Correlation between copy number variation genes (focal events) and molecular subtypes
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 427 patients, 173 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 2p cnv correlated to 'CN_CNMF'.

  • 2q cnv correlated to 'CN_CNMF'.

  • 3p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 3q cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

  • 4q cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  '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_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 6p cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 6q cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 9p cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9q 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 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

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

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

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

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

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

  • 18p cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  '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',  'MRNASEQ_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',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 22q cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', 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, 173 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
18p 259 (61%) 168 3.64e-10
(1.58e-07) 		1.1e-08
(4.67e-06) 		1.45e-37
(6.93e-35) 		2.34e-12
(1.05e-09) 		0.000604
(0.191) 		0.000561
(0.178) 		1.27e-19
(5.93e-17) 		3.47e-13
(1.58e-10) 		0.633
(1.00) 		0.0855
(1.00) 		1.68e-12
(7.54e-10) 		0.0594
(1.00)
20q 308 (72%) 119 1e-10
(4.38e-08) 		4.1e-12
(1.83e-09) 		8.06e-38
(3.87e-35) 		3.36e-12
(1.5e-09) 		0.00142
(0.427) 		5.05e-05
(0.0179) 		1.42e-23
(6.7e-21) 		4.29e-20
(2.02e-17) 		0.903
(1.00) 		5.91e-05
(0.0208) 		1.43e-12
(6.48e-10) 		0.121
(1.00)
14q 162 (38%) 265 0.000225
(0.0748) 		0.000141
(0.0476) 		2.77e-25
(1.31e-22) 		8.29e-06
(0.00313) 		0.00502
(1.00) 		0.107
(1.00) 		4.2e-11
(1.86e-08) 		2.3e-10
(1e-07) 		0.478
(1.00) 		0.000441
(0.143) 		1.81e-06
(0.000716) 		0.126
(1.00)
17p 247 (58%) 180 5.28e-08
(2.2e-05) 		9.71e-08
(4e-05) 		2.59e-33
(1.24e-30) 		9.38e-12
(4.17e-09) 		0.00332
(0.937) 		8.59e-05
(0.0298) 		1.7e-14
(7.76e-12) 		1.33e-16
(6.15e-14) 		0.45
(1.00) 		0.0157
(1.00) 		5.59e-11
(2.46e-08) 		0.0549
(1.00)
20p 272 (64%) 155 9.01e-06
(0.00338) 		6.33e-09
(2.68e-06) 		7.55e-22
(3.57e-19) 		1.51e-06
(6e-04) 		0.0176
(1.00) 		0.0376
(1.00) 		4.24e-13
(1.92e-10) 		7.32e-10
(3.16e-07) 		0.751
(1.00) 		0.000309
(0.102) 		7.66e-06
(0.00289) 		0.719
(1.00)
22q 148 (35%) 279 0.000223
(0.0744) 		0.000316
(0.104) 		8.17e-19
(3.81e-16) 		8.46e-05
(0.0295) 		0.101
(1.00) 		0.58
(1.00) 		2e-08
(8.37e-06) 		1.47e-05
(0.00544) 		0.166
(1.00) 		0.000495
(0.159) 		5.66e-06
(0.00216) 		0.375
(1.00)
4q 130 (30%) 297 4.51e-06
(0.00174) 		0.000717
(0.221) 		6.26e-18
(2.91e-15) 		1.5e-05
(0.00553) 		0.00938
(1.00) 		0.102
(1.00) 		3.41e-05
(0.0123) 		4.27e-07
(0.000173) 		0.2
(1.00) 		0.0023
(0.68) 		7.61e-06
(0.00288) 		0.317
(1.00)
8p 256 (60%) 171 0.0891
(1.00) 		0.0132
(1.00) 		1.55e-24
(7.37e-22) 		0.000546
(0.174) 		0.000319
(0.104) 		4.32e-05
(0.0154) 		8.4e-08
(3.48e-05) 		2.26e-06
(0.000889) 		0.313
(1.00) 		0.167
(1.00) 		1.39e-05
(0.00513) 		0.165
(1.00)
11p 99 (23%) 328 8.99e-05
(0.0311) 		2.69e-05
(0.00983) 		3.22e-13
(1.47e-10) 		5.82e-07
(0.000234) 		0.127
(1.00) 		0.107
(1.00) 		3.54e-05
(0.0127) 		8.56e-06
(0.00322) 		0.691
(1.00) 		0.026
(1.00) 		4.13e-06
(0.0016) 		0.169
(1.00)
11q 107 (25%) 320 3.14e-06
(0.00122) 		7.47e-07
(0.000298) 		8.2e-15
(3.75e-12) 		1.32e-07
(5.41e-05) 		0.0939
(1.00) 		0.218
(1.00) 		1.76e-06
(7e-04) 		2.43e-06
(0.000953) 		0.84
(1.00) 		0.00507
(1.00) 		2.06e-07
(8.35e-05) 		0.273
(1.00)
13q 257 (60%) 170 0.000138
(0.0469) 		0.000124
(0.0421) 		2.16e-29
(1.03e-26) 		0.00028
(0.0926) 		0.00594
(1.00) 		0.00834
(1.00) 		1.57e-10
(6.84e-08) 		3.29e-11
(1.46e-08) 		0.6
(1.00) 		0.0161
(1.00) 		1.33e-07
(5.42e-05) 		0.795
(1.00)
18q 266 (62%) 161 3.12e-10
(1.35e-07) 		2.45e-09
(1.05e-06) 		4.1e-37
(1.96e-34) 		9.13e-12
(4.07e-09) 		0.00809
(1.00) 		0.00173
(0.519) 		5.35e-21
(2.52e-18) 		4.66e-15
(2.14e-12) 		0.45
(1.00) 		0.0607
(1.00) 		4.33e-11
(1.91e-08) 		0.241
(1.00)
4p 136 (32%) 291 2.82e-05
(0.0102) 		0.00394
(1.00) 		3.57e-17
(1.65e-14) 		9.08e-05
(0.0313) 		0.0566
(1.00) 		0.0909
(1.00) 		7.17e-07
(0.000287) 		9.19e-08
(3.8e-05) 		0.595
(1.00) 		0.0468
(1.00) 		6.52e-06
(0.00248) 		0.65
(1.00)
7p 234 (55%) 193 0.0062
(1.00) 		0.00107
(0.326) 		1.94e-15
(8.94e-13) 		0.000798
(0.246) 		0.000462
(0.149) 		0.0159
(1.00) 		3.75e-09
(1.61e-06) 		4.45e-09
(1.9e-06) 		0.599
(1.00) 		0.00669
(1.00) 		4.46e-06
(0.00172) 		0.968
(1.00)
16q 124 (29%) 303 4.54e-06
(0.00174) 		2.45e-05
(0.00897) 		2.67e-17
(1.24e-14) 		0.0891
(1.00) 		0.0368
(1.00) 		0.253
(1.00) 		0.000671
(0.208) 		0.000123
(0.0421) 		0.929
(1.00) 		0.00111
(0.337) 		0.000301
(0.0994) 		0.564
(1.00)
15q 156 (37%) 271 0.00305
(0.872) 		0.00361
(1.00) 		2.82e-19
(1.32e-16) 		0.00251
(0.731) 		0.00263
(0.757) 		0.0369
(1.00) 		5.74e-09
(2.44e-06) 		7.51e-08
(3.12e-05) 		0.938
(1.00) 		4.24e-05
(0.0151) 		1.38e-05
(0.00512) 		0.28
(1.00)
16p 129 (30%) 298 5.11e-06
(0.00195) 		1.37e-05
(0.00509) 		9.76e-18
(4.53e-15) 		0.0282
(1.00) 		0.0449
(1.00) 		0.193
(1.00) 		0.000653
(0.203) 		8.48e-05
(0.0295) 		0.695
(1.00) 		0.00176
(0.525) 		0.0021
(0.622) 		0.531
(1.00)
17q 136 (32%) 291 0.00556
(1.00) 		0.101
(1.00) 		1.61e-12
(7.25e-10) 		0.000627
(0.197) 		0.145
(1.00) 		0.0265
(1.00) 		1.99e-08
(8.37e-06) 		5.48e-07
(0.000221) 		0.319
(1.00) 		0.124
(1.00) 		0.000449
(0.146) 		0.045
(1.00)
6p 112 (26%) 315 0.108
(1.00) 		0.000232
(0.0769) 		7.15e-07
(0.000287) 		0.0217
(1.00) 		0.118
(1.00) 		0.457
(1.00) 		0.0069
(1.00) 		0.000496
(0.159) 		0.696
(1.00) 		0.0277
(1.00) 		0.000107
(0.0368) 		0.813
(1.00)
7q 214 (50%) 213 0.00407
(1.00) 		0.00312
(0.887) 		8.54e-11
(3.74e-08) 		0.00736
(1.00) 		0.00519
(1.00) 		0.0162
(1.00) 		1.07e-07
(4.39e-05) 		4.02e-08
(1.68e-05) 		0.471
(1.00) 		0.00254
(0.736) 		1.13e-05
(0.00424) 		0.89
(1.00)
10p 96 (22%) 331 0.00733
(1.00) 		0.0578
(1.00) 		7.54e-10
(3.25e-07) 		0.0217
(1.00) 		0.0595
(1.00) 		0.0233
(1.00) 		2.99e-06
(0.00117) 		4.44e-06
(0.00172) 		0.184
(1.00) 		0.000954
(0.291) 		2.08e-06
(0.000822) 		0.399
(1.00)
10q 86 (20%) 341 0.0037
(1.00) 		0.0203
(1.00) 		8.43e-11
(3.7e-08) 		0.0516
(1.00) 		0.0789
(1.00) 		0.1
(1.00) 		2.74e-05
(0.00996) 		5.34e-05
(0.0189) 		0.471
(1.00) 		0.0131
(1.00) 		2.67e-06
(0.00104) 		0.639
(1.00)
1p 121 (28%) 306 0.0144
(1.00) 		0.0228
(1.00) 		2.96e-13
(1.35e-10) 		0.00234
(0.688) 		0.0335
(1.00) 		0.112
(1.00) 		7e-05
(0.0245) 		5.02e-08
(2.09e-05) 		0.571
(1.00) 		0.0468
(1.00) 		0.00308
(0.878) 		0.025
(1.00)
1q 127 (30%) 300 0.479
(1.00) 		0.308
(1.00) 		1.27e-08
(5.34e-06) 		0.0331
(1.00) 		0.0969
(1.00) 		0.0252
(1.00) 		0.00319
(0.902) 		2.34e-05
(0.00857) 		0.726
(1.00) 		0.0935
(1.00) 		6.73e-05
(0.0236) 		0.202
(1.00)
5q 113 (26%) 314 0.348
(1.00) 		0.254
(1.00) 		3.85e-09
(1.64e-06) 		0.132
(1.00) 		0.069
(1.00) 		0.231
(1.00) 		0.000597
(0.189) 		1.57e-07
(6.41e-05) 		0.864
(1.00) 		0.296
(1.00) 		0.0047
(1.00) 		0.862
(1.00)
9p 123 (29%) 304 0.149
(1.00) 		0.0228
(1.00) 		1.79e-07
(7.3e-05) 		0.0221
(1.00) 		0.00355
(0.996) 		0.304
(1.00) 		0.000642
(0.2) 		0.000493
(0.159) 		0.343
(1.00) 		0.355
(1.00) 		0.0127
(1.00) 		0.776
(1.00)
19p 105 (25%) 322 0.324
(1.00) 		0.0257
(1.00) 		2.13e-07
(8.61e-05) 		0.1
(1.00) 		0.105
(1.00) 		0.107
(1.00) 		0.000219
(0.0735) 		0.000146
(0.0491) 		0.509
(1.00) 		0.03
(1.00) 		0.00841
(1.00) 		0.663
(1.00)
21q 138 (32%) 289 0.00417
(1.00) 		0.00248
(0.724) 		4.94e-11
(2.18e-08) 		0.108
(1.00) 		0.146
(1.00) 		0.181
(1.00) 		0.00259
(0.748) 		0.00064
(0.2) 		0.318
(1.00) 		0.126
(1.00) 		0.000424
(0.138) 		0.556
(1.00)
3p 92 (22%) 335 0.193
(1.00) 		0.0347
(1.00) 		1.63e-08
(6.85e-06) 		0.0982
(1.00) 		0.199
(1.00) 		0.0794
(1.00) 		0.000636
(0.2) 		0.00623
(1.00) 		0.663
(1.00) 		0.195
(1.00) 		0.00355
(0.996) 		0.141
(1.00)
3q 92 (22%) 335 0.0907
(1.00) 		0.0242
(1.00) 		3.11e-09
(1.34e-06) 		0.091
(1.00) 		0.154
(1.00) 		0.398
(1.00) 		0.000151
(0.0506) 		0.00279
(0.801) 		0.239
(1.00) 		0.258
(1.00) 		0.00508
(1.00) 		0.276
(1.00)
5p 117 (27%) 310 0.295
(1.00) 		0.177
(1.00) 		2.32e-06
(0.00091) 		0.49
(1.00) 		0.174
(1.00) 		0.774
(1.00) 		0.0355
(1.00) 		1.24e-05
(0.00463) 		0.656
(1.00) 		0.325
(1.00) 		0.0125
(1.00) 		0.675
(1.00)
8q 235 (55%) 192 0.766
(1.00) 		0.0713
(1.00) 		1.81e-19
(8.47e-17) 		0.00489
(1.00) 		0.0204
(1.00) 		0.000941
(0.288) 		0.0014
(0.422) 		4.89e-05
(0.0174) 		0.951
(1.00) 		0.263
(1.00) 		0.00728
(1.00) 		0.026
(1.00)
2p 80 (19%) 347 0.037
(1.00) 		0.0815
(1.00) 		2.88e-05
(0.0104) 		0.017
(1.00) 		0.0618
(1.00) 		0.301
(1.00) 		0.00531
(1.00) 		0.0113
(1.00) 		0.592
(1.00) 		0.0474
(1.00) 		0.149
(1.00) 		0.00737
(1.00)
2q 77 (18%) 350 0.11
(1.00) 		0.0705
(1.00) 		2.89e-05
(0.0104) 		0.022
(1.00) 		0.2
(1.00) 		0.613
(1.00) 		0.0207
(1.00) 		0.0358
(1.00) 		0.745
(1.00) 		0.125
(1.00) 		0.282
(1.00) 		0.249
(1.00)
6q 116 (27%) 311 0.102
(1.00) 		0.00233
(0.688) 		3.24e-05
(0.0116) 		0.0614
(1.00) 		0.393
(1.00) 		0.181
(1.00) 		0.141
(1.00) 		0.0266
(1.00) 		0.797
(1.00) 		0.0614
(1.00) 		0.000853
(0.262) 		0.817
(1.00)
9q 114 (27%) 313 0.343
(1.00) 		0.113
(1.00) 		4.85e-06
(0.00186) 		0.0278
(1.00) 		0.00411
(1.00) 		0.471
(1.00) 		0.00238
(0.698) 		0.00553
(1.00) 		0.23
(1.00) 		0.431
(1.00) 		0.0155
(1.00) 		0.49
(1.00)
19q 108 (25%) 319 0.106
(1.00) 		0.0258
(1.00) 		0.000102
(0.0353) 		0.156
(1.00) 		0.0356
(1.00) 		0.028
(1.00) 		0.00533
(1.00) 		0.00123
(0.372) 		0.711
(1.00) 		0.0375
(1.00) 		0.0525
(1.00) 		0.511
(1.00)
xq 114 (27%) 313 0.00682
(1.00) 		0.0626
(1.00) 		0.000112
(0.0383) 		0.216
(1.00) 		0.0171
(1.00) 		0.00791
(1.00) 		0.102
(1.00) 		0.167
(1.00) 		0.0219
(1.00) 		0.475
(1.00) 		0.0167
(1.00) 		0.0741
(1.00)
12p 131 (31%) 296 0.985
(1.00) 		0.205
(1.00) 		0.142
(1.00) 		0.81
(1.00) 		0.239
(1.00) 		0.661
(1.00) 		0.177
(1.00) 		0.109
(1.00) 		0.359
(1.00) 		0.268
(1.00) 		0.599
(1.00) 		0.559
(1.00)
12q 127 (30%) 300 0.875
(1.00) 		0.521
(1.00) 		0.265
(1.00) 		0.759
(1.00) 		0.199
(1.00) 		0.62
(1.00) 		0.123
(1.00) 		0.103
(1.00) 		0.215
(1.00) 		0.219
(1.00) 		0.558
(1.00) 		0.121
(1.00)
'1p' versus 'CN_CNMF'

P value = 2.96e-13 (Fisher's exact test), Q value = 1.3e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
1P MUTATED 83 27 11
1P WILD-TYPE 88 168 50

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

'1p' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.024

Table S2.  Gene #1: '1p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
1P MUTATED 53 22 40
1P WILD-TYPE 78 112 104

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

'1p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.02e-08 (Fisher's exact test), Q value = 2.1e-05

Table S3.  Gene #1: '1p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
1P MUTATED 47 59 9
1P WILD-TYPE 118 84 92

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

'1q' versus 'CN_CNMF'

P value = 1.27e-08 (Fisher's exact test), Q value = 5.3e-06

Table S4.  Gene #2: '1q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
1Q MUTATED 78 33 16
1Q WILD-TYPE 93 162 45

Figure S4.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #3: 'CN_CNMF'

'1q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.34e-05 (Fisher's exact test), Q value = 0.0086

Table S5.  Gene #2: '1q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
1Q MUTATED 49 56 13
1Q WILD-TYPE 116 87 88

Figure S5.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.73e-05 (Fisher's exact test), Q value = 0.024

Table S6.  Gene #2: '1q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
1Q MUTATED 34 10 22
1Q WILD-TYPE 45 68 41

Figure S6.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p' versus 'CN_CNMF'

P value = 2.88e-05 (Fisher's exact test), Q value = 0.01

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
2P MUTATED 50 21 9
2P WILD-TYPE 121 174 52

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

'2q' versus 'CN_CNMF'

P value = 2.89e-05 (Fisher's exact test), Q value = 0.01

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
2Q MUTATED 48 19 10
2Q WILD-TYPE 123 176 51

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

'3p' versus 'CN_CNMF'

P value = 1.63e-08 (Fisher's exact test), Q value = 6.9e-06

Table S9.  Gene #5: '3p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
3P MUTATED 62 23 7
3P WILD-TYPE 109 172 54

Figure S9.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #3: 'CN_CNMF'

'3p' versus 'MRNASEQ_CNMF'

P value = 0.000636 (Fisher's exact test), Q value = 0.2

Table S10.  Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
3P MUTATED 43 18 29
3P WILD-TYPE 88 116 115

Figure S10.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q' versus 'CN_CNMF'

P value = 3.11e-09 (Fisher's exact test), Q value = 1.3e-06

Table S11.  Gene #6: '3q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
3Q MUTATED 63 21 8
3Q WILD-TYPE 108 174 53

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

'3q' versus 'MRNASEQ_CNMF'

P value = 0.000151 (Fisher's exact test), Q value = 0.051

Table S12.  Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
3Q MUTATED 45 18 27
3Q WILD-TYPE 86 116 117

Figure S12.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p' versus 'MRNA_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.01

Table S13.  Gene #7: '4p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
4P MUTATED 8 29 1 10
4P WILD-TYPE 27 32 28 11

Figure S13.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p' versus 'CN_CNMF'

P value = 3.57e-17 (Fisher's exact test), Q value = 1.6e-14

Table S14.  Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
4P MUTATED 95 28 13
4P WILD-TYPE 76 167 48

Figure S14.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #3: 'CN_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 9.08e-05 (Fisher's exact test), Q value = 0.031

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
4P MUTATED 50 14 21
4P WILD-TYPE 64 74 47

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

'4p' versus 'MRNASEQ_CNMF'

P value = 7.17e-07 (Fisher's exact test), Q value = 0.00029

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
4P MUTATED 62 23 48
4P WILD-TYPE 69 111 96

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

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.19e-08 (Fisher's exact test), Q value = 3.8e-05

Table S17.  Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
4P MUTATED 57 64 12
4P WILD-TYPE 108 79 89

Figure S17.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.52e-06 (Fisher's exact test), Q value = 0.0025

Table S18.  Gene #7: '4p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
4P MUTATED 34 8 22
4P WILD-TYPE 45 70 41

Figure S18.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q' versus 'MRNA_CNMF'

P value = 4.51e-06 (Fisher's exact test), Q value = 0.0017

Table S19.  Gene #8: '4q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
4Q MUTATED 7 30 1 11
4Q WILD-TYPE 28 31 28 10

Figure S19.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000717 (Fisher's exact test), Q value = 0.22

Table S20.  Gene #8: '4q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
4Q MUTATED 23 5 21
4Q WILD-TYPE 33 38 26

Figure S20.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q' versus 'CN_CNMF'

P value = 6.26e-18 (Fisher's exact test), Q value = 2.9e-15

Table S21.  Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
4Q MUTATED 93 25 12
4Q WILD-TYPE 78 170 49

Figure S21.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #3: 'CN_CNMF'

'4q' versus 'METHLYATION_CNMF'

P value = 1.5e-05 (Fisher's exact test), Q value = 0.0055

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
4Q MUTATED 48 11 20
4Q WILD-TYPE 66 77 48

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

'4q' versus 'MRNASEQ_CNMF'

P value = 3.41e-05 (Fisher's exact test), Q value = 0.012

Table S23.  Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
4Q MUTATED 55 23 48
4Q WILD-TYPE 76 111 96

Figure S23.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.27e-07 (Fisher's exact test), Q value = 0.00017

Table S24.  Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
4Q MUTATED 57 58 11
4Q WILD-TYPE 108 85 90

Figure S24.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.61e-06 (Fisher's exact test), Q value = 0.0029

Table S25.  Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
4Q MUTATED 29 6 22
4Q WILD-TYPE 50 72 41

Figure S25.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p' versus 'CN_CNMF'

P value = 2.32e-06 (Fisher's exact test), Q value = 0.00091

Table S26.  Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
5P MUTATED 67 31 19
5P WILD-TYPE 104 164 42

Figure S26.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #3: 'CN_CNMF'

'5p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0046

Table S27.  Gene #9: '5p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
5P MUTATED 51 52 11
5P WILD-TYPE 114 91 90

Figure S27.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q' versus 'CN_CNMF'

P value = 3.85e-09 (Fisher's exact test), Q value = 1.6e-06

Table S28.  Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
5Q MUTATED 70 25 18
5Q WILD-TYPE 101 170 43

Figure S28.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #3: 'CN_CNMF'

'5q' versus 'MRNASEQ_CNMF'

P value = 0.000597 (Fisher's exact test), Q value = 0.19

Table S29.  Gene #10: '5q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
5Q MUTATED 50 23 38
5Q WILD-TYPE 81 111 106

Figure S29.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.57e-07 (Fisher's exact test), Q value = 6.4e-05

Table S30.  Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
5Q MUTATED 49 54 8
5Q WILD-TYPE 116 89 93

Figure S30.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p' versus 'MRNA_CHIERARCHICAL'

P value = 0.000232 (Fisher's exact test), Q value = 0.077

Table S31.  Gene #11: '6p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
6P MUTATED 8 8 23
6P WILD-TYPE 48 35 24

Figure S31.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p' versus 'CN_CNMF'

P value = 7.15e-07 (Fisher's exact test), Q value = 0.00029

Table S32.  Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
6P MUTATED 68 30 14
6P WILD-TYPE 103 165 47

Figure S32.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #3: 'CN_CNMF'

'6p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000496 (Fisher's exact test), Q value = 0.16

Table S33.  Gene #11: '6p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
6P MUTATED 46 49 13
6P WILD-TYPE 119 94 88

Figure S33.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.037

Table S34.  Gene #11: '6p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
6P MUTATED 31 8 16
6P WILD-TYPE 48 70 47

Figure S34.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q' versus 'CN_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.012

Table S35.  Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
6Q MUTATED 66 34 16
6Q WILD-TYPE 105 161 45

Figure S35.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'CN_CNMF'

P value = 1.94e-15 (Fisher's exact test), Q value = 8.9e-13

Table S36.  Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
7P MUTATED 129 66 39
7P WILD-TYPE 42 129 22

Figure S36.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #3: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 0.000798 (Fisher's exact test), Q value = 0.25

Table S37.  Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
7P MUTATED 82 41 37
7P WILD-TYPE 32 47 31

Figure S37.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p' versus 'RPPA_CNMF'

P value = 0.000462 (Fisher's exact test), Q value = 0.15

Table S38.  Gene #13: '7p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 127 26 94
7P MUTATED 53 63 19 38
7P WILD-TYPE 25 64 7 56

Figure S38.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 3.75e-09 (Fisher's exact test), Q value = 1.6e-06

Table S39.  Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
7P MUTATED 99 52 73
7P WILD-TYPE 32 82 71

Figure S39.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.45e-09 (Fisher's exact test), Q value = 1.9e-06

Table S40.  Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
7P MUTATED 84 105 35
7P WILD-TYPE 81 38 66

Figure S40.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.46e-06 (Fisher's exact test), Q value = 0.0017

Table S41.  Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
7P MUTATED 58 28 41
7P WILD-TYPE 21 50 22

Figure S41.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q' versus 'CN_CNMF'

P value = 8.54e-11 (Fisher's exact test), Q value = 3.7e-08

Table S42.  Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
7Q MUTATED 116 64 34
7Q WILD-TYPE 55 131 27

Figure S42.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #3: 'CN_CNMF'

'7q' versus 'MRNASEQ_CNMF'

P value = 1.07e-07 (Fisher's exact test), Q value = 4.4e-05

Table S43.  Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
7Q MUTATED 91 48 66
7Q WILD-TYPE 40 86 78

Figure S43.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.02e-08 (Fisher's exact test), Q value = 1.7e-05

Table S44.  Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
7Q MUTATED 74 98 33
7Q WILD-TYPE 91 45 68

Figure S44.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0042

Table S45.  Gene #14: '7q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
7Q MUTATED 52 25 41
7Q WILD-TYPE 27 53 22

Figure S45.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p' versus 'CN_CNMF'

P value = 1.55e-24 (Fisher's exact test), Q value = 7.4e-22

Table S46.  Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
8P MUTATED 128 69 59
8P WILD-TYPE 43 126 2

Figure S46.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #3: 'CN_CNMF'

'8p' versus 'METHLYATION_CNMF'

P value = 0.000546 (Fisher's exact test), Q value = 0.17

Table S47.  Gene #15: '8p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
8P MUTATED 88 46 40
8P WILD-TYPE 26 42 28

Figure S47.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p' versus 'RPPA_CNMF'

P value = 0.000319 (Fisher's exact test), Q value = 0.1

Table S48.  Gene #15: '8p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 127 26 94
8P MUTATED 59 71 16 41
8P WILD-TYPE 19 56 10 53

Figure S48.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p' versus 'RPPA_CHIERARCHICAL'

P value = 4.32e-05 (Fisher's exact test), Q value = 0.015

Table S49.  Gene #15: '8p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
8P MUTATED 13 21 50 103
8P WILD-TYPE 13 35 13 77

Figure S49.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p' versus 'MRNASEQ_CNMF'

P value = 8.4e-08 (Fisher's exact test), Q value = 3.5e-05

Table S50.  Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
8P MUTATED 103 62 78
8P WILD-TYPE 28 72 66

Figure S50.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.26e-06 (Fisher's exact test), Q value = 0.00089

Table S51.  Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
8P MUTATED 92 107 44
8P WILD-TYPE 73 36 57

Figure S51.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.39e-05 (Fisher's exact test), Q value = 0.0051

Table S52.  Gene #15: '8p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
8P MUTATED 60 33 46
8P WILD-TYPE 19 45 17

Figure S52.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q' versus 'CN_CNMF'

P value = 1.81e-19 (Fisher's exact test), Q value = 8.5e-17

Table S53.  Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
8Q MUTATED 109 68 58
8Q WILD-TYPE 62 127 3

Figure S53.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #3: 'CN_CNMF'

'8q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.89e-05 (Fisher's exact test), Q value = 0.017

Table S54.  Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
8Q MUTATED 86 97 40
8Q WILD-TYPE 79 46 61

Figure S54.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p' versus 'CN_CNMF'

P value = 1.79e-07 (Fisher's exact test), Q value = 7.3e-05

Table S55.  Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
9P MUTATED 75 36 12
9P WILD-TYPE 96 159 49

Figure S55.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #3: 'CN_CNMF'

'9p' versus 'MRNASEQ_CNMF'

P value = 0.000642 (Fisher's exact test), Q value = 0.2

Table S56.  Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
9P MUTATED 53 26 38
9P WILD-TYPE 78 108 106

Figure S56.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000493 (Fisher's exact test), Q value = 0.16

Table S57.  Gene #17: '9p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
9P MUTATED 42 57 18
9P WILD-TYPE 123 86 83

Figure S57.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q' versus 'CN_CNMF'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0019

Table S58.  Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
9Q MUTATED 68 34 12
9Q WILD-TYPE 103 161 49

Figure S58.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #3: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 7.54e-10 (Fisher's exact test), Q value = 3.2e-07

Table S59.  Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
10P MUTATED 63 18 15
10P WILD-TYPE 108 177 46

Figure S59.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'CN_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 2.99e-06 (Fisher's exact test), Q value = 0.0012

Table S60.  Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
10P MUTATED 50 18 25
10P WILD-TYPE 81 116 119

Figure S60.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.44e-06 (Fisher's exact test), Q value = 0.0017

Table S61.  Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
10P MUTATED 30 52 11
10P WILD-TYPE 135 91 90

Figure S61.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.00082

Table S62.  Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
10P MUTATED 33 6 18
10P WILD-TYPE 46 72 45

Figure S62.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q' versus 'CN_CNMF'

P value = 8.43e-11 (Fisher's exact test), Q value = 3.7e-08

Table S63.  Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
10Q MUTATED 58 13 15
10Q WILD-TYPE 113 182 46

Figure S63.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'CN_CNMF'

'10q' versus 'MRNASEQ_CNMF'

P value = 2.74e-05 (Fisher's exact test), Q value = 0.01

Table S64.  Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
10Q MUTATED 44 15 25
10Q WILD-TYPE 87 119 119

Figure S64.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.34e-05 (Fisher's exact test), Q value = 0.019

Table S65.  Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
10Q MUTATED 30 45 9
10Q WILD-TYPE 135 98 92

Figure S65.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.67e-06 (Fisher's exact test), Q value = 0.001

Table S66.  Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
10Q MUTATED 29 4 15
10Q WILD-TYPE 50 74 48

Figure S66.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p' versus 'MRNA_CNMF'

P value = 8.99e-05 (Fisher's exact test), Q value = 0.031

Table S67.  Gene #21: '11p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
11P MUTATED 4 19 1 11
11P WILD-TYPE 31 42 28 10

Figure S67.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p' versus 'MRNA_CHIERARCHICAL'

P value = 2.69e-05 (Fisher's exact test), Q value = 0.0098

Table S68.  Gene #21: '11p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
11P MUTATED 12 2 21
11P WILD-TYPE 44 41 26

Figure S68.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p' versus 'CN_CNMF'

P value = 3.22e-13 (Fisher's exact test), Q value = 1.5e-10

Table S69.  Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
11P MUTATED 72 19 8
11P WILD-TYPE 99 176 53

Figure S69.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #3: 'CN_CNMF'

'11p' versus 'METHLYATION_CNMF'

P value = 5.82e-07 (Fisher's exact test), Q value = 0.00023

Table S70.  Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
11P MUTATED 43 6 14
11P WILD-TYPE 71 82 54

Figure S70.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p' versus 'MRNASEQ_CNMF'

P value = 3.54e-05 (Fisher's exact test), Q value = 0.013

Table S71.  Gene #21: '11p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
11P MUTATED 44 15 38
11P WILD-TYPE 87 119 106

Figure S71.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.56e-06 (Fisher's exact test), Q value = 0.0032

Table S72.  Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
11P MUTATED 42 47 8
11P WILD-TYPE 123 96 93

Figure S72.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.13e-06 (Fisher's exact test), Q value = 0.0016

Table S73.  Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
11P MUTATED 26 4 20
11P WILD-TYPE 53 74 43

Figure S73.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q' versus 'MRNA_CNMF'

P value = 3.14e-06 (Fisher's exact test), Q value = 0.0012

Table S74.  Gene #22: '11q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
11Q MUTATED 3 22 1 12
11Q WILD-TYPE 32 39 28 9

Figure S74.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q' versus 'MRNA_CHIERARCHICAL'

P value = 7.47e-07 (Fisher's exact test), Q value = 3e-04

Table S75.  Gene #22: '11q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
11Q MUTATED 14 1 23
11Q WILD-TYPE 42 42 24

Figure S75.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q' versus 'CN_CNMF'

P value = 8.2e-15 (Fisher's exact test), Q value = 3.8e-12

Table S76.  Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
11Q MUTATED 77 18 12
11Q WILD-TYPE 94 177 49

Figure S76.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #3: 'CN_CNMF'

'11q' versus 'METHLYATION_CNMF'

P value = 1.32e-07 (Fisher's exact test), Q value = 5.4e-05

Table S77.  Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
11Q MUTATED 47 7 14
11Q WILD-TYPE 67 81 54

Figure S77.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q' versus 'MRNASEQ_CNMF'

P value = 1.76e-06 (Fisher's exact test), Q value = 7e-04

Table S78.  Gene #22: '11q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
11Q MUTATED 49 15 41
11Q WILD-TYPE 82 119 103

Figure S78.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.43e-06 (Fisher's exact test), Q value = 0.00095

Table S79.  Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
11Q MUTATED 44 52 9
11Q WILD-TYPE 121 91 92

Figure S79.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.06e-07 (Fisher's exact test), Q value = 8.3e-05

Table S80.  Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
11Q MUTATED 29 4 23
11Q WILD-TYPE 50 74 40

Figure S80.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q' versus 'MRNA_CNMF'

P value = 0.000138 (Fisher's exact test), Q value = 0.047

Table S81.  Gene #25: '13q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
13Q MUTATED 15 48 11 15
13Q WILD-TYPE 20 13 18 6

Figure S81.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000124 (Fisher's exact test), Q value = 0.042

Table S82.  Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
13Q MUTATED 38 15 36
13Q WILD-TYPE 18 28 11

Figure S82.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q' versus 'CN_CNMF'

P value = 2.16e-29 (Fisher's exact test), Q value = 1e-26

Table S83.  Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
13Q MUTATED 154 66 37
13Q WILD-TYPE 17 129 24

Figure S83.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #3: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.093

Table S84.  Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
13Q MUTATED 85 42 38
13Q WILD-TYPE 29 46 30

Figure S84.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q' versus 'MRNASEQ_CNMF'

P value = 1.57e-10 (Fisher's exact test), Q value = 6.8e-08

Table S85.  Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
13Q MUTATED 105 54 87
13Q WILD-TYPE 26 80 57

Figure S85.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.29e-11 (Fisher's exact test), Q value = 1.5e-08

Table S86.  Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
13Q MUTATED 101 111 34
13Q WILD-TYPE 64 32 67

Figure S86.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.33e-07 (Fisher's exact test), Q value = 5.4e-05

Table S87.  Gene #25: '13q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
13Q MUTATED 62 29 45
13Q WILD-TYPE 17 49 18

Figure S87.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q' versus 'MRNA_CNMF'

P value = 0.000225 (Fisher's exact test), Q value = 0.075

Table S88.  Gene #26: '14q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
14Q MUTATED 9 35 5 12
14Q WILD-TYPE 26 26 24 9

Figure S88.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000141 (Fisher's exact test), Q value = 0.048

Table S89.  Gene #26: '14q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
14Q MUTATED 24 8 29
14Q WILD-TYPE 32 35 18

Figure S89.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 2.77e-25 (Fisher's exact test), Q value = 1.3e-22

Table S90.  Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
14Q MUTATED 116 31 15
14Q WILD-TYPE 55 164 46

Figure S90.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'CN_CNMF'

'14q' versus 'METHLYATION_CNMF'

P value = 8.29e-06 (Fisher's exact test), Q value = 0.0031

Table S91.  Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
14Q MUTATED 60 19 19
14Q WILD-TYPE 54 69 49

Figure S91.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q' versus 'MRNASEQ_CNMF'

P value = 4.2e-11 (Fisher's exact test), Q value = 1.9e-08

Table S92.  Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
14Q MUTATED 75 23 59
14Q WILD-TYPE 56 111 85

Figure S92.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.3e-10 (Fisher's exact test), Q value = 1e-07

Table S93.  Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
14Q MUTATED 69 75 13
14Q WILD-TYPE 96 68 88

Figure S93.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000441 (Fisher's exact test), Q value = 0.14

Table S94.  Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 174 143
14Q MUTATED 16 74 63
14Q WILD-TYPE 64 100 80

Figure S94.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.81e-06 (Fisher's exact test), Q value = 0.00072

Table S95.  Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
14Q MUTATED 42 12 26
14Q WILD-TYPE 37 66 37

Figure S95.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q' versus 'CN_CNMF'

P value = 2.82e-19 (Fisher's exact test), Q value = 1.3e-16

Table S96.  Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
15Q MUTATED 106 32 18
15Q WILD-TYPE 65 163 43

Figure S96.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #3: 'CN_CNMF'

'15q' versus 'MRNASEQ_CNMF'

P value = 5.74e-09 (Fisher's exact test), Q value = 2.4e-06

Table S97.  Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
15Q MUTATED 74 27 53
15Q WILD-TYPE 57 107 91

Figure S97.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.51e-08 (Fisher's exact test), Q value = 3.1e-05

Table S98.  Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
15Q MUTATED 66 72 16
15Q WILD-TYPE 99 71 85

Figure S98.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.24e-05 (Fisher's exact test), Q value = 0.015

Table S99.  Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 174 143
15Q MUTATED 14 66 67
15Q WILD-TYPE 66 108 76

Figure S99.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0051

Table S100.  Gene #27: '15q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
15Q MUTATED 38 13 30
15Q WILD-TYPE 41 65 33

Figure S100.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p' versus 'MRNA_CNMF'

P value = 5.11e-06 (Fisher's exact test), Q value = 0.002

Table S101.  Gene #28: '16p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
16P MUTATED 6 26 2 14
16P WILD-TYPE 29 35 27 7

Figure S101.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p' versus 'MRNA_CHIERARCHICAL'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.0051

Table S102.  Gene #28: '16p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
16P MUTATED 16 5 27
16P WILD-TYPE 40 38 20

Figure S102.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p' versus 'CN_CNMF'

P value = 9.76e-18 (Fisher's exact test), Q value = 4.5e-15

Table S103.  Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
16P MUTATED 92 24 13
16P WILD-TYPE 79 171 48

Figure S103.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #3: 'CN_CNMF'

'16p' versus 'MRNASEQ_CNMF'

P value = 0.000653 (Fisher's exact test), Q value = 0.2

Table S104.  Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
16P MUTATED 53 26 48
16P WILD-TYPE 78 108 96

Figure S104.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.48e-05 (Fisher's exact test), Q value = 0.03

Table S105.  Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
16P MUTATED 56 56 15
16P WILD-TYPE 109 87 86

Figure S105.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MRNA_CNMF'

P value = 4.54e-06 (Fisher's exact test), Q value = 0.0017

Table S106.  Gene #29: '16q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
16Q MUTATED 5 24 2 14
16Q WILD-TYPE 30 37 27 7

Figure S106.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q' versus 'MRNA_CHIERARCHICAL'

P value = 2.45e-05 (Fisher's exact test), Q value = 0.009

Table S107.  Gene #29: '16q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
16Q MUTATED 16 4 25
16Q WILD-TYPE 40 39 22

Figure S107.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q' versus 'CN_CNMF'

P value = 2.67e-17 (Fisher's exact test), Q value = 1.2e-14

Table S108.  Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
16Q MUTATED 88 21 15
16Q WILD-TYPE 83 174 46

Figure S108.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #3: 'CN_CNMF'

'16q' versus 'MRNASEQ_CNMF'

P value = 0.000671 (Fisher's exact test), Q value = 0.21

Table S109.  Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
16Q MUTATED 50 24 47
16Q WILD-TYPE 81 110 97

Figure S109.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000123 (Fisher's exact test), Q value = 0.042

Table S110.  Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
16Q MUTATED 54 53 14
16Q WILD-TYPE 111 90 87

Figure S110.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000301 (Fisher's exact test), Q value = 0.099

Table S111.  Gene #29: '16q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
16Q MUTATED 31 10 22
16Q WILD-TYPE 48 68 41

Figure S111.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p' versus 'MRNA_CNMF'

P value = 5.28e-08 (Fisher's exact test), Q value = 2.2e-05

Table S112.  Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
17P MUTATED 11 49 9 17
17P WILD-TYPE 24 12 20 4

Figure S112.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p' versus 'MRNA_CHIERARCHICAL'

P value = 9.71e-08 (Fisher's exact test), Q value = 4e-05

Table S113.  Gene #30: '17p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
17P MUTATED 36 11 39
17P WILD-TYPE 20 32 8

Figure S113.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p' versus 'CN_CNMF'

P value = 2.59e-33 (Fisher's exact test), Q value = 1.2e-30

Table S114.  Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
17P MUTATED 150 54 43
17P WILD-TYPE 21 141 18

Figure S114.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 9.38e-12 (Fisher's exact test), Q value = 4.2e-09

Table S115.  Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
17P MUTATED 94 32 32
17P WILD-TYPE 20 56 36

Figure S115.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p' versus 'RPPA_CHIERARCHICAL'

P value = 8.59e-05 (Fisher's exact test), Q value = 0.03

Table S116.  Gene #30: '17p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
17P MUTATED 8 22 46 107
17P WILD-TYPE 18 34 17 73

Figure S116.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p' versus 'MRNASEQ_CNMF'

P value = 1.7e-14 (Fisher's exact test), Q value = 7.8e-12

Table S117.  Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
17P MUTATED 106 45 87
17P WILD-TYPE 25 89 57

Figure S117.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.33e-16 (Fisher's exact test), Q value = 6.1e-14

Table S118.  Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
17P MUTATED 98 114 26
17P WILD-TYPE 67 29 75

Figure S118.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.59e-11 (Fisher's exact test), Q value = 2.5e-08

Table S119.  Gene #30: '17p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
17P MUTATED 66 24 39
17P WILD-TYPE 13 54 24

Figure S119.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q' versus 'CN_CNMF'

P value = 1.61e-12 (Fisher's exact test), Q value = 7.3e-10

Table S120.  Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
17Q MUTATED 87 30 19
17Q WILD-TYPE 84 165 42

Figure S120.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #3: 'CN_CNMF'

'17q' versus 'METHLYATION_CNMF'

P value = 0.000627 (Fisher's exact test), Q value = 0.2

Table S121.  Gene #31: '17q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
17Q MUTATED 52 18 20
17Q WILD-TYPE 62 70 48

Figure S121.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q' versus 'MRNASEQ_CNMF'

P value = 1.99e-08 (Fisher's exact test), Q value = 8.4e-06

Table S122.  Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
17Q MUTATED 67 23 44
17Q WILD-TYPE 64 111 100

Figure S122.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.48e-07 (Fisher's exact test), Q value = 0.00022

Table S123.  Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
17Q MUTATED 52 67 15
17Q WILD-TYPE 113 76 86

Figure S123.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000449 (Fisher's exact test), Q value = 0.15

Table S124.  Gene #31: '17q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
17Q MUTATED 37 14 23
17Q WILD-TYPE 42 64 40

Figure S124.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p' versus 'MRNA_CNMF'

P value = 3.64e-10 (Fisher's exact test), Q value = 1.6e-07

Table S125.  Gene #32: '18p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
18P MUTATED 9 51 8 16
18P WILD-TYPE 26 10 21 5

Figure S125.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p' versus 'MRNA_CHIERARCHICAL'

P value = 1.1e-08 (Fisher's exact test), Q value = 4.7e-06

Table S126.  Gene #32: '18p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
18P MUTATED 37 9 38
18P WILD-TYPE 19 34 9

Figure S126.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p' versus 'CN_CNMF'

P value = 1.45e-37 (Fisher's exact test), Q value = 6.9e-35

Table S127.  Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
18P MUTATED 157 57 45
18P WILD-TYPE 14 138 16

Figure S127.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #3: 'CN_CNMF'

'18p' versus 'METHLYATION_CNMF'

P value = 2.34e-12 (Fisher's exact test), Q value = 1.1e-09

Table S128.  Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
18P MUTATED 99 36 35
18P WILD-TYPE 15 52 33

Figure S128.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p' versus 'RPPA_CNMF'

P value = 0.000604 (Fisher's exact test), Q value = 0.19

Table S129.  Gene #32: '18p' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 127 26 94
18P MUTATED 52 85 17 39
18P WILD-TYPE 26 42 9 55

Figure S129.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p' versus 'RPPA_CHIERARCHICAL'

P value = 0.000561 (Fisher's exact test), Q value = 0.18

Table S130.  Gene #32: '18p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
18P MUTATED 9 24 44 116
18P WILD-TYPE 17 32 19 64

Figure S130.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p' versus 'MRNASEQ_CNMF'

P value = 1.27e-19 (Fisher's exact test), Q value = 5.9e-17

Table S131.  Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
18P MUTATED 117 48 85
18P WILD-TYPE 14 86 59

Figure S131.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.47e-13 (Fisher's exact test), Q value = 1.6e-10

Table S132.  Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
18P MUTATED 98 117 35
18P WILD-TYPE 67 26 66

Figure S132.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.68e-12 (Fisher's exact test), Q value = 7.5e-10

Table S133.  Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
18P MUTATED 69 25 43
18P WILD-TYPE 10 53 20

Figure S133.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q' versus 'MRNA_CNMF'

P value = 3.12e-10 (Fisher's exact test), Q value = 1.4e-07

Table S134.  Gene #33: '18q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
18Q MUTATED 9 52 9 16
18Q WILD-TYPE 26 9 20 5

Figure S134.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q' versus 'MRNA_CHIERARCHICAL'

P value = 2.45e-09 (Fisher's exact test), Q value = 1.1e-06

Table S135.  Gene #33: '18q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
18Q MUTATED 38 9 39
18Q WILD-TYPE 18 34 8

Figure S135.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q' versus 'CN_CNMF'

P value = 4.1e-37 (Fisher's exact test), Q value = 2e-34

Table S136.  Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
18Q MUTATED 157 60 49
18Q WILD-TYPE 14 135 12

Figure S136.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #3: 'CN_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 9.13e-12 (Fisher's exact test), Q value = 4.1e-09

Table S137.  Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
18Q MUTATED 100 38 37
18Q WILD-TYPE 14 50 31

Figure S137.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q' versus 'MRNASEQ_CNMF'

P value = 5.35e-21 (Fisher's exact test), Q value = 2.5e-18

Table S138.  Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
18Q MUTATED 119 48 89
18Q WILD-TYPE 12 86 55

Figure S138.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.66e-15 (Fisher's exact test), Q value = 2.1e-12

Table S139.  Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
18Q MUTATED 100 121 35
18Q WILD-TYPE 65 22 66

Figure S139.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.33e-11 (Fisher's exact test), Q value = 1.9e-08

Table S140.  Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
18Q MUTATED 69 28 44
18Q WILD-TYPE 10 50 19

Figure S140.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p' versus 'CN_CNMF'

P value = 2.13e-07 (Fisher's exact test), Q value = 8.6e-05

Table S141.  Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
19P MUTATED 64 25 16
19P WILD-TYPE 107 170 45

Figure S141.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #3: 'CN_CNMF'

'19p' versus 'MRNASEQ_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.073

Table S142.  Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
19P MUTATED 49 22 30
19P WILD-TYPE 82 112 114

Figure S142.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000146 (Fisher's exact test), Q value = 0.049

Table S143.  Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
19P MUTATED 39 50 12
19P WILD-TYPE 126 93 89

Figure S143.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q' versus 'CN_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.035

Table S144.  Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
19Q MUTATED 62 33 13
19Q WILD-TYPE 109 162 48

Figure S144.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'MRNA_CNMF'

P value = 9.01e-06 (Fisher's exact test), Q value = 0.0034

Table S145.  Gene #36: '20p' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
20P MUTATED 13 51 15 17
20P WILD-TYPE 22 10 14 4

Figure S145.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p' versus 'MRNA_CHIERARCHICAL'

P value = 6.33e-09 (Fisher's exact test), Q value = 2.7e-06

Table S146.  Gene #36: '20p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
20P MUTATED 45 12 39
20P WILD-TYPE 11 31 8

Figure S146.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p' versus 'CN_CNMF'

P value = 7.55e-22 (Fisher's exact test), Q value = 3.6e-19

Table S147.  Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
20P MUTATED 150 78 44
20P WILD-TYPE 21 117 17

Figure S147.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #3: 'CN_CNMF'

'20p' versus 'METHLYATION_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 6e-04

Table S148.  Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
20P MUTATED 92 43 36
20P WILD-TYPE 22 45 32

Figure S148.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p' versus 'MRNASEQ_CNMF'

P value = 4.24e-13 (Fisher's exact test), Q value = 1.9e-10

Table S149.  Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
20P MUTATED 110 54 97
20P WILD-TYPE 21 80 47

Figure S149.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.32e-10 (Fisher's exact test), Q value = 3.2e-07

Table S150.  Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
20P MUTATED 109 113 39
20P WILD-TYPE 56 30 62

Figure S150.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000309 (Fisher's exact test), Q value = 0.1

Table S151.  Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 174 143
20P MUTATED 36 114 103
20P WILD-TYPE 44 60 40

Figure S151.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.66e-06 (Fisher's exact test), Q value = 0.0029

Table S152.  Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
20P MUTATED 61 33 46
20P WILD-TYPE 18 45 17

Figure S152.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q' versus 'MRNA_CNMF'

P value = 1e-10 (Fisher's exact test), Q value = 4.4e-08

Table S153.  Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
20Q MUTATED 13 59 16 18
20Q WILD-TYPE 22 2 13 3

Figure S153.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q' versus 'MRNA_CHIERARCHICAL'

P value = 4.1e-12 (Fisher's exact test), Q value = 1.8e-09

Table S154.  Gene #37: '20q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
20Q MUTATED 50 13 43
20Q WILD-TYPE 6 30 4

Figure S154.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q' versus 'CN_CNMF'

P value = 8.06e-38 (Fisher's exact test), Q value = 3.9e-35

Table S155.  Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
20Q MUTATED 169 85 54
20Q WILD-TYPE 2 110 7

Figure S155.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #3: 'CN_CNMF'

'20q' versus 'METHLYATION_CNMF'

P value = 3.36e-12 (Fisher's exact test), Q value = 1.5e-09

Table S156.  Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
20Q MUTATED 107 46 43
20Q WILD-TYPE 7 42 25

Figure S156.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q' versus 'RPPA_CHIERARCHICAL'

P value = 5.05e-05 (Fisher's exact test), Q value = 0.018

Table S157.  Gene #37: '20q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 56 63 180
20Q MUTATED 13 29 54 133
20Q WILD-TYPE 13 27 9 47

Figure S157.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q' versus 'MRNASEQ_CNMF'

P value = 1.42e-23 (Fisher's exact test), Q value = 6.7e-21

Table S158.  Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
20Q MUTATED 128 60 106
20Q WILD-TYPE 3 74 38

Figure S158.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.29e-20 (Fisher's exact test), Q value = 2e-17

Table S159.  Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
20Q MUTATED 120 134 40
20Q WILD-TYPE 45 9 61

Figure S159.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.91e-05 (Fisher's exact test), Q value = 0.021

Table S160.  Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 174 143
20Q MUTATED 43 126 117
20Q WILD-TYPE 37 48 26

Figure S160.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.43e-12 (Fisher's exact test), Q value = 6.5e-10

Table S161.  Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
20Q MUTATED 74 34 52
20Q WILD-TYPE 5 44 11

Figure S161.  Get High-res Image Gene #37: '20q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q' versus 'CN_CNMF'

P value = 4.94e-11 (Fisher's exact test), Q value = 2.2e-08

Table S162.  Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
21Q MUTATED 88 37 13
21Q WILD-TYPE 83 158 48

Figure S162.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #3: 'CN_CNMF'

'21q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.2

Table S163.  Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
21Q MUTATED 48 63 22
21Q WILD-TYPE 117 80 79

Figure S163.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000424 (Fisher's exact test), Q value = 0.14

Table S164.  Gene #38: '21q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
21Q MUTATED 34 14 28
21Q WILD-TYPE 45 64 35

Figure S164.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q' versus 'MRNA_CNMF'

P value = 0.000223 (Fisher's exact test), Q value = 0.074

Table S165.  Gene #39: '22q' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 61 29 21
22Q MUTATED 8 34 4 9
22Q WILD-TYPE 27 27 25 12

Figure S165.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q' versus 'MRNA_CHIERARCHICAL'

P value = 0.000316 (Fisher's exact test), Q value = 0.1

Table S166.  Gene #39: '22q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 43 47
22Q MUTATED 25 6 24
22Q WILD-TYPE 31 37 23

Figure S166.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q' versus 'CN_CNMF'

P value = 8.17e-19 (Fisher's exact test), Q value = 3.8e-16

Table S167.  Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
22Q MUTATED 103 33 12
22Q WILD-TYPE 68 162 49

Figure S167.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #3: 'CN_CNMF'

'22q' versus 'METHLYATION_CNMF'

P value = 8.46e-05 (Fisher's exact test), Q value = 0.03

Table S168.  Gene #39: '22q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 88 68
22Q MUTATED 49 14 26
22Q WILD-TYPE 65 74 42

Figure S168.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 2e-08 (Fisher's exact test), Q value = 8.4e-06

Table S169.  Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 134 144
22Q MUTATED 67 23 54
22Q WILD-TYPE 64 111 90

Figure S169.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.0054

Table S170.  Gene #39: '22q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 143 101
22Q MUTATED 64 63 17
22Q WILD-TYPE 101 80 84

Figure S170.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000495 (Fisher's exact test), Q value = 0.16

Table S171.  Gene #39: '22q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 174 143
22Q MUTATED 13 66 56
22Q WILD-TYPE 67 108 87

Figure S171.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.66e-06 (Fisher's exact test), Q value = 0.0022

Table S172.  Gene #39: '22q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 78 63
22Q MUTATED 33 9 27
22Q WILD-TYPE 46 69 36

Figure S172.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq' versus 'CN_CNMF'

P value = 0.000112 (Fisher's exact test), Q value = 0.038

Table S173.  Gene #40: 'xq' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 195 61
XQ MUTATED 59 33 22
XQ WILD-TYPE 112 162 39

Figure S173.  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 = COAD-TP.transferedmergedcluster.txt

  • Number of patients = 427

  • 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.

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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