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 59 arm-level events and 10 molecular subtypes across 499 patients, 248 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 4q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 12q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xp gain cnv correlated to 'METHLYATION_CNMF'.

  • xq gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1p loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

  • 11q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 21q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 59 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 248 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
7q gain 20 (4%) 479 0.00657
(0.0257) 		0.00032
(0.00255) 		0.143
(0.252) 		0.0166
(0.0505) 		0.00032
(0.00255) 		2e-05
(0.000381) 		0.00302
(0.0134) 		1e-05
(0.000311) 		0.00025
(0.00214) 		7e-05
(0.000843)
17p gain 16 (3%) 483 0.00019
(0.00184) 		2e-05
(0.000381) 		0.323
(0.47) 		0.0313
(0.0832) 		1e-05
(0.000311) 		1e-05
(0.000311) 		0.00044
(0.00317) 		1e-05
(0.000311) 		7e-05
(0.000843) 		3e-05
(0.000506)
17q gain 18 (4%) 481 0.00035
(0.00265) 		1e-05
(0.000311) 		0.7
(0.799) 		0.017
(0.051) 		4e-05
(0.000638) 		1e-05
(0.000311) 		0.00047
(0.00334) 		1e-05
(0.000311) 		8e-05
(0.000908) 		2e-05
(0.000381)
5p gain 21 (4%) 478 0.00888
(0.0325) 		0.00585
(0.0235) 		0.126
(0.228) 		0.262
(0.407) 		0.0127
(0.0439) 		8e-05
(0.000908) 		0.00261
(0.0118) 		0.00013
(0.00139) 		0.00637
(0.0251) 		0.00146
(0.0073)
5q gain 17 (3%) 482 0.00067
(0.00416) 		0.00027
(0.00221) 		0.267
(0.407) 		0.0881
(0.177) 		0.00057
(0.00374) 		0.0001
(0.00109) 		0.00124
(0.00671) 		1e-05
(0.000311) 		0.00135
(0.00705) 		0.00052
(0.00349)
7p gain 18 (4%) 481 0.00539
(0.0219) 		0.0013
(0.00691) 		0.237
(0.375) 		0.0587
(0.133) 		0.00195
(0.00935) 		0.00014
(0.00147) 		0.0117
(0.0417) 		4e-05
(0.000638) 		0.00214
(0.00994) 		0.00089
(0.0053)
12p gain 15 (3%) 484 0.00048
(0.00337) 		2e-05
(0.000381) 		0.767
(0.859) 		0.0893
(0.179) 		5e-05
(0.000737) 		1e-05
(0.000311) 		0.00026
(0.00216) 		1e-05
(0.000311) 		0.00022
(0.00197) 		5e-05
(0.000737)
12q gain 15 (3%) 484 0.00051
(0.00349) 		5e-05
(0.000737) 		0.766
(0.859) 		0.088
(0.177) 		2e-05
(0.000381) 		1e-05
(0.000311) 		0.0002
(0.0019) 		2e-05
(0.000381) 		0.00026
(0.00216) 		7e-05
(0.000843)
16p gain 15 (3%) 484 0.0004
(0.00295) 		0.00142
(0.00716) 		0.7
(0.799) 		0.0856
(0.175) 		0.00052
(0.00349) 		3e-05
(0.000506) 		0.00627
(0.0248) 		6e-05
(0.000823) 		0.00033
(0.00256) 		6e-05
(0.000823)
16q gain 13 (3%) 486 0.00142
(0.00716) 		0.0071
(0.0272) 		0.446
(0.589) 		0.296
(0.446) 		0.0027
(0.0121) 		0.00039
(0.00291) 		0.0309
(0.0828) 		0.00022
(0.00197) 		0.00255
(0.0116) 		0.00067
(0.00416)
19q gain 10 (2%) 489 0.012
(0.0418) 		0.00195
(0.00935) 		0.368
(0.515) 		0.0712
(0.15) 		0.00019
(0.00184) 		2e-05
(0.000381) 		0.00913
(0.0333) 		1e-05
(0.000311) 		0.00443
(0.0183) 		9e-05
(0.001)
2p loss 10 (2%) 489 0.00231
(0.0106) 		0.00198
(0.00942) 		0.637
(0.749) 		0.092
(0.18) 		0.00017
(0.0017) 		8e-05
(0.000908) 		0.0134
(0.0452) 		2e-05
(0.000381) 		0.00139
(0.00713) 		1e-05
(0.000311)
2q loss 10 (2%) 489 0.00202
(0.00953) 		0.00168
(0.00819) 		0.577
(0.709) 		0.0943
(0.183) 		0.00015
(0.00155) 		3e-05
(0.000506) 		0.0136
(0.0457) 		2e-05
(0.000381) 		0.0013
(0.00691) 		2e-05
(0.000381)
22q loss 89 (18%) 410 1e-05
(0.000311) 		1e-05
(0.000311) 		0.41
(0.558) 		0.509
(0.65) 		1e-05
(0.000311) 		1e-05
(0.000311) 		0.00478
(0.0196) 		6e-05
(0.000823) 		3e-05
(0.000506) 		7e-05
(0.000843)
1q gain 26 (5%) 473 0.196
(0.327) 		1e-05
(0.000311) 		0.0512
(0.12) 		0.0559
(0.129) 		0.00016
(0.00163) 		1e-05
(0.000311) 		0.0153
(0.0489) 		0.0478
(0.114) 		0.0399
(0.103) 		0.0149
(0.0477)
14q gain 11 (2%) 488 0.00089
(0.0053) 		0.00043
(0.00313) 		0.483
(0.628) 		0.17
(0.294) 		0.00133
(0.00701) 		0.00022
(0.00197) 		0.0565
(0.13) 		7e-05
(0.000843) 		0.00119
(0.00656) 		0.00023
(0.00203)
6q loss 7 (1%) 492 0.0197
(0.0565) 		0.0297
(0.0806) 		0.102
(0.193) 		0.579
(0.71) 		0.047
(0.113) 		0.0186
(0.0541) 		0.312
(0.462) 		0.00067
(0.00416) 		0.0408
(0.104) 		0.00097
(0.00567)
13q loss 14 (3%) 485 0.0132
(0.0448) 		0.0702
(0.149) 		0.0075
(0.0282) 		0.132
(0.237) 		0.0116
(0.0413) 		0.00858
(0.0316) 		0.121
(0.221) 		0.00052
(0.00349) 		0.01
(0.0363) 		0.00033
(0.00256)
15q loss 8 (2%) 491 0.172
(0.294) 		0.012
(0.0418) 		0.154
(0.27) 		0.095
(0.184) 		0.00124
(0.00671) 		0.00022
(0.00197) 		0.014
(0.0462) 		2e-05
(0.000381) 		0.0043
(0.018) 		7e-05
(0.000843)
19p loss 5 (1%) 494 0.727
(0.825) 		0.031
(0.0828) 		0.122
(0.222) 		0.261
(0.406) 		0.0242
(0.0677) 		0.0141
(0.0462) 		0.0428
(0.106) 		0.00104
(0.00596) 		0.00226
(0.0104) 		0.00107
(0.00607)
19p gain 8 (2%) 491 0.00765
(0.0286) 		0.012
(0.0418) 		0.00149
(0.00739) 		0.00024
(0.00208) 		0.0531
(0.124) 		2e-05
(0.000381) 		0.0682
(0.148) 		0.00098
(0.00567)
20p gain 12 (2%) 487 0.0039
(0.0172) 		0.0176
(0.052) 		0.446
(0.589) 		0.102
(0.193) 		0.00692
(0.0267) 		0.00088
(0.0053) 		0.0562
(0.129) 		0.00066
(0.00416) 		0.0507
(0.12) 		0.02
(0.0569)
20q gain 12 (2%) 487 0.00403
(0.0174) 		0.0165
(0.0505) 		0.445
(0.589) 		0.102
(0.193) 		0.0073
(0.0278) 		0.00109
(0.00612) 		0.0571
(0.131) 		0.0006
(0.00389) 		0.0513
(0.12) 		0.0196
(0.0563)
xq gain 7 (1%) 492 0.0793
(0.164) 		0.0294
(0.0806) 		0.776
(0.863) 		0.518
(0.657) 		0.0471
(0.113) 		0.018
(0.0528) 		0.0984
(0.188) 		0.00608
(0.0242) 		0.0157
(0.0493) 		0.0259
(0.0714)
11p loss 7 (1%) 492 0.239
(0.376) 		0.0299
(0.0806) 		0.785
(0.87) 		0.959
(1.00) 		0.0145
(0.0468) 		0.0185
(0.0541) 		0.0985
(0.188) 		0.00093
(0.00549) 		0.0413
(0.104) 		0.00139
(0.00713)
11q loss 9 (2%) 490 0.437
(0.585) 		0.0155
(0.0491) 		0.605
(0.732) 		0.831
(0.913) 		0.0398
(0.103) 		0.0189
(0.0548) 		0.0814
(0.167) 		0.00209
(0.00979) 		0.0119
(0.0418) 		0.00035
(0.00265)
4p gain 5 (1%) 494 0.0885
(0.178) 		0.0322
(0.0846) 		0.0238
(0.0671) 		0.0144
(0.0468) 		0.474
(0.62) 		0.0139
(0.0462) 		0.0673
(0.146) 		0.0128
(0.0439)
4q gain 5 (1%) 494 0.0901
(0.18) 		0.0318
(0.0842) 		0.0244
(0.068) 		0.0141
(0.0462) 		0.473
(0.62) 		0.0145
(0.0468) 		0.0673
(0.146) 		0.0132
(0.0448)
8p loss 4 (1%) 495 0.202
(0.331) 		0.299
(0.449) 		0.0697
(0.149) 		0.0472
(0.113) 		0.0434
(0.107) 		0.00435
(0.0181) 		0.0399
(0.103) 		0.017
(0.051)
8q loss 4 (1%) 495 0.202
(0.331) 		0.299
(0.449) 		0.0693
(0.149) 		0.0472
(0.113) 		0.0418
(0.104) 		0.00404
(0.0174) 		0.0417
(0.104) 		0.0166
(0.0505)
9q loss 25 (5%) 474 0.00057
(0.00374) 		0.035
(0.0915) 		0.572
(0.707) 		0.118
(0.215) 		0.269
(0.409) 		0.0599
(0.134) 		0.0534
(0.124) 		0.00745
(0.0282) 		0.0108
(0.0388) 		0.0171
(0.0511)
10p loss 7 (1%) 492 0.0807
(0.166) 		0.275
(0.417) 		0.365
(0.513) 		0.444
(0.589) 		0.0323
(0.0846) 		0.0157
(0.0493) 		0.314
(0.463) 		0.00081
(0.00498) 		0.0415
(0.104) 		0.00118
(0.00656)
11p gain 6 (1%) 493 0.0413
(0.104) 		0.18
(0.305) 		0.884
(0.966) 		0.303
(0.451) 		0.0703
(0.149) 		0.0467
(0.113) 		0.00165
(0.00811) 		0.00685
(0.0266) 		0.138
(0.245) 		0.0924
(0.18)
9p loss 19 (4%) 480 0.0242
(0.0677) 		0.092
(0.18) 		0.941
(1.00) 		0.648
(0.754) 		0.0582
(0.132) 		0.0622
(0.139) 		0.21
(0.342) 		0.00842
(0.0312) 		0.0173
(0.0513) 		0.0252
(0.0699)
3q loss 4 (1%) 495 0.201
(0.331) 		0.0867
(0.176) 		0.365
(0.513) 		0.444
(0.589) 		0.0698
(0.149) 		0.048
(0.114) 		0.334
(0.483) 		0.00409
(0.0174) 		0.216
(0.348) 		0.00411
(0.0174)
10q loss 6 (1%) 493 0.144
(0.253) 		0.422
(0.57) 		0.0712
(0.15) 		0.0472
(0.113) 		0.435
(0.585) 		0.00424
(0.0179) 		0.102
(0.193) 		0.0041
(0.0174)
11q gain 5 (1%) 494 0.0878
(0.177) 		0.316
(0.465) 		0.883
(0.966) 		0.302
(0.451) 		0.174
(0.296) 		0.123
(0.223) 		0.00555
(0.0224) 		0.023
(0.0652) 		0.4
(0.546) 		0.266
(0.407)
1q loss 3 (1%) 496 0.255
(0.399) 		0.224
(0.357) 		0.171
(0.294) 		0.173
(0.296) 		0.765
(0.859) 		0.0166
(0.0505) 		0.565
(0.704) 		0.0166
(0.0505)
3p loss 3 (1%) 496 0.256
(0.399) 		0.222
(0.354) 		0.17
(0.294) 		0.17
(0.294) 		0.766
(0.859) 		0.0164
(0.0505) 		0.565
(0.704) 		0.0168
(0.0507)
8p gain 6 (1%) 493 0.0412
(0.104) 		0.959
(1.00) 		1
(1.00) 		0.646
(0.753) 		0.704
(0.802) 		0.544
(0.686) 		0.721
(0.82) 		0.451
(0.593) 		1
(1.00) 		0.451
(0.593)
xp gain 8 (2%) 491 0.0589
(0.133) 		0.0299
(0.0806) 		0.773
(0.863) 		0.518
(0.657) 		0.0722
(0.152) 		0.0602
(0.135) 		0.279
(0.422) 		0.0733
(0.153) 		0.0593
(0.133) 		0.157
(0.275)
1p loss 4 (1%) 495 0.488
(0.628) 		0.613
(0.738) 		0.341
(0.489) 		0.318
(0.466) 		0.682
(0.79) 		0.0648
(0.144) 		0.345
(0.493) 		0.0412
(0.104)
6p loss 4 (1%) 495 0.2
(0.331) 		0.302
(0.451) 		0.552
(0.692) 		0.411
(0.559) 		0.684
(0.791) 		0.0666
(0.146) 		0.346
(0.493) 		0.0405
(0.104)
21q loss 8 (2%) 491 0.6
(0.727) 		0.699
(0.799) 		0.631
(0.747) 		0.219
(0.351) 		0.326
(0.473) 		0.428
(0.576) 		0.11
(0.204) 		0.0295
(0.0806) 		0.354
(0.501) 		0.0529
(0.124)
1p gain 4 (1%) 495 0.7
(0.799) 		0.694
(0.799) 		0.504
(0.645) 		0.614
(0.738) 		0.482
(0.628) 		0.137
(0.245) 		0.625
(0.746) 		0.36
(0.508)
3p gain 3 (1%) 496 0.623
(0.746) 		0.776
(0.863) 		0.641
(0.751) 		0.587
(0.717) 		0.765
(0.859) 		0.189
(0.317) 		0.563
(0.704) 		0.187
(0.314)
8q gain 7 (1%) 492 0.0791
(0.164) 		0.826
(0.909) 		1
(1.00) 		0.644
(0.753) 		0.912
(0.993) 		0.517
(0.657) 		0.766
(0.859) 		0.63
(0.747) 		0.882
(0.966) 		0.628
(0.747)
9p gain 3 (1%) 496 0.623
(0.746) 		0.776
(0.863) 		0.642
(0.751) 		0.589
(0.718) 		0.598
(0.727) 		1
(1.00) 		0.895
(0.976) 		1
(1.00)
9q gain 4 (1%) 495 0.486
(0.628) 		0.921
(1.00) 		0.377
(0.524) 		0.377
(0.524) 		0.438
(0.585) 		1
(1.00) 		0.587
(0.717) 		1
(1.00)
13q gain 5 (1%) 494 0.392
(0.54) 		0.135
(0.242) 		0.633
(0.747) 		0.216
(0.348) 		0.0689
(0.149) 		0.103
(0.194) 		0.573
(0.707) 		0.0744
(0.155) 		0.219
(0.351) 		0.183
(0.309)
18p gain 6 (1%) 493 0.181
(0.306) 		0.42
(0.569) 		0.211
(0.342) 		0.266
(0.407) 		0.227
(0.359) 		0.112
(0.207) 		0.526
(0.665) 		0.108
(0.201)
18q gain 6 (1%) 493 0.177
(0.302) 		0.42
(0.569) 		0.208
(0.341) 		0.266
(0.407) 		0.227
(0.359) 		0.11
(0.205) 		0.526
(0.665) 		0.108
(0.202)
21q gain 5 (1%) 494 0.391
(0.54) 		0.687
(0.792) 		0.338
(0.487) 		0.493
(0.632) 		0.141
(0.25) 		0.308
(0.458) 		0.792
(0.875) 		0.572
(0.707)
17p loss 8 (2%) 491 0.215
(0.348) 		0.795
(0.876) 		0.635
(0.748) 		0.392
(0.54) 		0.764
(0.859) 		0.6
(0.727) 		0.311
(0.46) 		0.162
(0.283) 		0.264
(0.407) 		0.164
(0.285)
17q loss 4 (1%) 495 0.485
(0.628) 		0.577
(0.709) 		1
(1.00) 		0.667
(0.775) 		0.19
(0.318) 		0.573
(0.707) 		0.792
(0.875) 		0.565
(0.704)
18p loss 4 (1%) 495 0.485
(0.628) 		0.115
(0.212) 		0.633
(0.747) 		0.394
(0.54) 		0.338
(0.487) 		0.317
(0.465) 		0.368
(0.515) 		0.091
(0.18) 		0.349
(0.497) 		0.266
(0.407)
18q loss 4 (1%) 495 0.489
(0.629) 		0.113
(0.208) 		0.629
(0.747) 		0.393
(0.54) 		0.342
(0.489) 		0.32
(0.467) 		0.371
(0.517) 		0.091
(0.18) 		0.351
(0.498) 		0.263
(0.407)
xp loss 4 (1%) 495 0.488
(0.628) 		0.613
(0.738) 		0.0652
(0.144) 		0.199
(0.33) 		0.55
(0.692) 		0.218
(0.35) 		0.0806
(0.166) 		0.0919
(0.18) 		0.138
(0.245) 		0.0915
(0.18)
xq loss 5 (1%) 494 0.331
(0.48) 		0.687
(0.792) 		0.0653
(0.144) 		0.202
(0.331) 		0.437
(0.585) 		0.393
(0.54) 		0.244
(0.383) 		0.0982
(0.188) 		0.128
(0.232) 		0.0964
(0.186)
'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
1Q GAIN MUTATED 11 2 7 1 5
1Q GAIN WILD-TYPE 35 145 77 41 175

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0016

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
1Q GAIN MUTATED 17 2 5 2
1Q GAIN WILD-TYPE 141 165 53 112

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
1Q GAIN MUTATED 17 2 1 2 4
1Q GAIN WILD-TYPE 87 132 85 93 74

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.049

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
1Q GAIN MUTATED 15 3 3 5
1Q GAIN WILD-TYPE 150 142 116 64

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
1Q GAIN MUTATED 15 3 8
1Q GAIN WILD-TYPE 163 125 184

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

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.1

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
1Q GAIN MUTATED 12 2 4 4
1Q GAIN WILD-TYPE 119 123 104 100

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.048

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
1Q GAIN MUTATED 14 2 6
1Q GAIN WILD-TYPE 149 118 179

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.085

Table S8.  Gene #4: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
4P GAIN MUTATED 0 5 0 0 0
4P GAIN WILD-TYPE 46 142 84 42 180

Figure S8.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.067

Table S9.  Gene #4: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
4P GAIN MUTATED 0 5 0 0
4P GAIN WILD-TYPE 158 162 58 114

Figure S9.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.047

Table S10.  Gene #4: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
4P GAIN MUTATED 0 5 0 0 0
4P GAIN WILD-TYPE 104 129 86 95 78

Figure S10.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.046

Table S11.  Gene #4: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
4P GAIN MUTATED 1 4 0
4P GAIN WILD-TYPE 177 124 192

Figure S11.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.044

Table S12.  Gene #4: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
4P GAIN MUTATED 1 4 0
4P GAIN WILD-TYPE 162 116 185

Figure S12.  Get High-res Image Gene #4: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.084

Table S13.  Gene #5: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
4Q GAIN MUTATED 0 5 0 0 0
4Q GAIN WILD-TYPE 46 142 84 42 180

Figure S13.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.068

Table S14.  Gene #5: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
4Q GAIN MUTATED 0 5 0 0
4Q GAIN WILD-TYPE 158 162 58 114

Figure S14.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.046

Table S15.  Gene #5: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
4Q GAIN MUTATED 0 5 0 0 0
4Q GAIN WILD-TYPE 104 129 86 95 78

Figure S15.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.047

Table S16.  Gene #5: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
4Q GAIN MUTATED 1 4 0
4Q GAIN WILD-TYPE 177 124 192

Figure S16.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.045

Table S17.  Gene #5: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
4Q GAIN MUTATED 1 4 0
4Q GAIN WILD-TYPE 162 116 185

Figure S17.  Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 0.00888 (Fisher's exact test), Q value = 0.033

Table S18.  Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
5P GAIN MUTATED 4 1 16
5P GAIN WILD-TYPE 128 137 213

Figure S18.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00585 (Fisher's exact test), Q value = 0.023

Table S19.  Gene #6: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
5P GAIN MUTATED 2 14 2 0 3
5P GAIN WILD-TYPE 44 133 82 42 177

Figure S19.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.044

Table S20.  Gene #6: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
5P GAIN MUTATED 5 14 1 1
5P GAIN WILD-TYPE 153 153 57 113

Figure S20.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00091

Table S21.  Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
5P GAIN MUTATED 6 14 0 1 0
5P GAIN WILD-TYPE 98 120 86 94 78

Figure S21.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.012

Table S22.  Gene #6: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
5P GAIN MUTATED 8 12 0 1
5P GAIN WILD-TYPE 157 133 119 68

Figure S22.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0014

Table S23.  Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
5P GAIN MUTATED 7 13 1
5P GAIN WILD-TYPE 171 115 191

Figure S23.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00637 (Fisher's exact test), Q value = 0.025

Table S24.  Gene #6: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
5P GAIN MUTATED 6 10 2 0
5P GAIN WILD-TYPE 125 115 106 104

Figure S24.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0073

Table S25.  Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
5P GAIN MUTATED 7 10 1
5P GAIN WILD-TYPE 156 110 184

Figure S25.  Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0042

Table S26.  Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
5Q GAIN MUTATED 2 0 15
5Q GAIN WILD-TYPE 130 138 214

Figure S26.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0022

Table S27.  Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
5Q GAIN MUTATED 1 14 1 0 1
5Q GAIN WILD-TYPE 45 133 83 42 179

Figure S27.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0037

Table S28.  Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
5Q GAIN MUTATED 2 14 0 1
5Q GAIN WILD-TYPE 156 153 58 113

Figure S28.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S29.  Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
5Q GAIN MUTATED 2 14 0 1 0
5Q GAIN WILD-TYPE 102 120 86 94 78

Figure S29.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0067

Table S30.  Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
5Q GAIN MUTATED 4 12 0 1
5Q GAIN WILD-TYPE 161 133 119 68

Figure S30.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S31.  Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
5Q GAIN MUTATED 3 13 1
5Q GAIN WILD-TYPE 175 115 191

Figure S31.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.007

Table S32.  Gene #7: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
5Q GAIN MUTATED 3 10 1 0
5Q GAIN WILD-TYPE 128 115 107 104

Figure S32.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0035

Table S33.  Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
5Q GAIN MUTATED 3 10 1
5Q GAIN WILD-TYPE 160 110 184

Figure S33.  Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 0.00539 (Fisher's exact test), Q value = 0.022

Table S34.  Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
7P GAIN MUTATED 2 1 15
7P GAIN WILD-TYPE 130 137 214

Figure S34.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0069

Table S35.  Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
7P GAIN MUTATED 1 13 3 0 1
7P GAIN WILD-TYPE 45 134 81 42 179

Figure S35.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.0094

Table S36.  Gene #8: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
7P GAIN MUTATED 2 14 1 1
7P GAIN WILD-TYPE 156 153 57 113

Figure S36.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

Table S37.  Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
7P GAIN MUTATED 2 14 1 1 0
7P GAIN WILD-TYPE 102 120 85 94 78

Figure S37.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.042

Table S38.  Gene #8: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
7P GAIN MUTATED 5 10 0 3
7P GAIN WILD-TYPE 160 135 119 66

Figure S38.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00064

Table S39.  Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
7P GAIN MUTATED 4 13 1
7P GAIN WILD-TYPE 174 115 191

Figure S39.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.0099

Table S40.  Gene #8: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
7P GAIN MUTATED 4 10 1 0
7P GAIN WILD-TYPE 127 115 107 104

Figure S40.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0053

Table S41.  Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
7P GAIN MUTATED 4 10 1
7P GAIN WILD-TYPE 159 110 184

Figure S41.  Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 0.00657 (Fisher's exact test), Q value = 0.026

Table S42.  Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
7Q GAIN MUTATED 3 1 16
7Q GAIN WILD-TYPE 129 137 213

Figure S42.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0026

Table S43.  Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
7Q GAIN MUTATED 1 15 3 0 1
7Q GAIN WILD-TYPE 45 132 81 42 179

Figure S43.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.051

Table S44.  Gene #9: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 47 27 9
7Q GAIN MUTATED 4 1 0 2 0 5 0
7Q GAIN WILD-TYPE 42 27 33 27 47 22 9

Figure S44.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0026

Table S45.  Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
7Q GAIN MUTATED 2 16 1 1
7Q GAIN WILD-TYPE 156 151 57 113

Figure S45.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S46.  Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
7Q GAIN MUTATED 2 16 1 1 0
7Q GAIN WILD-TYPE 102 118 85 94 78

Figure S46.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.013

Table S47.  Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
7Q GAIN MUTATED 5 12 0 3
7Q GAIN WILD-TYPE 160 133 119 66

Figure S47.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S48.  Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
7Q GAIN MUTATED 4 15 1
7Q GAIN WILD-TYPE 174 113 191

Figure S48.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0021

Table S49.  Gene #9: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
7Q GAIN MUTATED 4 12 1 0
7Q GAIN WILD-TYPE 127 113 107 104

Figure S49.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00084

Table S50.  Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
7Q GAIN MUTATED 4 12 1
7Q GAIN WILD-TYPE 159 108 184

Figure S50.  Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.1

Table S51.  Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
8P GAIN MUTATED 0 0 6
8P GAIN WILD-TYPE 132 138 223

Figure S51.  Get High-res Image Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.1

Table S52.  Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
11P GAIN MUTATED 0 0 6
11P GAIN WILD-TYPE 132 138 223

Figure S52.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 0.11

Table S53.  Gene #14: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
11P GAIN MUTATED 0 5 0 1 0
11P GAIN WILD-TYPE 104 129 86 94 78

Figure S53.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0081

Table S54.  Gene #14: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
11P GAIN MUTATED 0 6 0 0
11P GAIN WILD-TYPE 165 139 119 69

Figure S54.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00685 (Fisher's exact test), Q value = 0.027

Table S55.  Gene #14: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
11P GAIN MUTATED 0 5 1
11P GAIN WILD-TYPE 178 123 191

Figure S55.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.00555 (Fisher's exact test), Q value = 0.022

Table S56.  Gene #15: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
11Q GAIN MUTATED 0 5 0 0
11Q GAIN WILD-TYPE 165 140 119 69

Figure S56.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.065

Table S57.  Gene #15: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
11Q GAIN MUTATED 0 4 1
11Q GAIN WILD-TYPE 178 124 191

Figure S57.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0034

Table S58.  Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
12P GAIN MUTATED 1 0 14
12P GAIN WILD-TYPE 131 138 215

Figure S58.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S59.  Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
12P GAIN MUTATED 0 14 0 0 1
12P GAIN WILD-TYPE 46 133 84 42 179

Figure S59.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00074

Table S60.  Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
12P GAIN MUTATED 0 14 0 1
12P GAIN WILD-TYPE 158 153 58 113

Figure S60.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S61.  Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
12P GAIN MUTATED 0 14 0 1 0
12P GAIN WILD-TYPE 104 120 86 94 78

Figure S61.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0022

Table S62.  Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
12P GAIN MUTATED 2 12 0 1
12P GAIN WILD-TYPE 163 133 119 68

Figure S62.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S63.  Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
12P GAIN MUTATED 1 13 1
12P GAIN WILD-TYPE 177 115 191

Figure S63.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.002

Table S64.  Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
12P GAIN MUTATED 1 10 1 0
12P GAIN WILD-TYPE 130 115 107 104

Figure S64.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00074

Table S65.  Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
12P GAIN MUTATED 1 10 1
12P GAIN WILD-TYPE 162 110 184

Figure S65.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0035

Table S66.  Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
12Q GAIN MUTATED 1 0 14
12Q GAIN WILD-TYPE 131 138 215

Figure S66.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00074

Table S67.  Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
12Q GAIN MUTATED 0 14 0 0 1
12Q GAIN WILD-TYPE 46 133 84 42 179

Figure S67.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S68.  Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
12Q GAIN MUTATED 0 14 0 1
12Q GAIN WILD-TYPE 158 153 58 113

Figure S68.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S69.  Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
12Q GAIN MUTATED 0 14 0 1 0
12Q GAIN WILD-TYPE 104 120 86 94 78

Figure S69.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0019

Table S70.  Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
12Q GAIN MUTATED 2 12 0 1
12Q GAIN WILD-TYPE 163 133 119 68

Figure S70.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S71.  Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
12Q GAIN MUTATED 1 13 1
12Q GAIN WILD-TYPE 177 115 191

Figure S71.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0022

Table S72.  Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
12Q GAIN MUTATED 1 10 1 0
12Q GAIN WILD-TYPE 130 115 107 104

Figure S72.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00084

Table S73.  Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
12Q GAIN MUTATED 1 10 1
12Q GAIN WILD-TYPE 162 110 184

Figure S73.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0053

Table S74.  Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
14Q GAIN MUTATED 0 0 11
14Q GAIN WILD-TYPE 132 138 218

Figure S74.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0031

Table S75.  Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
14Q GAIN MUTATED 1 10 0 0 0
14Q GAIN WILD-TYPE 45 137 84 42 180

Figure S75.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.007

Table S76.  Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
14Q GAIN MUTATED 1 10 0 0
14Q GAIN WILD-TYPE 157 157 58 114

Figure S76.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.002

Table S77.  Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
14Q GAIN MUTATED 0 10 0 0 1
14Q GAIN WILD-TYPE 104 124 86 95 77

Figure S77.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00084

Table S78.  Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
14Q GAIN MUTATED 2 9 0
14Q GAIN WILD-TYPE 176 119 192

Figure S78.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0066

Table S79.  Gene #19: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
14Q GAIN MUTATED 2 8 0 0
14Q GAIN WILD-TYPE 129 117 108 104

Figure S79.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.002

Table S80.  Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
14Q GAIN MUTATED 2 8 0
14Q GAIN WILD-TYPE 161 112 185

Figure S80.  Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0029

Table S81.  Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
16P GAIN MUTATED 1 0 14
16P GAIN WILD-TYPE 131 138 215

Figure S81.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0072

Table S82.  Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
16P GAIN MUTATED 0 12 2 0 1
16P GAIN WILD-TYPE 46 135 82 42 179

Figure S82.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0035

Table S83.  Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
16P GAIN MUTATED 1 13 0 1
16P GAIN WILD-TYPE 157 154 58 113

Figure S83.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00051

Table S84.  Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
16P GAIN MUTATED 1 13 0 1 0
16P GAIN WILD-TYPE 103 121 86 94 78

Figure S84.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00627 (Fisher's exact test), Q value = 0.025

Table S85.  Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
16P GAIN MUTATED 3 10 0 2
16P GAIN WILD-TYPE 162 135 119 67

Figure S85.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S86.  Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
16P GAIN MUTATED 2 12 1
16P GAIN WILD-TYPE 176 116 191

Figure S86.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0026

Table S87.  Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
16P GAIN MUTATED 2 11 1 0
16P GAIN WILD-TYPE 129 114 107 104

Figure S87.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S88.  Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
16P GAIN MUTATED 2 11 1
16P GAIN WILD-TYPE 161 109 184

Figure S88.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0072

Table S89.  Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
16Q GAIN MUTATED 1 0 12
16Q GAIN WILD-TYPE 131 138 217

Figure S89.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.0071 (Fisher's exact test), Q value = 0.027

Table S90.  Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
16Q GAIN MUTATED 0 10 2 0 1
16Q GAIN WILD-TYPE 46 137 82 42 179

Figure S90.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.0027 (Fisher's exact test), Q value = 0.012

Table S91.  Gene #21: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
16Q GAIN MUTATED 1 11 0 1
16Q GAIN WILD-TYPE 157 156 58 113

Figure S91.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0029

Table S92.  Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
16Q GAIN MUTATED 1 11 0 1 0
16Q GAIN WILD-TYPE 103 123 86 94 78

Figure S92.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.083

Table S93.  Gene #21: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
16Q GAIN MUTATED 3 8 0 2
16Q GAIN WILD-TYPE 162 137 119 67

Figure S93.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.002

Table S94.  Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
16Q GAIN MUTATED 2 10 1
16Q GAIN WILD-TYPE 176 118 191

Figure S94.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.012

Table S95.  Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
16Q GAIN MUTATED 2 9 1 0
16Q GAIN WILD-TYPE 129 116 107 104

Figure S95.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0042

Table S96.  Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
16Q GAIN MUTATED 2 9 1
16Q GAIN WILD-TYPE 161 111 184

Figure S96.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0018

Table S97.  Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
17P GAIN MUTATED 1 0 15
17P GAIN WILD-TYPE 131 138 214

Figure S97.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S98.  Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
17P GAIN MUTATED 0 15 0 0 1
17P GAIN WILD-TYPE 46 132 84 42 179

Figure S98.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.083

Table S99.  Gene #22: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 47 27 9
17P GAIN MUTATED 1 1 0 2 0 4 0
17P GAIN WILD-TYPE 45 27 33 27 47 23 9

Figure S99.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S100.  Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
17P GAIN MUTATED 0 15 0 1
17P GAIN WILD-TYPE 158 152 58 113

Figure S100.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S101.  Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
17P GAIN MUTATED 0 15 0 1 0
17P GAIN WILD-TYPE 104 119 86 94 78

Figure S101.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0032

Table S102.  Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
17P GAIN MUTATED 2 12 0 2
17P GAIN WILD-TYPE 163 133 119 67

Figure S102.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S103.  Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
17P GAIN MUTATED 1 14 1
17P GAIN WILD-TYPE 177 114 191

Figure S103.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00084

Table S104.  Gene #22: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
17P GAIN MUTATED 1 11 1 0
17P GAIN WILD-TYPE 130 114 107 104

Figure S104.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00051

Table S105.  Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
17P GAIN MUTATED 1 11 1
17P GAIN WILD-TYPE 162 109 184

Figure S105.  Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0026

Table S106.  Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
17Q GAIN MUTATED 2 0 16
17Q GAIN WILD-TYPE 130 138 213

Figure S106.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S107.  Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
17Q GAIN MUTATED 1 16 0 0 1
17Q GAIN WILD-TYPE 45 131 84 42 179

Figure S107.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.051

Table S108.  Gene #23: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 28 33 29 47 27 9
17Q GAIN MUTATED 1 1 0 3 0 4 0
17Q GAIN WILD-TYPE 45 27 33 26 47 23 9

Figure S108.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00064

Table S109.  Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
17Q GAIN MUTATED 1 16 0 1
17Q GAIN WILD-TYPE 157 151 58 113

Figure S109.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S110.  Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
17Q GAIN MUTATED 1 16 0 1 0
17Q GAIN WILD-TYPE 103 118 86 94 78

Figure S110.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0033

Table S111.  Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
17Q GAIN MUTATED 3 13 0 2
17Q GAIN WILD-TYPE 162 132 119 67

Figure S111.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S112.  Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
17Q GAIN MUTATED 2 15 1
17Q GAIN WILD-TYPE 176 113 191

Figure S112.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00091

Table S113.  Gene #23: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
17Q GAIN MUTATED 2 12 1 0
17Q GAIN WILD-TYPE 129 113 107 104

Figure S113.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S114.  Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
17Q GAIN MUTATED 2 12 1
17Q GAIN WILD-TYPE 161 108 184

Figure S114.  Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.00765 (Fisher's exact test), Q value = 0.029

Table S115.  Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
19P GAIN MUTATED 0 0 8
19P GAIN WILD-TYPE 132 138 221

Figure S115.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.042

Table S116.  Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
19P GAIN MUTATED 0 7 1 0 0
19P GAIN WILD-TYPE 46 140 83 42 180

Figure S116.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0074

Table S117.  Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
19P GAIN MUTATED 0 8 0 0
19P GAIN WILD-TYPE 158 159 58 114

Figure S117.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0021

Table S118.  Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
19P GAIN MUTATED 0 8 0 0 0
19P GAIN WILD-TYPE 104 126 86 95 78

Figure S118.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S119.  Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
19P GAIN MUTATED 0 8 0
19P GAIN WILD-TYPE 178 120 192

Figure S119.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0057

Table S120.  Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
19P GAIN MUTATED 0 5 0
19P GAIN WILD-TYPE 163 115 185

Figure S120.  Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.042

Table S121.  Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
19Q GAIN MUTATED 1 0 9
19Q GAIN WILD-TYPE 131 138 220

Figure S121.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.0094

Table S122.  Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
19Q GAIN MUTATED 0 9 1 0 0
19Q GAIN WILD-TYPE 46 138 83 42 180

Figure S122.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0018

Table S123.  Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
19Q GAIN MUTATED 0 10 0 0
19Q GAIN WILD-TYPE 158 157 58 114

Figure S123.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S124.  Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
19Q GAIN MUTATED 0 10 0 0 0
19Q GAIN WILD-TYPE 104 124 86 95 78

Figure S124.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00913 (Fisher's exact test), Q value = 0.033

Table S125.  Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
19Q GAIN MUTATED 1 7 0 2
19Q GAIN WILD-TYPE 164 138 119 67

Figure S125.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S126.  Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
19Q GAIN MUTATED 0 10 0
19Q GAIN WILD-TYPE 178 118 192

Figure S126.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00443 (Fisher's exact test), Q value = 0.018

Table S127.  Gene #27: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
19Q GAIN MUTATED 1 6 0 0
19Q GAIN WILD-TYPE 130 119 108 104

Figure S127.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.001

Table S128.  Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
19Q GAIN MUTATED 0 7 0
19Q GAIN WILD-TYPE 163 113 185

Figure S128.  Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.017

Table S129.  Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
20P GAIN MUTATED 1 0 11
20P GAIN WILD-TYPE 131 138 218

Figure S129.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.052

Table S130.  Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
20P GAIN MUTATED 0 9 2 0 1
20P GAIN WILD-TYPE 46 138 82 42 179

Figure S130.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00692 (Fisher's exact test), Q value = 0.027

Table S131.  Gene #28: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
20P GAIN MUTATED 1 10 0 1
20P GAIN WILD-TYPE 157 157 58 113

Figure S131.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0053

Table S132.  Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
20P GAIN MUTATED 1 10 0 1 0
20P GAIN WILD-TYPE 103 124 86 94 78

Figure S132.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0042

Table S133.  Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
20P GAIN MUTATED 2 9 1
20P GAIN WILD-TYPE 176 119 191

Figure S133.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.057

Table S134.  Gene #28: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
20P GAIN MUTATED 2 6 1
20P GAIN WILD-TYPE 161 114 184

Figure S134.  Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.017

Table S135.  Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
20Q GAIN MUTATED 1 0 11
20Q GAIN WILD-TYPE 131 138 218

Figure S135.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.051

Table S136.  Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
20Q GAIN MUTATED 0 9 2 0 1
20Q GAIN WILD-TYPE 46 138 82 42 179

Figure S136.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0073 (Fisher's exact test), Q value = 0.028

Table S137.  Gene #29: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
20Q GAIN MUTATED 1 10 0 1
20Q GAIN WILD-TYPE 157 157 58 113

Figure S137.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0061

Table S138.  Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
20Q GAIN MUTATED 1 10 0 1 0
20Q GAIN WILD-TYPE 103 124 86 94 78

Figure S138.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0039

Table S139.  Gene #29: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
20Q GAIN MUTATED 2 9 1
20Q GAIN WILD-TYPE 176 119 191

Figure S139.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.056

Table S140.  Gene #29: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
20Q GAIN MUTATED 2 6 1
20Q GAIN WILD-TYPE 161 114 184

Figure S140.  Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.081

Table S141.  Gene #31: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
XP GAIN MUTATED 0 6 2 0 0
XP GAIN WILD-TYPE 46 141 82 42 180

Figure S141.  Get High-res Image Gene #31: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.081

Table S142.  Gene #32: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
XQ GAIN MUTATED 0 6 1 0 0
XQ GAIN WILD-TYPE 46 141 83 42 180

Figure S142.  Get High-res Image Gene #32: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 0.11

Table S143.  Gene #32: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
XQ GAIN MUTATED 1 6 0 0
XQ GAIN WILD-TYPE 157 161 58 114

Figure S143.  Get High-res Image Gene #32: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.053

Table S144.  Gene #32: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
XQ GAIN MUTATED 1 6 0 0 0
XQ GAIN WILD-TYPE 103 128 86 95 78

Figure S144.  Get High-res Image Gene #32: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00608 (Fisher's exact test), Q value = 0.024

Table S145.  Gene #32: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
XQ GAIN MUTATED 2 5 0
XQ GAIN WILD-TYPE 176 123 192

Figure S145.  Get High-res Image Gene #32: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.049

Table S146.  Gene #32: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
XQ GAIN MUTATED 1 5 0 0
XQ GAIN WILD-TYPE 130 120 108 104

Figure S146.  Get High-res Image Gene #32: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 0.071

Table S147.  Gene #32: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
XQ GAIN MUTATED 2 4 0
XQ GAIN WILD-TYPE 161 116 185

Figure S147.  Get High-res Image Gene #32: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.1

Table S148.  Gene #33: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
1P LOSS MUTATED 1 3 0
1P LOSS WILD-TYPE 162 117 185

Figure S148.  Get High-res Image Gene #33: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.051

Table S149.  Gene #34: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
1Q LOSS MUTATED 0 3 0
1Q LOSS WILD-TYPE 178 125 192

Figure S149.  Get High-res Image Gene #34: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.051

Table S150.  Gene #34: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
1Q LOSS MUTATED 0 3 0
1Q LOSS WILD-TYPE 163 117 185

Figure S150.  Get High-res Image Gene #34: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.011

Table S151.  Gene #35: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
2P LOSS MUTATED 0 0 10
2P LOSS WILD-TYPE 132 138 219

Figure S151.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0094

Table S152.  Gene #35: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
2P LOSS MUTATED 0 9 1 0 0
2P LOSS WILD-TYPE 46 138 83 42 180

Figure S152.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0017

Table S153.  Gene #35: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
2P LOSS MUTATED 0 10 0 0
2P LOSS WILD-TYPE 158 157 58 114

Figure S153.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00091

Table S154.  Gene #35: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
2P LOSS MUTATED 0 10 0 0 0
2P LOSS WILD-TYPE 104 124 86 95 78

Figure S154.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.045

Table S155.  Gene #35: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
2P LOSS MUTATED 1 6 0 3
2P LOSS WILD-TYPE 164 139 119 66

Figure S155.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S156.  Gene #35: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
2P LOSS MUTATED 0 10 0
2P LOSS WILD-TYPE 178 118 192

Figure S156.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0071

Table S157.  Gene #35: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
2P LOSS MUTATED 1 7 0 0
2P LOSS WILD-TYPE 130 118 108 104

Figure S157.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S158.  Gene #35: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
2P LOSS MUTATED 0 8 0
2P LOSS WILD-TYPE 163 112 185

Figure S158.  Get High-res Image Gene #35: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0095

Table S159.  Gene #36: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
2Q LOSS MUTATED 0 0 10
2Q LOSS WILD-TYPE 132 138 219

Figure S159.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.0082

Table S160.  Gene #36: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
2Q LOSS MUTATED 0 9 1 0 0
2Q LOSS WILD-TYPE 46 138 83 42 180

Figure S160.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0016

Table S161.  Gene #36: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
2Q LOSS MUTATED 0 10 0 0
2Q LOSS WILD-TYPE 158 157 58 114

Figure S161.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00051

Table S162.  Gene #36: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
2Q LOSS MUTATED 0 10 0 0 0
2Q LOSS WILD-TYPE 104 124 86 95 78

Figure S162.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.046

Table S163.  Gene #36: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
2Q LOSS MUTATED 1 6 0 3
2Q LOSS WILD-TYPE 164 139 119 66

Figure S163.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S164.  Gene #36: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
2Q LOSS MUTATED 0 10 0
2Q LOSS WILD-TYPE 178 118 192

Figure S164.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0069

Table S165.  Gene #36: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
2Q LOSS MUTATED 1 7 0 0
2Q LOSS WILD-TYPE 130 118 108 104

Figure S165.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S166.  Gene #36: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
2Q LOSS MUTATED 0 8 0
2Q LOSS WILD-TYPE 163 112 185

Figure S166.  Get High-res Image Gene #36: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.051

Table S167.  Gene #37: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
3P LOSS MUTATED 0 3 0
3P LOSS WILD-TYPE 178 125 192

Figure S167.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.051

Table S168.  Gene #37: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
3P LOSS MUTATED 0 3 0
3P LOSS WILD-TYPE 163 117 185

Figure S168.  Get High-res Image Gene #37: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.048 (Fisher's exact test), Q value = 0.11

Table S169.  Gene #38: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
3Q LOSS MUTATED 0 4 0 0 0
3Q LOSS WILD-TYPE 104 130 86 95 78

Figure S169.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00409 (Fisher's exact test), Q value = 0.017

Table S170.  Gene #38: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
3Q LOSS MUTATED 0 4 0
3Q LOSS WILD-TYPE 178 124 192

Figure S170.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00411 (Fisher's exact test), Q value = 0.017

Table S171.  Gene #38: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
3Q LOSS MUTATED 0 4 0
3Q LOSS WILD-TYPE 163 116 185

Figure S171.  Get High-res Image Gene #38: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0405 (Fisher's exact test), Q value = 0.1

Table S172.  Gene #39: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
6P LOSS MUTATED 1 3 0
6P LOSS WILD-TYPE 162 117 185

Figure S172.  Get High-res Image Gene #39: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.056

Table S173.  Gene #40: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
6Q LOSS MUTATED 0 0 7
6Q LOSS WILD-TYPE 132 138 222

Figure S173.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.081

Table S174.  Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
6Q LOSS MUTATED 0 6 1 0 0
6Q LOSS WILD-TYPE 46 141 83 42 180

Figure S174.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.11

Table S175.  Gene #40: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
6Q LOSS MUTATED 1 6 0 0
6Q LOSS WILD-TYPE 157 161 58 114

Figure S175.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.054

Table S176.  Gene #40: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
6Q LOSS MUTATED 1 6 0 0 0
6Q LOSS WILD-TYPE 103 128 86 95 78

Figure S176.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0042

Table S177.  Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
6Q LOSS MUTATED 1 6 0
6Q LOSS WILD-TYPE 177 122 192

Figure S177.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.1

Table S178.  Gene #40: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
6Q LOSS MUTATED 2 5 0 0
6Q LOSS WILD-TYPE 129 120 108 104

Figure S178.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0057

Table S179.  Gene #40: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
6Q LOSS MUTATED 1 6 0
6Q LOSS WILD-TYPE 162 114 185

Figure S179.  Get High-res Image Gene #40: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.11

Table S180.  Gene #41: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
8P LOSS MUTATED 0 4 0 0 0
8P LOSS WILD-TYPE 104 130 86 95 78

Figure S180.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.11

Table S181.  Gene #41: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
8P LOSS MUTATED 0 2 0 2
8P LOSS WILD-TYPE 165 143 119 67

Figure S181.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00435 (Fisher's exact test), Q value = 0.018

Table S182.  Gene #41: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
8P LOSS MUTATED 0 4 0
8P LOSS WILD-TYPE 178 124 192

Figure S182.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.1

Table S183.  Gene #41: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
8P LOSS MUTATED 0 3 0 0
8P LOSS WILD-TYPE 131 122 108 104

Figure S183.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.051

Table S184.  Gene #41: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
8P LOSS MUTATED 0 3 0
8P LOSS WILD-TYPE 163 117 185

Figure S184.  Get High-res Image Gene #41: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.11

Table S185.  Gene #42: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
8Q LOSS MUTATED 0 4 0 0 0
8Q LOSS WILD-TYPE 104 130 86 95 78

Figure S185.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.1

Table S186.  Gene #42: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
8Q LOSS MUTATED 0 2 0 2
8Q LOSS WILD-TYPE 165 143 119 67

Figure S186.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00404 (Fisher's exact test), Q value = 0.017

Table S187.  Gene #42: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
8Q LOSS MUTATED 0 4 0
8Q LOSS WILD-TYPE 178 124 192

Figure S187.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.1

Table S188.  Gene #42: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
8Q LOSS MUTATED 0 3 0 0
8Q LOSS WILD-TYPE 131 122 108 104

Figure S188.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.051

Table S189.  Gene #42: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
8Q LOSS MUTATED 0 3 0
8Q LOSS WILD-TYPE 163 117 185

Figure S189.  Get High-res Image Gene #42: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.068

Table S190.  Gene #43: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
9P LOSS MUTATED 9 1 9
9P LOSS WILD-TYPE 123 137 220

Figure S190.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00842 (Fisher's exact test), Q value = 0.031

Table S191.  Gene #43: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
9P LOSS MUTATED 7 10 2
9P LOSS WILD-TYPE 171 118 190

Figure S191.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.051

Table S192.  Gene #43: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
9P LOSS MUTATED 7 8 0 2
9P LOSS WILD-TYPE 124 117 108 102

Figure S192.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.07

Table S193.  Gene #43: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
9P LOSS MUTATED 7 8 2
9P LOSS WILD-TYPE 156 112 183

Figure S193.  Get High-res Image Gene #43: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0037

Table S194.  Gene #44: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
9Q LOSS MUTATED 14 1 10
9Q LOSS WILD-TYPE 118 137 219

Figure S194.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.092

Table S195.  Gene #44: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
9Q LOSS MUTATED 4 11 6 0 4
9Q LOSS WILD-TYPE 42 136 78 42 176

Figure S195.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.028

Table S196.  Gene #44: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
9Q LOSS MUTATED 11 11 3
9Q LOSS WILD-TYPE 167 117 189

Figure S196.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.039

Table S197.  Gene #44: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
9Q LOSS MUTATED 11 9 1 2
9Q LOSS WILD-TYPE 120 116 107 102

Figure S197.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.051

Table S198.  Gene #44: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
9Q LOSS MUTATED 11 9 3
9Q LOSS WILD-TYPE 152 111 182

Figure S198.  Get High-res Image Gene #44: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.085

Table S199.  Gene #45: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
10P LOSS MUTATED 0 6 0 1
10P LOSS WILD-TYPE 158 161 58 113

Figure S199.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.049

Table S200.  Gene #45: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
10P LOSS MUTATED 0 6 0 1 0
10P LOSS WILD-TYPE 104 128 86 94 78

Figure S200.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.005

Table S201.  Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
10P LOSS MUTATED 1 6 0
10P LOSS WILD-TYPE 177 122 192

Figure S201.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.1

Table S202.  Gene #45: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
10P LOSS MUTATED 2 5 0 0
10P LOSS WILD-TYPE 129 120 108 104

Figure S202.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0066

Table S203.  Gene #45: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
10P LOSS MUTATED 1 6 0
10P LOSS WILD-TYPE 162 114 185

Figure S203.  Get High-res Image Gene #45: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.11

Table S204.  Gene #46: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
10Q LOSS MUTATED 0 5 0 1 0
10Q LOSS WILD-TYPE 104 129 86 94 78

Figure S204.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.018

Table S205.  Gene #46: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
10Q LOSS MUTATED 1 5 0
10Q LOSS WILD-TYPE 177 123 192

Figure S205.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0041 (Fisher's exact test), Q value = 0.017

Table S206.  Gene #46: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
10Q LOSS MUTATED 1 5 0
10Q LOSS WILD-TYPE 162 115 185

Figure S206.  Get High-res Image Gene #46: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.081

Table S207.  Gene #47: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
11P LOSS MUTATED 0 6 1 0 0
11P LOSS WILD-TYPE 46 141 83 42 180

Figure S207.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.047

Table S208.  Gene #47: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
11P LOSS MUTATED 0 6 1 0
11P LOSS WILD-TYPE 158 161 57 114

Figure S208.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.054

Table S209.  Gene #47: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
11P LOSS MUTATED 1 6 0 0 0
11P LOSS WILD-TYPE 103 128 86 95 78

Figure S209.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0055

Table S210.  Gene #47: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
11P LOSS MUTATED 1 6 0
11P LOSS WILD-TYPE 177 122 192

Figure S210.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.1

Table S211.  Gene #47: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
11P LOSS MUTATED 2 5 0 0
11P LOSS WILD-TYPE 129 120 108 104

Figure S211.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0071

Table S212.  Gene #47: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
11P LOSS MUTATED 1 6 0
11P LOSS WILD-TYPE 162 114 185

Figure S212.  Get High-res Image Gene #47: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.049

Table S213.  Gene #48: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
11Q LOSS MUTATED 1 7 1 0 0
11Q LOSS WILD-TYPE 45 140 83 42 180

Figure S213.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.1

Table S214.  Gene #48: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
11Q LOSS MUTATED 1 7 1 0
11Q LOSS WILD-TYPE 157 160 57 114

Figure S214.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.055

Table S215.  Gene #48: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
11Q LOSS MUTATED 1 7 0 0 1
11Q LOSS WILD-TYPE 103 127 86 95 77

Figure S215.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00209 (Fisher's exact test), Q value = 0.0098

Table S216.  Gene #48: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
11Q LOSS MUTATED 1 7 1
11Q LOSS WILD-TYPE 177 121 191

Figure S216.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.042

Table S217.  Gene #48: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
11Q LOSS MUTATED 2 6 0 0
11Q LOSS WILD-TYPE 129 119 108 104

Figure S217.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0026

Table S218.  Gene #48: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
11Q LOSS MUTATED 1 7 0
11Q LOSS WILD-TYPE 162 113 185

Figure S218.  Get High-res Image Gene #48: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.045

Table S219.  Gene #49: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
13Q LOSS MUTATED 3 0 11
13Q LOSS WILD-TYPE 129 138 218

Figure S219.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.0075 (Fisher's exact test), Q value = 0.028

Table S220.  Gene #49: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 64 64 42 49
13Q LOSS MUTATED 1 1 6 1
13Q LOSS WILD-TYPE 63 63 36 48

Figure S220.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.041

Table S221.  Gene #49: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
13Q LOSS MUTATED 0 9 2 3
13Q LOSS WILD-TYPE 158 158 56 111

Figure S221.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00858 (Fisher's exact test), Q value = 0.032

Table S222.  Gene #49: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
13Q LOSS MUTATED 0 9 2 3 0
13Q LOSS WILD-TYPE 104 125 84 92 78

Figure S222.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0035

Table S223.  Gene #49: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
13Q LOSS MUTATED 0 9 5
13Q LOSS WILD-TYPE 178 119 187

Figure S223.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.036

Table S224.  Gene #49: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
13Q LOSS MUTATED 1 9 2 1
13Q LOSS WILD-TYPE 130 116 106 103

Figure S224.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0026

Table S225.  Gene #49: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
13Q LOSS MUTATED 0 9 4
13Q LOSS WILD-TYPE 163 111 181

Figure S225.  Get High-res Image Gene #49: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.042

Table S226.  Gene #50: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
15Q LOSS MUTATED 0 7 1 0 0
15Q LOSS WILD-TYPE 46 140 83 42 180

Figure S226.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0067

Table S227.  Gene #50: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
15Q LOSS MUTATED 0 8 0 0
15Q LOSS WILD-TYPE 158 159 58 114

Figure S227.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.002

Table S228.  Gene #50: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
15Q LOSS MUTATED 0 8 0 0 0
15Q LOSS WILD-TYPE 104 126 86 95 78

Figure S228.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.046

Table S229.  Gene #50: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
15Q LOSS MUTATED 1 3 0 4
15Q LOSS WILD-TYPE 164 142 119 65

Figure S229.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S230.  Gene #50: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
15Q LOSS MUTATED 0 8 0
15Q LOSS WILD-TYPE 178 120 192

Figure S230.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0043 (Fisher's exact test), Q value = 0.018

Table S231.  Gene #50: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
15Q LOSS MUTATED 1 6 0 0
15Q LOSS WILD-TYPE 130 119 108 104

Figure S231.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00084

Table S232.  Gene #50: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
15Q LOSS MUTATED 0 7 0
15Q LOSS WILD-TYPE 163 113 185

Figure S232.  Get High-res Image Gene #50: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.083

Table S233.  Gene #55: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
19P LOSS MUTATED 0 5 0 0 0
19P LOSS WILD-TYPE 46 142 84 42 180

Figure S233.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.068

Table S234.  Gene #55: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
19P LOSS MUTATED 0 5 0 0
19P LOSS WILD-TYPE 158 162 58 114

Figure S234.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.046

Table S235.  Gene #55: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
19P LOSS MUTATED 0 5 0 0 0
19P LOSS WILD-TYPE 104 129 86 95 78

Figure S235.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.11

Table S236.  Gene #55: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
19P LOSS MUTATED 0 4 0 1
19P LOSS WILD-TYPE 165 141 119 68

Figure S236.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.006

Table S237.  Gene #55: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
19P LOSS MUTATED 0 5 0
19P LOSS WILD-TYPE 178 123 192

Figure S237.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.01

Table S238.  Gene #55: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
19P LOSS MUTATED 0 5 0 0
19P LOSS WILD-TYPE 131 120 108 104

Figure S238.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0061

Table S239.  Gene #55: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
19P LOSS MUTATED 0 5 0
19P LOSS WILD-TYPE 163 115 185

Figure S239.  Get High-res Image Gene #55: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.081

Table S240.  Gene #56: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
21Q LOSS MUTATED 4 4 0
21Q LOSS WILD-TYPE 174 124 192

Figure S240.  Get High-res Image Gene #56: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S241.  Gene #57: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 138 229
22Q LOSS MUTATED 75 0 14
22Q LOSS WILD-TYPE 57 138 215

Figure S241.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S242.  Gene #57: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 147 84 42 180
22Q LOSS MUTATED 3 46 9 2 29
22Q LOSS WILD-TYPE 43 101 75 40 151

Figure S242.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S243.  Gene #57: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 167 58 114
22Q LOSS MUTATED 8 47 8 26
22Q LOSS WILD-TYPE 150 120 50 88

Figure S243.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S244.  Gene #57: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 104 134 86 95 78
22Q LOSS MUTATED 9 42 13 23 2
22Q LOSS WILD-TYPE 95 92 73 72 76

Figure S244.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00478 (Fisher's exact test), Q value = 0.02

Table S245.  Gene #57: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 165 145 119 69
22Q LOSS MUTATED 21 40 19 9
22Q LOSS WILD-TYPE 144 105 100 60

Figure S245.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S246.  Gene #57: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 178 128 192
22Q LOSS MUTATED 21 40 28
22Q LOSS WILD-TYPE 157 88 164

Figure S246.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00051

Table S247.  Gene #57: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 125 108 104
22Q LOSS MUTATED 17 39 8 17
22Q LOSS WILD-TYPE 114 86 100 87

Figure S247.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00084

Table S248.  Gene #57: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 163 120 185
22Q LOSS MUTATED 21 38 22
22Q LOSS WILD-TYPE 142 82 163

Figure S248.  Get High-res Image Gene #57: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/22511440/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/22542946/THCA-TP.transferedmergedcluster.txt

  • Number of patients = 499

  • Number of significantly arm-level cnvs = 59

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Made with Nozzle