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 8 molecular subtypes across 370 patients, 257 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 2p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

  • 2q gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • 3q gain cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 7q gain cnv correlated to 'METHLYATION_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 10q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 13q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 16q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 18q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

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

  • 22q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • xp gain cnv correlated to 'CN_CNMF'.

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

  • 1p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 3q loss cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 5p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 7p loss cnv correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 8q loss cnv correlated to 'CN_CNMF'.

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

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

  • 10p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

  • 15q loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 18p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 20q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

  • xp loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • xq loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 257 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		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
1p loss 81 (22%) 289 0.00269
(0.0157) 		1e-05
(0.000173) 		1e-05
(0.000173) 		1e-05
(0.000173) 		0.00399
(0.0199) 		0.00754
(0.0315) 		0.00048
(0.00437) 		0.00447
(0.0217)
13q loss 122 (33%) 248 0.00025
(0.00278) 		0.0359
(0.098) 		0.00676
(0.0288) 		0.0003
(0.00317) 		0.00272
(0.0157) 		0.00494
(0.023) 		0.0203
(0.0648) 		0.00123
(0.00849)
16p loss 109 (29%) 261 2e-05
(0.00032) 		5e-05
(0.000729) 		1e-05
(0.000173) 		1e-05
(0.000173) 		0.00401
(0.0199) 		1e-05
(0.000173) 		1e-05
(0.000173) 		1e-05
(0.000173)
19p gain 56 (15%) 314 0.585
(0.692) 		0.00392
(0.0199) 		0.00104
(0.00767) 		0.00846
(0.0349) 		0.0135
(0.0491) 		0.00483
(0.023) 		0.00064
(0.00531) 		0.037
(0.0999)
19q gain 72 (19%) 298 0.394
(0.523) 		0.00106
(0.00773) 		0.00227
(0.0138) 		6e-05
(0.00082) 		0.00034
(0.00348) 		0.00099
(0.00753) 		1e-05
(0.000173) 		0.00083
(0.00656)
4q loss 148 (40%) 222 1e-05
(0.000173) 		0.00508
(0.0233) 		1e-05
(0.000173) 		0.00083
(0.00656) 		0.248
(0.395) 		0.00532
(0.0239) 		1e-05
(0.000173) 		0.00924
(0.0365)
5q loss 39 (11%) 331 0.0028
(0.0158) 		0.00729
(0.0309) 		0.0231
(0.0703) 		0.00015
(0.00189) 		0.532
(0.641) 		0.0478
(0.124) 		0.00127
(0.00859) 		0.00121
(0.00844)
9p loss 118 (32%) 252 3e-05
(0.000458) 		0.0221
(0.0686) 		0.00034
(0.00348) 		0.00493
(0.023) 		0.108
(0.225) 		0.00924
(0.0365) 		0.0297
(0.085) 		0.0117
(0.0444)
16q loss 145 (39%) 225 1e-05
(0.000173) 		1e-05
(0.000173) 		1e-05
(0.000173) 		1e-05
(0.000173) 		0.17
(0.309) 		1e-05
(0.000173) 		1e-05
(0.000173) 		1e-05
(0.000173)
17p loss 185 (50%) 185 1e-05
(0.000173) 		0.022
(0.0686) 		0.00535
(0.0239) 		0.0232
(0.0703) 		0.00361
(0.0189) 		0.00053
(0.00452) 		0.445
(0.563) 		0.00051
(0.00446)
8q gain 188 (51%) 182 1e-05
(0.000173) 		0.0864
(0.191) 		1e-05
(0.000173) 		1e-05
(0.000173) 		0.0277
(0.0807) 		0.00336
(0.018) 		0.132
(0.26) 		0.00023
(0.00265)
10q gain 37 (10%) 333 0.00101
(0.00753) 		0.0299
(0.0853) 		2e-05
(0.00032) 		0.0723
(0.166) 		0.0664
(0.158) 		0.0438
(0.115) 		0.0367
(0.0999) 		0.0339
(0.0937)
xq gain 64 (17%) 306 0.00108
(0.00779) 		0.0685
(0.162) 		0.00222
(0.0136) 		0.0135
(0.0491) 		0.00634
(0.0274) 		0.00052
(0.00449) 		0.162
(0.299) 		0.00026
(0.00284)
3p loss 52 (14%) 318 0.032
(0.0906) 		0.43
(0.552) 		0.00779
(0.0323) 		0.0095
(0.0373) 		0.00747
(0.0314) 		0.32
(0.45) 		0.00115
(0.00811) 		0.0494
(0.126)
4p loss 107 (29%) 263 1e-05
(0.000173) 		0.0595
(0.145) 		0.001
(0.00753) 		0.0141
(0.0507) 		0.988
(0.988) 		0.0178
(0.0605) 		0.00482
(0.023) 		0.00281
(0.0158)
9q loss 107 (29%) 263 0.00037
(0.00368) 		0.0124
(0.0465) 		0.0121
(0.0456) 		0.00324
(0.0176) 		0.269
(0.413) 		0.0162
(0.0561) 		0.117
(0.235) 		0.00139
(0.00921)
1q gain 222 (60%) 148 1e-05
(0.000173) 		7e-05
(0.000918) 		1e-05
(0.000173) 		0.0003
(0.00317) 		0.156
(0.291) 		0.00493
(0.023) 		0.416
(0.538) 		0.0534
(0.135)
6p gain 117 (32%) 253 1e-05
(0.000173) 		0.00231
(0.0139) 		0.00546
(0.0242) 		0.0273
(0.0801) 		0.145
(0.276) 		0.00252
(0.015) 		0.322
(0.452) 		0.105
(0.221)
8p gain 80 (22%) 290 3e-05
(0.000458) 		0.249
(0.395) 		0.0208
(0.0655) 		0.0357
(0.098) 		0.0108
(0.0416) 		0.115
(0.235) 		0.147
(0.28) 		0.0157
(0.0551)
10p gain 61 (16%) 309 0.00041
(0.0039) 		0.428
(0.552) 		0.00382
(0.0199) 		0.0209
(0.0656) 		0.275
(0.415) 		0.418
(0.539) 		0.0222
(0.0686) 		0.0184
(0.0619)
12p gain 41 (11%) 329 0.0164
(0.0561) 		0.308
(0.44) 		0.0114
(0.0436) 		0.00064
(0.00531) 		0.788
(0.841) 		0.367
(0.502) 		0.00144
(0.00942) 		0.0243
(0.0718)
17q gain 95 (26%) 275 0.00148
(0.00952) 		0.0455
(0.118) 		0.237
(0.387) 		0.121
(0.243) 		0.0197
(0.0639) 		0.00043
(0.00403) 		0.609
(0.712) 		0.0237
(0.0705)
20p gain 108 (29%) 262 1e-05
(0.000173) 		0.181
(0.318) 		0.0329
(0.0918) 		0.00217
(0.0134) 		0.171
(0.31) 		0.0323
(0.0909) 		6e-05
(0.00082) 		0.0746
(0.171)
10p loss 45 (12%) 325 0.0235
(0.0704) 		0.225
(0.372) 		0.00089
(0.00687) 		0.00282
(0.0158) 		0.611
(0.712) 		0.00653
(0.028) 		0.392
(0.522) 		0.0199
(0.0642)
10q loss 76 (21%) 294 0.00871
(0.0354) 		0.0932
(0.2) 		1e-05
(0.000173) 		1e-05
(0.000173) 		0.316
(0.448) 		4e-05
(0.000596) 		0.45
(0.567) 		1e-05
(0.000173)
14q loss 107 (29%) 263 1e-05
(0.000173) 		0.164
(0.3) 		2e-05
(0.00032) 		1e-05
(0.000173) 		0.48
(0.591) 		0.176
(0.315) 		0.00025
(0.00278) 		0.0158
(0.0551)
3p gain 35 (9%) 335 0.037
(0.0999) 		0.0449
(0.118) 		0.00272
(0.0157) 		0.0903
(0.196) 		0.134
(0.261) 		0.518
(0.631) 		0.0235
(0.0704) 		0.253
(0.396)
4p gain 27 (7%) 343 0.0145
(0.0516) 		0.014
(0.0506) 		0.00532
(0.0239) 		0.00137
(0.00917) 		0.299
(0.435) 		0.444
(0.563) 		0.0687
(0.162) 		0.206
(0.349)
12q gain 47 (13%) 323 0.0231
(0.0703) 		0.483
(0.593) 		0.0133
(0.049) 		0.00269
(0.0157) 		0.343
(0.477) 		0.622
(0.721) 		0.00051
(0.00446) 		0.0704
(0.164)
22q gain 48 (13%) 322 1e-05
(0.000173) 		0.246
(0.395) 		0.0459
(0.119) 		0.00198
(0.0126) 		0.611
(0.712) 		0.737
(0.804) 		0.00204
(0.0129) 		0.135
(0.262)
5p loss 28 (8%) 342 0.0243
(0.0718) 		0.215
(0.36) 		0.0561
(0.14) 		0.0164
(0.0561) 		0.263
(0.406) 		0.1
(0.212) 		0.00911
(0.0364) 		0.0186
(0.0619)
11p loss 65 (18%) 305 0.461
(0.578) 		0.984
(0.985) 		0.0199
(0.0642) 		0.00457
(0.022) 		0.645
(0.737) 		0.176
(0.315) 		0.00125
(0.00854) 		0.00555
(0.0244)
15q loss 67 (18%) 303 0.0578
(0.142) 		0.0658
(0.157) 		6e-05
(0.00082) 		7e-05
(0.000918) 		0.154
(0.288) 		0.249
(0.395) 		1e-05
(0.000173) 		0.018
(0.0608)
1p gain 57 (15%) 313 0.292
(0.43) 		0.209
(0.353) 		0.0292
(0.0841) 		0.38
(0.512) 		0.967
(0.976) 		0.0393
(0.105) 		0.111
(0.23) 		0.0227
(0.0698)
2q gain 41 (11%) 329 0.0855
(0.19) 		0.294
(0.43) 		0.0133
(0.049) 		0.00045
(0.00416) 		0.695
(0.778) 		0.763
(0.823) 		0.00338
(0.018) 		0.373
(0.505)
18q gain 28 (8%) 342 0.0194
(0.0633) 		0.629
(0.725) 		0.0569
(0.141) 		0.00302
(0.0165) 		0.83
(0.879) 		0.0537
(0.135) 		0.0191
(0.063) 		0.283
(0.423)
20q gain 112 (30%) 258 1e-05
(0.000173) 		0.191
(0.332) 		0.177
(0.315) 		0.00864
(0.0354) 		0.306
(0.439) 		0.0748
(0.171) 		8e-05
(0.00103) 		0.0876
(0.192)
7q loss 21 (6%) 349 0.435
(0.556) 		0.263
(0.406) 		0.0898
(0.196) 		0.0846
(0.19) 		0.563
(0.67) 		0.0261
(0.0768) 		0.00017
(0.00207) 		0.00507
(0.0233)
8p loss 190 (51%) 180 0.00021
(0.00246) 		0.0638
(0.153) 		0.0194
(0.0633) 		0.851
(0.893) 		0.244
(0.395) 		0.0291
(0.0841) 		0.449
(0.567) 		0.438
(0.558)
18p loss 74 (20%) 296 0.0485
(0.124) 		0.0114
(0.0436) 		0.715
(0.785) 		0.00285
(0.0158) 		0.528
(0.638) 		0.713
(0.785) 		0.0681
(0.161) 		0.224
(0.371)
18q loss 79 (21%) 291 0.00416
(0.0205) 		0.004
(0.0199) 		0.646
(0.737) 		0.00041
(0.0039) 		0.205
(0.349) 		0.403
(0.53) 		0.116
(0.235) 		0.304
(0.438)
19p loss 55 (15%) 315 1e-05
(0.000173) 		0.556
(0.664) 		0.0324
(0.091) 		0.1
(0.212) 		0.15
(0.283) 		0.0815
(0.184) 		0.282
(0.423) 		0.0036
(0.0189)
xp loss 94 (25%) 276 0.0333
(0.0925) 		0.0571
(0.141) 		0.18
(0.318) 		0.0202
(0.0647) 		0.125
(0.247) 		0.232
(0.38) 		0.0044
(0.0215) 		0.287
(0.425)
2p gain 44 (12%) 326 0.161
(0.296) 		0.284
(0.424) 		0.115
(0.234) 		0.00036
(0.00363) 		0.55
(0.658) 		0.94
(0.953) 		0.00895
(0.036) 		0.383
(0.513)
3q gain 38 (10%) 332 0.298
(0.434) 		0.135
(0.263) 		0.0039
(0.0199) 		0.0921
(0.199) 		0.213
(0.359) 		0.51
(0.622) 		0.0151
(0.0534) 		0.611
(0.712)
6q gain 67 (18%) 303 0.0007
(0.00567) 		0.159
(0.295) 		0.038
(0.102) 		0.602
(0.707) 		0.204
(0.349) 		0.187
(0.327) 		0.205
(0.349) 		0.388
(0.519)
7p gain 111 (30%) 259 0.0452
(0.118) 		0.0847
(0.19) 		0.983
(0.985) 		0.904
(0.933) 		0.0436
(0.115) 		0.0714
(0.166) 		0.257
(0.399) 		0.335
(0.468)
11p gain 17 (5%) 353 0.471
(0.582) 		0.294
(0.43) 		0.439
(0.558) 		0.0484
(0.124) 		0.303
(0.438) 		0.468
(0.581) 		0.0153
(0.0539) 		0.273
(0.415)
18p gain 36 (10%) 334 0.0234
(0.0704) 		0.218
(0.364) 		0.0599
(0.145) 		0.0187
(0.0619) 		0.768
(0.824) 		0.193
(0.336) 		0.0871
(0.192) 		0.457
(0.574)
2p loss 33 (9%) 337 0.0592
(0.144) 		0.711
(0.785) 		0.0105
(0.0406) 		0.0393
(0.105) 		0.376
(0.507) 		0.71
(0.785) 		0.2
(0.344) 		0.267
(0.412)
2q loss 38 (10%) 332 0.188
(0.327) 		0.603
(0.707) 		0.0103
(0.0401) 		0.0205
(0.0651) 		0.256
(0.399) 		0.593
(0.7) 		0.6
(0.706) 		0.405
(0.531)
3q loss 40 (11%) 330 0.328
(0.459) 		0.667
(0.753) 		0.0187
(0.0619) 		0.069
(0.162) 		0.0779
(0.177) 		0.316
(0.448) 		0.00525
(0.0239) 		0.275
(0.415)
7p loss 16 (4%) 354 0.365
(0.501) 		0.288
(0.426) 		0.0559
(0.14) 		0.351
(0.485) 		0.879
(0.913) 		0.226
(0.373) 		0.00578
(0.0253) 		0.04
(0.106)
11q loss 73 (20%) 297 0.141
(0.271) 		0.78
(0.835) 		0.195
(0.338) 		0.123
(0.245) 		0.663
(0.751) 		0.304
(0.438) 		0.00297
(0.0164) 		0.0161
(0.056)
12p loss 65 (18%) 305 0.00085
(0.00664) 		0.116
(0.235) 		0.028
(0.0814) 		0.273
(0.415) 		0.408
(0.532) 		0.164
(0.3) 		0.624
(0.721) 		0.431
(0.552)
19q loss 39 (11%) 331 1e-05
(0.000173) 		0.382
(0.513) 		0.114
(0.233) 		0.582
(0.692) 		0.0311
(0.0882) 		0.153
(0.288) 		0.473
(0.583) 		0.247
(0.395)
21q loss 110 (30%) 260 0.0005
(0.00446) 		0.74
(0.806) 		0.00021
(0.00246) 		0.124
(0.247) 		0.495
(0.606) 		0.931
(0.948) 		0.122
(0.245) 		0.308
(0.44)
22q loss 70 (19%) 300 0.0358
(0.098) 		0.0719
(0.166) 		0.00206
(0.0129) 		0.159
(0.295) 		0.505
(0.617) 		0.462
(0.578) 		0.106
(0.222) 		0.874
(0.911)
5p gain 135 (36%) 235 0.00016
(0.00198) 		0.0906
(0.196) 		0.901
(0.931) 		0.802
(0.853) 		0.228
(0.376) 		0.176
(0.315) 		0.302
(0.438) 		0.584
(0.692)
5q gain 107 (29%) 263 0.00394
(0.0199) 		0.126
(0.248) 		0.667
(0.753) 		0.944
(0.956) 		0.644
(0.737) 		0.852
(0.893) 		0.929
(0.947) 		0.891
(0.924)
7q gain 111 (30%) 259 0.373
(0.505) 		0.00069
(0.00566) 		0.964
(0.974) 		0.878
(0.913) 		0.218
(0.364) 		0.208
(0.352) 		0.521
(0.632) 		0.341
(0.475)
13q gain 23 (6%) 347 0.00875
(0.0354) 		0.328
(0.459) 		0.285
(0.424) 		0.409
(0.533) 		0.0795
(0.181) 		0.294
(0.43) 		0.181
(0.318) 		0.213
(0.359)
16p gain 31 (8%) 339 0.175
(0.315) 		0.914
(0.936) 		0.00594
(0.0258) 		0.982
(0.985) 		0.767
(0.824) 		0.252
(0.396) 		0.101
(0.213) 		0.318
(0.449)
16q gain 17 (5%) 353 0.907
(0.934) 		0.0587
(0.144) 		0.0011
(0.00784) 		0.314
(0.447) 		0.125
(0.247) 		0.912
(0.936) 		0.16
(0.296) 		0.706
(0.785)
xp gain 42 (11%) 328 0.00041
(0.0039) 		0.298
(0.434) 		0.0576
(0.142) 		0.653
(0.742) 		0.437
(0.557) 		0.155
(0.289) 		0.984
(0.985) 		0.0537
(0.135)
8q loss 43 (12%) 327 0.00145
(0.00942) 		0.113
(0.232) 		0.271
(0.414) 		0.549
(0.658) 		0.76
(0.822) 		0.935
(0.949) 		0.69
(0.774) 		0.901
(0.931)
20q loss 13 (4%) 357 0.352
(0.485) 		0.205
(0.349) 		0.138
(0.268) 		0.111
(0.23) 		0.466
(0.579) 		0.64
(0.737) 		0.0135
(0.0491) 		0.256
(0.399)
xq loss 70 (19%) 300 0.0125
(0.0465) 		0.141
(0.271) 		0.398
(0.526) 		0.308
(0.44) 		0.133
(0.26) 		0.698
(0.779) 		0.125
(0.247) 		0.746
(0.811)
4q gain 7 (2%) 363 0.799
(0.851) 		0.622
(0.721) 		0.756
(0.821) 		0.406
(0.531) 		0.248
(0.395) 		0.848
(0.893) 		0.276
(0.415) 		0.555
(0.664)
9p gain 19 (5%) 351 0.465
(0.579) 		0.406
(0.531) 		0.854
(0.893) 		0.669
(0.754) 		0.708
(0.785) 		0.401
(0.528) 		0.096
(0.206) 		0.367
(0.502)
9q gain 21 (6%) 349 0.0844
(0.19) 		0.594
(0.7) 		0.249
(0.395) 		0.392
(0.522) 		0.765
(0.824) 		0.414
(0.538) 		0.112
(0.231) 		0.233
(0.381)
11q gain 18 (5%) 352 0.911
(0.936) 		0.782
(0.835) 		0.471
(0.582) 		0.246
(0.395) 		0.369
(0.502) 		0.7
(0.78) 		0.18
(0.318) 		0.345
(0.478)
14q gain 23 (6%) 347 0.45
(0.567) 		0.469
(0.581) 		0.253
(0.396) 		0.152
(0.286) 		0.761
(0.822) 		0.15
(0.283) 		0.0659
(0.157) 		0.651
(0.742)
15q gain 33 (9%) 337 0.646
(0.737) 		0.549
(0.658) 		0.979
(0.985) 		0.719
(0.789) 		0.85
(0.893) 		0.287
(0.425) 		0.529
(0.638) 		0.829
(0.878)
17p gain 30 (8%) 340 0.1
(0.212) 		0.0854
(0.19) 		0.496
(0.607) 		0.0997
(0.212) 		0.396
(0.525) 		0.759
(0.822) 		0.0531
(0.135) 		0.144
(0.276)
21q gain 26 (7%) 344 0.178
(0.316) 		0.81
(0.86) 		0.0701
(0.164) 		0.388
(0.519) 		0.924
(0.944) 		0.222
(0.37) 		0.25
(0.395) 		0.525
(0.635)
1q loss 22 (6%) 348 0.369
(0.502) 		0.852
(0.893) 		0.23
(0.378) 		0.238
(0.387) 		0.356
(0.49) 		0.243
(0.393) 		0.287
(0.425) 		0.0624
(0.151)
6p loss 28 (8%) 342 0.641
(0.737) 		0.77
(0.826) 		0.318
(0.449) 		0.714
(0.785) 		0.679
(0.762) 		0.724
(0.793) 		0.27
(0.413) 		0.242
(0.392)
6q loss 92 (25%) 278 0.188
(0.327) 		0.431
(0.552) 		0.252
(0.396) 		0.734
(0.802) 		0.52
(0.631) 		0.14
(0.27) 		0.671
(0.755) 		0.833
(0.88)
12q loss 36 (10%) 334 0.0881
(0.193) 		0.415
(0.538) 		0.4
(0.528) 		0.66
(0.749) 		0.878
(0.913) 		0.916
(0.937) 		0.699
(0.779) 		0.933
(0.949)
17q loss 39 (11%) 331 0.37
(0.502) 		0.198
(0.342) 		0.35
(0.484) 		0.17
(0.309) 		0.176
(0.315) 		0.625
(0.721) 		0.27
(0.413) 		0.463
(0.578)
20p loss 26 (7%) 344 0.263
(0.406) 		0.275
(0.415) 		0.623
(0.721) 		0.107
(0.223) 		0.0866
(0.191) 		0.855
(0.893) 		0.712
(0.785) 		0.304
(0.438)
'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.084

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
1P GAIN MUTATED 18 10 9 9 9
1P GAIN WILD-TYPE 43 87 59 60 60

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0393 (Fisher's exact test), Q value = 0.1

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
1P GAIN MUTATED 12 8 11 20 5
1P GAIN WILD-TYPE 32 87 45 102 43

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 0.07

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
1P GAIN MUTATED 17 10 13 10 5
1P GAIN WILD-TYPE 50 76 86 25 48

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
1Q GAIN MUTATED 82 87 53
1Q GAIN WILD-TYPE 27 37 84

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00092

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
1Q GAIN MUTATED 36 103 83
1Q GAIN WILD-TYPE 52 64 32

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
1Q GAIN MUTATED 36 40 55 39 47
1Q GAIN WILD-TYPE 25 57 13 30 22

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0032

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
1Q GAIN MUTATED 28 35 52 63 39
1Q GAIN WILD-TYPE 26 21 62 21 17

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00493 (Fisher's exact test), Q value = 0.023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
1Q GAIN MUTATED 27 43 40 73 35
1Q GAIN WILD-TYPE 17 52 16 49 13

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0036

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
2P GAIN MUTATED 13 2 6 16 5
2P GAIN WILD-TYPE 41 54 108 68 51

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00895 (Fisher's exact test), Q value = 0.036

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
2P GAIN MUTATED 18 11 6 6
2P GAIN WILD-TYPE 74 76 113 36

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.049

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
2Q GAIN MUTATED 6 3 13 9 8
2Q GAIN WILD-TYPE 55 94 55 60 61

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0042

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
2Q GAIN MUTATED 10 2 4 16 7
2Q GAIN WILD-TYPE 44 54 110 68 49

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

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00338 (Fisher's exact test), Q value = 0.018

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
2Q GAIN MUTATED 18 9 5 6
2Q GAIN WILD-TYPE 74 78 114 36

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.1

Table S14.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
3P GAIN MUTATED 10 18 7
3P GAIN WILD-TYPE 99 106 130

Figure S14.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.12

Table S15.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
3P GAIN MUTATED 5 23 7
3P GAIN WILD-TYPE 83 144 108

Figure S15.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
3P GAIN MUTATED 10 8 7 0 10
3P GAIN WILD-TYPE 51 89 61 69 59

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

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.07

Table S17.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
3P GAIN MUTATED 12 2 10 6
3P GAIN WILD-TYPE 80 85 109 36

Figure S17.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.02

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
3Q GAIN MUTATED 13 9 6 1 9
3Q GAIN WILD-TYPE 48 88 62 68 60

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

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.053

Table S19.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
3Q GAIN MUTATED 10 3 11 9
3Q GAIN WILD-TYPE 82 84 108 33

Figure S19.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.052

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
4P GAIN MUTATED 6 16 5
4P GAIN WILD-TYPE 103 108 132

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

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.051

Table S21.  Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
4P GAIN MUTATED 6 6 15
4P GAIN WILD-TYPE 82 161 100

Figure S21.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00532 (Fisher's exact test), Q value = 0.024

Table S22.  Gene #7: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
4P GAIN MUTATED 2 6 12 5 1
4P GAIN WILD-TYPE 59 91 56 64 68

Figure S22.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0092

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
4P GAIN MUTATED 5 3 3 14 1
4P GAIN WILD-TYPE 49 53 111 70 55

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

'5p gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.002

Table S24.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
5P GAIN MUTATED 47 56 32
5P GAIN WILD-TYPE 62 68 105

Figure S24.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.02

Table S25.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
5Q GAIN MUTATED 42 38 27
5Q GAIN WILD-TYPE 67 86 110

Figure S25.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S26.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
6P GAIN MUTATED 37 58 22
6P GAIN WILD-TYPE 72 66 115

Figure S26.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.014

Table S27.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
6P GAIN MUTATED 15 61 41
6P GAIN WILD-TYPE 73 106 74

Figure S27.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.024

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
6P GAIN MUTATED 23 22 26 15 31
6P GAIN WILD-TYPE 38 75 42 54 38

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

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.08

Table S29.  Gene #11: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
6P GAIN MUTATED 16 11 32 33 25
6P GAIN WILD-TYPE 38 45 82 51 31

Figure S29.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.015

Table S30.  Gene #11: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
6P GAIN MUTATED 19 18 19 37 23
6P GAIN WILD-TYPE 25 77 37 85 25

Figure S30.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0057

Table S31.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
6Q GAIN MUTATED 24 31 12
6Q GAIN WILD-TYPE 85 93 125

Figure S31.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.1

Table S32.  Gene #12: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
6Q GAIN MUTATED 18 12 14 8 15
6Q GAIN WILD-TYPE 43 85 54 61 54

Figure S32.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.12

Table S33.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
7P GAIN MUTATED 35 45 31
7P GAIN WILD-TYPE 74 79 106

Figure S33.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0436 (Fisher's exact test), Q value = 0.12

Table S34.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
7P GAIN MUTATED 14 49 11 34
7P GAIN WILD-TYPE 51 78 38 90

Figure S34.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0057

Table S35.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
7Q GAIN MUTATED 20 67 24
7Q GAIN WILD-TYPE 68 100 91

Figure S35.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00046

Table S36.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
8P GAIN MUTATED 39 25 16
8P GAIN WILD-TYPE 70 99 121

Figure S36.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.065

Table S37.  Gene #15: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
8P GAIN MUTATED 14 11 13 21 19
8P GAIN WILD-TYPE 47 86 55 48 50

Figure S37.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.098

Table S38.  Gene #15: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
8P GAIN MUTATED 12 14 14 25 13
8P GAIN WILD-TYPE 42 42 100 59 43

Figure S38.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.042

Table S39.  Gene #15: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
8P GAIN MUTATED 5 29 14 31
8P GAIN WILD-TYPE 60 98 35 93

Figure S39.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.055

Table S40.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
8P GAIN MUTATED 17 9 28 7 16
8P GAIN WILD-TYPE 50 77 71 28 37

Figure S40.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S41.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
8Q GAIN MUTATED 97 61 30
8Q GAIN WILD-TYPE 12 63 107

Figure S41.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S42.  Gene #16: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
8Q GAIN MUTATED 37 25 38 38 45
8Q GAIN WILD-TYPE 24 72 30 31 24

Figure S42.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S43.  Gene #16: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
8Q GAIN MUTATED 31 31 33 52 36
8Q GAIN WILD-TYPE 23 25 81 32 20

Figure S43.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.081

Table S44.  Gene #16: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
8Q GAIN MUTATED 22 70 26 67
8Q GAIN WILD-TYPE 43 57 23 57

Figure S44.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00336 (Fisher's exact test), Q value = 0.018

Table S45.  Gene #16: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
8Q GAIN MUTATED 20 34 29 71 31
8Q GAIN WILD-TYPE 24 61 27 51 17

Figure S45.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
8Q GAIN MUTATED 42 29 56 14 35
8Q GAIN WILD-TYPE 25 57 43 21 18

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

'10p gain' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0039

Table S47.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
10P GAIN MUTATED 21 30 10
10P GAIN WILD-TYPE 88 94 127

Figure S47.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00382 (Fisher's exact test), Q value = 0.02

Table S48.  Gene #19: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
10P GAIN MUTATED 9 9 21 7 13
10P GAIN WILD-TYPE 52 88 47 62 56

Figure S48.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.066

Table S49.  Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
10P GAIN MUTATED 11 6 11 22 9
10P GAIN WILD-TYPE 43 50 103 62 47

Figure S49.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.069

Table S50.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
10P GAIN MUTATED 23 12 12 9
10P GAIN WILD-TYPE 69 75 107 33

Figure S50.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.062

Table S51.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
10P GAIN MUTATED 18 7 17 8 6
10P GAIN WILD-TYPE 49 79 82 27 47

Figure S51.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0075

Table S52.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
10Q GAIN MUTATED 16 17 4
10Q GAIN WILD-TYPE 93 107 133

Figure S52.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.085

Table S53.  Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
10Q GAIN MUTATED 3 18 16
10Q GAIN WILD-TYPE 85 149 99

Figure S53.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S54.  Gene #20: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
10Q GAIN MUTATED 1 4 18 4 10
10Q GAIN WILD-TYPE 60 93 50 65 59

Figure S54.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.12

Table S55.  Gene #20: '10q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
10Q GAIN MUTATED 3 4 11 14 5
10Q GAIN WILD-TYPE 41 91 45 108 43

Figure S55.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.1

Table S56.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
10Q GAIN MUTATED 13 6 6 7
10Q GAIN WILD-TYPE 79 81 113 35

Figure S56.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.094

Table S57.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
10Q GAIN MUTATED 11 2 11 3 5
10Q GAIN WILD-TYPE 56 84 88 32 48

Figure S57.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0484 (Fisher's exact test), Q value = 0.12

Table S58.  Gene #21: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
11P GAIN MUTATED 5 2 3 7 0
11P GAIN WILD-TYPE 49 54 111 77 56

Figure S58.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.054

Table S59.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
11P GAIN MUTATED 5 5 1 5
11P GAIN WILD-TYPE 87 82 118 37

Figure S59.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.056

Table S60.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
12P GAIN MUTATED 12 21 8
12P GAIN WILD-TYPE 97 103 129

Figure S60.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.044

Table S61.  Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
12P GAIN MUTATED 12 5 12 8 4
12P GAIN WILD-TYPE 49 92 56 61 65

Figure S61.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0053

Table S62.  Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
12P GAIN MUTATED 14 2 10 13 2
12P GAIN WILD-TYPE 40 54 104 71 54

Figure S62.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0094

Table S63.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
12P GAIN MUTATED 18 10 4 5
12P GAIN WILD-TYPE 74 77 115 37

Figure S63.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 0.072

Table S64.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
12P GAIN MUTATED 13 7 11 5 1
12P GAIN WILD-TYPE 54 79 88 30 52

Figure S64.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.07

Table S65.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
12Q GAIN MUTATED 14 23 10
12Q GAIN WILD-TYPE 95 101 127

Figure S65.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.049

Table S66.  Gene #24: '12q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
12Q GAIN MUTATED 13 7 13 10 4
12Q GAIN WILD-TYPE 48 90 55 59 65

Figure S66.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00269 (Fisher's exact test), Q value = 0.016

Table S67.  Gene #24: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
12Q GAIN MUTATED 14 4 12 15 2
12Q GAIN WILD-TYPE 40 52 102 69 54

Figure S67.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0045

Table S68.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
12Q GAIN MUTATED 21 11 5 6
12Q GAIN WILD-TYPE 71 76 114 36

Figure S68.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.00875 (Fisher's exact test), Q value = 0.035

Table S69.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
13Q GAIN MUTATED 6 14 3
13Q GAIN WILD-TYPE 103 110 134

Figure S69.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00594 (Fisher's exact test), Q value = 0.026

Table S70.  Gene #28: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
16P GAIN MUTATED 8 6 1 12 4
16P GAIN WILD-TYPE 53 91 67 57 65

Figure S70.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0078

Table S71.  Gene #29: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
16Q GAIN MUTATED 2 2 0 10 3
16Q GAIN WILD-TYPE 59 95 68 59 66

Figure S71.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.0095

Table S72.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
17Q GAIN MUTATED 27 45 23
17Q GAIN WILD-TYPE 82 79 114

Figure S72.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.12

Table S73.  Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
17Q GAIN MUTATED 14 47 34
17Q GAIN WILD-TYPE 74 120 81

Figure S73.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.064

Table S74.  Gene #31: '17q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
17Q GAIN MUTATED 21 42 8 24
17Q GAIN WILD-TYPE 44 85 41 100

Figure S74.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.004

Table S75.  Gene #31: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
17Q GAIN MUTATED 22 21 17 20 15
17Q GAIN WILD-TYPE 22 74 39 102 33

Figure S75.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.071

Table S76.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
17Q GAIN MUTATED 23 19 17 14 16
17Q GAIN WILD-TYPE 44 67 82 21 37

Figure S76.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.07

Table S77.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
18P GAIN MUTATED 10 19 7
18P GAIN WILD-TYPE 99 105 130

Figure S77.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.062

Table S78.  Gene #32: '18p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
18P GAIN MUTATED 10 4 7 13 2
18P GAIN WILD-TYPE 44 52 107 71 54

Figure S78.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.063

Table S79.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
18Q GAIN MUTATED 7 16 5
18Q GAIN WILD-TYPE 102 108 132

Figure S79.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00302 (Fisher's exact test), Q value = 0.017

Table S80.  Gene #33: '18q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
18Q GAIN MUTATED 9 4 5 10 0
18Q GAIN WILD-TYPE 45 52 109 74 56

Figure S80.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.063

Table S81.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
18Q GAIN MUTATED 12 9 3 3
18Q GAIN WILD-TYPE 80 78 116 39

Figure S81.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.02

Table S82.  Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
19P GAIN MUTATED 14 15 27
19P GAIN WILD-TYPE 74 152 88

Figure S82.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0077

Table S83.  Gene #34: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
19P GAIN MUTATED 7 11 17 17 3
19P GAIN WILD-TYPE 54 86 51 52 66

Figure S83.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00846 (Fisher's exact test), Q value = 0.035

Table S84.  Gene #34: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
19P GAIN MUTATED 10 11 11 20 3
19P GAIN WILD-TYPE 44 45 103 64 53

Figure S84.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.049

Table S85.  Gene #34: '19p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
19P GAIN MUTATED 6 12 9 28
19P GAIN WILD-TYPE 59 115 40 96

Figure S85.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.023

Table S86.  Gene #34: '19p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
19P GAIN MUTATED 4 12 11 27 1
19P GAIN WILD-TYPE 40 83 45 95 47

Figure S86.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0053

Table S87.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
19P GAIN MUTATED 18 19 6 8
19P GAIN WILD-TYPE 74 68 113 34

Figure S87.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.1

Table S88.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
19P GAIN MUTATED 11 11 23 3 3
19P GAIN WILD-TYPE 56 75 76 32 50

Figure S88.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0077

Table S89.  Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
19Q GAIN MUTATED 16 21 35
19Q GAIN WILD-TYPE 72 146 80

Figure S89.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.014

Table S90.  Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
19Q GAIN MUTATED 10 14 21 20 6
19Q GAIN WILD-TYPE 51 83 47 49 63

Figure S90.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00082

Table S91.  Gene #35: '19q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
19Q GAIN MUTATED 11 15 12 29 4
19Q GAIN WILD-TYPE 43 41 102 55 52

Figure S91.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0035

Table S92.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
19Q GAIN MUTATED 7 14 13 37
19Q GAIN WILD-TYPE 58 113 36 87

Figure S92.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0075

Table S93.  Gene #35: '19q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
19Q GAIN MUTATED 7 13 17 32 2
19Q GAIN WILD-TYPE 37 82 39 90 46

Figure S93.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S94.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
19Q GAIN MUTATED 23 24 7 12
19Q GAIN WILD-TYPE 69 63 112 30

Figure S94.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0066

Table S95.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
19Q GAIN MUTATED 19 12 27 6 2
19Q GAIN WILD-TYPE 48 74 72 29 51

Figure S95.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S96.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
20P GAIN MUTATED 28 58 22
20P GAIN WILD-TYPE 81 66 115

Figure S96.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.092

Table S97.  Gene #36: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
20P GAIN MUTATED 21 23 30 18 16
20P GAIN WILD-TYPE 40 74 38 51 53

Figure S97.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.013

Table S98.  Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
20P GAIN MUTATED 19 15 26 38 10
20P GAIN WILD-TYPE 35 41 88 46 46

Figure S98.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.091

Table S99.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
20P GAIN MUTATED 18 21 22 37 9
20P GAIN WILD-TYPE 26 74 34 85 39

Figure S99.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00082

Table S100.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
20P GAIN MUTATED 34 23 20 22
20P GAIN WILD-TYPE 58 64 99 20

Figure S100.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S101.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
20Q GAIN MUTATED 30 59 23
20Q GAIN WILD-TYPE 79 65 114

Figure S101.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00864 (Fisher's exact test), Q value = 0.035

Table S102.  Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
20Q GAIN MUTATED 18 15 31 38 10
20Q GAIN WILD-TYPE 36 41 83 46 46

Figure S102.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.001

Table S103.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
20Q GAIN MUTATED 36 23 21 22
20Q GAIN WILD-TYPE 56 64 98 20

Figure S103.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S104.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
22Q GAIN MUTATED 13 29 6
22Q GAIN WILD-TYPE 96 95 131

Figure S104.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.12

Table S105.  Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
22Q GAIN MUTATED 7 8 17 8 8
22Q GAIN WILD-TYPE 54 89 51 61 61

Figure S105.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00198 (Fisher's exact test), Q value = 0.013

Table S106.  Gene #39: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
22Q GAIN MUTATED 14 5 8 17 4
22Q GAIN WILD-TYPE 40 51 106 67 52

Figure S106.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00204 (Fisher's exact test), Q value = 0.013

Table S107.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
22Q GAIN MUTATED 17 10 6 10
22Q GAIN WILD-TYPE 75 77 113 32

Figure S107.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0039

Table S108.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
XP GAIN MUTATED 22 14 6
XP GAIN WILD-TYPE 87 110 131

Figure S108.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0078

Table S109.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
XQ GAIN MUTATED 30 21 13
XQ GAIN WILD-TYPE 79 103 124

Figure S109.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.014

Table S110.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
XQ GAIN MUTATED 6 16 8 10 24
XQ GAIN WILD-TYPE 55 81 60 59 45

Figure S110.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.049

Table S111.  Gene #41: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
XQ GAIN MUTATED 7 7 21 10 19
XQ GAIN WILD-TYPE 47 49 93 74 37

Figure S111.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.00634 (Fisher's exact test), Q value = 0.027

Table S112.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
XQ GAIN MUTATED 6 34 7 16
XQ GAIN WILD-TYPE 59 93 42 108

Figure S112.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0045

Table S113.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
XQ GAIN MUTATED 5 15 9 14 20
XQ GAIN WILD-TYPE 39 80 47 108 28

Figure S113.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0028

Table S114.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
XQ GAIN MUTATED 12 11 11 3 21
XQ GAIN WILD-TYPE 55 75 88 32 32

Figure S114.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.016

Table S115.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
1P LOSS MUTATED 23 39 19
1P LOSS WILD-TYPE 86 85 118

Figure S115.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S116.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
1P LOSS MUTATED 10 27 44
1P LOSS WILD-TYPE 78 140 71

Figure S116.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S117.  Gene #42: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
1P LOSS MUTATED 9 13 36 14 8
1P LOSS WILD-TYPE 52 84 32 55 61

Figure S117.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S118.  Gene #42: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
1P LOSS MUTATED 12 9 14 38 7
1P LOSS WILD-TYPE 42 47 100 46 49

Figure S118.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00399 (Fisher's exact test), Q value = 0.02

Table S119.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
1P LOSS MUTATED 5 26 14 35
1P LOSS WILD-TYPE 60 101 35 89

Figure S119.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00754 (Fisher's exact test), Q value = 0.032

Table S120.  Gene #42: '1p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
1P LOSS MUTATED 5 17 17 36 5
1P LOSS WILD-TYPE 39 78 39 86 43

Figure S120.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0044

Table S121.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
1P LOSS MUTATED 26 20 13 16
1P LOSS WILD-TYPE 66 67 106 26

Figure S121.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00447 (Fisher's exact test), Q value = 0.022

Table S122.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
1P LOSS MUTATED 16 15 34 4 6
1P LOSS WILD-TYPE 51 71 65 31 47

Figure S122.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.041

Table S123.  Gene #44: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
2P LOSS MUTATED 12 8 6 6 1
2P LOSS WILD-TYPE 49 89 62 63 68

Figure S123.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0393 (Fisher's exact test), Q value = 0.1

Table S124.  Gene #44: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
2P LOSS MUTATED 6 7 10 10 0
2P LOSS WILD-TYPE 48 49 104 74 56

Figure S124.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.04

Table S125.  Gene #45: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
2Q LOSS MUTATED 11 13 8 5 1
2Q LOSS WILD-TYPE 50 84 60 64 68

Figure S125.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.065

Table S126.  Gene #45: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
2Q LOSS MUTATED 5 7 16 10 0
2Q LOSS WILD-TYPE 49 49 98 74 56

Figure S126.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.091

Table S127.  Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
3P LOSS MUTATED 11 26 15
3P LOSS WILD-TYPE 98 98 122

Figure S127.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00779 (Fisher's exact test), Q value = 0.032

Table S128.  Gene #46: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
3P LOSS MUTATED 9 7 16 14 5
3P LOSS WILD-TYPE 52 90 52 55 64

Figure S128.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0095 (Fisher's exact test), Q value = 0.037

Table S129.  Gene #46: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
3P LOSS MUTATED 14 5 10 17 5
3P LOSS WILD-TYPE 40 51 104 67 51

Figure S129.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00747 (Fisher's exact test), Q value = 0.031

Table S130.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
3P LOSS MUTATED 3 16 5 27
3P LOSS WILD-TYPE 62 111 44 97

Figure S130.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0081

Table S131.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
3P LOSS MUTATED 20 17 7 3
3P LOSS WILD-TYPE 72 70 112 39

Figure S131.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0494 (Fisher's exact test), Q value = 0.13

Table S132.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
3P LOSS MUTATED 12 10 20 2 3
3P LOSS WILD-TYPE 55 76 79 33 50

Figure S132.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.062

Table S133.  Gene #47: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
3Q LOSS MUTATED 7 6 15 7 4
3Q LOSS WILD-TYPE 54 91 53 62 65

Figure S133.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00525 (Fisher's exact test), Q value = 0.024

Table S134.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
3Q LOSS MUTATED 18 9 6 2
3Q LOSS WILD-TYPE 74 78 113 40

Figure S134.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S135.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
4P LOSS MUTATED 25 60 22
4P LOSS WILD-TYPE 84 64 115

Figure S135.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0075

Table S136.  Gene #48: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
4P LOSS MUTATED 26 27 28 13 12
4P LOSS WILD-TYPE 35 70 40 56 57

Figure S136.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.051

Table S137.  Gene #48: '4p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
4P LOSS MUTATED 15 11 38 33 9
4P LOSS WILD-TYPE 39 45 76 51 47

Figure S137.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.06

Table S138.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
4P LOSS MUTATED 14 27 25 33 7
4P LOSS WILD-TYPE 30 68 31 89 41

Figure S138.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00482 (Fisher's exact test), Q value = 0.023

Table S139.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
4P LOSS MUTATED 39 21 25 14
4P LOSS WILD-TYPE 53 66 94 28

Figure S139.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.016

Table S140.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
4P LOSS MUTATED 30 27 24 11 7
4P LOSS WILD-TYPE 37 59 75 24 46

Figure S140.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S141.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
4Q LOSS MUTATED 34 85 29
4Q LOSS WILD-TYPE 75 39 108

Figure S141.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00508 (Fisher's exact test), Q value = 0.023

Table S142.  Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
4Q LOSS MUTATED 26 63 59
4Q LOSS WILD-TYPE 62 104 56

Figure S142.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S143.  Gene #49: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
4Q LOSS MUTATED 32 35 45 18 16
4Q LOSS WILD-TYPE 29 62 23 51 53

Figure S143.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0066

Table S144.  Gene #49: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
4Q LOSS MUTATED 24 19 44 47 12
4Q LOSS WILD-TYPE 30 37 70 37 44

Figure S144.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00532 (Fisher's exact test), Q value = 0.024

Table S145.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
4Q LOSS MUTATED 18 37 30 53 9
4Q LOSS WILD-TYPE 26 58 26 69 39

Figure S145.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S146.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
4Q LOSS MUTATED 49 33 32 26
4Q LOSS WILD-TYPE 43 54 87 16

Figure S146.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00924 (Fisher's exact test), Q value = 0.037

Table S147.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
4Q LOSS MUTATED 35 36 44 14 11
4Q LOSS WILD-TYPE 32 50 55 21 42

Figure S147.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.072

Table S148.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
5P LOSS MUTATED 4 16 8
5P LOSS WILD-TYPE 105 108 129

Figure S148.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.056

Table S149.  Gene #50: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
5P LOSS MUTATED 7 1 6 12 2
5P LOSS WILD-TYPE 47 55 108 72 54

Figure S149.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00911 (Fisher's exact test), Q value = 0.036

Table S150.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
5P LOSS MUTATED 12 2 6 6
5P LOSS WILD-TYPE 80 85 113 36

Figure S150.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.062

Table S151.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
5P LOSS MUTATED 10 5 7 4 0
5P LOSS WILD-TYPE 57 81 92 31 53

Figure S151.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.0028 (Fisher's exact test), Q value = 0.016

Table S152.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
5Q LOSS MUTATED 7 23 9
5Q LOSS WILD-TYPE 102 101 128

Figure S152.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00729 (Fisher's exact test), Q value = 0.031

Table S153.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
5Q LOSS MUTATED 7 11 21
5Q LOSS WILD-TYPE 81 156 94

Figure S153.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.07

Table S154.  Gene #51: '5q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
5Q LOSS MUTATED 10 7 13 6 3
5Q LOSS WILD-TYPE 51 90 55 63 66

Figure S154.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0019

Table S155.  Gene #51: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
5Q LOSS MUTATED 13 1 9 14 2
5Q LOSS WILD-TYPE 41 55 105 70 54

Figure S155.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.12

Table S156.  Gene #51: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
5Q LOSS MUTATED 6 11 8 14 0
5Q LOSS WILD-TYPE 38 84 48 108 48

Figure S156.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.0086

Table S157.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
5Q LOSS MUTATED 19 5 6 6
5Q LOSS WILD-TYPE 73 82 113 36

Figure S157.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0084

Table S158.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
5Q LOSS MUTATED 15 8 9 4 0
5Q LOSS WILD-TYPE 52 78 90 31 53

Figure S158.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00578 (Fisher's exact test), Q value = 0.025

Table S159.  Gene #54: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
7P LOSS MUTATED 10 3 1 2
7P LOSS WILD-TYPE 82 84 118 40

Figure S159.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.11

Table S160.  Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
7P LOSS MUTATED 7 5 2 2 0
7P LOSS WILD-TYPE 60 81 97 33 53

Figure S160.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.077

Table S161.  Gene #55: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
7Q LOSS MUTATED 6 6 5 4 0
7Q LOSS WILD-TYPE 38 89 51 118 48

Figure S161.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0021

Table S162.  Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
7Q LOSS MUTATED 14 3 1 3
7Q LOSS WILD-TYPE 78 84 118 39

Figure S162.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00507 (Fisher's exact test), Q value = 0.023

Table S163.  Gene #55: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
7Q LOSS MUTATED 7 5 3 6 0
7Q LOSS WILD-TYPE 60 81 96 29 53

Figure S163.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0025

Table S164.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
8P LOSS MUTATED 66 73 51
8P LOSS WILD-TYPE 43 51 86

Figure S164.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.063

Table S165.  Gene #56: '8p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
8P LOSS MUTATED 34 48 44 25 35
8P LOSS WILD-TYPE 27 49 24 44 34

Figure S165.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.084

Table S166.  Gene #56: '8p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
8P LOSS MUTATED 23 45 38 53 28
8P LOSS WILD-TYPE 21 50 18 69 20

Figure S166.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0094

Table S167.  Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
8Q LOSS MUTATED 6 25 12
8Q LOSS WILD-TYPE 103 99 125

Figure S167.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00046

Table S168.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
9P LOSS MUTATED 31 58 29
9P LOSS WILD-TYPE 78 66 108

Figure S168.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.069

Table S169.  Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
9P LOSS MUTATED 22 48 48
9P LOSS WILD-TYPE 66 119 67

Figure S169.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0035

Table S170.  Gene #58: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
9P LOSS MUTATED 24 26 34 21 11
9P LOSS WILD-TYPE 37 71 34 48 58

Figure S170.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00493 (Fisher's exact test), Q value = 0.023

Table S171.  Gene #58: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
9P LOSS MUTATED 21 17 30 38 10
9P LOSS WILD-TYPE 33 39 84 46 46

Figure S171.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00924 (Fisher's exact test), Q value = 0.037

Table S172.  Gene #58: '9p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
9P LOSS MUTATED 15 28 22 47 6
9P LOSS WILD-TYPE 29 67 34 75 42

Figure S172.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.085

Table S173.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
9P LOSS MUTATED 31 31 30 21
9P LOSS WILD-TYPE 61 56 89 21

Figure S173.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.044

Table S174.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
9P LOSS MUTATED 28 26 39 12 8
9P LOSS WILD-TYPE 39 60 60 23 45

Figure S174.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0037

Table S175.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
9Q LOSS MUTATED 28 52 27
9Q LOSS WILD-TYPE 81 72 110

Figure S175.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.046

Table S176.  Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
9Q LOSS MUTATED 19 43 45
9Q LOSS WILD-TYPE 69 124 70

Figure S176.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.046

Table S177.  Gene #59: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
9Q LOSS MUTATED 23 27 26 20 10
9Q LOSS WILD-TYPE 38 70 42 49 59

Figure S177.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.018

Table S178.  Gene #59: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
9Q LOSS MUTATED 19 15 30 35 7
9Q LOSS WILD-TYPE 35 41 84 49 49

Figure S178.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.056

Table S179.  Gene #59: '9q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
9Q LOSS MUTATED 14 25 20 41 5
9Q LOSS WILD-TYPE 30 70 36 81 43

Figure S179.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0092

Table S180.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
9Q LOSS MUTATED 26 22 35 12 5
9Q LOSS WILD-TYPE 41 64 64 23 48

Figure S180.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.07

Table S181.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
10P LOSS MUTATED 6 20 19
10P LOSS WILD-TYPE 103 104 118

Figure S181.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0069

Table S182.  Gene #60: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
10P LOSS MUTATED 13 17 3 10 2
10P LOSS WILD-TYPE 48 80 65 59 67

Figure S182.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 0.016

Table S183.  Gene #60: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
10P LOSS MUTATED 12 4 21 6 2
10P LOSS WILD-TYPE 42 52 93 78 54

Figure S183.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00653 (Fisher's exact test), Q value = 0.028

Table S184.  Gene #60: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
10P LOSS MUTATED 4 20 2 17 2
10P LOSS WILD-TYPE 40 75 54 105 46

Figure S184.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.064

Table S185.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
10P LOSS MUTATED 6 19 13 3 2
10P LOSS WILD-TYPE 61 67 86 32 51

Figure S185.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 0.00871 (Fisher's exact test), Q value = 0.035

Table S186.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
10Q LOSS MUTATED 12 32 32
10Q LOSS WILD-TYPE 97 92 105

Figure S186.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S187.  Gene #61: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
10Q LOSS MUTATED 28 25 4 14 4
10Q LOSS WILD-TYPE 33 72 64 55 65

Figure S187.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S188.  Gene #61: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
10Q LOSS MUTATED 23 8 30 9 5
10Q LOSS WILD-TYPE 31 48 84 75 51

Figure S188.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6e-04

Table S189.  Gene #61: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
10Q LOSS MUTATED 10 34 7 23 2
10Q LOSS WILD-TYPE 34 61 49 99 46

Figure S189.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S190.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
10Q LOSS MUTATED 15 32 17 9 1
10Q LOSS WILD-TYPE 52 54 82 26 52

Figure S190.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.064

Table S191.  Gene #62: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
11P LOSS MUTATED 20 11 12 11 10
11P LOSS WILD-TYPE 41 86 56 58 59

Figure S191.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00457 (Fisher's exact test), Q value = 0.022

Table S192.  Gene #62: '11p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
11P LOSS MUTATED 15 5 15 23 6
11P LOSS WILD-TYPE 39 51 99 61 50

Figure S192.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0085

Table S193.  Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
11P LOSS MUTATED 27 12 11 9
11P LOSS WILD-TYPE 65 75 108 33

Figure S193.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00555 (Fisher's exact test), Q value = 0.024

Table S194.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
11P LOSS MUTATED 22 13 14 6 4
11P LOSS WILD-TYPE 45 73 85 29 49

Figure S194.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00297 (Fisher's exact test), Q value = 0.016

Table S195.  Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
11Q LOSS MUTATED 30 12 16 9
11Q LOSS WILD-TYPE 62 75 103 33

Figure S195.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.056

Table S196.  Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
11Q LOSS MUTATED 22 19 15 6 5
11Q LOSS WILD-TYPE 45 67 84 29 48

Figure S196.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0066

Table S197.  Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
12P LOSS MUTATED 15 35 15
12P LOSS WILD-TYPE 94 89 122

Figure S197.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.081

Table S198.  Gene #64: '12p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
12P LOSS MUTATED 19 20 9 9 8
12P LOSS WILD-TYPE 42 77 59 60 61

Figure S198.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0028

Table S199.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
13Q LOSS MUTATED 27 59 36
13Q LOSS WILD-TYPE 82 65 101

Figure S199.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.098

Table S200.  Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
13Q LOSS MUTATED 29 45 48
13Q LOSS WILD-TYPE 59 122 67

Figure S200.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00676 (Fisher's exact test), Q value = 0.029

Table S201.  Gene #66: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
13Q LOSS MUTATED 27 28 27 25 12
13Q LOSS WILD-TYPE 34 69 41 44 57

Figure S201.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0032

Table S202.  Gene #66: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
13Q LOSS MUTATED 26 11 37 36 9
13Q LOSS WILD-TYPE 28 45 77 48 47

Figure S202.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.016

Table S203.  Gene #66: '13q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
13Q LOSS MUTATED 26 28 14 53
13Q LOSS WILD-TYPE 39 99 35 71

Figure S203.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00494 (Fisher's exact test), Q value = 0.023

Table S204.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
13Q LOSS MUTATED 19 35 15 46 6
13Q LOSS WILD-TYPE 25 60 41 76 42

Figure S204.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.065

Table S205.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
13Q LOSS MUTATED 35 37 28 16
13Q LOSS WILD-TYPE 57 50 91 26

Figure S205.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.0085

Table S206.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
13Q LOSS MUTATED 22 33 40 15 6
13Q LOSS WILD-TYPE 45 53 59 20 47

Figure S206.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S207.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
14Q LOSS MUTATED 17 64 26
14Q LOSS WILD-TYPE 92 60 111

Figure S207.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S208.  Gene #67: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
14Q LOSS MUTATED 32 18 25 21 10
14Q LOSS WILD-TYPE 29 79 43 48 59

Figure S208.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S209.  Gene #67: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
14Q LOSS MUTATED 30 10 25 33 8
14Q LOSS WILD-TYPE 24 46 89 51 48

Figure S209.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0028

Table S210.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
14Q LOSS MUTATED 40 29 20 13
14Q LOSS WILD-TYPE 52 58 99 29

Figure S210.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.055

Table S211.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
14Q LOSS MUTATED 26 23 33 13 7
14Q LOSS WILD-TYPE 41 63 66 22 46

Figure S211.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00082

Table S212.  Gene #68: '15q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
15Q LOSS MUTATED 22 9 19 10 6
15Q LOSS WILD-TYPE 39 88 49 59 63

Figure S212.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00092

Table S213.  Gene #68: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
15Q LOSS MUTATED 20 5 12 22 7
15Q LOSS WILD-TYPE 34 51 102 62 49

Figure S213.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S214.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
15Q LOSS MUTATED 28 10 11 15
15Q LOSS WILD-TYPE 64 77 108 27

Figure S214.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.061

Table S215.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
15Q LOSS MUTATED 20 12 22 6 4
15Q LOSS WILD-TYPE 47 74 77 29 49

Figure S215.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S216.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
16P LOSS MUTATED 25 57 27
16P LOSS WILD-TYPE 84 67 110

Figure S216.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00073

Table S217.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
16P LOSS MUTATED 27 32 50
16P LOSS WILD-TYPE 61 135 65

Figure S217.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S218.  Gene #69: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
16P LOSS MUTATED 21 19 51 12 4
16P LOSS WILD-TYPE 40 78 17 57 65

Figure S218.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S219.  Gene #69: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
16P LOSS MUTATED 22 13 25 44 3
16P LOSS WILD-TYPE 32 43 89 40 53

Figure S219.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.02

Table S220.  Gene #69: '16p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
16P LOSS MUTATED 13 34 25 36
16P LOSS WILD-TYPE 52 93 24 88

Figure S220.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S221.  Gene #69: '16p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
16P LOSS MUTATED 10 21 27 48 2
16P LOSS WILD-TYPE 34 74 29 74 46

Figure S221.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S222.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
16P LOSS MUTATED 39 22 16 27
16P LOSS WILD-TYPE 53 65 103 15

Figure S222.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S223.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
16P LOSS MUTATED 30 19 42 8 5
16P LOSS WILD-TYPE 37 67 57 27 48

Figure S223.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S224.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
16Q LOSS MUTATED 43 69 33
16Q LOSS WILD-TYPE 66 55 104

Figure S224.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S225.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
16Q LOSS MUTATED 25 51 69
16Q LOSS WILD-TYPE 63 116 46

Figure S225.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S226.  Gene #70: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
16Q LOSS MUTATED 30 33 58 15 7
16Q LOSS WILD-TYPE 31 64 10 54 62

Figure S226.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S227.  Gene #70: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
16Q LOSS MUTATED 23 16 46 53 5
16Q LOSS WILD-TYPE 31 40 68 31 51

Figure S227.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S228.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
16Q LOSS MUTATED 15 33 33 60 3
16Q LOSS WILD-TYPE 29 62 23 62 45

Figure S228.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S229.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
16Q LOSS MUTATED 53 31 28 27
16Q LOSS WILD-TYPE 39 56 91 15

Figure S229.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S230.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
16Q LOSS MUTATED 39 32 49 11 8
16Q LOSS WILD-TYPE 28 54 50 24 45

Figure S230.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S231.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
17P LOSS MUTATED 36 84 65
17P LOSS WILD-TYPE 73 40 72

Figure S231.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.069

Table S232.  Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
17P LOSS MUTATED 42 96 47
17P LOSS WILD-TYPE 46 71 68

Figure S232.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00535 (Fisher's exact test), Q value = 0.024

Table S233.  Gene #71: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
17P LOSS MUTATED 42 53 30 29 28
17P LOSS WILD-TYPE 19 44 38 40 41

Figure S233.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.07

Table S234.  Gene #71: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
17P LOSS MUTATED 32 23 68 36 23
17P LOSS WILD-TYPE 22 33 46 48 33

Figure S234.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00361 (Fisher's exact test), Q value = 0.019

Table S235.  Gene #71: '17p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
17P LOSS MUTATED 46 60 23 55
17P LOSS WILD-TYPE 19 67 26 69

Figure S235.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0045

Table S236.  Gene #71: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
17P LOSS MUTATED 34 54 23 52 21
17P LOSS WILD-TYPE 10 41 33 70 27

Figure S236.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0045

Table S237.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
17P LOSS MUTATED 28 52 46 28 22
17P LOSS WILD-TYPE 39 34 53 7 31

Figure S237.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.12

Table S238.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
18P LOSS MUTATED 18 34 22
18P LOSS WILD-TYPE 91 90 115

Figure S238.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.044

Table S239.  Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
18P LOSS MUTATED 14 26 34
18P LOSS WILD-TYPE 74 141 81

Figure S239.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00285 (Fisher's exact test), Q value = 0.016

Table S240.  Gene #73: '18p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
18P LOSS MUTATED 10 5 18 29 12
18P LOSS WILD-TYPE 44 51 96 55 44

Figure S240.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.021

Table S241.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
18Q LOSS MUTATED 19 39 21
18Q LOSS WILD-TYPE 90 85 116

Figure S241.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.004 (Fisher's exact test), Q value = 0.02

Table S242.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 88 167 115
18Q LOSS MUTATED 13 29 37
18Q LOSS WILD-TYPE 75 138 78

Figure S242.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0039

Table S243.  Gene #74: '18q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
18Q LOSS MUTATED 8 5 21 32 13
18Q LOSS WILD-TYPE 46 51 93 52 43

Figure S243.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S244.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
19P LOSS MUTATED 9 37 9
19P LOSS WILD-TYPE 100 87 128

Figure S244.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.091

Table S245.  Gene #75: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
19P LOSS MUTATED 17 14 10 7 6
19P LOSS WILD-TYPE 44 83 58 62 63

Figure S245.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0036 (Fisher's exact test), Q value = 0.019

Table S246.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 99 35 53
19P LOSS MUTATED 17 12 10 10 3
19P LOSS WILD-TYPE 50 74 89 25 50

Figure S246.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S247.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
19Q LOSS MUTATED 6 29 4
19Q LOSS WILD-TYPE 103 95 133

Figure S247.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.088

Table S248.  Gene #76: '19q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 127 49 124
19Q LOSS MUTATED 12 16 3 7
19Q LOSS WILD-TYPE 53 111 46 117

Figure S248.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.049

Table S249.  Gene #78: '20q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
20Q LOSS MUTATED 8 3 1 0
20Q LOSS WILD-TYPE 84 84 118 42

Figure S249.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0045

Table S250.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
21Q LOSS MUTATED 37 48 25
21Q LOSS WILD-TYPE 72 76 112

Figure S250.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0025

Table S251.  Gene #79: '21q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
21Q LOSS MUTATED 32 17 21 18 19
21Q LOSS WILD-TYPE 29 80 47 51 50

Figure S251.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.098

Table S252.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
22Q LOSS MUTATED 12 28 30
22Q LOSS WILD-TYPE 97 96 107

Figure S252.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.013

Table S253.  Gene #80: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 61 97 68 69 69
22Q LOSS MUTATED 23 19 8 12 8
22Q LOSS WILD-TYPE 38 78 60 57 61

Figure S253.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.092

Table S254.  Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
XP LOSS MUTATED 22 42 30
XP LOSS WILD-TYPE 87 82 107

Figure S254.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0202 (Fisher's exact test), Q value = 0.065

Table S255.  Gene #81: 'xp loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
XP LOSS MUTATED 14 10 39 13 17
XP LOSS WILD-TYPE 40 46 75 71 39

Figure S255.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0044 (Fisher's exact test), Q value = 0.022

Table S256.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 87 119 42
XP LOSS MUTATED 23 18 42 4
XP LOSS WILD-TYPE 69 69 77 38

Figure S256.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.046

Table S257.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 124 137
XQ LOSS MUTATED 14 34 22
XQ LOSS WILD-TYPE 95 90 115

Figure S257.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/15089886/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/15111045/LIHC-TP.transferedmergedcluster.txt

  • Number of patients = 370

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 8

  • 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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