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 82 arm-level events and 10 molecular subtypes across 295 patients, 217 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 1q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 3p gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

  • 9q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 13q gain cnv correlated to 'MIRSEQ_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 15q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 21q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 22q gain cnv correlated to 'MRNASEQ_CNMF'.

  • xp gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • xq gain cnv correlated to 'METHLYATION_CNMF'.

  • 1p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 2p loss cnv correlated to 'CN_CNMF'.

  • 2q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 4q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'CN_CNMF'.

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

  • 6q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'METHLYATION_CNMF'.

  • 7q loss cnv correlated to 'METHLYATION_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 12p loss cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'METHLYATION_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 16p loss cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • 18p loss cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20p loss cnv correlated to 'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 22q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • xp loss cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 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, 217 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
9q gain 50 (17%) 245 0.00146
(0.0184) 		0.00551
(0.0434) 		0.278
(0.491) 		0.558
(0.731) 		0.0135
(0.078) 		0.00052
(0.00907) 		0.0112
(0.0699) 		0.0104
(0.0677) 		0.0461
(0.179) 		0.0347
(0.148)
3p loss 77 (26%) 218 1e-05
(0.000482) 		0.00577
(0.0442) 		0.375
(0.583) 		0.0568
(0.207) 		0.0123
(0.0744) 		0.00026
(0.00547) 		0.0116
(0.0707) 		0.00294
(0.0277) 		0.0115
(0.0707) 		0.00153
(0.0189)
8q loss 25 (8%) 270 0.00156
(0.0189) 		1e-05
(0.000482) 		0.669
(0.799) 		0.075
(0.242) 		8e-05
(0.00205) 		3e-05
(0.00102) 		0.00721
(0.0514) 		5e-05
(0.00132) 		0.00607
(0.0457) 		0.00825
(0.0564)
16q loss 43 (15%) 252 0.242
(0.459) 		0.00793
(0.0551) 		0.739
(0.853) 		0.176
(0.385) 		0.00491
(0.0396) 		0.00249
(0.0251) 		0.0108
(0.0686) 		0.00251
(0.0251) 		0.0404
(0.167) 		0.00043
(0.00801)
18q loss 73 (25%) 222 0.00104
(0.0155) 		0.00957
(0.0633) 		0.45
(0.641) 		0.204
(0.422) 		4e-05
(0.00113) 		0.00103
(0.0155) 		0.111
(0.301) 		0.00027
(0.00553) 		0.0173
(0.0935) 		2e-05
(0.000745)
3q gain 176 (60%) 119 4e-05
(0.00113) 		0.276
(0.49) 		1
(1.00) 		0.32
(0.532) 		0.00113
(0.016) 		4e-05
(0.00113) 		0.349
(0.559) 		0.00022
(0.00475) 		0.00651
(0.0477) 		1e-05
(0.000482)
8q gain 91 (31%) 204 0.002
(0.0222) 		1e-05
(0.000482) 		0.383
(0.584) 		0.501
(0.687) 		0.00607
(0.0457) 		0.00127
(0.0171) 		0.17
(0.378) 		0.00862
(0.0579) 		0.442
(0.632) 		0.00213
(0.0233)
20q gain 114 (39%) 181 1e-05
(0.000482) 		0.0345
(0.148) 		0.213
(0.431) 		0.00176
(0.0206) 		0.225
(0.443) 		0.0477
(0.183) 		0.241
(0.459) 		0.0285
(0.13) 		0.0126
(0.0754) 		0.321
(0.532)
4p loss 130 (44%) 165 1e-05
(0.000482) 		0.0436
(0.175) 		0.939
(0.977) 		1
(1.00) 		0.00633
(0.0471) 		0.00228
(0.0243) 		0.31
(0.526) 		0.0012
(0.0164) 		0.537
(0.716) 		0.00571
(0.0442)
13q loss 80 (27%) 215 1e-05
(0.000482) 		0.246
(0.463) 		0.973
(0.989) 		0.179
(0.39) 		0.0137
(0.0781) 		0.0272
(0.126) 		0.0178
(0.0941) 		0.00193
(0.022) 		0.182
(0.393) 		0.0456
(0.178)
1p gain 92 (31%) 203 1e-05
(0.000482) 		0.402
(0.598) 		0.751
(0.86) 		0.864
(0.933) 		0.00013
(0.00314) 		0.00216
(0.0233) 		0.162
(0.375) 		4e-05
(0.00113) 		0.126
(0.328) 		0.00157
(0.0189)
1q gain 141 (48%) 154 1e-05
(0.000482) 		0.335
(0.541) 		0.348
(0.559) 		0.38
(0.584) 		0.00398
(0.0352) 		0.00575
(0.0442) 		0.273
(0.487) 		0.00271
(0.0258) 		0.0677
(0.226) 		0.00267
(0.0258)
2q gain 38 (13%) 257 4e-05
(0.00113) 		0.044
(0.175) 		0.0672
(0.226) 		0.172
(0.381) 		0.0245
(0.117) 		0.00707
(0.0509) 		0.304
(0.519) 		0.00371
(0.0334) 		0.589
(0.748) 		0.628
(0.773)
5p gain 115 (39%) 180 1e-05
(0.000482) 		0.234
(0.452) 		0.553
(0.729) 		0.65
(0.786) 		0.0786
(0.248) 		0.0251
(0.119) 		0.00434
(0.037) 		0.00497
(0.0396) 		0.0295
(0.133) 		0.224
(0.443)
20p gain 101 (34%) 194 1e-05
(0.000482) 		0.021
(0.103) 		0.819
(0.899) 		0.0127
(0.0754) 		0.156
(0.363) 		0.0971
(0.281) 		0.0436
(0.175) 		0.122
(0.32) 		0.0169
(0.0918) 		0.377
(0.584)
8p loss 82 (28%) 213 1e-05
(0.000482) 		0.944
(0.977) 		0.882
(0.944) 		0.222
(0.443) 		0.0164
(0.0897) 		0.308
(0.523) 		0.0203
(0.103) 		0.0439
(0.175) 		0.00685
(0.0497) 		0.395
(0.594)
11p loss 100 (34%) 195 1e-05
(0.000482) 		0.335
(0.541) 		0.0255
(0.12) 		0.0264
(0.123) 		0.0342
(0.148) 		0.0866
(0.265) 		0.466
(0.659) 		0.0622
(0.216) 		0.669
(0.799) 		0.0204
(0.103)
19p loss 60 (20%) 235 1e-05
(0.000482) 		0.569
(0.739) 		0.706
(0.824) 		0.122
(0.32) 		0.00039
(0.00744) 		0.00142
(0.0182) 		0.101
(0.286) 		0.00056
(0.00957) 		0.0442
(0.175) 		0.0998
(0.284)
21q loss 49 (17%) 246 0.00061
(0.01) 		0.244
(0.462) 		0.606
(0.759) 		0.0243
(0.117) 		0.00879
(0.0586) 		0.00442
(0.037) 		0.46
(0.652) 		0.0269
(0.125) 		0.13
(0.33) 		0.234
(0.452)
2p gain 65 (22%) 230 3e-05
(0.00102) 		0.395
(0.594) 		0.0181
(0.0941) 		0.119
(0.317) 		0.018
(0.0941) 		0.0507
(0.188) 		0.129
(0.329) 		0.00112
(0.016) 		0.247
(0.463) 		0.117
(0.315)
6p gain 52 (18%) 243 0.0005
(0.00891) 		0.0448
(0.177) 		0.763
(0.865) 		0.011
(0.0692) 		0.0104
(0.0677) 		0.139
(0.343) 		0.944
(0.977) 		0.0737
(0.239) 		0.269
(0.484) 		0.165
(0.378)
7q gain 38 (13%) 257 0.00199
(0.0222) 		0.07
(0.23) 		1
(1.00) 		0.137
(0.342) 		0.477
(0.667) 		0.211
(0.429) 		0.00076
(0.0122) 		0.156
(0.363) 		0.00101
(0.0155) 		0.0418
(0.17)
3q loss 14 (5%) 281 0.0145
(0.0818) 		0.305
(0.519) 		0.775
(0.871) 		0.029
(0.131) 		0.0233
(0.113) 		0.428
(0.622) 		0.059
(0.211) 		0.371
(0.58) 		0.111
(0.301) 		0.00637
(0.0471)
6q loss 74 (25%) 221 0.00018
(0.0041) 		0.0234
(0.113) 		0.422
(0.62) 		0.602
(0.756) 		0.23
(0.45) 		0.0302
(0.135) 		0.148
(0.355) 		0.0362
(0.154) 		0.223
(0.443) 		0.169
(0.378)
7p gain 37 (13%) 258 0.00311
(0.0287) 		0.0927
(0.273) 		0.0791
(0.248) 		0.21
(0.427) 		0.0599
(0.213) 		0.423
(0.62) 		0.0005
(0.00891) 		0.128
(0.328) 		0.00475
(0.0389) 		0.169
(0.378)
9p gain 51 (17%) 244 0.00759
(0.0532) 		0.114
(0.307) 		0.242
(0.459) 		0.223
(0.443) 		0.327
(0.536) 		0.0105
(0.0677) 		0.127
(0.328) 		0.013
(0.0763) 		0.353
(0.562) 		0.0771
(0.245)
19q gain 72 (24%) 223 1e-05
(0.000482) 		0.266
(0.482) 		0.623
(0.773) 		0.532
(0.714) 		0.159
(0.368) 		0.0328
(0.145) 		0.469
(0.661) 		0.0256
(0.12) 		0.305
(0.519) 		0.225
(0.443)
2q loss 34 (12%) 261 0.021
(0.103) 		0.183
(0.395) 		0.947
(0.977) 		0.172
(0.381) 		0.00234
(0.0246) 		0.0573
(0.208) 		0.124
(0.326) 		0.0323
(0.144) 		0.567
(0.738) 		0.157
(0.364)
4q loss 95 (32%) 200 1e-05
(0.000482) 		0.555
(0.729) 		0.679
(0.806) 		0.953
(0.978) 		0.0709
(0.232) 		0.0176
(0.0941) 		1
(1.00) 		0.0483
(0.183) 		0.182
(0.393) 		0.278
(0.491)
6p loss 46 (16%) 249 0.0128
(0.0754) 		0.0395
(0.165) 		0.494
(0.68) 		0.317
(0.53) 		0.189
(0.405) 		0.0408
(0.168) 		0.524
(0.707) 		0.168
(0.378) 		0.426
(0.622) 		0.0946
(0.277)
17p loss 94 (32%) 201 0.00432
(0.037) 		0.033
(0.145) 		0.048
(0.183) 		0.591
(0.748) 		0.103
(0.289) 		0.0527
(0.194) 		0.118
(0.315) 		0.0768
(0.245) 		0.252
(0.466) 		0.581
(0.746)
17q loss 34 (12%) 261 0.0135
(0.078) 		0.0208
(0.103) 		0.00733
(0.0518) 		0.393
(0.593) 		0.0605
(0.214) 		0.283
(0.497) 		0.102
(0.288) 		0.34
(0.547) 		0.739
(0.853) 		0.698
(0.82)
20p loss 22 (7%) 273 0.954
(0.978) 		0.922
(0.97) 		0.152
(0.361) 		0.927
(0.972) 		0.018
(0.0941) 		0.0915
(0.272) 		0.0628
(0.216) 		0.168
(0.378) 		0.00463
(0.0383) 		0.00441
(0.037)
4q gain 14 (5%) 281 0.0381
(0.161) 		0.415
(0.612) 		0.0463
(0.179) 		0.364
(0.573) 		0.883
(0.944) 		0.465
(0.659) 		0.834
(0.907) 		0.285
(0.5) 		0.792
(0.883) 		0.287
(0.501)
6q gain 35 (12%) 260 0.0137
(0.0781) 		0.0401
(0.167) 		0.215
(0.434) 		0.0919
(0.272) 		0.23
(0.45) 		0.247
(0.463) 		0.741
(0.854) 		0.265
(0.482) 		0.315
(0.53) 		0.665
(0.798)
8p gain 53 (18%) 242 2e-05
(0.000745) 		0.0864
(0.265) 		0.767
(0.867) 		0.549
(0.726) 		0.0332
(0.145) 		0.167
(0.378) 		0.826
(0.902) 		0.0763
(0.244) 		0.887
(0.945) 		0.134
(0.339)
11q gain 8 (3%) 287 0.377
(0.584) 		0.259
(0.474) 		0.108
(0.297) 		0.67
(0.799) 		0.0506
(0.188) 		0.00164
(0.0195) 		0.18
(0.39) 		0.0229
(0.112) 		0.175
(0.385) 		0.0774
(0.245)
12q gain 50 (17%) 245 0.0481
(0.183) 		0.8
(0.886) 		0.382
(0.584) 		0.78
(0.877) 		0.0024
(0.0249) 		0.327
(0.536) 		1
(1.00) 		0.27
(0.485) 		0.723
(0.839) 		0.582
(0.746)
18p gain 49 (17%) 246 0.00183
(0.0211) 		0.753
(0.86) 		0.579
(0.746) 		0.762
(0.865) 		0.0389
(0.164) 		0.165
(0.378) 		0.782
(0.878) 		0.289
(0.503) 		0.899
(0.955) 		0.193
(0.412)
18q gain 32 (11%) 263 0.00011
(0.00273) 		0.792
(0.883) 		0.302
(0.519) 		0.218
(0.438) 		0.00118
(0.0164) 		0.251
(0.466) 		0.315
(0.53) 		0.334
(0.541) 		0.97
(0.989) 		0.0631
(0.216)
xp gain 40 (14%) 255 0.58
(0.746) 		0.0333
(0.145) 		0.587
(0.748) 		0.435
(0.626) 		0.138
(0.343) 		0.0279
(0.128) 		0.731
(0.847) 		0.167
(0.378) 		0.65
(0.786) 		0.317
(0.53)
1p loss 13 (4%) 282 0.146
(0.355) 		0.934
(0.977) 		0.765
(0.867) 		0.4
(0.597) 		0.00031
(0.0062) 		0.0193
(0.0992) 		0.0988
(0.282) 		0.2
(0.419) 		0.398
(0.595) 		0.139
(0.343)
9q loss 48 (16%) 247 0.0147
(0.0827) 		0.0891
(0.269) 		0.225
(0.443) 		0.495
(0.68) 		0.136
(0.342) 		0.0863
(0.265) 		0.377
(0.584) 		0.536
(0.716) 		0.0107
(0.0686) 		0.385
(0.585)
11q loss 115 (39%) 180 1e-05
(0.000482) 		0.287
(0.501) 		0.15
(0.359) 		0.29
(0.504) 		0.0501
(0.188) 		0.0889
(0.269) 		0.298
(0.514) 		0.00803
(0.0553) 		0.424
(0.62) 		0.0709
(0.232)
16p loss 32 (11%) 263 0.105
(0.294) 		0.642
(0.783) 		0.627
(0.773) 		0.617
(0.769) 		0.0427
(0.173) 		0.364
(0.573) 		0.276
(0.49) 		0.0112
(0.0699) 		0.153
(0.361) 		0.504
(0.689)
18p loss 54 (18%) 241 0.478
(0.668) 		0.0636
(0.217) 		0.966
(0.987) 		0.17
(0.378) 		0.0151
(0.0843) 		0.0652
(0.221) 		0.311
(0.526) 		0.0625
(0.216) 		0.234
(0.452) 		0.00014
(0.00328)
22q loss 71 (24%) 224 0.00403
(0.0352) 		0.633
(0.776) 		0.302
(0.519) 		0.117
(0.314) 		0.225
(0.443) 		0.0197
(0.101) 		0.954
(0.978) 		0.209
(0.425) 		0.389
(0.588) 		0.435
(0.626)
xp loss 65 (22%) 230 0.0886
(0.269) 		0.0659
(0.223) 		0.529
(0.712) 		0.705
(0.824) 		0.269
(0.484) 		0.624
(0.773) 		0.00243
(0.0249) 		0.195
(0.414) 		0.0646
(0.22) 		0.0116
(0.0707)
3p gain 78 (26%) 217 0.201
(0.419) 		0.0925
(0.273) 		0.752
(0.86) 		0.00495
(0.0396) 		0.388
(0.588) 		0.887
(0.945) 		0.148
(0.355) 		0.615
(0.767) 		0.678
(0.806) 		0.583
(0.746)
5q gain 48 (16%) 247 2e-05
(0.000745) 		1
(1.00) 		0.652
(0.786) 		0.953
(0.978) 		0.176
(0.385) 		0.842
(0.913) 		0.335
(0.541) 		0.773
(0.871) 		0.25
(0.466) 		0.939
(0.977)
11p gain 9 (3%) 286 0.886
(0.945) 		0.914
(0.966) 		0.198
(0.417) 		0.897
(0.954) 		0.398
(0.595) 		0.155
(0.362) 		0.697
(0.82) 		0.0205
(0.103) 		0.635
(0.777) 		0.517
(0.701)
12p gain 53 (18%) 242 0.114
(0.307) 		0.667
(0.799) 		0.374
(0.583) 		0.72
(0.837) 		0.00107
(0.0157) 		0.671
(0.799) 		0.793
(0.883) 		0.353
(0.562) 		0.773
(0.871) 		0.637
(0.778)
13q gain 25 (8%) 270 0.357
(0.567) 		0.128
(0.328) 		0.233
(0.452) 		0.626
(0.773) 		0.107
(0.296) 		0.0575
(0.208) 		0.0157
(0.087) 		0.0899
(0.269) 		0.0683
(0.226) 		0.0529
(0.194)
14q gain 47 (16%) 248 0.00359
(0.0327) 		0.562
(0.733) 		0.96
(0.983) 		0.224
(0.443) 		0.215
(0.434) 		1
(1.00) 		0.368
(0.578) 		0.147
(0.355) 		0.0503
(0.188) 		0.121
(0.319)
15q gain 52 (18%) 243 0.00254
(0.0251) 		0.453
(0.644) 		0.131
(0.333) 		0.614
(0.767) 		0.871
(0.936) 		0.87
(0.936) 		0.872
(0.936) 		0.762
(0.865) 		0.941
(0.977) 		0.832
(0.906)
16p gain 45 (15%) 250 0.00135
(0.0176) 		0.553
(0.729) 		0.383
(0.584) 		0.761
(0.865) 		0.428
(0.622) 		0.337
(0.544) 		0.0683
(0.226) 		0.0854
(0.264) 		0.411
(0.609) 		0.576
(0.746)
16q gain 40 (14%) 255 2e-05
(0.000745) 		0.406
(0.604) 		0.367
(0.577) 		0.291
(0.505) 		0.579
(0.746) 		0.437
(0.628) 		0.151
(0.36) 		0.0872
(0.266) 		0.0913
(0.272) 		0.488
(0.676)
17p gain 22 (7%) 273 0.00037
(0.00722) 		0.262
(0.478) 		0.942
(0.977) 		0.973
(0.989) 		0.109
(0.297) 		0.334
(0.541) 		0.33
(0.539) 		0.651
(0.786) 		0.0579
(0.208) 		0.971
(0.989)
17q gain 43 (15%) 252 0.00061
(0.01) 		0.108
(0.297) 		0.206
(0.422) 		0.0527
(0.194) 		0.189
(0.405) 		0.413
(0.611) 		0.591
(0.748) 		0.825
(0.902) 		0.205
(0.422) 		0.663
(0.797)
19p gain 45 (15%) 250 2e-05
(0.000745) 		0.361
(0.57) 		0.516
(0.701) 		0.94
(0.977) 		0.511
(0.697) 		0.56
(0.732) 		1
(1.00) 		0.484
(0.674) 		0.807
(0.889) 		0.706
(0.824)
21q gain 37 (13%) 258 0.109
(0.297) 		0.837
(0.909) 		0.543
(0.72) 		0.716
(0.834) 		0.0181
(0.0941) 		0.357
(0.567) 		0.975
(0.989) 		0.76
(0.865) 		0.752
(0.86) 		0.514
(0.699)
22q gain 29 (10%) 266 0.555
(0.729) 		0.49
(0.677) 		0.774
(0.871) 		0.581
(0.746) 		0.00021
(0.00465) 		0.252
(0.466) 		0.799
(0.886) 		0.334
(0.541) 		0.805
(0.889) 		0.315
(0.53)
xq gain 43 (15%) 252 0.537
(0.716) 		0.0454
(0.178) 		0.0848
(0.263) 		0.432
(0.625) 		0.242
(0.459) 		0.139
(0.343) 		0.179
(0.39) 		0.147
(0.355) 		0.254
(0.468) 		0.393
(0.593)
1q loss 9 (3%) 286 0.382
(0.584) 		0.913
(0.966) 		0.441
(0.632) 		0.683
(0.809) 		0.0343
(0.148) 		0.155
(0.362) 		0.0613
(0.216) 		0.438
(0.63) 		0.202
(0.421) 		0.384
(0.584)
2p loss 18 (6%) 277 0.016
(0.0879) 		0.785
(0.88) 		0.909
(0.963) 		0.258
(0.474) 		0.325
(0.535) 		0.236
(0.454) 		0.529
(0.712) 		0.271
(0.485) 		0.561
(0.733) 		0.796
(0.885)
5q loss 49 (17%) 246 5e-05
(0.00132) 		0.572
(0.742) 		0.805
(0.889) 		0.447
(0.638) 		0.652
(0.786) 		0.947
(0.977) 		0.118
(0.315) 		0.242
(0.459) 		0.325
(0.535) 		0.0675
(0.226)
7p loss 26 (9%) 269 0.384
(0.584) 		0.00862
(0.0579) 		0.737
(0.852) 		0.0962
(0.281) 		0.0592
(0.211) 		0.25
(0.466) 		0.126
(0.328) 		0.826
(0.902) 		0.278
(0.491) 		0.275
(0.49)
7q loss 36 (12%) 259 0.595
(0.751) 		0.0416
(0.17) 		0.197
(0.416) 		0.0734
(0.239) 		0.453
(0.644) 		0.164
(0.378) 		0.0984
(0.282) 		0.204
(0.422) 		0.141
(0.345) 		0.188
(0.403)
9p loss 53 (18%) 242 0.0013
(0.0172) 		0.794
(0.883) 		0.082
(0.257) 		0.482
(0.672) 		0.474
(0.665) 		0.604
(0.758) 		0.926
(0.972) 		0.873
(0.936) 		0.282
(0.497) 		0.859
(0.93)
10p loss 66 (22%) 229 0.00271
(0.0258) 		0.428
(0.622) 		0.745
(0.856) 		0.974
(0.989) 		0.419
(0.616) 		0.53
(0.712) 		0.631
(0.774) 		0.601
(0.756) 		0.321
(0.532) 		0.133
(0.337)
10q loss 73 (25%) 222 0.00401
(0.0352) 		0.423
(0.62) 		0.92
(0.968) 		0.9
(0.955) 		0.198
(0.417) 		0.208
(0.425) 		0.51
(0.696) 		0.251
(0.466) 		0.235
(0.453) 		0.127
(0.328)
12p loss 40 (14%) 255 0.883
(0.944) 		0.0844
(0.263) 		0.493
(0.679) 		0.00086
(0.0136) 		0.137
(0.342) 		0.489
(0.676) 		0.316
(0.53) 		0.801
(0.887) 		0.172
(0.381) 		0.397
(0.595)
12q loss 15 (5%) 280 0.724
(0.84) 		0.0184
(0.0949) 		0.743
(0.855) 		0.806
(0.889) 		0.649
(0.786) 		0.414
(0.611) 		0.204
(0.422) 		0.538
(0.716) 		0.262
(0.478) 		0.654
(0.788)
15q loss 47 (16%) 248 0.05
(0.188) 		0.979
(0.993) 		0.916
(0.966) 		0.683
(0.809) 		0.165
(0.378) 		0.591
(0.748) 		0.167
(0.378) 		0.51
(0.696) 		0.155
(0.362) 		0.384
(0.584)
19q loss 30 (10%) 265 0.00312
(0.0287) 		0.106
(0.296) 		0.379
(0.584) 		0.63
(0.774) 		0.229
(0.448) 		0.292
(0.505) 		0.476
(0.667) 		0.107
(0.297) 		0.179
(0.39) 		0.239
(0.459)
4p gain 11 (4%) 284 0.59
(0.748) 		0.141
(0.346) 		0.3
(0.516) 		0.206
(0.422) 		0.647
(0.786) 		0.596
(0.751) 		0.467
(0.659) 		0.596
(0.751) 		0.637
(0.778) 		0.942
(0.977)
10p gain 25 (8%) 270 0.128
(0.328) 		0.518
(0.701) 		0.943
(0.977) 		0.695
(0.82) 		0.821
(0.9) 		0.473
(0.665) 		0.0616
(0.216) 		0.697
(0.82) 		0.327
(0.536) 		0.787
(0.88)
10q gain 17 (6%) 278 0.432
(0.625) 		0.859
(0.93) 		0.625
(0.773) 		0.698
(0.82) 		0.36
(0.57) 		0.2
(0.419) 		0.242
(0.459) 		0.916
(0.966) 		0.699
(0.82) 		0.626
(0.773)
5p loss 17 (6%) 278 0.577
(0.746) 		0.628
(0.773) 		0.353
(0.562) 		0.556
(0.729) 		0.828
(0.903) 		0.488
(0.676) 		0.815
(0.896) 		0.541
(0.719) 		0.701
(0.822) 		0.142
(0.346)
14q loss 35 (12%) 260 0.373
(0.582) 		0.0973
(0.281) 		0.303
(0.519) 		0.09
(0.269) 		0.0626
(0.216) 		0.139
(0.343) 		0.947
(0.977) 		0.0978
(0.281) 		0.194
(0.412) 		0.151
(0.36)
20q loss 12 (4%) 283 0.148
(0.355) 		0.867
(0.935) 		0.537
(0.716) 		0.591
(0.748) 		0.268
(0.484) 		0.0969
(0.281) 		1
(1.00) 		0.487
(0.676) 		1
(1.00) 		0.322
(0.534)
xq loss 58 (20%) 237 0.266
(0.482) 		0.104
(0.292) 		0.547
(0.724) 		0.679
(0.806) 		0.252
(0.466) 		1
(1.00) 		0.0758
(0.244) 		0.954
(0.978) 		0.259
(0.474) 		0.323
(0.534)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
1P GAIN MUTATED 3 38 35 6 10
1P GAIN WILD-TYPE 12 74 21 53 43

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0031

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
1P GAIN MUTATED 19 46 14 12
1P GAIN WILD-TYPE 38 52 55 56

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00216 (Fisher's exact test), Q value = 0.023

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
1P GAIN MUTATED 13 71 7
1P GAIN WILD-TYPE 59 114 28

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
1P GAIN MUTATED 9 31 36 10 6
1P GAIN WILD-TYPE 51 64 36 15 37

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.019

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
1P GAIN MUTATED 9 36 30 7 4
1P GAIN WILD-TYPE 20 43 69 35 29

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
1Q GAIN MUTATED 5 57 42 13 24
1Q GAIN WILD-TYPE 10 55 14 46 29

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00398 (Fisher's exact test), Q value = 0.035

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
1Q GAIN MUTATED 28 60 27 24
1Q GAIN WILD-TYPE 29 38 42 44

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00575 (Fisher's exact test), Q value = 0.044

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
1Q GAIN MUTATED 24 101 14
1Q GAIN WILD-TYPE 48 84 21

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00271 (Fisher's exact test), Q value = 0.026

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
1Q GAIN MUTATED 19 52 42 14 14
1Q GAIN WILD-TYPE 41 43 30 11 29

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.026

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
1Q GAIN MUTATED 14 46 52 12 9
1Q GAIN WILD-TYPE 15 33 47 30 24

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.001

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
2P GAIN MUTATED 1 41 9 4 10
2P GAIN WILD-TYPE 14 71 47 55 43

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.094

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 41 64
2P GAIN MUTATED 17 3 17
2P GAIN WILD-TYPE 42 38 47

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.094

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
2P GAIN MUTATED 16 12 21 16
2P GAIN WILD-TYPE 41 86 48 52

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.016

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
2P GAIN MUTATED 18 19 6 11 11
2P GAIN WILD-TYPE 42 76 66 14 32

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S15.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
2Q GAIN MUTATED 1 27 4 0 6
2Q GAIN WILD-TYPE 14 85 52 59 47

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.18

Table S16.  Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
2Q GAIN MUTATED 12 8 18
2Q GAIN WILD-TYPE 60 107 90

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.12

Table S17.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
2Q GAIN MUTATED 10 5 11 12
2Q GAIN WILD-TYPE 47 93 58 56

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00707 (Fisher's exact test), Q value = 0.051

Table S18.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
2Q GAIN MUTATED 13 16 9
2Q GAIN WILD-TYPE 59 169 26

Figure S18.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00371 (Fisher's exact test), Q value = 0.033

Table S19.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
2Q GAIN MUTATED 12 10 2 5 9
2Q GAIN WILD-TYPE 48 85 70 20 34

Figure S19.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00495 (Fisher's exact test), Q value = 0.04

Table S20.  Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
3P GAIN MUTATED 10 11 7 5 11
3P GAIN WILD-TYPE 22 36 38 18 6

Figure S20.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S21.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
3Q GAIN MUTATED 6 71 45 22 32
3Q GAIN WILD-TYPE 9 41 11 37 21

Figure S21.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.016

Table S22.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
3Q GAIN MUTATED 36 72 34 32
3Q GAIN WILD-TYPE 21 26 35 36

Figure S22.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S23.  Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
3Q GAIN MUTATED 30 129 15
3Q GAIN WILD-TYPE 42 56 20

Figure S23.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0047

Table S24.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
3Q GAIN MUTATED 23 60 55 16 22
3Q GAIN WILD-TYPE 37 35 17 9 21

Figure S24.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00651 (Fisher's exact test), Q value = 0.048

Table S25.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
3Q GAIN MUTATED 48 55 65
3Q GAIN WILD-TYPE 53 24 37

Figure S25.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S26.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
3Q GAIN MUTATED 12 58 69 15 14
3Q GAIN WILD-TYPE 17 21 30 27 19

Figure S26.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.16

Table S27.  Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
4Q GAIN MUTATED 0 2 3 2 7
4Q GAIN WILD-TYPE 15 110 53 57 46

Figure S27.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'RPPA_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.18

Table S28.  Gene #8: '4q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 41 64
4Q GAIN MUTATED 2 0 7
4Q GAIN WILD-TYPE 57 41 57

Figure S28.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S29.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
5P GAIN MUTATED 6 65 26 10 8
5P GAIN WILD-TYPE 9 47 30 49 45

Figure S29.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.12

Table S30.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
5P GAIN MUTATED 20 75 19
5P GAIN WILD-TYPE 52 110 16

Figure S30.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.037

Table S31.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
5P GAIN MUTATED 36 21 58
5P GAIN WILD-TYPE 69 54 57

Figure S31.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00497 (Fisher's exact test), Q value = 0.04

Table S32.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
5P GAIN MUTATED 14 45 22 13 21
5P GAIN WILD-TYPE 46 50 50 12 22

Figure S32.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.13

Table S33.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
5P GAIN MUTATED 38 22 48
5P GAIN WILD-TYPE 63 57 54

Figure S33.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S34.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
5Q GAIN MUTATED 2 28 14 2 2
5Q GAIN WILD-TYPE 13 84 42 57 51

Figure S34.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
6P GAIN MUTATED 0 33 4 9 6
6P GAIN WILD-TYPE 15 79 52 50 47

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

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.18

Table S36.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
6P GAIN MUTATED 18 13 21
6P GAIN WILD-TYPE 54 102 87

Figure S36.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.069

Table S37.  Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
6P GAIN MUTATED 7 4 5 7 7
6P GAIN WILD-TYPE 25 43 40 16 10

Figure S37.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.068

Table S38.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
6P GAIN MUTATED 15 8 14 15
6P GAIN WILD-TYPE 42 90 55 53

Figure S38.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.078

Table S39.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
6Q GAIN MUTATED 0 23 4 5 3
6Q GAIN WILD-TYPE 15 89 52 54 50

Figure S39.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.17

Table S40.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
6Q GAIN MUTATED 14 8 13
6Q GAIN WILD-TYPE 58 107 95

Figure S40.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.029

Table S41.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
7P GAIN MUTATED 3 17 9 0 8
7P GAIN WILD-TYPE 12 95 47 59 45

Figure S41.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0089

Table S42.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
7P GAIN MUTATED 9 3 25
7P GAIN WILD-TYPE 96 72 90

Figure S42.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00475 (Fisher's exact test), Q value = 0.039

Table S43.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
7P GAIN MUTATED 9 4 21
7P GAIN WILD-TYPE 92 75 81

Figure S43.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.022

Table S44.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
7Q GAIN MUTATED 1 19 10 0 8
7Q GAIN WILD-TYPE 14 93 46 59 45

Figure S44.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.012

Table S45.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
7Q GAIN MUTATED 10 3 25
7Q GAIN WILD-TYPE 95 72 90

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

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.016

Table S46.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
7Q GAIN MUTATED 11 3 22
7Q GAIN WILD-TYPE 90 76 80

Figure S46.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.17

Table S47.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
7Q GAIN MUTATED 2 5 21 5 3
7Q GAIN WILD-TYPE 27 74 78 37 30

Figure S47.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S48.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
8P GAIN MUTATED 6 12 22 5 8
8P GAIN WILD-TYPE 9 100 34 54 45

Figure S48.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.15

Table S49.  Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
8P GAIN MUTATED 12 23 5 13
8P GAIN WILD-TYPE 45 75 64 55

Figure S49.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.022

Table S50.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
8Q GAIN MUTATED 7 33 27 9 15
8Q GAIN WILD-TYPE 8 79 29 50 38

Figure S50.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S51.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
8Q GAIN MUTATED 7 49 35
8Q GAIN WILD-TYPE 65 66 73

Figure S51.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00607 (Fisher's exact test), Q value = 0.046

Table S52.  Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
8Q GAIN MUTATED 21 34 10 25
8Q GAIN WILD-TYPE 36 64 59 43

Figure S52.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.017

Table S53.  Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
8Q GAIN MUTATED 11 70 9
8Q GAIN WILD-TYPE 61 115 26

Figure S53.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00862 (Fisher's exact test), Q value = 0.058

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
8Q GAIN MUTATED 9 39 21 6 16
8Q GAIN WILD-TYPE 51 56 51 19 27

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

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00213 (Fisher's exact test), Q value = 0.023

Table S55.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
8Q GAIN MUTATED 7 22 39 16 2
8Q GAIN WILD-TYPE 22 57 60 26 31

Figure S55.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.00759 (Fisher's exact test), Q value = 0.053

Table S56.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
9P GAIN MUTATED 1 19 19 6 6
9P GAIN WILD-TYPE 14 93 37 53 47

Figure S56.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.068

Table S57.  Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
9P GAIN MUTATED 6 34 11
9P GAIN WILD-TYPE 66 151 24

Figure S57.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.076

Table S58.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
9P GAIN MUTATED 6 15 15 1 14
9P GAIN WILD-TYPE 54 80 57 24 29

Figure S58.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.018

Table S59.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
9Q GAIN MUTATED 3 21 18 4 4
9Q GAIN WILD-TYPE 12 91 38 55 49

Figure S59.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.043

Table S60.  Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
9Q GAIN MUTATED 4 22 24
9Q GAIN WILD-TYPE 68 93 84

Figure S60.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.078

Table S61.  Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
9Q GAIN MUTATED 11 18 4 17
9Q GAIN WILD-TYPE 46 80 65 51

Figure S61.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0091

Table S62.  Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
9Q GAIN MUTATED 3 37 10
9Q GAIN WILD-TYPE 69 148 25

Figure S62.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.07

Table S63.  Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
9Q GAIN MUTATED 9 15 26
9Q GAIN WILD-TYPE 96 60 89

Figure S63.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.068

Table S64.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
9Q GAIN MUTATED 3 17 14 3 13
9Q GAIN WILD-TYPE 57 78 58 22 30

Figure S64.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0461 (Fisher's exact test), Q value = 0.18

Table S65.  Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
9Q GAIN MUTATED 10 14 23
9Q GAIN WILD-TYPE 91 65 79

Figure S65.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0347 (Fisher's exact test), Q value = 0.15

Table S66.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
9Q GAIN MUTATED 1 13 20 11 2
9Q GAIN WILD-TYPE 28 66 79 31 31

Figure S66.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.1

Table S67.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
11P GAIN MUTATED 1 2 0 2 4
11P GAIN WILD-TYPE 59 93 72 23 39

Figure S67.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00164 (Fisher's exact test), Q value = 0.019

Table S68.  Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
11Q GAIN MUTATED 3 1 4
11Q GAIN WILD-TYPE 69 184 31

Figure S68.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.11

Table S69.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
11Q GAIN MUTATED 2 1 0 1 4
11Q GAIN WILD-TYPE 58 94 72 24 39

Figure S69.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.016

Table S70.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
12P GAIN MUTATED 21 11 9 11
12P GAIN WILD-TYPE 36 87 60 57

Figure S70.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.18

Table S71.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
12Q GAIN MUTATED 2 26 12 6 4
12Q GAIN WILD-TYPE 13 86 44 53 49

Figure S71.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.025

Table S72.  Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
12Q GAIN MUTATED 20 11 9 10
12Q GAIN WILD-TYPE 37 87 60 58

Figure S72.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.087

Table S73.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
13Q GAIN MUTATED 15 6 4
13Q GAIN WILD-TYPE 90 69 111

Figure S73.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.033

Table S74.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
14Q GAIN MUTATED 0 28 9 3 7
14Q GAIN WILD-TYPE 15 84 47 56 46

Figure S74.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.025

Table S75.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
15Q GAIN MUTATED 4 27 12 2 7
15Q GAIN WILD-TYPE 11 85 44 57 46

Figure S75.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.018

Table S76.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
16P GAIN MUTATED 0 24 14 3 4
16P GAIN WILD-TYPE 15 88 42 56 49

Figure S76.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S77.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
16Q GAIN MUTATED 0 23 14 1 2
16Q GAIN WILD-TYPE 15 89 42 58 51

Figure S77.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0072

Table S78.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
17P GAIN MUTATED 0 18 3 1 0
17P GAIN WILD-TYPE 15 94 53 58 53

Figure S78.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.01

Table S79.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
17Q GAIN MUTATED 1 29 6 2 5
17Q GAIN WILD-TYPE 14 83 50 57 48

Figure S79.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.021

Table S80.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
18P GAIN MUTATED 2 21 18 4 4
18P GAIN WILD-TYPE 13 91 38 55 49

Figure S80.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.16

Table S81.  Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
18P GAIN MUTATED 16 18 7 8
18P GAIN WILD-TYPE 41 80 62 60

Figure S81.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0027

Table S82.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
18Q GAIN MUTATED 1 9 17 2 3
18Q GAIN WILD-TYPE 14 103 39 57 50

Figure S82.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.016

Table S83.  Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
18Q GAIN MUTATED 13 12 1 6
18Q GAIN WILD-TYPE 44 86 68 62

Figure S83.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S84.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
19P GAIN MUTATED 0 26 16 2 1
19P GAIN WILD-TYPE 15 86 40 57 52

Figure S84.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S85.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
19Q GAIN MUTATED 3 47 19 2 1
19Q GAIN WILD-TYPE 12 65 37 57 52

Figure S85.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.15

Table S86.  Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
19Q GAIN MUTATED 12 44 14
19Q GAIN WILD-TYPE 60 141 21

Figure S86.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.12

Table S87.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
19Q GAIN MUTATED 7 24 18 11 12
19Q GAIN WILD-TYPE 53 71 54 14 31

Figure S87.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S88.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
20P GAIN MUTATED 1 53 26 9 12
20P GAIN WILD-TYPE 14 59 30 50 41

Figure S88.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.1

Table S89.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
20P GAIN MUTATED 32 42 27
20P GAIN WILD-TYPE 40 73 81

Figure S89.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.075

Table S90.  Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
20P GAIN MUTATED 10 14 16 7 13
20P GAIN WILD-TYPE 22 33 29 16 4

Figure S90.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.0436 (Fisher's exact test), Q value = 0.18

Table S91.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
20P GAIN MUTATED 44 27 30
20P GAIN WILD-TYPE 61 48 85

Figure S91.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.092

Table S92.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
20P GAIN MUTATED 45 27 26
20P GAIN WILD-TYPE 56 52 76

Figure S92.  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 = 0.00048

Table S93.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
20Q GAIN MUTATED 1 55 29 9 20
20Q GAIN WILD-TYPE 14 57 27 50 33

Figure S93.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.15

Table S94.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
20Q GAIN MUTATED 37 42 35
20Q GAIN WILD-TYPE 35 73 73

Figure S94.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.021

Table S95.  Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
20Q GAIN MUTATED 10 13 20 8 14
20Q GAIN WILD-TYPE 22 34 25 15 3

Figure S95.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.18

Table S96.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
20Q GAIN MUTATED 37 66 11
20Q GAIN WILD-TYPE 35 119 24

Figure S96.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.13

Table S97.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
20Q GAIN MUTATED 30 32 23 15 14
20Q GAIN WILD-TYPE 30 63 49 10 29

Figure S97.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.075

Table S98.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
20Q GAIN MUTATED 51 27 32
20Q GAIN WILD-TYPE 50 52 70

Figure S98.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.094

Table S99.  Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
21Q GAIN MUTATED 9 19 6 3
21Q GAIN WILD-TYPE 48 79 63 65

Figure S99.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0047

Table S100.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
22Q GAIN MUTATED 15 5 3 6
22Q GAIN WILD-TYPE 42 93 66 62

Figure S100.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.15

Table S101.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
XP GAIN MUTATED 8 23 9
XP GAIN WILD-TYPE 64 92 99

Figure S101.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.13

Table S102.  Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
XP GAIN MUTATED 5 33 2
XP GAIN WILD-TYPE 67 152 33

Figure S102.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0454 (Fisher's exact test), Q value = 0.18

Table S103.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
XQ GAIN MUTATED 9 24 10
XQ GAIN WILD-TYPE 63 91 98

Figure S103.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0062

Table S104.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
1P LOSS MUTATED 2 0 2 9
1P LOSS WILD-TYPE 55 98 67 59

Figure S104.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.099

Table S105.  Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
1P LOSS MUTATED 3 5 5
1P LOSS WILD-TYPE 69 180 30

Figure S105.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.15

Table S106.  Gene #43: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
1Q LOSS MUTATED 1 1 1 6
1Q LOSS WILD-TYPE 56 97 68 62

Figure S106.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.088

Table S107.  Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
2P LOSS MUTATED 1 6 9 1 1
2P LOSS WILD-TYPE 14 106 47 58 52

Figure S107.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.1

Table S108.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
2Q LOSS MUTATED 2 10 14 4 4
2Q LOSS WILD-TYPE 13 102 42 55 49

Figure S108.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.025

Table S109.  Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
2Q LOSS MUTATED 3 21 3 7
2Q LOSS WILD-TYPE 54 77 66 61

Figure S109.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.14

Table S110.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
2Q LOSS MUTATED 3 16 10 4 1
2Q LOSS WILD-TYPE 57 79 62 21 42

Figure S110.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S111.  Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
3P LOSS MUTATED 9 29 15 0 24
3P LOSS WILD-TYPE 6 83 41 59 29

Figure S111.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00577 (Fisher's exact test), Q value = 0.044

Table S112.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
3P LOSS MUTATED 10 40 27
3P LOSS WILD-TYPE 62 75 81

Figure S112.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.074

Table S113.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
3P LOSS MUTATED 18 29 8 21
3P LOSS WILD-TYPE 39 69 61 47

Figure S113.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0055

Table S114.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
3P LOSS MUTATED 7 62 7
3P LOSS WILD-TYPE 65 123 28

Figure S114.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.071

Table S115.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
3P LOSS MUTATED 18 19 40
3P LOSS WILD-TYPE 87 56 75

Figure S115.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.028

Table S116.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
3P LOSS MUTATED 5 33 22 7 10
3P LOSS WILD-TYPE 55 62 50 18 33

Figure S116.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.071

Table S117.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
3P LOSS MUTATED 17 20 36
3P LOSS WILD-TYPE 84 59 66

Figure S117.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00153 (Fisher's exact test), Q value = 0.019

Table S118.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
3P LOSS MUTATED 3 20 31 17 2
3P LOSS WILD-TYPE 26 59 68 25 31

Figure S118.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.082

Table S119.  Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
3Q LOSS MUTATED 2 5 1 0 6
3Q LOSS WILD-TYPE 13 107 55 59 47

Figure S119.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.13

Table S120.  Gene #47: '3q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
3Q LOSS MUTATED 1 1 3 5 0
3Q LOSS WILD-TYPE 31 46 42 18 17

Figure S120.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.11

Table S121.  Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
3Q LOSS MUTATED 4 1 2 7
3Q LOSS WILD-TYPE 53 97 67 61

Figure S121.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.047

Table S122.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
3Q LOSS MUTATED 0 1 4 7 1
3Q LOSS WILD-TYPE 29 78 95 35 32

Figure S122.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S123.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
4P LOSS MUTATED 5 76 28 7 14
4P LOSS WILD-TYPE 10 36 28 52 39

Figure S123.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.0436 (Fisher's exact test), Q value = 0.18

Table S124.  Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
4P LOSS MUTATED 23 58 49
4P LOSS WILD-TYPE 49 57 59

Figure S124.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00633 (Fisher's exact test), Q value = 0.047

Table S125.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
4P LOSS MUTATED 29 50 18 31
4P LOSS WILD-TYPE 28 48 51 37

Figure S125.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00228 (Fisher's exact test), Q value = 0.024

Table S126.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
4P LOSS MUTATED 20 87 21
4P LOSS WILD-TYPE 52 98 14

Figure S126.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.016

Table S127.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
4P LOSS MUTATED 13 51 31 12 23
4P LOSS WILD-TYPE 47 44 41 13 20

Figure S127.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00571 (Fisher's exact test), Q value = 0.044

Table S128.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
4P LOSS MUTATED 9 37 52 19 6
4P LOSS WILD-TYPE 20 42 47 23 27

Figure S128.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S129.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
4Q LOSS MUTATED 3 65 23 3 1
4Q LOSS WILD-TYPE 12 47 33 56 52

Figure S129.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.094

Table S130.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
4Q LOSS MUTATED 21 55 19
4Q LOSS WILD-TYPE 51 130 16

Figure S130.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.18

Table S131.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
4Q LOSS MUTATED 15 32 20 6 22
4Q LOSS WILD-TYPE 45 63 52 19 21

Figure S131.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0013

Table S132.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
5Q LOSS MUTATED 1 34 6 3 5
5Q LOSS WILD-TYPE 14 78 50 56 48

Figure S132.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.075

Table S133.  Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
6P LOSS MUTATED 1 16 12 3 14
6P LOSS WILD-TYPE 14 96 44 56 39

Figure S133.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.17

Table S134.  Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
6P LOSS MUTATED 6 25 15
6P LOSS WILD-TYPE 66 90 93

Figure S134.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.17

Table S135.  Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
6P LOSS MUTATED 5 36 5
6P LOSS WILD-TYPE 67 149 30

Figure S135.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0041

Table S136.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
6Q LOSS MUTATED 4 31 15 3 21
6Q LOSS WILD-TYPE 11 81 41 56 32

Figure S136.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.11

Table S137.  Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
6Q LOSS MUTATED 10 36 28
6Q LOSS WILD-TYPE 62 79 80

Figure S137.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.14

Table S138.  Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
6Q LOSS MUTATED 10 54 10
6Q LOSS WILD-TYPE 62 131 25

Figure S138.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.15

Table S139.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
6Q LOSS MUTATED 8 28 17 11 10
6Q LOSS WILD-TYPE 52 67 55 14 33

Figure S139.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00862 (Fisher's exact test), Q value = 0.058

Table S140.  Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
7P LOSS MUTATED 13 8 5
7P LOSS WILD-TYPE 59 107 103

Figure S140.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.17

Table S141.  Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
7Q LOSS MUTATED 15 12 9
7Q LOSS WILD-TYPE 57 103 99

Figure S141.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S142.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
8P LOSS MUTATED 1 51 5 13 12
8P LOSS WILD-TYPE 14 61 51 46 41

Figure S142.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.09

Table S143.  Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
8P LOSS MUTATED 19 18 18 27
8P LOSS WILD-TYPE 38 80 51 41

Figure S143.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.1

Table S144.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
8P LOSS MUTATED 28 13 41
8P LOSS WILD-TYPE 77 62 74

Figure S144.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0439 (Fisher's exact test), Q value = 0.18

Table S145.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
8P LOSS MUTATED 19 22 14 8 19
8P LOSS WILD-TYPE 41 73 58 17 24

Figure S145.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00685 (Fisher's exact test), Q value = 0.05

Table S146.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
8P LOSS MUTATED 31 13 38
8P LOSS WILD-TYPE 70 66 64

Figure S146.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.019

Table S147.  Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
8Q LOSS MUTATED 0 18 0 5 2
8Q LOSS WILD-TYPE 15 94 56 54 51

Figure S147.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S148.  Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
8Q LOSS MUTATED 16 2 7
8Q LOSS WILD-TYPE 56 113 101

Figure S148.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.002

Table S149.  Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
8Q LOSS MUTATED 6 0 12 7
8Q LOSS WILD-TYPE 51 98 57 61

Figure S149.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.001

Table S150.  Gene #57: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
8Q LOSS MUTATED 16 5 4
8Q LOSS WILD-TYPE 56 180 31

Figure S150.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.00721 (Fisher's exact test), Q value = 0.051

Table S151.  Gene #57: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
8Q LOSS MUTATED 16 2 7
8Q LOSS WILD-TYPE 89 73 108

Figure S151.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0013

Table S152.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
8Q LOSS MUTATED 14 3 1 2 5
8Q LOSS WILD-TYPE 46 92 71 23 38

Figure S152.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00607 (Fisher's exact test), Q value = 0.046

Table S153.  Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
8Q LOSS MUTATED 16 2 7
8Q LOSS WILD-TYPE 85 77 95

Figure S153.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00825 (Fisher's exact test), Q value = 0.056

Table S154.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
8Q LOSS MUTATED 5 2 7 4 7
8Q LOSS WILD-TYPE 24 77 92 38 26

Figure S154.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.017

Table S155.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
9P LOSS MUTATED 2 34 6 5 6
9P LOSS WILD-TYPE 13 78 50 54 47

Figure S155.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.083

Table S156.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
9Q LOSS MUTATED 1 29 8 5 5
9Q LOSS WILD-TYPE 14 83 48 54 48

Figure S156.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.069

Table S157.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
9Q LOSS MUTATED 25 10 10
9Q LOSS WILD-TYPE 76 69 92

Figure S157.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 0.00271 (Fisher's exact test), Q value = 0.026

Table S158.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
10P LOSS MUTATED 3 36 15 6 6
10P LOSS WILD-TYPE 12 76 41 53 47

Figure S158.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.035

Table S159.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
10Q LOSS MUTATED 2 40 15 7 9
10Q LOSS WILD-TYPE 13 72 41 52 44

Figure S159.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S160.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
11P LOSS MUTATED 1 46 26 6 21
11P LOSS WILD-TYPE 14 66 30 53 32

Figure S160.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.12

Table S161.  Gene #62: '11p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 41 64
11P LOSS MUTATED 11 18 18
11P LOSS WILD-TYPE 48 23 46

Figure S161.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.12

Table S162.  Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
11P LOSS MUTATED 5 9 16 8 9
11P LOSS WILD-TYPE 27 38 29 15 8

Figure S162.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.15

Table S163.  Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
11P LOSS MUTATED 24 37 14 25
11P LOSS WILD-TYPE 33 61 55 43

Figure S163.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.1

Table S164.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
11P LOSS MUTATED 10 29 42 12 4
11P LOSS WILD-TYPE 19 50 57 30 29

Figure S164.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S165.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
11Q LOSS MUTATED 0 42 34 13 26
11Q LOSS WILD-TYPE 15 70 22 46 27

Figure S165.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00803 (Fisher's exact test), Q value = 0.055

Table S166.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
11Q LOSS MUTATED 17 50 29 8 11
11Q LOSS WILD-TYPE 43 45 43 17 32

Figure S166.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.014

Table S167.  Gene #64: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
12P LOSS MUTATED 2 4 6 10 0
12P LOSS WILD-TYPE 30 43 39 13 17

Figure S167.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.095

Table S168.  Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
12Q LOSS MUTATED 4 10 1
12Q LOSS WILD-TYPE 68 105 107

Figure S168.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S169.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
13Q LOSS MUTATED 2 43 15 2 18
13Q LOSS WILD-TYPE 13 69 41 57 35

Figure S169.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.078

Table S170.  Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
13Q LOSS MUTATED 19 24 10 25
13Q LOSS WILD-TYPE 38 74 59 43

Figure S170.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 0.13

Table S171.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
13Q LOSS MUTATED 12 52 14
13Q LOSS WILD-TYPE 60 133 21

Figure S171.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.094

Table S172.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
13Q LOSS MUTATED 22 16 42
13Q LOSS WILD-TYPE 83 59 73

Figure S172.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.022

Table S173.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
13Q LOSS MUTATED 7 29 16 12 16
13Q LOSS WILD-TYPE 53 66 56 13 27

Figure S173.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 0.18

Table S174.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
13Q LOSS MUTATED 8 21 30 13 2
13Q LOSS WILD-TYPE 21 58 69 29 31

Figure S174.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.05 (Fisher's exact test), Q value = 0.19

Table S175.  Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
15Q LOSS MUTATED 1 23 13 4 6
15Q LOSS WILD-TYPE 14 89 43 55 47

Figure S175.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.17

Table S176.  Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
16P LOSS MUTATED 11 5 7 9
16P LOSS WILD-TYPE 46 93 62 59

Figure S176.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.07

Table S177.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
16P LOSS MUTATED 6 10 2 6 8
16P LOSS WILD-TYPE 54 85 70 19 35

Figure S177.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00793 (Fisher's exact test), Q value = 0.055

Table S178.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
16Q LOSS MUTATED 19 12 12
16Q LOSS WILD-TYPE 53 103 96

Figure S178.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00491 (Fisher's exact test), Q value = 0.04

Table S179.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
16Q LOSS MUTATED 11 8 18 6
16Q LOSS WILD-TYPE 46 90 51 62

Figure S179.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00249 (Fisher's exact test), Q value = 0.025

Table S180.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
16Q LOSS MUTATED 20 20 3
16Q LOSS WILD-TYPE 52 165 32

Figure S180.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.069

Table S181.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
16Q LOSS MUTATED 24 9 10
16Q LOSS WILD-TYPE 81 66 105

Figure S181.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.025

Table S182.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
16Q LOSS MUTATED 16 12 3 6 6
16Q LOSS WILD-TYPE 44 83 69 19 37

Figure S182.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.17

Table S183.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
16Q LOSS MUTATED 22 11 9
16Q LOSS WILD-TYPE 79 68 93

Figure S183.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.008

Table S184.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
16Q LOSS MUTATED 4 6 14 4 14
16Q LOSS WILD-TYPE 25 73 85 38 19

Figure S184.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00432 (Fisher's exact test), Q value = 0.037

Table S185.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
17P LOSS MUTATED 4 46 20 8 16
17P LOSS WILD-TYPE 11 66 36 51 37

Figure S185.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.15

Table S186.  Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
17P LOSS MUTATED 19 47 28
17P LOSS WILD-TYPE 53 68 80

Figure S186.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.18

Table S187.  Gene #71: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 41 64
17P LOSS MUTATED 19 15 11
17P LOSS WILD-TYPE 40 26 53

Figure S187.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.078

Table S188.  Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
17Q LOSS MUTATED 2 13 12 1 6
17Q LOSS WILD-TYPE 13 99 44 58 47

Figure S188.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.1

Table S189.  Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
17Q LOSS MUTATED 5 21 8
17Q LOSS WILD-TYPE 67 94 100

Figure S189.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 0.00733 (Fisher's exact test), Q value = 0.052

Table S190.  Gene #72: '17q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 41 64
17Q LOSS MUTATED 10 3 1
17Q LOSS WILD-TYPE 49 38 63

Figure S190.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.084

Table S191.  Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
18P LOSS MUTATED 7 11 18 18
18P LOSS WILD-TYPE 50 87 51 50

Figure S191.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0033

Table S192.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
18P LOSS MUTATED 1 8 18 13 14
18P LOSS WILD-TYPE 28 71 81 29 19

Figure S192.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.016

Table S193.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
18Q LOSS MUTATED 1 40 5 14 13
18Q LOSS WILD-TYPE 14 72 51 45 40

Figure S193.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00957 (Fisher's exact test), Q value = 0.063

Table S194.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 115 108
18Q LOSS MUTATED 27 20 26
18Q LOSS WILD-TYPE 45 95 82

Figure S194.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S195.  Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
18Q LOSS MUTATED 14 9 26 24
18Q LOSS WILD-TYPE 43 89 43 44

Figure S195.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.016

Table S196.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
18Q LOSS MUTATED 27 33 13
18Q LOSS WILD-TYPE 45 152 22

Figure S196.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0055

Table S197.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
18Q LOSS MUTATED 25 15 11 5 17
18Q LOSS WILD-TYPE 35 80 61 20 26

Figure S197.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.093

Table S198.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
18Q LOSS MUTATED 34 12 27
18Q LOSS WILD-TYPE 67 67 75

Figure S198.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00075

Table S199.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
18Q LOSS MUTATED 4 10 23 17 19
18Q LOSS WILD-TYPE 25 69 76 25 14

Figure S199.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S200.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
19P LOSS MUTATED 2 40 4 1 13
19P LOSS WILD-TYPE 13 72 52 58 40

Figure S200.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0074

Table S201.  Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
19P LOSS MUTATED 13 8 16 23
19P LOSS WILD-TYPE 44 90 53 45

Figure S201.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.018

Table S202.  Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
19P LOSS MUTATED 17 28 15
19P LOSS WILD-TYPE 55 157 20

Figure S202.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0096

Table S203.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
19P LOSS MUTATED 13 16 6 11 14
19P LOSS WILD-TYPE 47 79 66 14 29

Figure S203.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.18

Table S204.  Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
19P LOSS MUTATED 25 9 25
19P LOSS WILD-TYPE 76 70 77

Figure S204.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.029

Table S205.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
19Q LOSS MUTATED 0 15 3 1 11
19Q LOSS WILD-TYPE 15 97 53 58 42

Figure S205.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.094

Table S206.  Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
20P LOSS MUTATED 1 5 5 11
20P LOSS WILD-TYPE 56 93 64 57

Figure S206.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00463 (Fisher's exact test), Q value = 0.038

Table S207.  Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 79 102
20P LOSS MUTATED 3 3 15
20P LOSS WILD-TYPE 98 76 87

Figure S207.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00441 (Fisher's exact test), Q value = 0.037

Table S208.  Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
20P LOSS MUTATED 1 3 4 9 4
20P LOSS WILD-TYPE 28 76 95 33 29

Figure S208.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.01

Table S209.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
21Q LOSS MUTATED 1 32 8 5 3
21Q LOSS WILD-TYPE 14 80 48 54 50

Figure S209.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 0.12

Table S210.  Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 47 45 23 17
21Q LOSS MUTATED 6 5 2 4 6
21Q LOSS WILD-TYPE 26 42 43 19 11

Figure S210.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00879 (Fisher's exact test), Q value = 0.059

Table S211.  Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 98 69 68
21Q LOSS MUTATED 14 8 10 17
21Q LOSS WILD-TYPE 43 90 59 51

Figure S211.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00442 (Fisher's exact test), Q value = 0.037

Table S212.  Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
21Q LOSS MUTATED 12 24 13
21Q LOSS WILD-TYPE 60 161 22

Figure S212.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.12

Table S213.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 95 72 25 43
21Q LOSS MUTATED 8 13 8 9 11
21Q LOSS WILD-TYPE 52 82 64 16 32

Figure S213.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.035

Table S214.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 112 56 59 53
22Q LOSS MUTATED 2 39 14 6 10
22Q LOSS WILD-TYPE 13 73 42 53 43

Figure S214.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.1

Table S215.  Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 185 35
22Q LOSS MUTATED 21 36 14
22Q LOSS WILD-TYPE 51 149 21

Figure S215.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.00243 (Fisher's exact test), Q value = 0.025

Table S216.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 105 75 115
XP LOSS MUTATED 21 8 36
XP LOSS WILD-TYPE 84 67 79

Figure S216.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.071

Table S217.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 79 99 42 33
XP LOSS MUTATED 8 8 27 14 6
XP LOSS WILD-TYPE 21 71 72 28 27

Figure S217.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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/CESC-TP/22507939/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/22541064/CESC-TP.transferedmergedcluster.txt

  • Number of patients = 295

  • Number of significantly arm-level cnvs = 82

  • 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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