Correlation between copy number variations of arm-level result and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between copy number variation 81 arm-level events and 10 molecular subtypes across 184 patients, 253 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'RPPA_CNMF'.

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 2q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 4q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

  • 7q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 9p gain cnv correlated to 'CN_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 17q gain cnv correlated to 'CN_CNMF'.

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

  • 18q gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

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

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

  • xp gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • xq gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'CN_CNMF'.

  • 2p loss cnv correlated to 'CN_CNMF'.

  • 2q loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 5p loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF'.

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

  • 6q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'CN_CNMF'.

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

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'CN_CNMF'.

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

  • 12p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 14q loss cnv correlated to 'METHLYATION_CNMF'.

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

  • 16p loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF'.

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

  • 17q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 21q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • xp loss cnv correlated to 'CN_CNMF'.

  • xq loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 81 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 253 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type 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
6q loss 83 (45%) 101 1e-05
(0.000279) 		1e-05
(0.000279) 		0.0429
(0.142) 		0.374
(0.571) 		0.00038
(0.0054) 		0.00038
(0.0054) 		0.00112
(0.0105) 		1e-05
(0.000279) 		1e-05
(0.000279) 		1e-05
(0.000279)
9p loss 75 (41%) 109 1e-05
(0.000279) 		0.0061
(0.0383) 		0.0218
(0.0916) 		0.31
(0.506) 		0.00332
(0.024) 		0.038
(0.131) 		0.0172
(0.0768) 		0.0134
(0.0653) 		0.00803
(0.0455) 		0.00718
(0.0421)
17p loss 80 (43%) 104 1e-05
(0.000279) 		1e-05
(0.000279) 		0.0114
(0.0595) 		0.191
(0.385) 		1e-05
(0.000279) 		1e-05
(0.000279) 		1e-05
(0.000279) 		5e-05
(0.00101) 		1e-05
(0.000279) 		1e-05
(0.000279)
18q loss 106 (58%) 78 1e-05
(0.000279) 		0.00029
(0.00467) 		0.0358
(0.128) 		0.592
(0.754) 		0.0021
(0.0172) 		0.00505
(0.0333) 		0.015
(0.0708) 		0.00311
(0.0231) 		0.0469
(0.151) 		5e-05
(0.00101)
1q gain 50 (27%) 134 0.00798
(0.0455) 		6e-05
(0.00116) 		0.328
(0.526) 		0.28
(0.473) 		0.0121
(0.0623) 		0.0639
(0.188) 		0.00551
(0.036) 		0.0376
(0.13) 		0.0003
(0.00467) 		0.0117
(0.061)
17p gain 9 (5%) 175 4e-05
(0.000876) 		0.0188
(0.082) 		0.453
(0.637) 		0.423
(0.626) 		0.00246
(0.0192) 		0.0007
(0.00777) 		0.00103
(0.0101) 		0.00254
(0.0194) 		0.222
(0.419) 		0.00956
(0.0516)
1p loss 36 (20%) 148 3e-05
(0.000675) 		1e-05
(0.000279) 		0.00191
(0.0161) 		0.00397
(0.027) 		0.0097
(0.052) 		0.0637
(0.188) 		0.164
(0.348) 		0.0505
(0.161) 		0.0289
(0.109) 		0.0237
(0.0943)
8p loss 41 (22%) 143 0.00102
(0.0101) 		0.00346
(0.0246) 		0.523
(0.701) 		0.34
(0.537) 		0.146
(0.326) 		0.0047
(0.0315) 		0.0155
(0.0723) 		0.0124
(0.0623) 		0.00686
(0.0407) 		0.00231
(0.0184)
12p loss 20 (11%) 164 0.0002
(0.00337) 		0.0371
(0.129) 		0.00073
(0.00799) 		0.00098
(0.0098) 		0.0616
(0.187) 		0.00824
(0.0463) 		0.0845
(0.229) 		0.00098
(0.0098) 		0.343
(0.54) 		0.00166
(0.0145)
20p loss 20 (11%) 164 0.00033
(0.00486) 		0.0451
(0.146) 		0.689
(0.825) 		0.686
(0.825) 		0.00651
(0.0398) 		0.0919
(0.244) 		0.0369
(0.129) 		0.0395
(0.135) 		0.00188
(0.0161) 		0.0139
(0.0672)
16p gain 22 (12%) 162 2e-05
(0.000523) 		0.00074
(0.00799) 		0.0252
(0.0977) 		0.0904
(0.241) 		0.155
(0.338) 		0.0585
(0.18) 		0.0686
(0.197) 		0.014
(0.0672) 		0.00201
(0.0166) 		0.0297
(0.111)
16q gain 23 (12%) 161 1e-05
(0.000279) 		0.00027
(0.00446) 		0.37
(0.567) 		0.577
(0.742) 		0.106
(0.265) 		0.0551
(0.172) 		0.0139
(0.0672) 		0.00078
(0.00831) 		0.00252
(0.0194) 		0.00323
(0.0238)
6p loss 64 (35%) 120 3e-05
(0.000675) 		0.00011
(0.00194) 		0.151
(0.332) 		0.357
(0.557) 		0.135
(0.309) 		0.0142
(0.0678) 		0.22
(0.419) 		0.00108
(0.0103) 		0.00333
(0.024) 		0.00012
(0.00207)
13q loss 20 (11%) 164 0.00046
(0.00591) 		0.009
(0.0493) 		0.83
(0.911) 		0.823
(0.907) 		0.00305
(0.0229) 		0.156
(0.338) 		0.0229
(0.0929) 		0.013
(0.0642) 		0.00191
(0.0161) 		0.0638
(0.188)
15q loss 30 (16%) 154 5e-05
(0.00101) 		0.00879
(0.0484) 		0.401
(0.597) 		0.358
(0.557) 		0.0211
(0.09) 		0.00197
(0.0165) 		0.0794
(0.218) 		0.00611
(0.0383) 		0.106
(0.265) 		0.00372
(0.0257)
19p loss 19 (10%) 165 0.00128
(0.0118) 		0.0223
(0.0928) 		0.29
(0.485) 		0.809
(0.905) 		0.0622
(0.187) 		0.0247
(0.0972) 		0.389
(0.583) 		0.00614
(0.0383) 		0.00033
(0.00486) 		0.0194
(0.0838)
21q loss 58 (32%) 126 1e-05
(0.000279) 		0.0225
(0.0929) 		0.348
(0.547) 		0.459
(0.641) 		0.0219
(0.0916) 		0.0938
(0.248) 		0.389
(0.583) 		0.032
(0.118) 		0.00044
(0.00588) 		0.0362
(0.128)
4p gain 11 (6%) 173 0.0156
(0.0723) 		0.578
(0.742) 		0.754
(0.876) 		0.304
(0.498) 		0.00138
(0.0126) 		0.0101
(0.0533) 		0.0352
(0.126) 		0.0207
(0.0888) 		0.779
(0.888) 		0.208
(0.408)
4q gain 8 (4%) 176 0.0006
(0.00715) 		0.223
(0.42) 		0.755
(0.876) 		0.302
(0.496) 		0.0218
(0.0916) 		0.0348
(0.125) 		0.0227
(0.0929) 		0.039
(0.134) 		0.52
(0.697) 		0.151
(0.332)
18p gain 28 (15%) 156 1e-05
(0.000279) 		0.0188
(0.082) 		0.165
(0.348) 		0.128
(0.302) 		0.026
(0.1) 		0.198
(0.395) 		0.147
(0.326) 		0.0227
(0.0929) 		0.0341
(0.124) 		0.103
(0.262)
22q loss 46 (25%) 138 1e-05
(0.000279) 		0.0056
(0.0363) 		0.764
(0.879) 		0.687
(0.825) 		0.22
(0.419) 		0.375
(0.571) 		0.31
(0.506) 		0.0407
(0.137) 		0.00105
(0.0101) 		0.0285
(0.108)
2q gain 16 (9%) 168 0.0361
(0.128) 		0.00152
(0.0136) 		0.178
(0.366) 		0.0967
(0.252) 		0.464
(0.646) 		0.181
(0.373) 		0.514
(0.692) 		0.00476
(0.0316) 		0.197
(0.394) 		0.0407
(0.137)
7p gain 52 (28%) 132 1e-05
(0.000279) 		0.0161
(0.0735) 		0.0583
(0.18) 		0.378
(0.573) 		0.352
(0.551) 		0.268
(0.463) 		0.279
(0.473) 		0.0471
(0.151) 		0.006
(0.0383) 		0.165
(0.348)
10p gain 10 (5%) 174 0.036
(0.128) 		0.201
(0.398) 		0.0269
(0.103) 		0.0274
(0.104) 		0.214
(0.415) 		0.814
(0.906) 		0.473
(0.654) 		0.901
(0.959) 		0.00079
(0.00831) 		1
(1.00)
12q gain 22 (12%) 162 1e-05
(0.000279) 		0.0169
(0.0756) 		0.0654
(0.19) 		0.721
(0.851) 		0.586
(0.749) 		0.113
(0.278) 		0.207
(0.407) 		0.0419
(0.14) 		0.00417
(0.0281) 		0.155
(0.338)
20p gain 34 (18%) 150 1e-05
(0.000279) 		0.0177
(0.0782) 		0.135
(0.309) 		0.221
(0.419) 		0.229
(0.428) 		0.156
(0.338) 		0.221
(0.419) 		0.0165
(0.0752) 		0.00622
(0.0385) 		0.254
(0.456)
20q gain 45 (24%) 139 1e-05
(0.000279) 		0.0313
(0.116) 		0.425
(0.627) 		0.159
(0.34) 		0.543
(0.717) 		0.176
(0.365) 		0.333
(0.531) 		0.0236
(0.0943) 		0.0004
(0.00559) 		0.209
(0.408)
xp gain 8 (4%) 176 3e-05
(0.000675) 		0.222
(0.419) 		0.294
(0.49) 		0.0721
(0.202) 		0.124
(0.297) 		0.0344
(0.125) 		0.0429
(0.142) 		0.0405
(0.137) 		0.722
(0.851) 		0.0711
(0.201)
4p loss 25 (14%) 159 0.0432
(0.142) 		0.00667
(0.0403) 		0.339
(0.537) 		0.767
(0.881) 		0.104
(0.264) 		0.102
(0.261) 		0.578
(0.742) 		0.0126
(0.0629) 		0.957
(0.994) 		0.00354
(0.0249)
12q loss 28 (15%) 156 1e-05
(0.000279) 		0.0611
(0.186) 		0.00689
(0.0407) 		0.0834
(0.227) 		0.156
(0.338) 		0.00236
(0.0186) 		0.121
(0.293) 		0.12
(0.291) 		0.241
(0.443) 		0.0244
(0.0963)
19q loss 12 (7%) 172 0.00653
(0.0398) 		0.132
(0.307) 		0.00232
(0.0184) 		0.156
(0.338) 		0.0399
(0.136) 		0.0145
(0.0685) 		0.489
(0.665) 		0.0522
(0.165) 		0.096
(0.252) 		0.0743
(0.207)
2p gain 14 (8%) 170 0.0214
(0.0907) 		0.00069
(0.00776) 		0.175
(0.364) 		0.0968
(0.252) 		0.633
(0.791) 		0.188
(0.382) 		0.441
(0.634) 		0.0156
(0.0723) 		0.128
(0.302) 		0.0999
(0.258)
5q gain 20 (11%) 164 1e-05
(0.000279) 		0.486
(0.664) 		0.834
(0.912) 		0.672
(0.818) 		0.326
(0.524) 		0.00987
(0.0526) 		0.111
(0.273) 		0.0346
(0.125) 		0.114
(0.28) 		0.145
(0.326)
8q gain 48 (26%) 136 3e-05
(0.000675) 		0.00828
(0.0463) 		0.72
(0.851) 		0.623
(0.781) 		0.297
(0.491) 		0.546
(0.718) 		0.397
(0.593) 		0.0794
(0.218) 		0.00114
(0.0106) 		0.0676
(0.196)
12p gain 30 (16%) 154 1e-05
(0.000279) 		0.00091
(0.00945) 		0.142
(0.32) 		0.727
(0.855) 		0.675
(0.821) 		0.257
(0.459) 		0.109
(0.269) 		0.0698
(0.199) 		0.00221
(0.0179) 		0.459
(0.641)
xq gain 13 (7%) 171 0.0003
(0.00467) 		0.69
(0.826) 		0.222
(0.419) 		0.711
(0.843) 		0.127
(0.301) 		0.00944
(0.0513) 		0.162
(0.344) 		0.0369
(0.129) 		0.812
(0.905) 		0.0867
(0.233)
3q loss 19 (10%) 165 0.0329
(0.121) 		0.425
(0.627) 		0.0131
(0.0643) 		0.0681
(0.196) 		0.533
(0.707) 		0.672
(0.818) 		0.786
(0.891) 		1
(1.00) 		0.00733
(0.0427) 		0.854
(0.922)
4q loss 25 (14%) 159 0.248
(0.45) 		0.0192
(0.0834) 		0.553
(0.725) 		0.27
(0.464) 		0.0549
(0.172) 		0.182
(0.373) 		0.201
(0.398) 		0.00285
(0.0216) 		0.71
(0.843) 		0.00097
(0.0098)
17q loss 22 (12%) 162 0.00061
(0.00716) 		0.221
(0.419) 		0.0438
(0.144) 		0.025
(0.0976) 		0.157
(0.338) 		0.387
(0.583) 		0.518
(0.695) 		0.313
(0.507) 		0.177
(0.365) 		0.318
(0.514)
3p gain 10 (5%) 174 0.0123
(0.0623) 		0.00802
(0.0455) 		0.268
(0.463) 		0.245
(0.446) 		0.539
(0.712) 		0.614
(0.775) 		0.839
(0.914) 		0.445
(0.637) 		0.529
(0.704) 		0.528
(0.704)
3q gain 20 (11%) 164 0.00044
(0.00588) 		3e-05
(0.000675) 		0.201
(0.398) 		0.322
(0.519) 		0.265
(0.462) 		0.279
(0.473) 		0.773
(0.885) 		0.0607
(0.186) 		0.174
(0.364) 		0.264
(0.462)
5p gain 28 (15%) 156 1e-05
(0.000279) 		0.36
(0.558) 		0.677
(0.822) 		0.776
(0.887) 		0.669
(0.818) 		0.158
(0.34) 		0.241
(0.443) 		0.126
(0.299) 		0.00683
(0.0407) 		0.455
(0.638)
6q gain 5 (3%) 179 0.016
(0.0735) 		0.654
(0.809) 		0.853
(0.922) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.031
(0.115) 		0.451
(0.637)
7q gain 48 (26%) 136 2e-05
(0.000523) 		0.0838
(0.228) 		0.169
(0.354) 		0.491
(0.666) 		0.755
(0.876) 		0.261
(0.462) 		0.669
(0.818) 		0.342
(0.538) 		0.0237
(0.0943) 		0.448
(0.637)
8p gain 26 (14%) 158 0.00357
(0.0249) 		0.0961
(0.252) 		0.823
(0.907) 		0.353
(0.551) 		0.757
(0.876) 		0.958
(0.994) 		0.223
(0.419) 		0.555
(0.727) 		0.0123
(0.0623) 		0.662
(0.814)
10q gain 13 (7%) 171 0.0272
(0.104) 		0.0571
(0.178) 		0.0581
(0.18) 		0.133
(0.308) 		0.147
(0.326) 		0.378
(0.573) 		0.296
(0.491) 		0.913
(0.966) 		0.00045
(0.00588) 		1
(1.00)
11p gain 13 (7%) 171 0.00063
(0.00729) 		0.0451
(0.146) 		0.144
(0.326) 		0.821
(0.907) 		0.756
(0.876) 		1
(1.00) 		0.729
(0.855) 		0.791
(0.892) 		0.428
(0.628) 		0.754
(0.876)
11q gain 15 (8%) 169 0.0059
(0.0379) 		0.0124
(0.0623) 		0.0644
(0.189) 		0.225
(0.421) 		0.939
(0.982) 		0.937
(0.981) 		0.501
(0.677) 		0.532
(0.707) 		0.284
(0.477) 		0.182
(0.373)
19p gain 17 (9%) 167 0.00067
(0.00764) 		0.691
(0.826) 		0.553
(0.725) 		0.109
(0.269) 		0.681
(0.824) 		0.62
(0.78) 		0.0128
(0.0636) 		0.335
(0.532) 		0.382
(0.578) 		0.598
(0.759)
10q loss 30 (16%) 154 8e-05
(0.00147) 		0.898
(0.958) 		0.758
(0.876) 		0.756
(0.876) 		0.184
(0.375) 		0.0167
(0.0753) 		0.53
(0.704) 		0.334
(0.531) 		0.228
(0.426) 		0.0991
(0.256)
11q loss 16 (9%) 168 0.0006
(0.00715) 		0.658
(0.811) 		0.133
(0.308) 		0.0463
(0.15) 		0.783
(0.89) 		0.819
(0.907) 		0.929
(0.976) 		0.574
(0.742) 		0.399
(0.595) 		0.821
(0.907)
16p loss 11 (6%) 173 0.00843
(0.0468) 		0.574
(0.742) 		0.0232
(0.0936) 		0.151
(0.332) 		0.671
(0.818) 		0.489
(0.665) 		0.634
(0.791) 		0.426
(0.627) 		0.278
(0.473) 		0.836
(0.913)
xq loss 18 (10%) 166 1e-05
(0.000279) 		0.0448
(0.146) 		0.471
(0.653) 		0.101
(0.26) 		0.367
(0.565) 		0.33
(0.528) 		0.266
(0.462) 		0.833
(0.912) 		0.493
(0.667) 		0.588
(0.75)
1p gain 18 (10%) 166 0.428
(0.628) 		0.078
(0.216) 		0.031
(0.115) 		0.0711
(0.201) 		0.759
(0.876) 		0.736
(0.863) 		1
(1.00) 		0.938
(0.981) 		0.134
(0.309) 		0.893
(0.955)
6p gain 7 (4%) 177 0.00054
(0.00673) 		0.528
(0.704) 		0.485
(0.664) 		0.24
(0.442) 		0.888
(0.953) 		1
(1.00) 		0.907
(0.962) 		0.875
(0.94) 		0.0602
(0.185) 		1
(1.00)
9p gain 8 (4%) 176 0.0109
(0.0572) 		1
(1.00) 		0.791
(0.892) 		0.211
(0.412) 		0.593
(0.754) 		0.638
(0.795) 		0.681
(0.824) 		0.789
(0.892) 		0.578
(0.742) 		0.448
(0.637)
9q gain 12 (7%) 172 8e-05
(0.00147) 		0.659
(0.811) 		0.962
(0.996) 		0.834
(0.912) 		0.927
(0.975) 		0.613
(0.774) 		0.63
(0.789) 		0.263
(0.462) 		0.264
(0.462) 		0.284
(0.477)
13q gain 29 (16%) 155 0.0167
(0.0753) 		0.787
(0.891) 		0.464
(0.646) 		0.453
(0.637) 		0.212
(0.412) 		0.474
(0.655) 		0.218
(0.419) 		0.126
(0.299) 		0.434
(0.63) 		0.793
(0.893)
14q gain 26 (14%) 158 1e-05
(0.000279) 		0.222
(0.419) 		0.824
(0.907) 		0.844
(0.918) 		0.276
(0.471) 		0.574
(0.742) 		0.171
(0.359) 		0.265
(0.462) 		0.105
(0.265) 		0.924
(0.974)
17q gain 17 (9%) 167 0.00045
(0.00588) 		0.248
(0.45) 		0.987
(1.00) 		0.864
(0.93) 		0.19
(0.384) 		0.0624
(0.187) 		0.0975
(0.253) 		0.0718
(0.202) 		0.122
(0.293) 		0.244
(0.446)
18q gain 12 (7%) 172 6e-05
(0.00116) 		0.684
(0.825) 		0.443
(0.636) 		0.244
(0.446) 		0.378
(0.573) 		0.49
(0.665) 		0.479
(0.659) 		0.125
(0.299) 		0.361
(0.559) 		0.0863
(0.233)
19q gain 28 (15%) 156 0.00053
(0.00671) 		0.316
(0.511) 		0.583
(0.746) 		0.0769
(0.213) 		0.896
(0.957) 		0.889
(0.953) 		0.0689
(0.197) 		0.688
(0.825) 		0.106
(0.265) 		1
(1.00)
1q loss 8 (4%) 176 0.0413
(0.138) 		0.411
(0.609) 		0.812
(0.905) 		0.233
(0.433) 		1
(1.00) 		0.511
(0.689) 		0.759
(0.876) 		0.697
(0.831) 		0.103
(0.262) 		0.783
(0.89)
2p loss 11 (6%) 173 0.0076
(0.044) 		0.577
(0.742) 		0.679
(0.824) 		0.815
(0.906) 		0.67
(0.818) 		0.193
(0.386) 		0.92
(0.972) 		0.761
(0.877) 		0.266
(0.462) 		0.849
(0.921)
2q loss 5 (3%) 179 0.00056
(0.00687) 		0.759
(0.876) 		0.453
(0.637) 		0.0895
(0.239) 		0.45
(0.637) 		0.292
(0.487) 		0.159
(0.34) 		0.362
(0.559)
3p loss 36 (20%) 148 0.00163
(0.0144) 		0.0504
(0.161) 		0.453
(0.637) 		0.305
(0.499) 		0.651
(0.807) 		0.906
(0.962) 		0.208
(0.408) 		0.3
(0.494) 		0.106
(0.265) 		0.556
(0.727)
5p loss 9 (5%) 175 0.00335
(0.024) 		0.855
(0.922) 		0.813
(0.905) 		0.853
(0.922) 		0.91
(0.965) 		0.239
(0.442) 		0.844
(0.918) 		1
(1.00) 		0.159
(0.34) 		0.805
(0.903)
5q loss 13 (7%) 171 0.00375
(0.0257) 		0.261
(0.462) 		0.409
(0.608) 		0.451
(0.637) 		0.935
(0.981) 		0.251
(0.451) 		0.622
(0.781) 		0.448
(0.637) 		0.137
(0.311) 		0.604
(0.765)
8q loss 16 (9%) 168 0.0183
(0.0806) 		0.28
(0.473) 		0.395
(0.591) 		0.655
(0.809) 		0.794
(0.893) 		0.437
(0.633) 		0.333
(0.531) 		0.452
(0.637) 		0.0511
(0.162) 		0.169
(0.354)
10p loss 36 (20%) 148 0.00031
(0.00474) 		0.297
(0.491) 		0.574
(0.742) 		0.996
(1.00) 		0.159
(0.34) 		0.192
(0.386) 		0.37
(0.567) 		0.148
(0.328) 		0.0621
(0.187) 		0.0955
(0.252)
11p loss 17 (9%) 167 0.00153
(0.0136) 		0.13
(0.306) 		0.471
(0.653) 		0.457
(0.64) 		0.943
(0.983) 		0.685
(0.825) 		0.476
(0.655) 		0.482
(0.662) 		0.475
(0.655) 		0.727
(0.855)
14q loss 16 (9%) 168 0.237
(0.44) 		0.0229
(0.0929) 		0.19
(0.384) 		0.571
(0.742) 		0.494
(0.668) 		0.0739
(0.206) 		0.375
(0.571) 		0.219
(0.419) 		0.77
(0.883) 		0.583
(0.746)
16q loss 13 (7%) 171 0.0251
(0.0976) 		0.941
(0.982) 		0.485
(0.664) 		0.922
(0.972) 		0.708
(0.842) 		0.121
(0.293) 		0.431
(0.63) 		0.245
(0.446) 		0.132
(0.307) 		0.281
(0.474)
xp loss 27 (15%) 157 9e-05
(0.00162) 		0.135
(0.309) 		0.104
(0.264) 		0.3
(0.494) 		0.438
(0.633) 		0.288
(0.482) 		0.136
(0.31) 		0.957
(0.994) 		0.25
(0.45) 		0.694
(0.828)
15q gain 14 (8%) 170 0.0883
(0.237) 		0.0632
(0.188) 		0.185
(0.377) 		0.784
(0.891) 		0.341
(0.538) 		0.131
(0.306) 		0.249
(0.45) 		1
(1.00) 		0.253
(0.454) 		0.867
(0.933)
22q gain 8 (4%) 176 0.352
(0.551) 		0.063
(0.188) 		0.438
(0.633) 		0.644
(0.8) 		0.108
(0.268) 		0.0799
(0.219) 		0.366
(0.563) 		0.0653
(0.19) 		0.146
(0.326) 		0.27
(0.464)
7p loss 3 (2%) 181 0.175
(0.364) 		0.617
(0.778) 		0.798
(0.896) 		0.773
(0.885) 		0.427
(0.628) 		1
(1.00) 		0.433
(0.63) 		0.315
(0.511)
7q loss 4 (2%) 180 0.0712
(0.201) 		0.238
(0.441) 		0.433
(0.63) 		0.713
(0.844) 		0.807
(0.904) 		1
(1.00) 		0.539
(0.712) 		1
(1.00) 		0.261
(0.462) 		0.562
(0.733)
9q loss 43 (23%) 141 0.116
(0.282) 		0.545
(0.718) 		0.257
(0.459) 		0.432
(0.63) 		0.272
(0.466) 		0.44
(0.634) 		0.199
(0.396) 		0.265
(0.462) 		0.218
(0.419) 		0.311
(0.506)
18p loss 55 (30%) 129 0.13
(0.304) 		0.268
(0.463) 		0.822
(0.907) 		0.95
(0.989) 		0.645
(0.8) 		0.639
(0.795) 		0.365
(0.562) 		0.901
(0.959) 		0.27
(0.464) 		0.274
(0.468)
20q loss 5 (3%) 179 0.265
(0.462) 		0.0673
(0.195) 		0.384
(0.579) 		0.846
(0.918) 		0.92
(0.972) 		0.825
(0.907) 		0.129
(0.303) 		0.605
(0.765)
'1p gain' versus 'RPPA_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
1P GAIN MUTATED 1 3 5 1 1
1P GAIN WILD-TYPE 34 17 11 17 15

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

'1q gain' versus 'CN_CNMF'

P value = 0.00798 (Fisher's exact test), Q value = 0.045

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
1Q GAIN MUTATED 14 28 8
1Q GAIN WILD-TYPE 71 47 16

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
1Q GAIN MUTATED 23 5 16 6
1Q GAIN WILD-TYPE 22 42 34 35

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.062

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
1Q GAIN MUTATED 28 14 5
1Q GAIN WILD-TYPE 55 34 41

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

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.036

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
1Q GAIN MUTATED 27 11 6 3
1Q GAIN WILD-TYPE 42 29 29 30

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.13

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
1Q GAIN MUTATED 34 9 4
1Q GAIN WILD-TYPE 68 33 29

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0047

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
1Q GAIN MUTATED 29 8 9
1Q GAIN WILD-TYPE 40 59 28

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.061

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
1Q GAIN MUTATED 25 17 4
1Q GAIN WILD-TYPE 61 30 36

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.091

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
2P GAIN MUTATED 2 10 2
2P GAIN WILD-TYPE 83 65 22

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0078

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
2P GAIN MUTATED 6 0 8 0
2P GAIN WILD-TYPE 39 47 42 41

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.072

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
2P GAIN MUTATED 13 0 1
2P GAIN WILD-TYPE 89 42 32

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.13

Table S12.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
2Q GAIN MUTATED 3 11 2
2Q GAIN WILD-TYPE 82 64 22

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.014

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
2Q GAIN MUTATED 6 0 9 1
2Q GAIN WILD-TYPE 39 47 41 40

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.032

Table S14.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
2Q GAIN MUTATED 15 0 1
2Q GAIN WILD-TYPE 87 42 32

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.14

Table S15.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
2Q GAIN MUTATED 13 2 1
2Q GAIN WILD-TYPE 73 45 39

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.062

Table S16.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
3P GAIN MUTATED 1 5 4
3P GAIN WILD-TYPE 84 70 20

Figure S16.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00802 (Fisher's exact test), Q value = 0.045

Table S17.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
3P GAIN MUTATED 5 0 5 0
3P GAIN WILD-TYPE 40 47 45 41

Figure S17.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0059

Table S18.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
3Q GAIN MUTATED 3 9 8
3Q GAIN WILD-TYPE 82 66 16

Figure S18.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00067

Table S19.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
3Q GAIN MUTATED 9 0 11 0
3Q GAIN WILD-TYPE 36 47 39 41

Figure S19.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.072

Table S20.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
4P GAIN MUTATED 3 3 5
4P GAIN WILD-TYPE 82 72 19

Figure S20.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.013

Table S21.  Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
4P GAIN MUTATED 3 0 8
4P GAIN WILD-TYPE 80 48 38

Figure S21.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.053

Table S22.  Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
4P GAIN MUTATED 1 5 5
4P GAIN WILD-TYPE 73 70 23

Figure S22.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.13

Table S23.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
4P GAIN MUTATED 3 1 1 6
4P GAIN WILD-TYPE 66 39 34 27

Figure S23.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.089

Table S24.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
4P GAIN MUTATED 6 0 5
4P GAIN WILD-TYPE 96 42 28

Figure S24.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0071

Table S25.  Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
4Q GAIN MUTATED 1 2 5
4Q GAIN WILD-TYPE 84 73 19

Figure S25.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.092

Table S26.  Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
4Q GAIN MUTATED 3 0 5
4Q GAIN WILD-TYPE 80 48 41

Figure S26.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0348 (Fisher's exact test), Q value = 0.13

Table S27.  Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
4Q GAIN MUTATED 1 3 4
4Q GAIN WILD-TYPE 73 72 24

Figure S27.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.093

Table S28.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
4Q GAIN MUTATED 2 1 0 5
4Q GAIN WILD-TYPE 67 39 35 28

Figure S28.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.13

Table S29.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
4Q GAIN MUTATED 4 0 4
4Q GAIN WILD-TYPE 98 42 29

Figure S29.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S30.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
5P GAIN MUTATED 3 11 14
5P GAIN WILD-TYPE 82 64 10

Figure S30.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.041

Table S31.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
5P GAIN MUTATED 14 4 10
5P GAIN WILD-TYPE 55 63 27

Figure S31.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S32.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
5Q GAIN MUTATED 2 7 11
5Q GAIN WILD-TYPE 83 68 13

Figure S32.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00987 (Fisher's exact test), Q value = 0.053

Table S33.  Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
5Q GAIN MUTATED 7 5 8
5Q GAIN WILD-TYPE 67 70 20

Figure S33.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.13

Table S34.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
5Q GAIN MUTATED 10 2 8
5Q GAIN WILD-TYPE 92 40 25

Figure S34.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0067

Table S35.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
6P GAIN MUTATED 1 1 5
6P GAIN WILD-TYPE 84 74 19

Figure S35.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.074

Table S36.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
6Q GAIN MUTATED 1 1 3
6Q GAIN WILD-TYPE 84 74 21

Figure S36.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.12

Table S37.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
6Q GAIN MUTATED 1 0 3
6Q GAIN WILD-TYPE 68 67 34

Figure S37.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S38.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
7P GAIN MUTATED 12 23 17
7P GAIN WILD-TYPE 73 52 7

Figure S38.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.074

Table S39.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
7P GAIN MUTATED 18 9 18 6
7P GAIN WILD-TYPE 27 38 32 35

Figure S39.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0471 (Fisher's exact test), Q value = 0.15

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
7P GAIN MUTATED 36 7 7
7P GAIN WILD-TYPE 66 35 26

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

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.006 (Fisher's exact test), Q value = 0.038

Table S41.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
7P GAIN MUTATED 26 10 13
7P GAIN WILD-TYPE 43 57 24

Figure S41.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00052

Table S42.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
7Q GAIN MUTATED 12 20 16
7Q GAIN WILD-TYPE 73 55 8

Figure S42.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.094

Table S43.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
7Q GAIN MUTATED 22 10 13
7Q GAIN WILD-TYPE 47 57 24

Figure S43.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.00357 (Fisher's exact test), Q value = 0.025

Table S44.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
8P GAIN MUTATED 5 14 7
8P GAIN WILD-TYPE 80 61 17

Figure S44.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.062

Table S45.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
8P GAIN MUTATED 11 4 10
8P GAIN WILD-TYPE 58 63 27

Figure S45.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00067

Table S46.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
8Q GAIN MUTATED 10 25 13
8Q GAIN WILD-TYPE 75 50 11

Figure S46.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00828 (Fisher's exact test), Q value = 0.046

Table S47.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
8Q GAIN MUTATED 18 8 16 5
8Q GAIN WILD-TYPE 27 39 34 36

Figure S47.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.011

Table S48.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
8Q GAIN MUTATED 23 8 15
8Q GAIN WILD-TYPE 46 59 22

Figure S48.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.057

Table S49.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
9P GAIN MUTATED 1 3 4
9P GAIN WILD-TYPE 84 72 20

Figure S49.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S50.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
9Q GAIN MUTATED 0 6 6
9Q GAIN WILD-TYPE 85 69 18

Figure S50.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.13

Table S51.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
10P GAIN MUTATED 1 7 2
10P GAIN WILD-TYPE 84 68 22

Figure S51.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
10P GAIN MUTATED 6 0 0 0 0
10P GAIN WILD-TYPE 29 20 16 18 16

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

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.1

Table S53.  Gene #19: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 12 20 22 15 11 18 7
10P GAIN MUTATED 1 0 3 0 0 0 2
10P GAIN WILD-TYPE 11 20 19 15 11 18 5

Figure S53.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0083

Table S54.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
10P GAIN MUTATED 2 0 6
10P GAIN WILD-TYPE 67 67 31

Figure S54.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.1

Table S55.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
10Q GAIN MUTATED 2 7 4
10Q GAIN WILD-TYPE 83 68 20

Figure S55.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0059

Table S56.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
10Q GAIN MUTATED 3 0 7
10Q GAIN WILD-TYPE 66 67 30

Figure S56.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0073

Table S57.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
11P GAIN MUTATED 1 6 6
11P GAIN WILD-TYPE 84 69 18

Figure S57.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.15

Table S58.  Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
11P GAIN MUTATED 5 0 6 2
11P GAIN WILD-TYPE 40 47 44 39

Figure S58.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 0.038

Table S59.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
11Q GAIN MUTATED 2 8 5
11Q GAIN WILD-TYPE 83 67 19

Figure S59.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.062

Table S60.  Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
11Q GAIN MUTATED 5 0 8 2
11Q GAIN WILD-TYPE 40 47 42 39

Figure S60.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S61.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
12P GAIN MUTATED 1 10 19
12P GAIN WILD-TYPE 84 65 5

Figure S61.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0094

Table S62.  Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
12P GAIN MUTATED 12 7 11 0
12P GAIN WILD-TYPE 33 40 39 41

Figure S62.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.018

Table S63.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
12P GAIN MUTATED 12 4 12
12P GAIN WILD-TYPE 57 63 25

Figure S63.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S64.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
12Q GAIN MUTATED 1 4 17
12Q GAIN WILD-TYPE 84 71 7

Figure S64.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.076

Table S65.  Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
12Q GAIN MUTATED 8 6 8 0
12Q GAIN WILD-TYPE 37 41 42 41

Figure S65.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.14

Table S66.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
12Q GAIN MUTATED 12 2 8
12Q GAIN WILD-TYPE 90 40 25

Figure S66.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00417 (Fisher's exact test), Q value = 0.028

Table S67.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
12Q GAIN MUTATED 8 3 10
12Q GAIN WILD-TYPE 61 64 27

Figure S67.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.075

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
13Q GAIN MUTATED 7 15 7
13Q GAIN WILD-TYPE 78 60 17

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

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S69.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
14Q GAIN MUTATED 3 12 11
14Q GAIN WILD-TYPE 82 63 13

Figure S69.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00052

Table S70.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
16P GAIN MUTATED 1 13 8
16P GAIN WILD-TYPE 84 62 16

Figure S70.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.008

Table S71.  Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
16P GAIN MUTATED 10 1 10 1
16P GAIN WILD-TYPE 35 46 40 40

Figure S71.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.098

Table S72.  Gene #28: '16p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
16P GAIN MUTATED 9 2 0 1 0
16P GAIN WILD-TYPE 26 18 16 17 16

Figure S72.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.067

Table S73.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
16P GAIN MUTATED 19 2 1
16P GAIN WILD-TYPE 83 40 32

Figure S73.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.017

Table S74.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
16P GAIN MUTATED 11 2 9
16P GAIN WILD-TYPE 58 65 28

Figure S74.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.11

Table S75.  Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
16P GAIN MUTATED 16 5 1
16P GAIN WILD-TYPE 70 42 39

Figure S75.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S76.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
16Q GAIN MUTATED 1 14 8
16Q GAIN WILD-TYPE 84 61 16

Figure S76.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0045

Table S77.  Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
16Q GAIN MUTATED 9 1 12 1
16Q GAIN WILD-TYPE 36 46 38 40

Figure S77.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.067

Table S78.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
16Q GAIN MUTATED 16 4 1 2
16Q GAIN WILD-TYPE 53 36 34 31

Figure S78.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0083

Table S79.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
16Q GAIN MUTATED 21 2 0
16Q GAIN WILD-TYPE 81 40 33

Figure S79.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.019

Table S80.  Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
16Q GAIN MUTATED 13 2 8
16Q GAIN WILD-TYPE 56 65 29

Figure S80.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00323 (Fisher's exact test), Q value = 0.024

Table S81.  Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
16Q GAIN MUTATED 17 6 0
16Q GAIN WILD-TYPE 69 41 40

Figure S81.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00088

Table S82.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
17P GAIN MUTATED 3 0 6
17P GAIN WILD-TYPE 82 75 18

Figure S82.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.082

Table S83.  Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
17P GAIN MUTATED 2 6 0 1
17P GAIN WILD-TYPE 43 41 50 40

Figure S83.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.019

Table S84.  Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
17P GAIN MUTATED 1 1 7
17P GAIN WILD-TYPE 82 47 39

Figure S84.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0078

Table S85.  Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
17P GAIN MUTATED 1 2 6
17P GAIN WILD-TYPE 73 73 22

Figure S85.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.01

Table S86.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
17P GAIN MUTATED 0 1 2 6
17P GAIN WILD-TYPE 69 39 33 27

Figure S86.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00254 (Fisher's exact test), Q value = 0.019

Table S87.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
17P GAIN MUTATED 2 1 6
17P GAIN WILD-TYPE 100 41 27

Figure S87.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00956 (Fisher's exact test), Q value = 0.052

Table S88.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
17P GAIN MUTATED 2 1 6
17P GAIN WILD-TYPE 84 46 34

Figure S88.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0059

Table S89.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
17Q GAIN MUTATED 2 8 7
17Q GAIN WILD-TYPE 83 67 17

Figure S89.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S90.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
18P GAIN MUTATED 2 16 10
18P GAIN WILD-TYPE 83 59 14

Figure S90.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.082

Table S91.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
18P GAIN MUTATED 8 4 13 2
18P GAIN WILD-TYPE 37 43 37 39

Figure S91.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.1

Table S92.  Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
18P GAIN MUTATED 19 3 5
18P GAIN WILD-TYPE 64 45 41

Figure S92.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 0.093

Table S93.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
18P GAIN MUTATED 22 2 3
18P GAIN WILD-TYPE 80 40 30

Figure S93.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.12

Table S94.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
18P GAIN MUTATED 16 5 5
18P GAIN WILD-TYPE 53 62 32

Figure S94.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0012

Table S95.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
18Q GAIN MUTATED 1 4 7
18Q GAIN WILD-TYPE 84 71 17

Figure S95.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0076

Table S96.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
19P GAIN MUTATED 4 5 8
19P GAIN WILD-TYPE 81 70 16

Figure S96.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.064

Table S97.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
19P GAIN MUTATED 8 2 0 7
19P GAIN WILD-TYPE 61 38 35 26

Figure S97.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0067

Table S98.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
19Q GAIN MUTATED 6 12 10
19Q GAIN WILD-TYPE 79 63 14

Figure S98.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S99.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
20P GAIN MUTATED 7 12 15
20P GAIN WILD-TYPE 78 63 9

Figure S99.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.078

Table S100.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
20P GAIN MUTATED 15 7 8 3
20P GAIN WILD-TYPE 30 40 42 38

Figure S100.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.075

Table S101.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
20P GAIN MUTATED 23 2 8
20P GAIN WILD-TYPE 79 40 25

Figure S101.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00622 (Fisher's exact test), Q value = 0.038

Table S102.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
20P GAIN MUTATED 16 5 11
20P GAIN WILD-TYPE 53 62 26

Figure S102.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S103.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
20Q GAIN MUTATED 8 21 16
20Q GAIN WILD-TYPE 77 54 8

Figure S103.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.12

Table S104.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
20Q GAIN MUTATED 16 10 14 4
20Q GAIN WILD-TYPE 29 37 36 37

Figure S104.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.094

Table S105.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
20Q GAIN MUTATED 31 4 8
20Q GAIN WILD-TYPE 71 38 25

Figure S105.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0056

Table S106.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
20Q GAIN MUTATED 22 6 14
20Q GAIN WILD-TYPE 47 61 23

Figure S106.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00067

Table S107.  Gene #39: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
XP GAIN MUTATED 0 2 6
XP GAIN WILD-TYPE 85 73 18

Figure S107.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.12

Table S108.  Gene #39: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
XP GAIN MUTATED 1 3 4
XP GAIN WILD-TYPE 73 72 24

Figure S108.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.14

Table S109.  Gene #39: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
XP GAIN MUTATED 4 0 0 4
XP GAIN WILD-TYPE 65 40 35 29

Figure S109.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0405 (Fisher's exact test), Q value = 0.14

Table S110.  Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
XP GAIN MUTATED 4 0 4
XP GAIN WILD-TYPE 98 42 29

Figure S110.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0047

Table S111.  Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
XQ GAIN MUTATED 2 4 7
XQ GAIN WILD-TYPE 83 71 17

Figure S111.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00944 (Fisher's exact test), Q value = 0.051

Table S112.  Gene #40: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
XQ GAIN MUTATED 2 5 6
XQ GAIN WILD-TYPE 72 70 22

Figure S112.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.13

Table S113.  Gene #40: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
XQ GAIN MUTATED 6 1 6
XQ GAIN WILD-TYPE 96 41 27

Figure S113.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00067

Table S114.  Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
1P LOSS MUTATED 5 24 7
1P LOSS WILD-TYPE 80 51 17

Figure S114.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S115.  Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
1P LOSS MUTATED 22 6 7 1
1P LOSS WILD-TYPE 23 41 43 40

Figure S115.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.016

Table S116.  Gene #41: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
1P LOSS MUTATED 14 2 0 1 3
1P LOSS WILD-TYPE 21 18 16 17 13

Figure S116.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.027

Table S117.  Gene #41: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 12 20 22 15 11 18 7
1P LOSS MUTATED 6 2 4 0 0 5 3
1P LOSS WILD-TYPE 6 18 18 15 11 13 4

Figure S117.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.0097 (Fisher's exact test), Q value = 0.052

Table S118.  Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
1P LOSS MUTATED 23 8 3
1P LOSS WILD-TYPE 60 40 43

Figure S118.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.11

Table S119.  Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
1P LOSS MUTATED 17 6 9
1P LOSS WILD-TYPE 52 61 28

Figure S119.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.094

Table S120.  Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
1P LOSS MUTATED 21 9 2
1P LOSS WILD-TYPE 65 38 38

Figure S120.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.14

Table S121.  Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
1Q LOSS MUTATED 1 4 3
1Q LOSS WILD-TYPE 84 71 21

Figure S121.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 0.0076 (Fisher's exact test), Q value = 0.044

Table S122.  Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
2P LOSS MUTATED 2 4 5
2P LOSS WILD-TYPE 83 71 19

Figure S122.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0069

Table S123.  Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
2Q LOSS MUTATED 0 1 4
2Q LOSS WILD-TYPE 85 74 20

Figure S123.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.014

Table S124.  Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
3P LOSS MUTATED 8 19 9
3P LOSS WILD-TYPE 77 56 15

Figure S124.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.12

Table S125.  Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
3Q LOSS MUTATED 5 8 6
3Q LOSS WILD-TYPE 80 67 18

Figure S125.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'RPPA_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.064

Table S126.  Gene #46: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
3Q LOSS MUTATED 9 1 1 0 0
3Q LOSS WILD-TYPE 26 19 15 18 16

Figure S126.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00733 (Fisher's exact test), Q value = 0.043

Table S127.  Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
3Q LOSS MUTATED 8 2 8
3Q LOSS WILD-TYPE 61 65 29

Figure S127.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.14

Table S128.  Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
4P LOSS MUTATED 6 15 4
4P LOSS WILD-TYPE 79 60 20

Figure S128.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00667 (Fisher's exact test), Q value = 0.04

Table S129.  Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
4P LOSS MUTATED 11 1 9 4
4P LOSS WILD-TYPE 34 46 41 37

Figure S129.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.063

Table S130.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
4P LOSS MUTATED 20 1 3
4P LOSS WILD-TYPE 82 41 30

Figure S130.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00354 (Fisher's exact test), Q value = 0.025

Table S131.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
4P LOSS MUTATED 19 2 2
4P LOSS WILD-TYPE 67 45 38

Figure S131.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.083

Table S132.  Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
4Q LOSS MUTATED 10 1 8 6
4Q LOSS WILD-TYPE 35 46 42 35

Figure S132.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00285 (Fisher's exact test), Q value = 0.022

Table S133.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
4Q LOSS MUTATED 17 0 7
4Q LOSS WILD-TYPE 85 42 26

Figure S133.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0098

Table S134.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
4Q LOSS MUTATED 17 0 6
4Q LOSS WILD-TYPE 69 47 34

Figure S134.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.024

Table S135.  Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
5P LOSS MUTATED 0 8 1
5P LOSS WILD-TYPE 85 67 23

Figure S135.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.026

Table S136.  Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
5Q LOSS MUTATED 1 8 4
5Q LOSS WILD-TYPE 84 67 20

Figure S136.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00067

Table S137.  Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
6P LOSS MUTATED 15 37 12
6P LOSS WILD-TYPE 70 38 12

Figure S137.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0019

Table S138.  Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
6P LOSS MUTATED 23 8 24 8
6P LOSS WILD-TYPE 22 39 26 33

Figure S138.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.068

Table S139.  Gene #51: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
6P LOSS MUTATED 21 34 5
6P LOSS WILD-TYPE 53 41 23

Figure S139.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.01

Table S140.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
6P LOSS MUTATED 46 7 7
6P LOSS WILD-TYPE 56 35 26

Figure S140.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.024

Table S141.  Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
6P LOSS MUTATED 31 13 16
6P LOSS WILD-TYPE 38 54 21

Figure S141.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0021

Table S142.  Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
6P LOSS MUTATED 43 11 6
6P LOSS WILD-TYPE 43 36 34

Figure S142.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S143.  Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
6Q LOSS MUTATED 18 51 14
6Q LOSS WILD-TYPE 67 24 10

Figure S143.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S144.  Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
6Q LOSS MUTATED 27 9 34 12
6Q LOSS WILD-TYPE 18 38 16 29

Figure S144.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.14

Table S145.  Gene #52: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
6Q LOSS MUTATED 23 8 4 6 8
6Q LOSS WILD-TYPE 12 12 12 12 8

Figure S145.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0054

Table S146.  Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
6Q LOSS MUTATED 49 18 11
6Q LOSS WILD-TYPE 34 30 35

Figure S146.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0054

Table S147.  Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
6Q LOSS MUTATED 29 44 5
6Q LOSS WILD-TYPE 45 31 23

Figure S147.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.011

Table S148.  Gene #52: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
6Q LOSS MUTATED 43 14 12 9
6Q LOSS WILD-TYPE 26 26 23 24

Figure S148.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S149.  Gene #52: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
6Q LOSS MUTATED 61 10 7
6Q LOSS WILD-TYPE 41 32 26

Figure S149.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S150.  Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
6Q LOSS MUTATED 46 13 19
6Q LOSS WILD-TYPE 23 54 18

Figure S150.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S151.  Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
6Q LOSS MUTATED 54 18 6
6Q LOSS WILD-TYPE 32 29 34

Figure S151.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.01

Table S152.  Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
8P LOSS MUTATED 9 23 9
8P LOSS WILD-TYPE 76 52 15

Figure S152.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00346 (Fisher's exact test), Q value = 0.025

Table S153.  Gene #55: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
8P LOSS MUTATED 10 7 20 4
8P LOSS WILD-TYPE 35 40 30 37

Figure S153.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0047 (Fisher's exact test), Q value = 0.031

Table S154.  Gene #55: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
8P LOSS MUTATED 11 26 3
8P LOSS WILD-TYPE 63 49 25

Figure S154.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.072

Table S155.  Gene #55: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
8P LOSS MUTATED 23 3 7 7
8P LOSS WILD-TYPE 46 37 28 26

Figure S155.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.062

Table S156.  Gene #55: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
8P LOSS MUTATED 31 4 5
8P LOSS WILD-TYPE 71 38 28

Figure S156.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00686 (Fisher's exact test), Q value = 0.041

Table S157.  Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
8P LOSS MUTATED 20 7 12
8P LOSS WILD-TYPE 49 60 25

Figure S157.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.018

Table S158.  Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
8P LOSS MUTATED 29 6 4
8P LOSS WILD-TYPE 57 41 36

Figure S158.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.081

Table S159.  Gene #56: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
8Q LOSS MUTATED 3 8 5
8Q LOSS WILD-TYPE 82 67 19

Figure S159.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S160.  Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
9P LOSS MUTATED 18 49 8
9P LOSS WILD-TYPE 67 26 16

Figure S160.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0061 (Fisher's exact test), Q value = 0.038

Table S161.  Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
9P LOSS MUTATED 20 12 29 13
9P LOSS WILD-TYPE 25 35 21 28

Figure S161.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.092

Table S162.  Gene #57: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
9P LOSS MUTATED 18 11 2 5 9
9P LOSS WILD-TYPE 17 9 14 13 7

Figure S162.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.024

Table S163.  Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
9P LOSS MUTATED 41 19 9
9P LOSS WILD-TYPE 42 29 37

Figure S163.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 0.13

Table S164.  Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
9P LOSS MUTATED 31 33 5
9P LOSS WILD-TYPE 43 42 23

Figure S164.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.077

Table S165.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
9P LOSS MUTATED 36 13 13 7
9P LOSS WILD-TYPE 33 27 22 26

Figure S165.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.065

Table S166.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
9P LOSS MUTATED 49 12 8
9P LOSS WILD-TYPE 53 30 25

Figure S166.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00803 (Fisher's exact test), Q value = 0.045

Table S167.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
9P LOSS MUTATED 35 17 16
9P LOSS WILD-TYPE 34 50 21

Figure S167.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00718 (Fisher's exact test), Q value = 0.042

Table S168.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
9P LOSS MUTATED 42 18 8
9P LOSS WILD-TYPE 44 29 32

Figure S168.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0047

Table S169.  Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
10P LOSS MUTATED 8 17 11
10P LOSS WILD-TYPE 77 58 13

Figure S169.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S170.  Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
10Q LOSS MUTATED 5 15 10
10Q LOSS WILD-TYPE 80 60 14

Figure S170.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.075

Table S171.  Gene #60: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
10Q LOSS MUTATED 6 19 4
10Q LOSS WILD-TYPE 68 56 24

Figure S171.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.014

Table S172.  Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
11P LOSS MUTATED 2 9 6
11P LOSS WILD-TYPE 83 66 18

Figure S172.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0071

Table S173.  Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
11Q LOSS MUTATED 2 7 7
11Q LOSS WILD-TYPE 83 68 17

Figure S173.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.15

Table S174.  Gene #62: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 12 20 22 15 11 18 7
11Q LOSS MUTATED 0 0 1 4 0 1 0
11Q LOSS WILD-TYPE 12 20 21 11 11 17 7

Figure S174.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0034

Table S175.  Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
12P LOSS MUTATED 3 17 0
12P LOSS WILD-TYPE 82 58 24

Figure S175.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.13

Table S176.  Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
12P LOSS MUTATED 7 1 9 3
12P LOSS WILD-TYPE 38 46 41 38

Figure S176.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.008

Table S177.  Gene #63: '12p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
12P LOSS MUTATED 9 0 0 0 0
12P LOSS WILD-TYPE 26 20 16 18 16

Figure S177.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0098

Table S178.  Gene #63: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 12 20 22 15 11 18 7
12P LOSS MUTATED 3 0 3 0 0 0 3
12P LOSS WILD-TYPE 9 20 19 15 11 18 4

Figure S178.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00824 (Fisher's exact test), Q value = 0.046

Table S179.  Gene #63: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
12P LOSS MUTATED 5 14 0
12P LOSS WILD-TYPE 69 61 28

Figure S179.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0098

Table S180.  Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
12P LOSS MUTATED 18 0 1
12P LOSS WILD-TYPE 84 42 32

Figure S180.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.014

Table S181.  Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
12P LOSS MUTATED 16 1 1
12P LOSS WILD-TYPE 70 46 39

Figure S181.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S182.  Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
12Q LOSS MUTATED 2 25 1
12Q LOSS WILD-TYPE 83 50 23

Figure S182.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.041

Table S183.  Gene #64: '12q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
12Q LOSS MUTATED 10 1 0 0 2
12Q LOSS WILD-TYPE 25 19 16 18 14

Figure S183.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.019

Table S184.  Gene #64: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
12Q LOSS MUTATED 8 18 0
12Q LOSS WILD-TYPE 66 57 28

Figure S184.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.096

Table S185.  Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
12Q LOSS MUTATED 17 7 1
12Q LOSS WILD-TYPE 69 40 39

Figure S185.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0059

Table S186.  Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
13Q LOSS MUTATED 2 12 6
13Q LOSS WILD-TYPE 83 63 18

Figure S186.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.009 (Fisher's exact test), Q value = 0.049

Table S187.  Gene #65: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
13Q LOSS MUTATED 6 2 11 1
13Q LOSS WILD-TYPE 39 45 39 40

Figure S187.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00305 (Fisher's exact test), Q value = 0.023

Table S188.  Gene #65: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
13Q LOSS MUTATED 16 2 1
13Q LOSS WILD-TYPE 67 46 45

Figure S188.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.093

Table S189.  Gene #65: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
13Q LOSS MUTATED 13 1 4 1
13Q LOSS WILD-TYPE 56 39 31 32

Figure S189.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.064

Table S190.  Gene #65: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
13Q LOSS MUTATED 17 1 1
13Q LOSS WILD-TYPE 85 41 32

Figure S190.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.016

Table S191.  Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
13Q LOSS MUTATED 13 1 5
13Q LOSS WILD-TYPE 56 66 32

Figure S191.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.093

Table S192.  Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
14Q LOSS MUTATED 9 1 4 2
14Q LOSS WILD-TYPE 36 46 46 39

Figure S192.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S193.  Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
15Q LOSS MUTATED 3 20 7
15Q LOSS WILD-TYPE 82 55 17

Figure S193.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00879 (Fisher's exact test), Q value = 0.048

Table S194.  Gene #67: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
15Q LOSS MUTATED 9 2 14 5
15Q LOSS WILD-TYPE 36 45 36 36

Figure S194.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.09

Table S195.  Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
15Q LOSS MUTATED 21 4 5
15Q LOSS WILD-TYPE 62 44 41

Figure S195.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00197 (Fisher's exact test), Q value = 0.016

Table S196.  Gene #67: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
15Q LOSS MUTATED 8 21 1
15Q LOSS WILD-TYPE 66 54 27

Figure S196.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00611 (Fisher's exact test), Q value = 0.038

Table S197.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
15Q LOSS MUTATED 25 2 3
15Q LOSS WILD-TYPE 77 40 30

Figure S197.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00372 (Fisher's exact test), Q value = 0.026

Table S198.  Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
15Q LOSS MUTATED 22 4 2
15Q LOSS WILD-TYPE 64 43 38

Figure S198.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00843 (Fisher's exact test), Q value = 0.047

Table S199.  Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
16P LOSS MUTATED 2 4 5
16P LOSS WILD-TYPE 83 71 19

Figure S199.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.094

Table S200.  Gene #68: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
16P LOSS MUTATED 0 0 2 0 2
16P LOSS WILD-TYPE 35 20 14 18 14

Figure S200.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.098

Table S201.  Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
16Q LOSS MUTATED 3 5 5
16Q LOSS WILD-TYPE 82 70 19

Figure S201.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S202.  Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
17P LOSS MUTATED 7 65 8
17P LOSS WILD-TYPE 78 10 16

Figure S202.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S203.  Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
17P LOSS MUTATED 28 7 37 8
17P LOSS WILD-TYPE 17 40 13 33

Figure S203.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.059

Table S204.  Gene #70: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
17P LOSS MUTATED 24 10 4 5 6
17P LOSS WILD-TYPE 11 10 12 13 10

Figure S204.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S205.  Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
17P LOSS MUTATED 49 22 6
17P LOSS WILD-TYPE 34 26 40

Figure S205.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S206.  Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
17P LOSS MUTATED 37 39 1
17P LOSS WILD-TYPE 37 36 27

Figure S206.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S207.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
17P LOSS MUTATED 47 16 8 6
17P LOSS WILD-TYPE 22 24 27 27

Figure S207.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S208.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
17P LOSS MUTATED 58 14 5
17P LOSS WILD-TYPE 44 28 28

Figure S208.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S209.  Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
17P LOSS MUTATED 46 13 17
17P LOSS WILD-TYPE 23 54 20

Figure S209.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S210.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
17P LOSS MUTATED 49 22 5
17P LOSS WILD-TYPE 37 25 35

Figure S210.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0072

Table S211.  Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
17Q LOSS MUTATED 3 17 2
17Q LOSS WILD-TYPE 82 58 22

Figure S211.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 0.0438 (Fisher's exact test), Q value = 0.14

Table S212.  Gene #71: '17q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
17Q LOSS MUTATED 10 2 2 0 1
17Q LOSS WILD-TYPE 25 18 14 18 15

Figure S212.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.098

Table S213.  Gene #71: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 12 20 22 15 11 18 7
17Q LOSS MUTATED 3 2 3 2 1 0 4
17Q LOSS WILD-TYPE 9 18 19 13 10 18 3

Figure S213.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S214.  Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
18Q LOSS MUTATED 36 62 8
18Q LOSS WILD-TYPE 49 13 16

Figure S214.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0047

Table S215.  Gene #73: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
18Q LOSS MUTATED 31 18 38 19
18Q LOSS WILD-TYPE 14 29 12 22

Figure S215.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.13

Table S216.  Gene #73: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
18Q LOSS MUTATED 25 12 7 5 9
18Q LOSS WILD-TYPE 10 8 9 13 7

Figure S216.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.017

Table S217.  Gene #73: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
18Q LOSS MUTATED 57 29 17
18Q LOSS WILD-TYPE 26 19 29

Figure S217.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00505 (Fisher's exact test), Q value = 0.033

Table S218.  Gene #73: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
18Q LOSS MUTATED 43 51 9
18Q LOSS WILD-TYPE 31 24 19

Figure S218.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.071

Table S219.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
18Q LOSS MUTATED 50 21 18 14
18Q LOSS WILD-TYPE 19 19 17 19

Figure S219.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00311 (Fisher's exact test), Q value = 0.023

Table S220.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
18Q LOSS MUTATED 70 20 13
18Q LOSS WILD-TYPE 32 22 20

Figure S220.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.15

Table S221.  Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
18Q LOSS MUTATED 48 33 20
18Q LOSS WILD-TYPE 21 34 17

Figure S221.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S222.  Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
18Q LOSS MUTATED 59 31 11
18Q LOSS WILD-TYPE 27 16 29

Figure S222.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.012

Table S223.  Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
19P LOSS MUTATED 2 12 5
19P LOSS WILD-TYPE 83 63 19

Figure S223.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.093

Table S224.  Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
19P LOSS MUTATED 8 1 8 2
19P LOSS WILD-TYPE 37 46 42 39

Figure S224.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.097

Table S225.  Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
19P LOSS MUTATED 6 13 0
19P LOSS WILD-TYPE 68 62 28

Figure S225.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00614 (Fisher's exact test), Q value = 0.038

Table S226.  Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
19P LOSS MUTATED 17 2 0
19P LOSS WILD-TYPE 85 40 33

Figure S226.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0049

Table S227.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
19P LOSS MUTATED 15 1 2
19P LOSS WILD-TYPE 54 66 35

Figure S227.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.084

Table S228.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
19P LOSS MUTATED 12 6 0
19P LOSS WILD-TYPE 74 41 40

Figure S228.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00653 (Fisher's exact test), Q value = 0.04

Table S229.  Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
19Q LOSS MUTATED 1 7 4
19Q LOSS WILD-TYPE 84 68 20

Figure S229.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.018

Table S230.  Gene #75: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 20 16 18 16
19Q LOSS MUTATED 0 1 0 0 4
19Q LOSS WILD-TYPE 35 19 16 18 12

Figure S230.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.14

Table S231.  Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
19Q LOSS MUTATED 10 1 1
19Q LOSS WILD-TYPE 73 47 45

Figure S231.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.069

Table S232.  Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
19Q LOSS MUTATED 2 10 0
19Q LOSS WILD-TYPE 72 65 28

Figure S232.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0049

Table S233.  Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
20P LOSS MUTATED 2 16 2
20P LOSS WILD-TYPE 83 59 22

Figure S233.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.15

Table S234.  Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
20P LOSS MUTATED 6 2 10 2
20P LOSS WILD-TYPE 39 45 40 39

Figure S234.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.00651 (Fisher's exact test), Q value = 0.04

Table S235.  Gene #76: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
20P LOSS MUTATED 11 8 0
20P LOSS WILD-TYPE 72 40 46

Figure S235.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.13

Table S236.  Gene #76: '20p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 40 35 33
20P LOSS MUTATED 11 6 2 0
20P LOSS WILD-TYPE 58 34 33 33

Figure S236.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.13

Table S237.  Gene #76: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
20P LOSS MUTATED 15 4 0
20P LOSS WILD-TYPE 87 38 33

Figure S237.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.016

Table S238.  Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
20P LOSS MUTATED 11 1 7
20P LOSS WILD-TYPE 58 66 30

Figure S238.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.067

Table S239.  Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
20P LOSS MUTATED 11 8 0
20P LOSS WILD-TYPE 75 39 40

Figure S239.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S240.  Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
21Q LOSS MUTATED 11 38 9
21Q LOSS WILD-TYPE 74 37 15

Figure S240.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.093

Table S241.  Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
21Q LOSS MUTATED 17 9 22 9
21Q LOSS WILD-TYPE 28 38 28 32

Figure S241.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.092

Table S242.  Gene #78: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 48 46
21Q LOSS MUTATED 30 18 7
21Q LOSS WILD-TYPE 53 30 39

Figure S242.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.12

Table S243.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
21Q LOSS MUTATED 39 11 5
21Q LOSS WILD-TYPE 63 31 28

Figure S243.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0059

Table S244.  Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
21Q LOSS MUTATED 31 10 12
21Q LOSS WILD-TYPE 38 57 25

Figure S244.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.13

Table S245.  Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
21Q LOSS MUTATED 29 18 6
21Q LOSS WILD-TYPE 57 29 34

Figure S245.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S246.  Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
22Q LOSS MUTATED 7 30 9
22Q LOSS WILD-TYPE 78 45 15

Figure S246.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0056 (Fisher's exact test), Q value = 0.036

Table S247.  Gene #79: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
22Q LOSS MUTATED 18 7 16 5
22Q LOSS WILD-TYPE 27 40 34 36

Figure S247.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.14

Table S248.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
22Q LOSS MUTATED 32 6 5
22Q LOSS WILD-TYPE 70 36 28

Figure S248.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.01

Table S249.  Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 67 37
22Q LOSS MUTATED 22 7 14
22Q LOSS WILD-TYPE 47 60 23

Figure S249.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.11

Table S250.  Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 86 47 40
22Q LOSS MUTATED 27 12 4
22Q LOSS WILD-TYPE 59 35 36

Figure S250.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S251.  Gene #80: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
XP LOSS MUTATED 3 18 6
XP LOSS WILD-TYPE 82 57 18

Figure S251.  Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S252.  Gene #81: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 75 24
XQ LOSS MUTATED 0 13 5
XQ LOSS WILD-TYPE 85 62 19

Figure S252.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.15

Table S253.  Gene #81: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 47 50 41
XQ LOSS MUTATED 7 5 6 0
XQ LOSS WILD-TYPE 38 42 44 41

Figure S253.  Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PAAD-TP/15096459/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PAAD-TP/15107801/PAAD-TP.transferedmergedcluster.txt

  • Number of patients = 184

  • Number of significantly arm-level cnvs = 81

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

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