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 63 arm-level events and 10 molecular subtypes across 66 patients, 185 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 3p gain cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • 7p gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 7q gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

  • 8q gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 12p gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

  • 14q gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 18p gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 19p gain cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 22q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xp gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • 3p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 16q loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 17q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 19q loss cnv correlated to 'MRNASEQ_CNMF'.

  • 21q loss cnv correlated to 'METHLYATION_CNMF'.

  • 22q loss cnv correlated to 'METHLYATION_CNMF'.

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

  • xq loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  '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 63 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, 185 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
1p loss 53 (80%) 13 0.414
(0.651) 		1e-05
(0.000233) 		0.719
(0.863) 		0.596
(0.805) 		0.00027
(0.00298) 		0.00028
(0.00304) 		0.396
(0.638) 		0.00123
(0.00993) 		0.00048
(0.00451) 		0.00204
(0.0144)
1q loss 51 (77%) 15 0.542
(0.773) 		1e-05
(0.000233) 		0.217
(0.453) 		0.336
(0.583) 		2e-05
(0.000371) 		6e-05
(0.000969) 		0.269
(0.512) 		0.00031
(0.0032) 		0.0048
(0.0317) 		0.0119
(0.0619)
2p loss 46 (70%) 20 0.712
(0.863) 		1e-05
(0.000233) 		0.126
(0.328) 		0.512
(0.745) 		1e-05
(0.000233) 		1e-05
(0.000233) 		0.45
(0.683) 		2e-05
(0.000371) 		1e-05
(0.000233) 		0.00041
(0.00391)
2q loss 46 (70%) 20 0.71
(0.863) 		1e-05
(0.000233) 		0.127
(0.328) 		0.511
(0.745) 		1e-05
(0.000233) 		1e-05
(0.000233) 		0.453
(0.686) 		1e-05
(0.000233) 		1e-05
(0.000233) 		0.00051
(0.00472)
6p loss 51 (77%) 15 0.624
(0.81) 		1e-05
(0.000233) 		0.161
(0.378) 		0.105
(0.29) 		1e-05
(0.000233) 		1e-05
(0.000233) 		0.609
(0.805) 		0.00133
(0.0105) 		0.00026
(0.00298) 		7e-05
(0.00108)
6q loss 51 (77%) 15 0.624
(0.81) 		1e-05
(0.000233) 		0.16
(0.377) 		0.105
(0.29) 		1e-05
(0.000233) 		1e-05
(0.000233) 		0.609
(0.805) 		0.00129
(0.0103) 		0.00015
(0.00193) 		0.00012
(0.00161)
10p loss 48 (73%) 18 0.595
(0.805) 		3e-05
(0.000525) 		0.0883
(0.251) 		0.107
(0.293) 		1e-05
(0.000233) 		1e-05
(0.000233) 		0.595
(0.805) 		0.00022
(0.00267) 		0.00159
(0.0121) 		0.00726
(0.0436)
10q loss 49 (74%) 17 0.423
(0.661) 		2e-05
(0.000371) 		0.175
(0.399) 		0.238
(0.48) 		1e-05
(0.000233) 		1e-05
(0.000233) 		0.569
(0.786) 		0.00036
(0.00359) 		0.00543
(0.0345) 		0.00178
(0.0132)
17p loss 50 (76%) 16 0.568
(0.786) 		1e-05
(0.000233) 		0.14
(0.343) 		0.0688
(0.214) 		1e-05
(0.000233) 		1e-05
(0.000233) 		0.31
(0.552) 		5e-05
(0.000829) 		7e-05
(0.00108) 		0.0011
(0.00912)
17q loss 50 (76%) 16 0.569
(0.786) 		1e-05
(0.000233) 		0.141
(0.344) 		0.0688
(0.214) 		1e-05
(0.000233) 		1e-05
(0.000233) 		0.309
(0.552) 		8e-05
(0.00117) 		0.0001
(0.00137) 		0.00121
(0.0099)
xp loss 38 (58%) 28 0.901
(0.97) 		0.00026
(0.00298) 		0.69
(0.855) 		0.722
(0.863) 		0.0003
(0.00315) 		0.00027
(0.00298) 		0.33
(0.575) 		3e-05
(0.000525) 		2e-05
(0.000371) 		0.011
(0.0587)
xq loss 38 (58%) 28 1
(1.00) 		0.00158
(0.0121) 		0.691
(0.855) 		0.719
(0.863) 		0.00087
(0.00751) 		0.00144
(0.0112) 		0.653
(0.826) 		0.00083
(0.00726) 		8e-05
(0.00117) 		0.0498
(0.17)
4p gain 23 (35%) 43 0.903
(0.971) 		0.643
(0.826) 		0.507
(0.745) 		0.174
(0.397) 		0.00103
(0.00865) 		0.00037
(0.00359) 		1
(1.00) 		0.0137
(0.0697) 		0.0103
(0.0557) 		0.00366
(0.0245)
4q gain 24 (36%) 42 0.81
(0.918) 		0.805
(0.917) 		0.344
(0.585) 		0.15
(0.357) 		0.0001
(0.00137) 		9e-05
(0.00129) 		0.951
(0.997) 		0.00908
(0.0502) 		0.0115
(0.0607) 		0.0152
(0.0737)
16p gain 22 (33%) 44 1
(1.00) 		0.799
(0.915) 		0.492
(0.732) 		0.295
(0.55) 		0.00161
(0.0121) 		0.00054
(0.00486) 		0.656
(0.826) 		0.00583
(0.036) 		0.00567
(0.0354) 		0.00906
(0.0502)
16q gain 21 (32%) 45 1
(1.00) 		0.943
(0.992) 		0.264
(0.506) 		0.364
(0.608) 		0.00037
(0.00359) 		0.00014
(0.00184) 		0.401
(0.642) 		0.00515
(0.0331) 		0.0019
(0.0138) 		0.00547
(0.0345)
18p gain 17 (26%) 49 1
(1.00) 		0.721
(0.863) 		0.761
(0.893) 		0.652
(0.826) 		0.0217
(0.0899) 		0.0129
(0.066) 		1
(1.00) 		0.048
(0.167) 		0.00247
(0.0171) 		0.0128
(0.066)
8p loss 10 (15%) 56 2e-05
(0.000371) 		0.0216
(0.0899) 		0.0244
(0.0972) 		0.0269
(0.105) 		0.345
(0.585) 		0.0765
(0.228) 		0.146
(0.35) 		0.547
(0.774) 		0.215
(0.452) 		0.0191
(0.0845)
13q loss 43 (65%) 23 0.375
(0.623) 		0.00027
(0.00298) 		0.295
(0.55) 		0.0521
(0.175) 		0.00016
(0.00202) 		4e-05
(0.000681) 		0.0823
(0.24) 		0.198
(0.439) 		0.00089
(0.00758) 		0.00766
(0.0443)
11q gain 15 (23%) 51 1
(1.00) 		0.868
(0.949) 		0.215
(0.452) 		0.0879
(0.251) 		2e-05
(0.000371) 		2e-05
(0.000371) 		0.748
(0.889) 		0.02
(0.0862) 		0.0904
(0.254) 		0.0257
(0.101)
18q gain 16 (24%) 50 0.874
(0.952) 		0.935
(0.992) 		0.929
(0.992) 		0.555
(0.78) 		0.0498
(0.17) 		0.0198
(0.0862) 		1
(1.00) 		0.0506
(0.171) 		0.00188
(0.0138) 		0.0162
(0.0767)
20p gain 22 (33%) 44 0.721
(0.863) 		0.711
(0.863) 		0.166
(0.385) 		0.0657
(0.208) 		0.0175
(0.081) 		0.0238
(0.0957) 		0.429
(0.661) 		0.0224
(0.0922) 		0.0152
(0.0737) 		0.203
(0.441)
20q gain 22 (33%) 44 0.722
(0.863) 		0.714
(0.863) 		0.167
(0.385) 		0.0665
(0.208) 		0.0182
(0.0836) 		0.0235
(0.0954) 		0.427
(0.661) 		0.0216
(0.0899) 		0.0153
(0.0737) 		0.201
(0.439)
xp gain 8 (12%) 58 0.773
(0.898) 		0.306
(0.552) 		0.403
(0.644) 		0.384
(0.628) 		0.00761
(0.0443) 		0.0196
(0.086) 		0.0752
(0.228) 		0.0838
(0.241) 		0.00734
(0.0436) 		0.0308
(0.118)
xq gain 8 (12%) 58 0.772
(0.898) 		0.306
(0.552) 		0.406
(0.645) 		0.385
(0.628) 		0.00782
(0.0448) 		0.0185
(0.0845) 		0.0757
(0.228) 		0.0839
(0.241) 		0.00795
(0.0451) 		0.0321
(0.121)
5p loss 10 (15%) 56 0.00807
(0.0454) 		0.21
(0.448) 		1
(1.00) 		0.822
(0.922) 		0.0144
(0.0719) 		0.019
(0.0845) 		0.227
(0.465) 		0.0148
(0.0728) 		0.384
(0.628) 		0.649
(0.826)
5q loss 10 (15%) 56 0.0068
(0.0412) 		0.21
(0.448) 		1
(1.00) 		0.822
(0.922) 		0.0147
(0.0728) 		0.0191
(0.0845) 		0.23
(0.47) 		0.0143
(0.0719) 		0.381
(0.628) 		0.652
(0.826)
8q gain 17 (26%) 49 0.24
(0.482) 		0.145
(0.35) 		0.39
(0.63) 		0.13
(0.329) 		0.0337
(0.126) 		0.0307
(0.118) 		0.444
(0.678) 		0.121
(0.322) 		0.00961
(0.0526) 		0.0553
(0.183)
11p gain 15 (23%) 51 1
(1.00) 		0.87
(0.95) 		0.561
(0.785) 		0.0889
(0.251) 		0.00052
(0.00475) 		0.0003
(0.00315) 		0.83
(0.924) 		0.0275
(0.106) 		0.337
(0.583) 		0.0528
(0.176)
12q gain 20 (30%) 46 1
(1.00) 		0.519
(0.754) 		0.787
(0.905) 		0.413
(0.651) 		0.0331
(0.124) 		0.0837
(0.241) 		0.943
(0.992) 		0.0317
(0.12) 		0.00082
(0.00726) 		0.177
(0.401)
14q gain 21 (32%) 45 1
(1.00) 		0.944
(0.992) 		0.2
(0.439) 		0.293
(0.55) 		0.0167
(0.0787) 		0.00483
(0.0317) 		0.767
(0.898) 		0.0586
(0.193) 		0.0214
(0.0899) 		0.0661
(0.208)
19p gain 20 (30%) 46 0.711
(0.863) 		0.225
(0.465) 		0.0699
(0.216) 		0.0264
(0.103) 		0.0192
(0.0845) 		0.0227
(0.0929) 		0.881
(0.957) 		0.13
(0.329) 		0.356
(0.598) 		0.607
(0.805)
22q gain 19 (29%) 47 1
(1.00) 		0.541
(0.773) 		0.254
(0.499) 		0.243
(0.487) 		0.335
(0.583) 		0.362
(0.607) 		0.481
(0.716) 		0.0238
(0.0957) 		0.00993
(0.0539) 		0.00227
(0.0159)
8q loss 9 (14%) 57 0.00019
(0.00235) 		0.017
(0.0793) 		0.0704
(0.216) 		0.082
(0.24) 		0.586
(0.802) 		0.12
(0.322) 		0.249
(0.494) 		0.587
(0.802) 		0.216
(0.453) 		0.0187
(0.0845)
16q loss 5 (8%) 61 0.48
(0.716) 		0.434
(0.667) 		0.853
(0.938) 		0.226
(0.465) 		0.0347
(0.128) 		0.00749
(0.0441) 		0.276
(0.523) 		0.0497
(0.17) 		0.539
(0.773) 		0.657
(0.826)
3p gain 8 (12%) 58 0.26
(0.501) 		0.507
(0.745) 		0.46
(0.694) 		0.0447
(0.157) 		0.839
(0.929) 		0.646
(0.826) 		0.204
(0.441) 		0.69
(0.855) 		0.0385
(0.139) 		0.625
(0.81)
3q gain 8 (12%) 58 0.26
(0.501) 		0.506
(0.745) 		0.458
(0.691) 		0.0437
(0.155) 		0.841
(0.929) 		0.648
(0.826) 		0.205
(0.441) 		0.689
(0.855) 		0.039
(0.14) 		0.626
(0.81)
8p gain 16 (24%) 50 0.329
(0.575) 		0.131
(0.329) 		0.382
(0.628) 		0.149
(0.357) 		0.0915
(0.256) 		0.0772
(0.228) 		0.305
(0.552) 		0.144
(0.349) 		0.0207
(0.0888) 		0.0467
(0.163)
19q gain 18 (27%) 48 1
(1.00) 		0.261
(0.502) 		0.109
(0.297) 		0.0734
(0.225) 		0.00357
(0.0242) 		0.0063
(0.0385) 		0.696
(0.856) 		0.146
(0.35) 		0.326
(0.572) 		0.506
(0.745)
9p loss 9 (14%) 57 1
(1.00) 		0.906
(0.972) 		0.664
(0.833) 		0.811
(0.918) 		0.0117
(0.0612) 		0.00504
(0.0327) 		0.257
(0.499) 		0.547
(0.774) 		0.225
(0.465) 		0.998
(1.00)
9q loss 10 (15%) 56 0.804
(0.917) 		0.829
(0.924) 		0.51
(0.745) 		0.55
(0.776) 		0.0209
(0.0889) 		0.0156
(0.0746) 		0.0766
(0.228) 		0.6
(0.805) 		0.708
(0.863) 		0.925
(0.991)
18q loss 9 (14%) 57 0.13
(0.329) 		0.0406
(0.145) 		0.39
(0.63) 		0.407
(0.646) 		0.0364
(0.132) 		0.168
(0.386) 		0.583
(0.8) 		0.783
(0.902) 		0.122
(0.323) 		0.496
(0.736)
7p gain 24 (36%) 42 0.571
(0.788) 		0.898
(0.968) 		0.0996
(0.276) 		0.135
(0.338) 		0.0768
(0.228) 		0.061
(0.197) 		0.844
(0.931) 		0.117
(0.316) 		0.0342
(0.127) 		0.14
(0.344)
7q gain 24 (36%) 42 0.575
(0.791) 		0.896
(0.968) 		0.0959
(0.267) 		0.136
(0.338) 		0.0753
(0.228) 		0.0615
(0.198) 		0.84
(0.929) 		0.117
(0.316) 		0.0348
(0.128) 		0.142
(0.344)
12p gain 19 (29%) 47 0.892
(0.968) 		0.737
(0.88) 		0.837
(0.929) 		0.463
(0.696) 		0.128
(0.329) 		0.159
(0.377) 		0.67
(0.837) 		0.0664
(0.208) 		0.00036
(0.00359) 		0.198
(0.439)
3p loss 9 (14%) 57 0.605
(0.805) 		0.436
(0.668) 		0.817
(0.92) 		0.167
(0.385) 		0.127
(0.328) 		0.0027
(0.0185) 		0.428
(0.661) 		0.201
(0.439) 		0.668
(0.836) 		0.853
(0.938)
3q loss 8 (12%) 58 0.425
(0.661) 		0.167
(0.385) 		0.896
(0.968) 		0.385
(0.628) 		0.0885
(0.251) 		0.00196
(0.014) 		0.306
(0.552) 		0.18
(0.407) 		0.309
(0.552) 		0.656
(0.826)
19q loss 3 (5%) 63 1
(1.00) 		1
(1.00) 		0.613
(0.805) 		0.308
(0.552) 		0.05
(0.17) 		0.821
(0.922) 		1
(1.00) 		0.865
(0.948) 		0.778
(0.899) 		0.624
(0.81)
21q loss 35 (53%) 31 0.402
(0.643) 		0.0355
(0.129) 		0.125
(0.328) 		0.188
(0.424) 		0.265
(0.506) 		0.195
(0.437) 		0.984
(1.00) 		0.127
(0.328) 		0.121
(0.322) 		0.225
(0.465)
22q loss 8 (12%) 58 1
(1.00) 		0.0247
(0.0978) 		0.879
(0.957) 		1
(1.00) 		0.528
(0.765) 		0.233
(0.475) 		0.611
(0.805) 		0.213
(0.451) 		0.86
(0.943) 		0.316
(0.558)
5p gain 8 (12%) 58 0.772
(0.898) 		0.797
(0.915) 		0.71
(0.863) 		0.199
(0.439) 		0.386
(0.628) 		0.446
(0.679) 		0.426
(0.661) 		0.0599
(0.195) 		0.311
(0.552) 		0.129
(0.329)
5q gain 8 (12%) 58 0.773
(0.898) 		0.8
(0.915) 		0.709
(0.863) 		0.197
(0.439) 		0.386
(0.628) 		0.446
(0.679) 		0.427
(0.661) 		0.0602
(0.195) 		0.311
(0.552) 		0.129
(0.329)
9p gain 10 (15%) 56 0.649
(0.826) 		0.563
(0.785) 		0.257
(0.499) 		0.234
(0.475) 		0.417
(0.655) 		0.813
(0.918) 		0.755
(0.89) 		0.602
(0.805) 		0.301
(0.552) 		0.304
(0.552)
9q gain 10 (15%) 56 0.649
(0.826) 		0.562
(0.785) 		0.256
(0.499) 		0.235
(0.477) 		0.418
(0.655) 		0.813
(0.918) 		0.758
(0.891) 		0.597
(0.805) 		0.301
(0.552) 		0.305
(0.552)
10p gain 4 (6%) 62 1
(1.00) 		0.285
(0.538) 		1
(1.00) 		0.55
(0.776) 		0.478
(0.716) 		0.205
(0.441) 		1
(1.00) 		0.167
(0.385) 		0.255
(0.499) 		0.777
(0.899)
15q gain 21 (32%) 45 0.301
(0.552) 		0.943
(0.992) 		0.2
(0.439) 		0.297
(0.551) 		0.136
(0.338) 		0.0619
(0.198) 		0.945
(0.993) 		0.213
(0.451) 		0.288
(0.542) 		0.41
(0.649)
21q gain 4 (6%) 62 1
(1.00) 		0.282
(0.533) 		0.556
(0.78) 		0.81
(0.918) 		0.339
(0.584) 		0.107
(0.292) 		0.675
(0.842) 		0.166
(0.385) 		0.758
(0.891) 		0.719
(0.863)
11p loss 7 (11%) 59 0.753
(0.89) 		0.694
(0.856) 		0.533
(0.767) 		0.253
(0.499) 		0.344
(0.585) 		0.318
(0.559) 		0.345
(0.585) 		0.938
(0.992) 		0.937
(0.992) 		0.604
(0.805)
11q loss 7 (11%) 59 0.753
(0.89) 		0.695
(0.856) 		0.53
(0.766) 		0.254
(0.499) 		0.341
(0.585) 		0.316
(0.558) 		0.347
(0.586) 		0.937
(0.992) 		0.939
(0.992) 		0.603
(0.805)
16p loss 3 (5%) 63 0.602
(0.805) 		0.613
(0.805) 		0.35
(0.59) 		0.591
(0.805) 		0.248
(0.494) 		0.124
(0.326) 		0.752
(0.89) 		0.481
(0.716) 		0.781
(0.901) 		0.624
(0.81)
18p loss 7 (11%) 59 0.381
(0.628) 		0.0514
(0.173) 		0.534
(0.767) 		0.512
(0.745) 		0.399
(0.641) 		0.14
(0.343) 		0.774
(0.898) 		0.938
(0.992) 		0.301
(0.552) 		0.825
(0.923)
20p loss 4 (6%) 62 1
(1.00) 		0.567
(0.786) 		0.365
(0.608) 		0.338
(0.584) 		0.544
(0.773) 		0.215
(0.452) 		0.744
(0.886) 		0.657
(0.826) 		0.346
(0.586) 		0.541
(0.773)
20q loss 3 (5%) 63 1
(1.00) 		0.249
(0.494) 		0.612
(0.805) 		0.59
(0.804) 		0.25
(0.494) 		0.0589
(0.193) 		0.645
(0.826) 		0.827
(0.924) 		0.0796
(0.234) 		0.624
(0.81)
'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.16

Table S1.  Gene #1: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
3P GAIN MUTATED 7 1 0
3P GAIN WILD-TYPE 22 19 14

Figure S1.  Get High-res Image Gene #1: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.14

Table S2.  Gene #1: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
3P GAIN MUTATED 0 0 2 4
3P GAIN WILD-TYPE 9 13 12 8

Figure S2.  Get High-res Image Gene #1: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.15

Table S3.  Gene #2: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
3Q GAIN MUTATED 7 1 0
3Q GAIN WILD-TYPE 22 19 14

Figure S3.  Get High-res Image Gene #2: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.14

Table S4.  Gene #2: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
3Q GAIN MUTATED 0 0 2 4
3Q GAIN WILD-TYPE 9 13 12 8

Figure S4.  Get High-res Image Gene #2: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0087

Table S5.  Gene #3: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
4P GAIN MUTATED 4 12 1 1 2 0 3
4P GAIN WILD-TYPE 13 3 4 5 12 4 2

Figure S5.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0036

Table S6.  Gene #3: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
4P GAIN MUTATED 4 13 3 1 1 1 0
4P GAIN WILD-TYPE 15 3 4 5 9 3 4

Figure S6.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.07

Table S7.  Gene #3: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
4P GAIN MUTATED 2 8 5 3 2 2 1
4P GAIN WILD-TYPE 16 3 7 3 3 3 8

Figure S7.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.056

Table S8.  Gene #3: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
4P GAIN MUTATED 1 10 4 4
4P GAIN WILD-TYPE 8 3 10 8

Figure S8.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00366 (Fisher's exact test), Q value = 0.025

Table S9.  Gene #3: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
4P GAIN MUTATED 3 6 3 4 1 0 2 0 0
4P GAIN WILD-TYPE 2 0 2 4 4 4 4 5 4

Figure S9.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0014

Table S10.  Gene #4: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
4Q GAIN MUTATED 4 13 1 1 2 0 3
4Q GAIN WILD-TYPE 13 2 4 5 12 4 2

Figure S10.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0013

Table S11.  Gene #4: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
4Q GAIN MUTATED 4 14 3 1 1 1 0
4Q GAIN WILD-TYPE 15 2 4 5 9 3 4

Figure S11.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00908 (Fisher's exact test), Q value = 0.05

Table S12.  Gene #4: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
4Q GAIN MUTATED 2 8 5 3 3 2 1
4Q GAIN WILD-TYPE 16 3 7 3 2 3 8

Figure S12.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.061

Table S13.  Gene #4: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
4Q GAIN MUTATED 1 10 4 5
4Q GAIN WILD-TYPE 8 3 10 7

Figure S13.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.074

Table S14.  Gene #4: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
4Q GAIN MUTATED 3 6 3 4 1 0 2 1 0
4Q GAIN WILD-TYPE 2 0 2 4 4 4 4 4 4

Figure S14.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.13

Table S15.  Gene #7: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
7P GAIN MUTATED 1 9 4 6
7P GAIN WILD-TYPE 8 4 10 6

Figure S15.  Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S16.  Gene #8: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
7Q GAIN MUTATED 1 9 4 6
7Q GAIN WILD-TYPE 8 4 10 6

Figure S16.  Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S17.  Gene #9: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
8P GAIN MUTATED 0 6 2 6
8P GAIN WILD-TYPE 9 7 12 6

Figure S17.  Get High-res Image Gene #9: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 0.16

Table S18.  Gene #9: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
8P GAIN MUTATED 1 5 0 3 1 0 3 1 0
8P GAIN WILD-TYPE 4 1 5 5 4 4 3 4 4

Figure S18.  Get High-res Image Gene #9: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.13

Table S19.  Gene #10: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
8Q GAIN MUTATED 2 9 1 1 2 0 2
8Q GAIN WILD-TYPE 15 6 4 5 12 4 3

Figure S19.  Get High-res Image Gene #10: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.12

Table S20.  Gene #10: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
8Q GAIN MUTATED 2 9 3 1 2 0 0
8Q GAIN WILD-TYPE 17 7 4 5 8 4 4

Figure S20.  Get High-res Image Gene #10: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00961 (Fisher's exact test), Q value = 0.053

Table S21.  Gene #10: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
8Q GAIN MUTATED 0 7 2 6
8Q GAIN WILD-TYPE 9 6 12 6

Figure S21.  Get High-res Image Gene #10: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0047

Table S22.  Gene #14: '11p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
11P GAIN MUTATED 1 10 0 1 1 0 2
11P GAIN WILD-TYPE 16 5 5 5 13 4 3

Figure S22.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0031

Table S23.  Gene #14: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
11P GAIN MUTATED 1 11 1 1 1 0 0
11P GAIN WILD-TYPE 18 5 6 5 9 4 4

Figure S23.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.11

Table S24.  Gene #14: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
11P GAIN MUTATED 1 4 3 2 3 2 0
11P GAIN WILD-TYPE 17 7 9 4 2 3 9

Figure S24.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00037

Table S25.  Gene #15: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
11Q GAIN MUTATED 1 11 0 1 0 0 2
11Q GAIN WILD-TYPE 16 4 5 5 14 4 3

Figure S25.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00037

Table S26.  Gene #15: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
11Q GAIN MUTATED 1 12 1 1 0 0 0
11Q GAIN WILD-TYPE 18 4 6 5 10 4 4

Figure S26.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.086

Table S27.  Gene #15: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
11Q GAIN MUTATED 1 5 3 2 3 1 0
11Q GAIN WILD-TYPE 17 6 9 4 2 4 9

Figure S27.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.1

Table S28.  Gene #15: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
11Q GAIN MUTATED 3 5 1 2 0 0 1 1 0
11Q GAIN WILD-TYPE 2 1 4 6 5 4 5 4 4

Figure S28.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S29.  Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
12P GAIN MUTATED 0 10 2 4
12P GAIN WILD-TYPE 9 3 12 8

Figure S29.  Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.12

Table S30.  Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
12Q GAIN MUTATED 4 10 0 2 3 0 1
12Q GAIN WILD-TYPE 13 5 5 4 11 4 4

Figure S30.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.12

Table S31.  Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
12Q GAIN MUTATED 1 7 4 1 2 2 3
12Q GAIN WILD-TYPE 17 4 8 5 3 3 6

Figure S31.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0073

Table S32.  Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
12Q GAIN MUTATED 0 10 3 5
12Q GAIN WILD-TYPE 9 3 11 7

Figure S32.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.079

Table S33.  Gene #18: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
14Q GAIN MUTATED 4 11 1 1 3 0 1
14Q GAIN WILD-TYPE 13 4 4 5 11 4 4

Figure S33.  Get High-res Image Gene #18: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.032

Table S34.  Gene #18: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
14Q GAIN MUTATED 4 12 1 1 2 1 0
14Q GAIN WILD-TYPE 15 4 6 5 8 3 4

Figure S34.  Get High-res Image Gene #18: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.09

Table S35.  Gene #18: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
14Q GAIN MUTATED 1 9 3 4
14Q GAIN WILD-TYPE 8 4 11 8

Figure S35.  Get High-res Image Gene #18: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.012

Table S36.  Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
16P GAIN MUTATED 4 12 1 1 2 0 2
16P GAIN WILD-TYPE 13 3 4 5 12 4 3

Figure S36.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0049

Table S37.  Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
16P GAIN MUTATED 4 13 2 1 1 1 0
16P GAIN WILD-TYPE 15 3 5 5 9 3 4

Figure S37.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00583 (Fisher's exact test), Q value = 0.036

Table S38.  Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
16P GAIN MUTATED 2 7 5 3 3 2 0
16P GAIN WILD-TYPE 16 4 7 3 2 3 9

Figure S38.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00567 (Fisher's exact test), Q value = 0.035

Table S39.  Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
16P GAIN MUTATED 1 10 3 4
16P GAIN WILD-TYPE 8 3 11 8

Figure S39.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00906 (Fisher's exact test), Q value = 0.05

Table S40.  Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
16P GAIN MUTATED 3 6 3 3 1 0 1 1 0
16P GAIN WILD-TYPE 2 0 2 5 4 4 5 4 4

Figure S40.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0036

Table S41.  Gene #21: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
16Q GAIN MUTATED 4 12 1 1 1 0 2
16Q GAIN WILD-TYPE 13 3 4 5 13 4 3

Figure S41.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0018

Table S42.  Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
16Q GAIN MUTATED 4 13 2 1 0 1 0
16Q GAIN WILD-TYPE 15 3 5 5 10 3 4

Figure S42.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00515 (Fisher's exact test), Q value = 0.033

Table S43.  Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
16Q GAIN MUTATED 2 7 5 3 3 1 0
16Q GAIN WILD-TYPE 16 4 7 3 2 4 9

Figure S43.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0019 (Fisher's exact test), Q value = 0.014

Table S44.  Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
16Q GAIN MUTATED 1 10 2 4
16Q GAIN WILD-TYPE 8 3 12 8

Figure S44.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00547 (Fisher's exact test), Q value = 0.034

Table S45.  Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
16Q GAIN MUTATED 3 6 3 2 1 0 1 1 0
16Q GAIN WILD-TYPE 2 0 2 6 4 4 5 4 4

Figure S45.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.09

Table S46.  Gene #22: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
18P GAIN MUTATED 1 8 1 1 2 1 3
18P GAIN WILD-TYPE 16 7 4 5 12 3 2

Figure S46.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.066

Table S47.  Gene #22: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
18P GAIN MUTATED 1 9 3 1 1 1 1
18P GAIN WILD-TYPE 18 7 4 5 9 3 3

Figure S47.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.048 (Fisher's exact test), Q value = 0.17

Table S48.  Gene #22: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
18P GAIN MUTATED 1 6 2 3 1 1 3
18P GAIN WILD-TYPE 17 5 10 3 4 4 6

Figure S48.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.017

Table S49.  Gene #22: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
18P GAIN MUTATED 1 9 1 4
18P GAIN WILD-TYPE 8 4 13 8

Figure S49.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.066

Table S50.  Gene #22: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
18P GAIN MUTATED 3 5 2 1 0 0 3 0 1
18P GAIN WILD-TYPE 2 1 3 7 5 4 3 5 3

Figure S50.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.17

Table S51.  Gene #23: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
18Q GAIN MUTATED 1 8 1 1 2 1 2
18Q GAIN WILD-TYPE 16 7 4 5 12 3 3

Figure S51.  Get High-res Image Gene #23: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.086

Table S52.  Gene #23: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
18Q GAIN MUTATED 1 9 2 1 1 1 1
18Q GAIN WILD-TYPE 18 7 5 5 9 3 3

Figure S52.  Get High-res Image Gene #23: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.014

Table S53.  Gene #23: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
18Q GAIN MUTATED 1 9 1 3
18Q GAIN WILD-TYPE 8 4 13 9

Figure S53.  Get High-res Image Gene #23: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.077

Table S54.  Gene #23: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
18Q GAIN MUTATED 3 5 2 1 0 0 2 0 1
18Q GAIN WILD-TYPE 2 1 3 7 5 4 4 5 3

Figure S54.  Get High-res Image Gene #23: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.1

Table S55.  Gene #24: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
19P GAIN MUTATED 13 2 5
19P GAIN WILD-TYPE 16 18 9

Figure S55.  Get High-res Image Gene #24: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.084

Table S56.  Gene #24: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
19P GAIN MUTATED 3 10 1 0 5 0 1
19P GAIN WILD-TYPE 14 5 4 6 9 4 4

Figure S56.  Get High-res Image Gene #24: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S57.  Gene #24: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
19P GAIN MUTATED 3 10 2 0 4 1 0
19P GAIN WILD-TYPE 16 6 5 6 6 3 4

Figure S57.  Get High-res Image Gene #24: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00357 (Fisher's exact test), Q value = 0.024

Table S58.  Gene #25: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
19Q GAIN MUTATED 2 10 1 0 5 0 0
19Q GAIN WILD-TYPE 15 5 4 6 9 4 5

Figure S58.  Get High-res Image Gene #25: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0063 (Fisher's exact test), Q value = 0.039

Table S59.  Gene #25: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
19Q GAIN MUTATED 2 10 1 0 4 1 0
19Q GAIN WILD-TYPE 17 6 6 6 6 3 4

Figure S59.  Get High-res Image Gene #25: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.081

Table S60.  Gene #26: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
20P GAIN MUTATED 4 10 1 0 4 0 3
20P GAIN WILD-TYPE 13 5 4 6 10 4 2

Figure S60.  Get High-res Image Gene #26: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.096

Table S61.  Gene #26: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
20P GAIN MUTATED 4 10 4 0 3 1 0
20P GAIN WILD-TYPE 15 6 3 6 7 3 4

Figure S61.  Get High-res Image Gene #26: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.092

Table S62.  Gene #26: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
20P GAIN MUTATED 1 6 5 1 3 3 3
20P GAIN WILD-TYPE 17 5 7 5 2 2 6

Figure S62.  Get High-res Image Gene #26: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.074

Table S63.  Gene #26: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
20P GAIN MUTATED 0 7 4 7
20P GAIN WILD-TYPE 9 6 10 5

Figure S63.  Get High-res Image Gene #26: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.084

Table S64.  Gene #27: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
20Q GAIN MUTATED 4 10 1 0 4 0 3
20Q GAIN WILD-TYPE 13 5 4 6 10 4 2

Figure S64.  Get High-res Image Gene #27: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.095

Table S65.  Gene #27: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
20Q GAIN MUTATED 4 10 4 0 3 1 0
20Q GAIN WILD-TYPE 15 6 3 6 7 3 4

Figure S65.  Get High-res Image Gene #27: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.09

Table S66.  Gene #27: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
20Q GAIN MUTATED 1 6 5 1 3 3 3
20Q GAIN WILD-TYPE 17 5 7 5 2 2 6

Figure S66.  Get High-res Image Gene #27: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.074

Table S67.  Gene #27: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
20Q GAIN MUTATED 0 7 4 7
20Q GAIN WILD-TYPE 9 6 10 5

Figure S67.  Get High-res Image Gene #27: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.096

Table S68.  Gene #29: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
22Q GAIN MUTATED 1 7 5 1 2 1 2
22Q GAIN WILD-TYPE 17 4 7 5 3 4 7

Figure S68.  Get High-res Image Gene #29: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00993 (Fisher's exact test), Q value = 0.054

Table S69.  Gene #29: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
22Q GAIN MUTATED 1 9 2 4
22Q GAIN WILD-TYPE 8 4 12 8

Figure S69.  Get High-res Image Gene #29: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00227 (Fisher's exact test), Q value = 0.016

Table S70.  Gene #29: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
22Q GAIN MUTATED 3 5 3 0 0 0 3 2 0
22Q GAIN WILD-TYPE 2 1 2 8 5 4 3 3 4

Figure S70.  Get High-res Image Gene #29: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00761 (Fisher's exact test), Q value = 0.044

Table S71.  Gene #30: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
XP GAIN MUTATED 0 6 1 1 0 0 0
XP GAIN WILD-TYPE 17 9 4 5 14 4 5

Figure S71.  Get High-res Image Gene #30: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.086

Table S72.  Gene #30: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
XP GAIN MUTATED 0 6 1 1 0 0 0
XP GAIN WILD-TYPE 19 10 6 5 10 4 4

Figure S72.  Get High-res Image Gene #30: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00734 (Fisher's exact test), Q value = 0.044

Table S73.  Gene #30: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
XP GAIN MUTATED 0 5 0 1
XP GAIN WILD-TYPE 9 8 14 11

Figure S73.  Get High-res Image Gene #30: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.12

Table S74.  Gene #30: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
XP GAIN MUTATED 2 3 0 0 0 0 0 1 0
XP GAIN WILD-TYPE 3 3 5 8 5 4 6 4 4

Figure S74.  Get High-res Image Gene #30: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00782 (Fisher's exact test), Q value = 0.045

Table S75.  Gene #31: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
XQ GAIN MUTATED 0 6 1 1 0 0 0
XQ GAIN WILD-TYPE 17 9 4 5 14 4 5

Figure S75.  Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.084

Table S76.  Gene #31: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
XQ GAIN MUTATED 0 6 1 1 0 0 0
XQ GAIN WILD-TYPE 19 10 6 5 10 4 4

Figure S76.  Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00795 (Fisher's exact test), Q value = 0.045

Table S77.  Gene #31: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
XQ GAIN MUTATED 0 5 0 1
XQ GAIN WILD-TYPE 9 8 14 11

Figure S77.  Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.12

Table S78.  Gene #31: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
XQ GAIN MUTATED 2 3 0 0 0 0 0 1 0
XQ GAIN WILD-TYPE 3 3 5 8 5 4 6 4 4

Figure S78.  Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S79.  Gene #32: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
1P LOSS MUTATED 19 27 7
1P LOSS WILD-TYPE 0 2 11

Figure S79.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.003

Table S80.  Gene #32: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
1P LOSS MUTATED 17 10 5 4 13 0 4
1P LOSS WILD-TYPE 0 5 0 2 1 4 1

Figure S80.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.003

Table S81.  Gene #32: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
1P LOSS MUTATED 19 11 6 4 9 4 0
1P LOSS WILD-TYPE 0 5 1 2 1 0 4

Figure S81.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.0099

Table S82.  Gene #32: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
1P LOSS MUTATED 18 8 11 4 4 5 3
1P LOSS WILD-TYPE 0 3 1 2 1 0 6

Figure S82.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0045

Table S83.  Gene #32: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
1P LOSS MUTATED 9 6 14 7
1P LOSS WILD-TYPE 0 7 0 5

Figure S83.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00204 (Fisher's exact test), Q value = 0.014

Table S84.  Gene #32: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
1P LOSS MUTATED 3 3 5 8 5 4 4 4 0
1P LOSS WILD-TYPE 2 3 0 0 0 0 2 1 4

Figure S84.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S85.  Gene #33: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
1Q LOSS MUTATED 19 26 6
1Q LOSS WILD-TYPE 0 3 12

Figure S85.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00037

Table S86.  Gene #33: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
1Q LOSS MUTATED 17 9 5 3 14 0 3
1Q LOSS WILD-TYPE 0 6 0 3 0 4 2

Figure S86.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00097

Table S87.  Gene #33: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
1Q LOSS MUTATED 19 10 5 3 10 4 0
1Q LOSS WILD-TYPE 0 6 2 3 0 0 4

Figure S87.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0032

Table S88.  Gene #33: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
1Q LOSS MUTATED 18 7 11 3 4 5 3
1Q LOSS WILD-TYPE 0 4 1 3 1 0 6

Figure S88.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.032

Table S89.  Gene #33: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
1Q LOSS MUTATED 9 6 13 7
1Q LOSS WILD-TYPE 0 7 1 5

Figure S89.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.062

Table S90.  Gene #33: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
1Q LOSS MUTATED 3 3 5 7 5 4 4 4 0
1Q LOSS WILD-TYPE 2 3 0 1 0 0 2 1 4

Figure S90.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S91.  Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
2P LOSS MUTATED 19 24 3
2P LOSS WILD-TYPE 0 5 15

Figure S91.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S92.  Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
2P LOSS MUTATED 17 9 4 0 13 0 3
2P LOSS WILD-TYPE 0 6 1 6 1 4 2

Figure S92.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S93.  Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
2P LOSS MUTATED 19 10 4 0 10 3 0
2P LOSS WILD-TYPE 0 6 3 6 0 1 4

Figure S93.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00037

Table S94.  Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
2P LOSS MUTATED 18 7 10 2 3 5 1
2P LOSS WILD-TYPE 0 4 2 4 2 0 8

Figure S94.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S95.  Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
2P LOSS MUTATED 9 4 14 5
2P LOSS WILD-TYPE 0 9 0 7

Figure S95.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S96.  Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
2P LOSS MUTATED 3 2 5 8 5 4 3 2 0
2P LOSS WILD-TYPE 2 4 0 0 0 0 3 3 4

Figure S96.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S97.  Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
2Q LOSS MUTATED 19 24 3
2Q LOSS WILD-TYPE 0 5 15

Figure S97.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S98.  Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
2Q LOSS MUTATED 17 9 4 0 13 0 3
2Q LOSS WILD-TYPE 0 6 1 6 1 4 2

Figure S98.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S99.  Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
2Q LOSS MUTATED 19 10 4 0 10 3 0
2Q LOSS WILD-TYPE 0 6 3 6 0 1 4

Figure S99.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S100.  Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
2Q LOSS MUTATED 18 7 10 2 3 5 1
2Q LOSS WILD-TYPE 0 4 2 4 2 0 8

Figure S100.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S101.  Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
2Q LOSS MUTATED 9 4 14 5
2Q LOSS WILD-TYPE 0 9 0 7

Figure S101.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0047

Table S102.  Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
2Q LOSS MUTATED 3 2 5 8 5 4 3 2 0
2Q LOSS WILD-TYPE 2 4 0 0 0 0 3 3 4

Figure S102.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.018

Table S103.  Gene #36: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
3P LOSS MUTATED 0 6 0 1 0 2 0
3P LOSS WILD-TYPE 19 10 7 5 10 2 4

Figure S103.  Get High-res Image Gene #36: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00196 (Fisher's exact test), Q value = 0.014

Table S104.  Gene #37: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
3Q LOSS MUTATED 0 6 0 0 0 2 0
3Q LOSS WILD-TYPE 19 10 7 6 10 2 4

Figure S104.  Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.00807 (Fisher's exact test), Q value = 0.045

Table S105.  Gene #38: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 26 2
5P LOSS MUTATED 10 0 0
5P LOSS WILD-TYPE 28 26 2

Figure S105.  Get High-res Image Gene #38: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.072

Table S106.  Gene #38: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
5P LOSS MUTATED 1 6 2 0 0 0 1
5P LOSS WILD-TYPE 16 9 3 6 14 4 4

Figure S106.  Get High-res Image Gene #38: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.084

Table S107.  Gene #38: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
5P LOSS MUTATED 1 6 3 0 0 0 0
5P LOSS WILD-TYPE 18 10 4 6 10 4 4

Figure S107.  Get High-res Image Gene #38: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.073

Table S108.  Gene #38: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
5P LOSS MUTATED 0 2 3 1 3 1 0
5P LOSS WILD-TYPE 18 9 9 5 2 4 9

Figure S108.  Get High-res Image Gene #38: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.0068 (Fisher's exact test), Q value = 0.041

Table S109.  Gene #39: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 26 2
5Q LOSS MUTATED 10 0 0
5Q LOSS WILD-TYPE 28 26 2

Figure S109.  Get High-res Image Gene #39: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.073

Table S110.  Gene #39: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
5Q LOSS MUTATED 1 6 2 0 0 0 1
5Q LOSS WILD-TYPE 16 9 3 6 14 4 4

Figure S110.  Get High-res Image Gene #39: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.084

Table S111.  Gene #39: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
5Q LOSS MUTATED 1 6 3 0 0 0 0
5Q LOSS WILD-TYPE 18 10 4 6 10 4 4

Figure S111.  Get High-res Image Gene #39: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.072

Table S112.  Gene #39: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
5Q LOSS MUTATED 0 2 3 1 3 1 0
5Q LOSS WILD-TYPE 18 9 9 5 2 4 9

Figure S112.  Get High-res Image Gene #39: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S113.  Gene #40: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
6P LOSS MUTATED 19 26 6
6P LOSS WILD-TYPE 0 3 12

Figure S113.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S114.  Gene #40: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
6P LOSS MUTATED 17 10 4 1 14 0 5
6P LOSS WILD-TYPE 0 5 1 5 0 4 0

Figure S114.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S115.  Gene #40: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
6P LOSS MUTATED 19 11 6 1 10 4 0
6P LOSS WILD-TYPE 0 5 1 5 0 0 4

Figure S115.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.01

Table S116.  Gene #40: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
6P LOSS MUTATED 18 8 10 3 4 5 3
6P LOSS WILD-TYPE 0 3 2 3 1 0 6

Figure S116.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.003

Table S117.  Gene #40: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
6P LOSS MUTATED 9 5 14 8
6P LOSS WILD-TYPE 0 8 0 4

Figure S117.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.0011

Table S118.  Gene #40: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
6P LOSS MUTATED 3 3 5 8 5 4 6 2 0
6P LOSS WILD-TYPE 2 3 0 0 0 0 0 3 4

Figure S118.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S119.  Gene #41: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
6Q LOSS MUTATED 19 26 6
6Q LOSS WILD-TYPE 0 3 12

Figure S119.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S120.  Gene #41: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
6Q LOSS MUTATED 17 10 4 1 14 0 5
6Q LOSS WILD-TYPE 0 5 1 5 0 4 0

Figure S120.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S121.  Gene #41: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
6Q LOSS MUTATED 19 11 6 1 10 4 0
6Q LOSS WILD-TYPE 0 5 1 5 0 0 4

Figure S121.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.01

Table S122.  Gene #41: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
6Q LOSS MUTATED 18 8 10 3 4 5 3
6Q LOSS WILD-TYPE 0 3 2 3 1 0 6

Figure S122.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S123.  Gene #41: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
6Q LOSS MUTATED 9 5 14 8
6Q LOSS WILD-TYPE 0 8 0 4

Figure S123.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0016

Table S124.  Gene #41: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
6Q LOSS MUTATED 3 3 5 8 5 4 6 2 0
6Q LOSS WILD-TYPE 2 3 0 0 0 0 0 3 4

Figure S124.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00037

Table S125.  Gene #42: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 26 2
8P LOSS MUTATED 0 10 0
8P LOSS WILD-TYPE 38 16 2

Figure S125.  Get High-res Image Gene #42: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.09

Table S126.  Gene #42: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
8P LOSS MUTATED 6 4 0
8P LOSS WILD-TYPE 13 25 18

Figure S126.  Get High-res Image Gene #42: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.097

Table S127.  Gene #42: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 17 20
8P LOSS MUTATED 2 1 7
8P LOSS WILD-TYPE 24 16 13

Figure S127.  Get High-res Image Gene #42: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

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

Table S128.  Gene #42: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
8P LOSS MUTATED 2 7 1
8P LOSS WILD-TYPE 27 13 13

Figure S128.  Get High-res Image Gene #42: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.084

Table S129.  Gene #42: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
8P LOSS MUTATED 0 0 3 2 0 0 0 0 0
8P LOSS WILD-TYPE 5 6 2 6 5 4 6 5 4

Figure S129.  Get High-res Image Gene #42: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0023

Table S130.  Gene #43: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 26 2
8Q LOSS MUTATED 0 9 0
8Q LOSS WILD-TYPE 38 17 2

Figure S130.  Get High-res Image Gene #43: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.079

Table S131.  Gene #43: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
8Q LOSS MUTATED 6 3 0
8Q LOSS WILD-TYPE 13 26 18

Figure S131.  Get High-res Image Gene #43: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.084

Table S132.  Gene #43: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
8Q LOSS MUTATED 0 0 3 2 0 0 0 0 0
8Q LOSS WILD-TYPE 5 6 2 6 5 4 6 5 4

Figure S132.  Get High-res Image Gene #43: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

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

Table S133.  Gene #44: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
9P LOSS MUTATED 0 2 3 1 1 0 2
9P LOSS WILD-TYPE 17 13 2 5 13 4 3

Figure S133.  Get High-res Image Gene #44: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00504 (Fisher's exact test), Q value = 0.033

Table S134.  Gene #44: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
9P LOSS MUTATED 0 3 4 1 0 1 0
9P LOSS WILD-TYPE 19 13 3 5 10 3 4

Figure S134.  Get High-res Image Gene #44: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.089

Table S135.  Gene #45: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
9Q LOSS MUTATED 0 2 3 1 2 0 2
9Q LOSS WILD-TYPE 17 13 2 5 12 4 3

Figure S135.  Get High-res Image Gene #45: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.075

Table S136.  Gene #45: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
9Q LOSS MUTATED 0 3 4 1 1 1 0
9Q LOSS WILD-TYPE 19 13 3 5 9 3 4

Figure S136.  Get High-res Image Gene #45: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00052

Table S137.  Gene #46: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
10P LOSS MUTATED 19 23 6
10P LOSS WILD-TYPE 0 6 12

Figure S137.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S138.  Gene #46: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
10P LOSS MUTATED 17 7 5 2 13 0 4
10P LOSS WILD-TYPE 0 8 0 4 1 4 1

Figure S138.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S139.  Gene #46: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
10P LOSS MUTATED 19 8 6 2 10 3 0
10P LOSS WILD-TYPE 0 8 1 4 0 1 4

Figure S139.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0027

Table S140.  Gene #46: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
10P LOSS MUTATED 18 6 11 2 4 4 3
10P LOSS WILD-TYPE 0 5 1 4 1 1 6

Figure S140.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.012

Table S141.  Gene #46: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
10P LOSS MUTATED 9 4 12 7
10P LOSS WILD-TYPE 0 9 2 5

Figure S141.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00726 (Fisher's exact test), Q value = 0.044

Table S142.  Gene #46: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
10P LOSS MUTATED 3 2 4 7 5 4 5 2 0
10P LOSS WILD-TYPE 2 4 1 1 0 0 1 3 4

Figure S142.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00037

Table S143.  Gene #47: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
10Q LOSS MUTATED 19 24 6
10Q LOSS WILD-TYPE 0 5 12

Figure S143.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S144.  Gene #47: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
10Q LOSS MUTATED 17 7 5 2 14 0 4
10Q LOSS WILD-TYPE 0 8 0 4 0 4 1

Figure S144.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S145.  Gene #47: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
10Q LOSS MUTATED 19 8 6 2 10 4 0
10Q LOSS WILD-TYPE 0 8 1 4 0 0 4

Figure S145.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S146.  Gene #47: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
10Q LOSS MUTATED 18 7 11 2 4 4 3
10Q LOSS WILD-TYPE 0 4 1 4 1 1 6

Figure S146.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00543 (Fisher's exact test), Q value = 0.034

Table S147.  Gene #47: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
10Q LOSS MUTATED 9 5 12 7
10Q LOSS WILD-TYPE 0 8 2 5

Figure S147.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00178 (Fisher's exact test), Q value = 0.013

Table S148.  Gene #47: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
10Q LOSS MUTATED 3 2 5 7 5 4 5 2 0
10Q LOSS WILD-TYPE 2 4 0 1 0 0 1 3 4

Figure S148.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.003

Table S149.  Gene #50: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
13Q LOSS MUTATED 13 25 5
13Q LOSS WILD-TYPE 6 4 13

Figure S149.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

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

Table S150.  Gene #50: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
13Q LOSS MUTATED 13 10 3 0 13 0 4
13Q LOSS WILD-TYPE 4 5 2 6 1 4 1

Figure S150.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00068

Table S151.  Gene #50: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
13Q LOSS MUTATED 15 10 5 0 10 3 0
13Q LOSS WILD-TYPE 4 6 2 6 0 1 4

Figure S151.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0076

Table S152.  Gene #50: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
13Q LOSS MUTATED 6 4 14 7
13Q LOSS WILD-TYPE 3 9 0 5

Figure S152.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00766 (Fisher's exact test), Q value = 0.044

Table S153.  Gene #50: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
13Q LOSS MUTATED 2 3 3 8 4 4 5 2 0
13Q LOSS WILD-TYPE 3 3 2 0 1 0 1 3 4

Figure S153.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.13

Table S154.  Gene #52: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
16Q LOSS MUTATED 0 0 0 0 4 0 1
16Q LOSS WILD-TYPE 17 15 5 6 10 4 4

Figure S154.  Get High-res Image Gene #52: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00749 (Fisher's exact test), Q value = 0.044

Table S155.  Gene #52: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
16Q LOSS MUTATED 0 0 1 0 4 0 0
16Q LOSS WILD-TYPE 19 16 6 6 6 4 4

Figure S155.  Get High-res Image Gene #52: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0497 (Fisher's exact test), Q value = 0.17

Table S156.  Gene #52: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
16Q LOSS MUTATED 1 0 0 0 0 2 2
16Q LOSS WILD-TYPE 17 11 12 6 5 3 7

Figure S156.  Get High-res Image Gene #52: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S157.  Gene #53: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
17P LOSS MUTATED 19 27 4
17P LOSS WILD-TYPE 0 2 14

Figure S157.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S158.  Gene #53: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
17P LOSS MUTATED 17 10 5 0 14 0 4
17P LOSS WILD-TYPE 0 5 0 6 0 4 1

Figure S158.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S159.  Gene #53: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
17P LOSS MUTATED 19 11 6 0 10 4 0
17P LOSS WILD-TYPE 0 5 1 6 0 0 4

Figure S159.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00083

Table S160.  Gene #53: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
17P LOSS MUTATED 18 8 11 3 3 5 2
17P LOSS WILD-TYPE 0 3 1 3 2 0 7

Figure S160.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0011

Table S161.  Gene #53: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
17P LOSS MUTATED 9 5 14 6
17P LOSS WILD-TYPE 0 8 0 6

Figure S161.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0091

Table S162.  Gene #53: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
17P LOSS MUTATED 3 3 5 8 5 4 4 2 0
17P LOSS WILD-TYPE 2 3 0 0 0 0 2 3 4

Figure S162.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S163.  Gene #54: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
17Q LOSS MUTATED 19 27 4
17Q LOSS WILD-TYPE 0 2 14

Figure S163.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S164.  Gene #54: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
17Q LOSS MUTATED 17 10 5 0 14 0 4
17Q LOSS WILD-TYPE 0 5 0 6 0 4 1

Figure S164.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S165.  Gene #54: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
17Q LOSS MUTATED 19 11 6 0 10 4 0
17Q LOSS WILD-TYPE 0 5 1 6 0 0 4

Figure S165.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.0012

Table S166.  Gene #54: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
17Q LOSS MUTATED 18 8 11 3 3 5 2
17Q LOSS WILD-TYPE 0 3 1 3 2 0 7

Figure S166.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0014

Table S167.  Gene #54: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
17Q LOSS MUTATED 9 5 14 6
17Q LOSS WILD-TYPE 0 8 0 6

Figure S167.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0099

Table S168.  Gene #54: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
17Q LOSS MUTATED 3 3 5 8 5 4 4 2 0
17Q LOSS WILD-TYPE 2 3 0 0 0 0 2 3 4

Figure S168.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.14

Table S169.  Gene #56: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
18Q LOSS MUTATED 0 7 2
18Q LOSS WILD-TYPE 19 22 16

Figure S169.  Get High-res Image Gene #56: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.13

Table S170.  Gene #56: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
18Q LOSS MUTATED 1 1 0 0 4 0 3
18Q LOSS WILD-TYPE 16 14 5 6 10 4 2

Figure S170.  Get High-res Image Gene #56: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.05 (Fisher's exact test), Q value = 0.17

Table S171.  Gene #57: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
19Q LOSS MUTATED 1 0 0 0 0 0 2
19Q LOSS WILD-TYPE 16 15 5 6 14 4 3

Figure S171.  Get High-res Image Gene #57: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.13

Table S172.  Gene #60: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
21Q LOSS MUTATED 13 17 5
21Q LOSS WILD-TYPE 6 12 13

Figure S172.  Get High-res Image Gene #60: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.098

Table S173.  Gene #61: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
22Q LOSS MUTATED 1 7 0
22Q LOSS WILD-TYPE 18 22 18

Figure S173.  Get High-res Image Gene #61: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.003

Table S174.  Gene #62: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
XP LOSS MUTATED 14 21 3
XP LOSS WILD-TYPE 5 8 15

Figure S174.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0031

Table S175.  Gene #62: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
XP LOSS MUTATED 14 4 4 2 12 0 2
XP LOSS WILD-TYPE 3 11 1 4 2 4 3

Figure S175.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.003

Table S176.  Gene #62: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
XP LOSS MUTATED 16 5 3 2 9 3 0
XP LOSS WILD-TYPE 3 11 4 4 1 1 4

Figure S176.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00052

Table S177.  Gene #62: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
XP LOSS MUTATED 18 4 7 2 2 4 1
XP LOSS WILD-TYPE 0 7 5 4 3 1 8

Figure S177.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00037

Table S178.  Gene #62: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
XP LOSS MUTATED 9 2 12 3
XP LOSS WILD-TYPE 0 11 2 9

Figure S178.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.059

Table S179.  Gene #62: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
XP LOSS MUTATED 3 1 2 6 5 4 2 3 0
XP LOSS WILD-TYPE 2 5 3 2 0 0 4 2 4

Figure S179.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.012

Table S180.  Gene #63: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 29 18
XQ LOSS MUTATED 13 21 4
XQ LOSS WILD-TYPE 6 8 14

Figure S180.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0075

Table S181.  Gene #63: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 17 15 5 6 14 4 5
XQ LOSS MUTATED 13 4 4 2 12 0 3
XQ LOSS WILD-TYPE 4 11 1 4 2 4 2

Figure S181.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.011

Table S182.  Gene #63: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
XQ LOSS MUTATED 15 5 4 2 9 3 0
XQ LOSS WILD-TYPE 4 11 3 4 1 1 4

Figure S182.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0073

Table S183.  Gene #63: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
XQ LOSS MUTATED 17 4 7 2 2 4 2
XQ LOSS WILD-TYPE 1 7 5 4 3 1 7

Figure S183.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0012

Table S184.  Gene #63: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 14 12
XQ LOSS MUTATED 9 2 11 4
XQ LOSS WILD-TYPE 0 11 3 8

Figure S184.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0498 (Fisher's exact test), Q value = 0.17

Table S185.  Gene #63: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 5 6 5 8 5 4 6 5 4
XQ LOSS MUTATED 3 1 2 6 5 3 3 3 0
XQ LOSS WILD-TYPE 2 5 3 2 0 1 3 2 4

Figure S185.  Get High-res Image Gene #63: 'xq 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/KICH-TP/22507962/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/22539844/KICH-TP.transferedmergedcluster.txt

  • Number of patients = 66

  • Number of significantly arm-level cnvs = 63

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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