 		0.326
(1.00) 		3.26e-05
(0.0124) 		0.17
(1.00)
21q 215 (37%) 374 0.00609
(1.00) 		0.0952
(1.00) 		8.27e-08
(3.5e-05) 		0.0622
(1.00) 		0.455
(1.00) 		0.0913
(1.00) 		0.000394
(0.139) 		0.000662
(0.228) 		0.0514
(1.00) 		0.031
(1.00) 		0.000446
(0.157) 		0.112
(1.00)
1q 186 (32%) 403 0.23
(1.00) 		0.566
(1.00) 		1.29e-08
(5.56e-06) 		0.0636
(1.00) 		0.183
(1.00) 		0.666
(1.00) 		0.0221
(1.00) 		9.63e-05
(0.0358) 		0.488
(1.00) 		0.931
(1.00) 		0.000566
(0.196) 		0.0463
(1.00)
2p 131 (22%) 458 0.0587
(1.00) 		0.0356
(1.00) 		3.19e-06
(0.00129) 		0.000684
(0.235) 		0.382
(1.00) 		0.412
(1.00) 		2.73e-05
(0.0105) 		0.00557
(1.00) 		0.061
(1.00) 		0.0967
(1.00) 		0.172
(1.00) 		0.00364
(1.00)
5q 175 (30%) 414 0.0766
(1.00) 		0.254
(1.00) 		1.7e-09
(7.49e-07) 		0.0637
(1.00) 		0.107
(1.00) 		0.517
(1.00) 		0.00602
(1.00) 		4.39e-05
(0.0166) 		0.923
(1.00) 		0.721
(1.00) 		6.66e-05
(0.025) 		0.15
(1.00)
8q 334 (57%) 255 0.17
(1.00) 		0.0171
(1.00) 		9.12e-44
(4.37e-41) 		0.00577
(1.00) 		0.132
(1.00) 		0.0789
(1.00) 		7.8e-06
(0.00308) 		2.65e-07
(0.000111) 		0.5
(1.00) 		0.257
(1.00) 		0.0176
(1.00) 		0.371
(1.00)
16p 177 (30%) 412 0.00241
(0.76) 		0.00431
(1.00) 		6.18e-16
(2.85e-13) 		0.0235
(1.00) 		0.0312
(1.00) 		0.358
(1.00) 		0.000212
(0.0767) 		6.94e-05
(0.026) 		0.471
(1.00) 		0.834
(1.00) 		0.0209
(1.00) 		0.0494
(1.00)
16q 177 (30%) 412 0.00482
(1.00) 		0.00226
(0.718) 		2.12e-17
(9.91e-15) 		0.0807
(1.00) 		0.0419
(1.00) 		0.43
(1.00) 		0.000577
(0.2) 		0.000106
(0.0392) 		0.596
(1.00) 		0.739
(1.00) 		0.00503
(1.00) 		0.0682
(1.00)
17q 191 (32%) 398 0.0452
(1.00) 		0.329
(1.00) 		1.32e-07
(5.55e-05) 		0.00224
(0.715) 		0.728
(1.00) 		0.273
(1.00) 		2.91e-05
(0.0112) 		3.26e-05
(0.0124) 		0.0107
(1.00) 		0.278
(1.00) 		0.0283
(1.00) 		0.0529
(1.00)
22q 215 (37%) 374 0.00021
(0.0761) 		0.000826
(0.279) 		3.7e-16
(1.72e-13) 		0.00675
(1.00) 		0.674
(1.00) 		0.714
(1.00) 		0.00295
(0.919) 		0.0012
(0.394) 		0.945
(1.00) 		0.161
(1.00) 		0.000129
(0.0474) 		0.169
(1.00)
1p 176 (30%) 413 0.00974
(1.00) 		0.12
(1.00) 		5.11e-11
(2.28e-08) 		0.00347
(1.00) 		0.157
(1.00) 		0.934
(1.00) 		0.0206
(1.00) 		1.9e-06
(0.000771) 		0.475
(1.00) 		0.272
(1.00) 		0.00118
(0.389) 		0.0193
(1.00)
2q 125 (21%) 464 0.0686
(1.00) 		0.0327
(1.00) 		4.75e-07
(0.000197) 		0.000369
(0.131) 		0.615
(1.00) 		0.704
(1.00) 		0.00115
(0.38) 		0.00283
(0.886) 		0.136
(1.00) 		0.252
(1.00) 		0.247
(1.00) 		0.0582
(1.00)
5p 178 (30%) 411 0.282
(1.00) 		0.762
(1.00) 		2.79e-07
(0.000117) 		0.163
(1.00) 		0.41
(1.00) 		0.5
(1.00) 		0.0214
(1.00) 		0.000179
(0.0651) 		0.92
(1.00) 		0.884
(1.00) 		0.000975
(0.326) 		0.0662
(1.00)
6p 164 (28%) 425 0.0206
(1.00) 		0.00854
(1.00) 		6.96e-07
(0.000286) 		0.195
(1.00) 		0.154
(1.00) 		0.981
(1.00) 		0.0645
(1.00) 		0.00156
(0.51) 		0.856
(1.00) 		0.817
(1.00) 		0.000704
(0.242) 		0.272
(1.00)
19p 160 (27%) 429 0.148
(1.00) 		0.134
(1.00) 		2.2e-11
(9.89e-09) 		0.0123
(1.00) 		0.119
(1.00) 		0.128
(1.00) 		0.00764
(1.00) 		0.000563
(0.196) 		0.125
(1.00) 		0.0781
(1.00) 		0.0281
(1.00) 		0.0686
(1.00)
3p 133 (23%) 456 0.418
(1.00) 		0.537
(1.00) 		6.35e-05
(0.024) 		0.601
(1.00) 		0.513
(1.00) 		0.314
(1.00) 		0.405
(1.00) 		0.0327
(1.00) 		0.125
(1.00) 		0.0814
(1.00) 		0.0017
(0.552) 		0.182
(1.00)
3q 136 (23%) 453 0.0621
(1.00) 		0.0695
(1.00) 		3.86e-06
(0.00155) 		0.253
(1.00) 		0.244
(1.00) 		0.485
(1.00) 		0.0436
(1.00) 		0.00478
(1.00) 		0.0255
(1.00) 		0.0685
(1.00) 		0.000814
(0.276) 		0.279
(1.00)
6q 173 (29%) 416 0.0491
(1.00) 		0.0416
(1.00) 		8.57e-06
(0.00337) 		0.121
(1.00) 		0.32
(1.00) 		0.928
(1.00) 		0.237
(1.00) 		0.0732
(1.00) 		0.844
(1.00) 		0.691
(1.00) 		0.0103
(1.00) 		0.731
(1.00)
9p 187 (32%) 402 0.354
(1.00) 		0.629
(1.00) 		0.00033
(0.117) 		0.00846
(1.00) 		0.22
(1.00) 		0.913
(1.00) 		0.0184
(1.00) 		0.000931
(0.312) 		0.344
(1.00) 		0.0384
(1.00) 		0.000744
(0.254) 		0.395
(1.00)
19q 160 (27%) 429 0.0733
(1.00) 		0.0902
(1.00) 		1.16e-07
(4.89e-05) 		0.0418
(1.00) 		0.0654
(1.00) 		0.262
(1.00) 		0.057
(1.00) 		0.00889
(1.00) 		0.426
(1.00) 		0.168
(1.00) 		0.0341
(1.00) 		0.0503
(1.00)
xq 172 (29%) 417 0.461
(1.00) 		0.76
(1.00) 		1.19e-06
(0.000485) 		0.013
(1.00) 		0.00163
(0.529) 		0.00266
(0.839) 		0.314
(1.00) 		0.0645
(1.00) 		0.0384
(1.00) 		0.522
(1.00) 		0.567
(1.00) 		0.209
(1.00)
9q 168 (29%) 421 0.5
(1.00) 		0.594
(1.00) 		0.00125
(0.411) 		0.00759
(1.00) 		0.115
(1.00) 		0.644
(1.00) 		0.032
(1.00) 		0.0205
(1.00) 		0.217
(1.00) 		0.168
(1.00) 		0.00387
(1.00) 		0.299
(1.00)
12p 191 (32%) 398 0.944
(1.00) 		0.937
(1.00) 		0.121
(1.00) 		0.344
(1.00) 		0.522
(1.00) 		0.97
(1.00) 		0.745
(1.00) 		0.227
(1.00) 		0.753
(1.00) 		0.571
(1.00) 		0.836
(1.00) 		0.95
(1.00)
12q 175 (30%) 414 0.86
(1.00) 		0.908
(1.00) 		0.0818
(1.00) 		0.485
(1.00) 		0.347
(1.00) 		0.984
(1.00) 		0.775
(1.00) 		0.355
(1.00) 		0.755
(1.00) 		0.822
(1.00) 		0.958
(1.00) 		0.684
(1.00)
'1p' versus 'CN_CNMF'

P value = 5.11e-11 (Fisher's exact test), Q value = 2.3e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
1P MUTATED 81 43 43 9
1P WILD-TYPE 93 202 114 4

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

'1p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.9e-06 (Fisher's exact test), Q value = 0.00077

Table S2.  Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
1P MUTATED 70 22 77
1P WILD-TYPE 166 119 109

Figure S2.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q' versus 'CN_CNMF'

P value = 1.29e-08 (Fisher's exact test), Q value = 5.6e-06

Table S3.  Gene #2: '1q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
1Q MUTATED 76 49 51 10
1Q WILD-TYPE 98 196 106 3

Figure S3.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #3: 'CN_CNMF'

'1q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.63e-05 (Fisher's exact test), Q value = 0.036

Table S4.  Gene #2: '1q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
1Q MUTATED 75 26 75
1Q WILD-TYPE 161 115 111

Figure S4.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000566 (Fisher's exact test), Q value = 0.2

Table S5.  Gene #2: '1q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
1Q MUTATED 34 21 38
1Q WILD-TYPE 66 88 47

Figure S5.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p' versus 'CN_CNMF'

P value = 3.19e-06 (Fisher's exact test), Q value = 0.0013

Table S6.  Gene #3: '2p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
2P MUTATED 56 33 35 7
2P WILD-TYPE 118 212 122 6

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

'2p' versus 'METHLYATION_CNMF'

P value = 0.000684 (Fisher's exact test), Q value = 0.24

Table S7.  Gene #3: '2p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
2P MUTATED 51 16 17
2P WILD-TYPE 105 100 74

Figure S7.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p' versus 'MRNASEQ_CNMF'

P value = 2.73e-05 (Fisher's exact test), Q value = 0.011

Table S8.  Gene #3: '2p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
2P MUTATED 24 14 47 40
2P WILD-TYPE 96 111 82 149

Figure S8.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q' versus 'CN_CNMF'

P value = 4.75e-07 (Fisher's exact test), Q value = 2e-04

Table S9.  Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
2Q MUTATED 53 30 34 8
2Q WILD-TYPE 121 215 123 5

Figure S9.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #3: 'CN_CNMF'

'2q' versus 'METHLYATION_CNMF'

P value = 0.000369 (Fisher's exact test), Q value = 0.13

Table S10.  Gene #4: '2q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
2Q MUTATED 49 15 14
2Q WILD-TYPE 107 101 77

Figure S10.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p' versus 'CN_CNMF'

P value = 6.35e-05 (Fisher's exact test), Q value = 0.024

Table S11.  Gene #5: '3p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
3P MUTATED 60 37 34 2
3P WILD-TYPE 114 208 123 11

Figure S11.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #3: 'CN_CNMF'

'3q' versus 'CN_CNMF'

P value = 3.86e-06 (Fisher's exact test), Q value = 0.0016

Table S12.  Gene #6: '3q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
3Q MUTATED 62 34 38 2
3Q WILD-TYPE 112 211 119 11

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

'4p' versus 'CN_CNMF'

P value = 2.05e-15 (Fisher's exact test), Q value = 9.4e-13

Table S13.  Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
4P MUTATED 94 44 54 10
4P WILD-TYPE 80 201 103 3

Figure S13.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.039

Table S14.  Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
4P MUTATED 72 26 26
4P WILD-TYPE 84 90 65

Figure S14.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p' versus 'MRNASEQ_CNMF'

P value = 1.4e-05 (Fisher's exact test), Q value = 0.0055

Table S15.  Gene #7: '4p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
4P MUTATED 40 23 61 70
4P WILD-TYPE 80 102 68 119

Figure S15.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.45e-06 (Fisher's exact test), Q value = 0.0022

Table S16.  Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
4P MUTATED 84 27 83
4P WILD-TYPE 152 114 103

Figure S16.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.78e-05 (Fisher's exact test), Q value = 0.0069

Table S17.  Gene #7: '4p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
4P MUTATED 48 20 32
4P WILD-TYPE 52 89 53

Figure S17.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q' versus 'CN_CNMF'

P value = 2.1e-17 (Fisher's exact test), Q value = 9.8e-15

Table S18.  Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
4Q MUTATED 94 39 54 10
4Q WILD-TYPE 80 206 103 3

Figure S18.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

'4q' versus 'METHLYATION_CNMF'

P value = 3.64e-06 (Fisher's exact test), Q value = 0.0015

Table S19.  Gene #8: '4q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
4Q MUTATED 71 20 28
4Q WILD-TYPE 85 96 63

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

'4q' versus 'MRNASEQ_CNMF'

P value = 3.4e-05 (Fisher's exact test), Q value = 0.013

Table S20.  Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
4Q MUTATED 39 22 57 71
4Q WILD-TYPE 81 103 72 118

Figure S20.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.98e-06 (Fisher's exact test), Q value = 0.002

Table S21.  Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
4Q MUTATED 85 25 79
4Q WILD-TYPE 151 116 107

Figure S21.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.051

Table S22.  Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
4Q MUTATED 43 19 31
4Q WILD-TYPE 57 90 54

Figure S22.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p' versus 'CN_CNMF'

P value = 2.79e-07 (Fisher's exact test), Q value = 0.00012

Table S23.  Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
5P MUTATED 65 44 62 7
5P WILD-TYPE 109 201 95 6

Figure S23.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

'5p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000179 (Fisher's exact test), Q value = 0.065

Table S24.  Gene #9: '5p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
5P MUTATED 77 25 71
5P WILD-TYPE 159 116 115

Figure S24.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q' versus 'CN_CNMF'

P value = 1.7e-09 (Fisher's exact test), Q value = 7.5e-07

Table S25.  Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
5Q MUTATED 68 38 64 5
5Q WILD-TYPE 106 207 93 8

Figure S25.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

'5q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.39e-05 (Fisher's exact test), Q value = 0.017

Table S26.  Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
5Q MUTATED 76 23 71
5Q WILD-TYPE 160 118 115

Figure S26.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.66e-05 (Fisher's exact test), Q value = 0.025

Table S27.  Gene #10: '5q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
5Q MUTATED 40 16 30
5Q WILD-TYPE 60 93 55

Figure S27.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p' versus 'CN_CNMF'

P value = 6.96e-07 (Fisher's exact test), Q value = 0.00029

Table S28.  Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
6P MUTATED 69 42 46 7
6P WILD-TYPE 105 203 111 6

Figure S28.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

'6p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000704 (Fisher's exact test), Q value = 0.24

Table S29.  Gene #11: '6p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
6P MUTATED 37 17 29
6P WILD-TYPE 63 92 56

Figure S29.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q' versus 'CN_CNMF'

P value = 8.57e-06 (Fisher's exact test), Q value = 0.0034

Table S30.  Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
6Q MUTATED 69 47 50 7
6Q WILD-TYPE 105 198 107 6

Figure S30.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'MRNA_CHIERARCHICAL'

P value = 0.000549 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
7P MUTATED 28 19 22 38
7P WILD-TYPE 14 31 41 22

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

'7p' versus 'CN_CNMF'

P value = 2.79e-21 (Fisher's exact test), Q value = 1.3e-18

Table S32.  Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
7P MUTATED 139 85 101 11
7P WILD-TYPE 35 160 56 2

Figure S32.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 6.44e-06 (Fisher's exact test), Q value = 0.0026

Table S33.  Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
7P MUTATED 118 56 50
7P WILD-TYPE 38 60 41

Figure S33.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 2.88e-08 (Fisher's exact test), Q value = 1.2e-05

Table S34.  Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
7P MUTATED 70 53 101 99
7P WILD-TYPE 50 72 28 90

Figure S34.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-09 (Fisher's exact test), Q value = 8.3e-07

Table S35.  Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
7P MUTATED 122 61 140
7P WILD-TYPE 114 80 46

Figure S35.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.5e-06 (Fisher's exact test), Q value = 0.0018

Table S36.  Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
7P MUTATED 72 47 62
7P WILD-TYPE 28 62 23

Figure S36.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q' versus 'MRNA_CNMF'

P value = 0.000268 (Fisher's exact test), Q value = 0.097

Table S37.  Gene #14: '7q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
7Q MUTATED 9 36 36 13
7Q WILD-TYPE 34 26 33 28

Figure S37.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q' versus 'CN_CNMF'

P value = 4.55e-14 (Fisher's exact test), Q value = 2.1e-11

Table S38.  Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
7Q MUTATED 122 82 87 11
7Q WILD-TYPE 52 163 70 2

Figure S38.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 0.000307 (Fisher's exact test), Q value = 0.11

Table S39.  Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
7Q MUTATED 105 52 44
7Q WILD-TYPE 51 64 47

Figure S39.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q' versus 'MRNASEQ_CNMF'

P value = 5.79e-07 (Fisher's exact test), Q value = 0.00024

Table S40.  Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
7Q MUTATED 58 49 93 90
7Q WILD-TYPE 62 76 36 99

Figure S40.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.59e-07 (Fisher's exact test), Q value = 0.00019

Table S41.  Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
7Q MUTATED 109 56 125
7Q WILD-TYPE 127 85 61

Figure S41.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.52e-05 (Fisher's exact test), Q value = 0.0097

Table S42.  Gene #14: '7q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
7Q MUTATED 64 42 58
7Q WILD-TYPE 36 67 27

Figure S42.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p' versus 'CN_CNMF'

P value = 1.79e-44 (Fisher's exact test), Q value = 8.6e-42

Table S43.  Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
8P MUTATED 131 78 150 10
8P WILD-TYPE 43 167 7 3

Figure S43.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

'8p' versus 'METHLYATION_CNMF'

P value = 0.000134 (Fisher's exact test), Q value = 0.049

Table S44.  Gene #15: '8p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
8P MUTATED 121 63 55
8P WILD-TYPE 35 53 36

Figure S44.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p' versus 'MRNASEQ_CNMF'

P value = 7.38e-07 (Fisher's exact test), Q value = 3e-04

Table S45.  Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
8P MUTATED 79 55 100 117
8P WILD-TYPE 41 70 29 72

Figure S45.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.2e-06 (Fisher's exact test), Q value = 0.00049

Table S46.  Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
8P MUTATED 142 68 141
8P WILD-TYPE 94 73 45

Figure S46.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.09e-05 (Fisher's exact test), Q value = 0.034

Table S47.  Gene #15: '8p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
8P MUTATED 77 55 62
8P WILD-TYPE 23 54 23

Figure S47.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q' versus 'CN_CNMF'

P value = 9.12e-44 (Fisher's exact test), Q value = 4.4e-41

Table S48.  Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
8Q MUTATED 97 75 151 11
8Q WILD-TYPE 77 170 6 2

Figure S48.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

'8q' versus 'MRNASEQ_CNMF'

P value = 7.8e-06 (Fisher's exact test), Q value = 0.0031

Table S49.  Gene #16: '8q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
8Q MUTATED 75 49 90 104
8Q WILD-TYPE 45 76 39 85

Figure S49.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.65e-07 (Fisher's exact test), Q value = 0.00011

Table S50.  Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
8Q MUTATED 128 58 132
8Q WILD-TYPE 108 83 54

Figure S50.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.12

Table S51.  Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
9P MUTATED 71 55 57 4
9P WILD-TYPE 103 190 100 9

Figure S51.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 4.8e-07 (Fisher's exact test), Q value = 2e-04

Table S52.  Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
10P MUTATED 54 33 45 8
10P WILD-TYPE 120 212 112 5

Figure S52.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.1

Table S53.  Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
10P MUTATED 32 16 45 39
10P WILD-TYPE 88 109 84 150

Figure S53.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.067

Table S54.  Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
10P MUTATED 47 22 63
10P WILD-TYPE 189 119 123

Figure S54.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.11

Table S55.  Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
10P MUTATED 35 15 29
10P WILD-TYPE 65 94 56

Figure S55.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q' versus 'CN_CNMF'

P value = 5.93e-11 (Fisher's exact test), Q value = 2.6e-08

Table S56.  Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
10Q MUTATED 48 23 48 9
10Q WILD-TYPE 126 222 109 4

Figure S56.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

'10q' versus 'MRNASEQ_CNMF'

P value = 0.000553 (Fisher's exact test), Q value = 0.19

Table S57.  Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
10Q MUTATED 24 14 42 42
10Q WILD-TYPE 96 111 87 147

Figure S57.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000109 (Fisher's exact test), Q value = 0.04

Table S58.  Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
10Q MUTATED 49 16 57
10Q WILD-TYPE 187 125 129

Figure S58.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000123 (Fisher's exact test), Q value = 0.045

Table S59.  Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
10Q MUTATED 33 11 23
10Q WILD-TYPE 67 98 62

Figure S59.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p' versus 'CN_CNMF'

P value = 1e-08 (Fisher's exact test), Q value = 4.3e-06

Table S60.  Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
11P MUTATED 68 33 47 5
11P WILD-TYPE 106 212 110 8

Figure S60.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

'11p' versus 'METHLYATION_CNMF'

P value = 6.95e-06 (Fisher's exact test), Q value = 0.0028

Table S61.  Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
11P MUTATED 59 14 24
11P WILD-TYPE 97 102 67

Figure S61.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.84e-05 (Fisher's exact test), Q value = 0.015

Table S62.  Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
11P MUTATED 63 20 67
11P WILD-TYPE 173 121 119

Figure S62.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.11

Table S63.  Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
11P MUTATED 35 15 29
11P WILD-TYPE 65 94 56

Figure S63.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q' versus 'CN_CNMF'

P value = 1.63e-09 (Fisher's exact test), Q value = 7.2e-07

Table S64.  Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
11Q MUTATED 70 34 53 5
11Q WILD-TYPE 104 211 104 8

Figure S64.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

'11q' versus 'METHLYATION_CNMF'

P value = 8.81e-07 (Fisher's exact test), Q value = 0.00036

Table S65.  Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
11Q MUTATED 63 14 25
11Q WILD-TYPE 93 102 66

Figure S65.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.47e-05 (Fisher's exact test), Q value = 0.035

Table S66.  Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
11Q MUTATED 66 23 70
11Q WILD-TYPE 170 118 116

Figure S66.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.012

Table S67.  Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
11Q MUTATED 38 15 32
11Q WILD-TYPE 62 94 53

Figure S67.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q' versus 'MRNA_CNMF'

P value = 9.09e-06 (Fisher's exact test), Q value = 0.0036

Table S68.  Gene #25: '13q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
13Q MUTATED 18 47 53 17
13Q WILD-TYPE 25 15 16 24

Figure S68.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q' versus 'CN_CNMF'

P value = 1.59e-34 (Fisher's exact test), Q value = 7.6e-32

Table S69.  Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
13Q MUTATED 165 95 105 9
13Q WILD-TYPE 9 150 52 4

Figure S69.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 2.23e-09 (Fisher's exact test), Q value = 9.8e-07

Table S70.  Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
13Q MUTATED 129 56 52
13Q WILD-TYPE 27 60 39

Figure S70.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q' versus 'MRNASEQ_CNMF'

P value = 4.9e-08 (Fisher's exact test), Q value = 2.1e-05

Table S71.  Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
13Q MUTATED 71 55 102 129
13Q WILD-TYPE 49 70 27 60

Figure S71.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.63e-09 (Fisher's exact test), Q value = 3.7e-06

Table S72.  Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
13Q MUTATED 148 64 145
13Q WILD-TYPE 88 77 41

Figure S72.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.94e-10 (Fisher's exact test), Q value = 2.6e-07

Table S73.  Gene #25: '13q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
13Q MUTATED 83 48 67
13Q WILD-TYPE 17 61 18

Figure S73.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q' versus 'CN_CNMF'

P value = 3.26e-25 (Fisher's exact test), Q value = 1.5e-22

Table S74.  Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
14Q MUTATED 124 50 54 7
14Q WILD-TYPE 50 195 103 6

Figure S74.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

'14q' versus 'METHLYATION_CNMF'

P value = 2.06e-05 (Fisher's exact test), Q value = 0.008

Table S75.  Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
14Q MUTATED 81 29 31
14Q WILD-TYPE 75 87 60

Figure S75.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q' versus 'MRNASEQ_CNMF'

P value = 4.5e-11 (Fisher's exact test), Q value = 2e-08

Table S76.  Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
14Q MUTATED 33 28 79 86
14Q WILD-TYPE 87 97 50 103

Figure S76.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.04e-05 (Fisher's exact test), Q value = 0.012

Table S77.  Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
14Q MUTATED 100 35 91
14Q WILD-TYPE 136 106 95

Figure S77.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.82e-08 (Fisher's exact test), Q value = 1.2e-05

Table S78.  Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
14Q MUTATED 58 21 37
14Q WILD-TYPE 42 88 48

Figure S78.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q' versus 'MRNA_CNMF'

P value = 0.000556 (Fisher's exact test), Q value = 0.19

Table S79.  Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
15Q MUTATED 13 33 36 8
15Q WILD-TYPE 30 29 33 33

Figure S79.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q' versus 'CN_CNMF'

P value = 8.29e-18 (Fisher's exact test), Q value = 3.9e-15

Table S80.  Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
15Q MUTATED 105 48 69 9
15Q WILD-TYPE 69 197 88 4

Figure S80.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

'15q' versus 'MRNASEQ_CNMF'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.0066

Table S81.  Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
15Q MUTATED 50 28 66 82
15Q WILD-TYPE 70 97 63 107

Figure S81.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.68e-07 (Fisher's exact test), Q value = 0.00015

Table S82.  Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
15Q MUTATED 101 31 94
15Q WILD-TYPE 135 110 92

Figure S82.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.75e-06 (Fisher's exact test), Q value = 0.0019

Table S83.  Gene #27: '15q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
15Q MUTATED 50 23 42
15Q WILD-TYPE 50 86 43

Figure S83.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p' versus 'CN_CNMF'

P value = 6.18e-16 (Fisher's exact test), Q value = 2.8e-13

Table S84.  Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
16P MUTATED 91 34 49 3
16P WILD-TYPE 83 211 108 10

Figure S84.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

'16p' versus 'MRNASEQ_CNMF'

P value = 0.000212 (Fisher's exact test), Q value = 0.077

Table S85.  Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
16P MUTATED 32 23 55 64
16P WILD-TYPE 88 102 74 125

Figure S85.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.94e-05 (Fisher's exact test), Q value = 0.026

Table S86.  Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
16P MUTATED 75 25 74
16P WILD-TYPE 161 116 112

Figure S86.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'CN_CNMF'

P value = 2.12e-17 (Fisher's exact test), Q value = 9.9e-15

Table S87.  Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
16Q MUTATED 91 31 52 3
16Q WILD-TYPE 83 214 105 10

Figure S87.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

'16q' versus 'MRNASEQ_CNMF'

P value = 0.000577 (Fisher's exact test), Q value = 0.2

Table S88.  Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
16Q MUTATED 31 24 54 63
16Q WILD-TYPE 89 101 75 126

Figure S88.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000106 (Fisher's exact test), Q value = 0.039

Table S89.  Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
16Q MUTATED 74 25 73
16Q WILD-TYPE 162 116 113

Figure S89.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MRNA_CNMF'

P value = 8.21e-07 (Fisher's exact test), Q value = 0.00034

Table S90.  Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
17P MUTATED 17 47 54 16
17P WILD-TYPE 26 15 15 25

Figure S90.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p' versus 'MRNA_CHIERARCHICAL'

P value = 8.06e-06 (Fisher's exact test), Q value = 0.0032

Table S91.  Gene #30: '17p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
17P MUTATED 36 30 25 43
17P WILD-TYPE 6 20 38 17

Figure S91.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p' versus 'CN_CNMF'

P value = 6.29e-27 (Fisher's exact test), Q value = 3e-24

Table S92.  Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
17P MUTATED 142 85 122 9
17P WILD-TYPE 32 160 35 4

Figure S92.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 7.3e-09 (Fisher's exact test), Q value = 3.2e-06

Table S93.  Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
17P MUTATED 123 54 45
17P WILD-TYPE 33 62 46

Figure S93.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p' versus 'MRNASEQ_CNMF'

P value = 3.09e-09 (Fisher's exact test), Q value = 1.4e-06

Table S94.  Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
17P MUTATED 70 50 102 121
17P WILD-TYPE 50 75 27 68

Figure S94.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.08e-09 (Fisher's exact test), Q value = 2.2e-06

Table S95.  Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
17P MUTATED 146 58 139
17P WILD-TYPE 90 83 47

Figure S95.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.32e-08 (Fisher's exact test), Q value = 1.4e-05

Table S96.  Gene #30: '17p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
17P MUTATED 80 45 56
17P WILD-TYPE 20 64 29

Figure S96.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q' versus 'CN_CNMF'

P value = 1.32e-07 (Fisher's exact test), Q value = 5.5e-05

Table S97.  Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
17Q MUTATED 77 48 62 4
17Q WILD-TYPE 97 197 95 9

Figure S97.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

'17q' versus 'MRNASEQ_CNMF'

P value = 2.91e-05 (Fisher's exact test), Q value = 0.011

Table S98.  Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
17Q MUTATED 31 29 64 61
17Q WILD-TYPE 89 96 65 128

Figure S98.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.012

Table S99.  Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
17Q MUTATED 74 29 82
17Q WILD-TYPE 162 112 104

Figure S99.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p' versus 'MRNA_CNMF'

P value = 1.01e-10 (Fisher's exact test), Q value = 4.5e-08

Table S100.  Gene #32: '18p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18P MUTATED 16 53 55 14
18P WILD-TYPE 27 9 14 27

Figure S100.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p' versus 'MRNA_CHIERARCHICAL'

P value = 1.79e-08 (Fisher's exact test), Q value = 7.7e-06

Table S101.  Gene #32: '18p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
18P MUTATED 37 30 23 48
18P WILD-TYPE 5 20 40 12

Figure S101.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p' versus 'CN_CNMF'

P value = 2.06e-37 (Fisher's exact test), Q value = 9.8e-35

Table S102.  Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
18P MUTATED 161 92 127 12
18P WILD-TYPE 13 153 30 1

Figure S102.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

'18p' versus 'METHLYATION_CNMF'

P value = 2.97e-16 (Fisher's exact test), Q value = 1.4e-13

Table S103.  Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
18P MUTATED 142 55 53
18P WILD-TYPE 14 61 38

Figure S103.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p' versus 'MRNASEQ_CNMF'

P value = 1.64e-18 (Fisher's exact test), Q value = 7.7e-16

Table S104.  Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
18P MUTATED 78 51 120 126
18P WILD-TYPE 42 74 9 63

Figure S104.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.58e-13 (Fisher's exact test), Q value = 7.1e-11

Table S105.  Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
18P MUTATED 153 64 158
18P WILD-TYPE 83 77 28

Figure S105.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.06e-13 (Fisher's exact test), Q value = 4.8e-11

Table S106.  Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
18P MUTATED 90 47 67
18P WILD-TYPE 10 62 18

Figure S106.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q' versus 'MRNA_CNMF'

P value = 1.2e-09 (Fisher's exact test), Q value = 5.3e-07

Table S107.  Gene #33: '18q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18Q MUTATED 18 54 56 16
18Q WILD-TYPE 25 8 13 25

Figure S107.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q' versus 'MRNA_CHIERARCHICAL'

P value = 4.13e-08 (Fisher's exact test), Q value = 1.8e-05

Table S108.  Gene #33: '18q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
18Q MUTATED 37 32 25 50
18Q WILD-TYPE 5 18 38 10

Figure S108.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q' versus 'CN_CNMF'

P value = 1.27e-38 (Fisher's exact test), Q value = 6.1e-36

Table S109.  Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
18Q MUTATED 159 97 138 13
18Q WILD-TYPE 15 148 19 0

Figure S109.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 2.79e-15 (Fisher's exact test), Q value = 1.3e-12

Table S110.  Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
18Q MUTATED 144 60 55
18Q WILD-TYPE 12 56 36

Figure S110.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q' versus 'MRNASEQ_CNMF'

P value = 6.06e-16 (Fisher's exact test), Q value = 2.8e-13

Table S111.  Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
18Q MUTATED 83 55 119 132
18Q WILD-TYPE 37 70 10 57

Figure S111.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.19e-13 (Fisher's exact test), Q value = 5.4e-11

Table S112.  Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
18Q MUTATED 159 68 162
18Q WILD-TYPE 77 73 24

Figure S112.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.37e-11 (Fisher's exact test), Q value = 1.5e-08

Table S113.  Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
18Q MUTATED 90 53 68
18Q WILD-TYPE 10 56 17

Figure S113.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p' versus 'CN_CNMF'

P value = 2.2e-11 (Fisher's exact test), Q value = 9.9e-09

Table S114.  Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
19P MUTATED 70 30 55 5
19P WILD-TYPE 104 215 102 8

Figure S114.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

'19p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000563 (Fisher's exact test), Q value = 0.2

Table S115.  Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
19P MUTATED 62 24 67
19P WILD-TYPE 174 117 119

Figure S115.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q' versus 'CN_CNMF'

P value = 1.16e-07 (Fisher's exact test), Q value = 4.9e-05

Table S116.  Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
19Q MUTATED 68 37 50 5
19Q WILD-TYPE 106 208 107 8

Figure S116.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'MRNA_CNMF'

P value = 2.27e-07 (Fisher's exact test), Q value = 9.5e-05

Table S117.  Gene #36: '20p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20P MUTATED 19 53 58 21
20P WILD-TYPE 24 9 11 20

Figure S117.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p' versus 'MRNA_CHIERARCHICAL'

P value = 3.83e-09 (Fisher's exact test), Q value = 1.7e-06

Table S118.  Gene #36: '20p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
20P MUTATED 36 40 24 51
20P WILD-TYPE 6 10 39 9

Figure S118.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p' versus 'CN_CNMF'

P value = 9.46e-17 (Fisher's exact test), Q value = 4.4e-14

Table S119.  Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
20P MUTATED 147 119 120 13
20P WILD-TYPE 27 126 37 0

Figure S119.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 1.35e-08 (Fisher's exact test), Q value = 5.8e-06

Table S120.  Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
20P MUTATED 130 59 54
20P WILD-TYPE 26 57 37

Figure S120.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p' versus 'MRNASEQ_CNMF'

P value = 1.24e-08 (Fisher's exact test), Q value = 5.4e-06

Table S121.  Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
20P MUTATED 74 62 109 136
20P WILD-TYPE 46 63 20 53

Figure S121.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.86e-07 (Fisher's exact test), Q value = 2e-04

Table S122.  Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
20P MUTATED 164 71 146
20P WILD-TYPE 72 70 40

Figure S122.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.96e-06 (Fisher's exact test), Q value = 0.0039

Table S123.  Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
20P MUTATED 77 55 67
20P WILD-TYPE 23 54 18

Figure S123.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q' versus 'MRNA_CNMF'

P value = 3.3e-14 (Fisher's exact test), Q value = 1.5e-11

Table S124.  Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20Q MUTATED 18 61 63 23
20Q WILD-TYPE 25 1 6 18

Figure S124.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q' versus 'MRNA_CHIERARCHICAL'

P value = 5.11e-13 (Fisher's exact test), Q value = 2.3e-10

Table S125.  Gene #37: '20q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 50 63 60
20Q MUTATED 39 43 26 57
20Q WILD-TYPE 3 7 37 3

Figure S125.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q' versus 'CN_CNMF'

P value = 6.98e-34 (Fisher's exact test), Q value = 3.3e-31

Table S126.  Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
20Q MUTATED 172 129 137 13
20Q WILD-TYPE 2 116 20 0

Figure S126.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 1.02e-16 (Fisher's exact test), Q value = 4.7e-14

Table S127.  Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 116 91
20Q MUTATED 151 67 62
20Q WILD-TYPE 5 49 29

Figure S127.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q' versus 'MRNASEQ_CNMF'

P value = 1.45e-17 (Fisher's exact test), Q value = 6.8e-15

Table S128.  Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
20Q MUTATED 87 66 126 150
20Q WILD-TYPE 33 59 3 39

Figure S128.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.24e-14 (Fisher's exact test), Q value = 2.8e-11

Table S129.  Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
20Q MUTATED 180 78 171
20Q WILD-TYPE 56 63 15

Figure S129.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.05e-12 (Fisher's exact test), Q value = 2.7e-09

Table S130.  Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
20Q MUTATED 93 60 76
20Q WILD-TYPE 7 49 9

Figure S130.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000705 (Fisher's exact test), Q value = 0.24

Table S131.  Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 105 115 41
20Q MUTATED 31 84 77 37
20Q WILD-TYPE 2 21 38 4

Figure S131.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q' versus 'CN_CNMF'

P value = 8.27e-08 (Fisher's exact test), Q value = 3.5e-05

Table S132.  Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
21Q MUTATED 89 60 58 8
21Q WILD-TYPE 85 185 99 5

Figure S132.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

'21q' versus 'MRNASEQ_CNMF'

P value = 0.000394 (Fisher's exact test), Q value = 0.14

Table S133.  Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 120 125 129 189
21Q MUTATED 42 31 65 67
21Q WILD-TYPE 78 94 64 122

Figure S133.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000662 (Fisher's exact test), Q value = 0.23

Table S134.  Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 236 141 186
21Q MUTATED 80 38 87
21Q WILD-TYPE 156 103 99

Figure S134.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000446 (Fisher's exact test), Q value = 0.16

Table S135.  Gene #38: '21q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
21Q MUTATED 50 27 37
21Q WILD-TYPE 50 82 48

Figure S135.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.076

Table S136.  Gene #39: '22q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
22Q MUTATED 13 34 30 6
22Q WILD-TYPE 30 28 39 35

Figure S136.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q' versus 'CN_CNMF'

P value = 3.7e-16 (Fisher's exact test), Q value = 1.7e-13

Table S137.  Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
22Q MUTATED 106 51 51 7
22Q WILD-TYPE 68 194 106 6

Figure S137.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

'22q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000129 (Fisher's exact test), Q value = 0.047

Table S138.  Gene #39: '22q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 109 85
22Q MUTATED 46 22 35
22Q WILD-TYPE 54 87 50

Figure S138.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq' versus 'CN_CNMF'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00048

Table S139.  Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 174 245 157 13
XQ MUTATED 69 44 57 2
XQ WILD-TYPE 105 201 100 11

Figure S139.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

  • Molecular subtype file = COADREAD-TP.transferedmergedcluster.txt

  • Number of patients = 589

  • Number of significantly focal cnvs = 40

  • Number of molecular subtypes = 12

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

Fisher's exact test

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

Q value calculation

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

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] 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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