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 8 molecular subtypes across 66 patients, 151 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 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 'MRNASEQ_CNMF'.

  • 7q gain cnv correlated to 'MRNASEQ_CNMF'.

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

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

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

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

  • 12q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

  • 15q gain cnv correlated to 'MRNASEQ_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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

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

  • xp gain cnv correlated to 'MRNASEQ_CNMF'.

  • xq gain cnv correlated to 'MRNASEQ_CNMF'.

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

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

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

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

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

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

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

  • 8p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 9p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 9q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

  • 21q loss cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • xq loss cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', 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 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 151 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
2p loss 46 (70%) 20 0.087
(0.236) 		1e-05
(0.000187) 		1e-05
(0.000187) 		1e-05
(0.000187) 		0.0827
(0.229) 		1e-05
(0.000187) 		0.0306
(0.12) 		0.00071
(0.00585)
2q loss 46 (70%) 20 0.0875
(0.236) 		1e-05
(0.000187) 		1e-05
(0.000187) 		1e-05
(0.000187) 		0.084
(0.23) 		1e-05
(0.000187) 		0.0306
(0.12) 		0.00067
(0.00571)
17p loss 50 (76%) 16 0.301
(0.527) 		1e-05
(0.000187) 		1e-05
(0.000187) 		1e-05
(0.000187) 		0.0511
(0.168) 		8e-05
(0.00101) 		0.0491
(0.164) 		0.00226
(0.0148)
17q loss 50 (76%) 16 0.3
(0.527) 		1e-05
(0.000187) 		1e-05
(0.000187) 		1e-05
(0.000187) 		0.0535
(0.173) 		5e-05
(0.00072) 		0.0491
(0.164) 		0.00193
(0.0131)
4p gain 24 (36%) 42 0.0552
(0.177) 		1
(1.00) 		2e-05
(0.000315) 		7e-05
(0.000928) 		0.77
(0.896) 		0.0086
(0.0451) 		0.0349
(0.129) 		0.0174
(0.0775)
4q gain 24 (36%) 42 0.0556
(0.177) 		1
(1.00) 		2e-05
(0.000315) 		5e-05
(0.00072) 		0.772
(0.896) 		0.00898
(0.0462) 		0.0349
(0.129) 		0.0173
(0.0775)
16p gain 21 (32%) 45 0.105
(0.265) 		1
(1.00) 		1e-05
(0.000187) 		0.00012
(0.00137) 		0.159
(0.349) 		0.00522
(0.0306) 		0.0312
(0.12) 		0.00706
(0.0376)
16q gain 21 (32%) 45 0.104
(0.265) 		1
(1.00) 		1e-05
(0.000187) 		0.0001
(0.00117) 		0.16
(0.349) 		0.0053
(0.0307) 		0.0312
(0.12) 		0.00703
(0.0376)
1p loss 53 (80%) 13 0.672
(0.853) 		2e-05
(0.000315) 		0.00043
(0.0038) 		0.00038
(0.00355) 		0.163
(0.351) 		0.00085
(0.0068) 		0.176
(0.37) 		0.00366
(0.0225)
1q loss 52 (79%) 14 0.478
(0.7) 		1e-05
(0.000187) 		2e-05
(0.000315) 		6e-05
(0.00084) 		0.229
(0.44) 		0.00042
(0.00378) 		0.176
(0.37) 		0.00449
(0.0266)
6p loss 51 (77%) 15 0.331
(0.56) 		0.00018
(0.00197) 		3e-05
(0.000458) 		1e-05
(0.000187) 		0.35
(0.579) 		0.00127
(0.00922) 		0.176
(0.37) 		0.00031
(0.003)
6q loss 51 (77%) 15 0.328
(0.558) 		8e-05
(0.00101) 		7e-05
(0.000928) 		1e-05
(0.000187) 		0.351
(0.579) 		0.00118
(0.00875) 		0.176
(0.37) 		0.00028
(0.00288)
10p loss 48 (73%) 18 0.339
(0.569) 		0.00029
(0.00292) 		0.0001
(0.00117) 		1e-05
(0.000187) 		0.273
(0.497) 		0.00016
(0.00179) 		0.759
(0.896) 		0.0102
(0.0506)
10q loss 49 (74%) 17 0.247
(0.466) 		0.0003
(0.00296) 		1e-05
(0.000187) 		1e-05
(0.000187) 		0.228
(0.44) 		0.00019
(0.00204) 		0.538
(0.754) 		0.00292
(0.0188)
xp loss 38 (58%) 28 0.125
(0.298) 		0.00294
(0.0188) 		0.00025
(0.00262) 		0.00039
(0.00357) 		0.189
(0.392) 		1e-05
(0.000187) 		0.239
(0.455) 		0.0124
(0.0609)
18p gain 17 (26%) 49 0.517
(0.737) 		0.807
(0.93) 		0.00218
(0.0145) 		0.0136
(0.0658) 		0.937
(1.00) 		0.0488
(0.164) 		0.341
(0.57) 		0.048
(0.164)
13q loss 43 (65%) 23 0.261
(0.486) 		0.00059
(0.00513) 		0.00381
(0.0229) 		9e-05
(0.00111) 		0.852
(0.953) 		0.197
(0.402) 		0.541
(0.755) 		0.00567
(0.0321)
xq loss 39 (59%) 27 0.601
(0.806) 		0.0734
(0.209) 		0.00654
(0.0362) 		0.00341
(0.0212) 		0.329
(0.558) 		0.001
(0.00771) 		0.77
(0.896) 		0.0374
(0.135)
8p gain 17 (26%) 49 0.41
(0.646) 		0.416
(0.651) 		0.00372
(0.0226) 		0.0324
(0.122) 		0.467
(0.687) 		0.0987
(0.257) 		1
(1.00) 		0.0284
(0.115)
8q gain 18 (27%) 48 0.339
(0.569) 		0.374
(0.606) 		0.0011
(0.00827) 		0.0101
(0.0503) 		0.695
(0.853) 		0.088
(0.236) 		0.751
(0.896) 		0.0427
(0.149)
11p gain 15 (23%) 51 0.285
(0.51) 		0.679
(0.853) 		2e-05
(0.000315) 		0.00038
(0.00355) 		0.872
(0.968) 		0.0271
(0.111) 		0.197
(0.402) 		0.0769
(0.218)
11q gain 15 (23%) 51 0.279
(0.503) 		0.676
(0.853) 		1e-05
(0.000187) 		1e-05
(0.000187) 		0.619
(0.821) 		0.0199
(0.0859) 		0.197
(0.402) 		0.104
(0.265)
14q gain 21 (32%) 45 0.107
(0.267) 		0.828
(0.933) 		0.00072
(0.00585) 		0.00546
(0.0313) 		0.426
(0.658) 		0.0561
(0.177) 		0.0312
(0.12) 		0.0794
(0.221)
19p gain 19 (29%) 47 0.483
(0.703) 		0.275
(0.498) 		0.0225
(0.0955) 		0.00893
(0.0462) 		0.661
(0.853) 		0.0387
(0.137) 		1
(1.00) 		0.709
(0.865)
19q gain 17 (26%) 49 0.52
(0.738) 		0.308
(0.537) 		0.00128
(0.00922) 		0.00144
(0.0102) 		0.408
(0.646) 		0.0474
(0.164) 		1
(1.00) 		0.657
(0.853)
20p gain 20 (30%) 46 0.217
(0.423) 		0.596
(0.806) 		0.0301
(0.12) 		0.0317
(0.121) 		0.709
(0.865) 		0.0313
(0.12) 		0.535
(0.751) 		0.182
(0.38)
3q loss 8 (12%) 58 0.0212
(0.0906) 		0.369
(0.6) 		0.0258
(0.106) 		0.00204
(0.0137) 		0.568
(0.787) 		0.182
(0.38) 		0.142
(0.322) 		0.693
(0.853)
5p loss 10 (15%) 56 0.0992
(0.257) 		0.251
(0.471) 		0.00068
(0.00571) 		0.0186
(0.0824) 		0.426
(0.658) 		0.0144
(0.0687) 		0.451
(0.671) 		0.345
(0.575)
5q loss 10 (15%) 56 0.0986
(0.257) 		0.255
(0.476) 		0.0009
(0.00709) 		0.0193
(0.0838) 		0.427
(0.658) 		0.0144
(0.0687) 		0.451
(0.671) 		0.346
(0.575)
16q loss 5 (8%) 61 0.719
(0.867) 		0.384
(0.612) 		0.00584
(0.0327) 		0.00677
(0.0371) 		0.428
(0.658) 		0.049
(0.164) 		0.0724
(0.207) 		0.689
(0.853)
18q gain 16 (24%) 50 0.639
(0.841) 		0.928
(1.00) 		0.00101
(0.00771) 		0.0191
(0.0837) 		0.822
(0.933) 		0.0515
(0.169) 		0.119
(0.285) 		0.0622
(0.188)
20q gain 21 (32%) 45 0.227
(0.44) 		0.389
(0.619) 		0.0685
(0.2) 		0.0172
(0.0775) 		0.677
(0.853) 		0.0359
(0.132) 		0.762
(0.896) 		0.0983
(0.257)
22q gain 19 (29%) 47 0.9
(0.982) 		0.714
(0.867) 		0.069
(0.2) 		0.362
(0.592) 		0.555
(0.771) 		0.0233
(0.0969) 		1
(1.00) 		0.0094
(0.0479)
3p loss 9 (14%) 57 0.036
(0.132) 		0.897
(0.982) 		0.0642
(0.19) 		0.00328
(0.0207) 		0.904
(0.982) 		0.204
(0.409) 		0.381
(0.609) 		0.847
(0.949)
8p loss 9 (14%) 57 1e-05
(0.000187) 		0.0864
(0.235) 		0.0533
(0.173) 		0.0386
(0.137) 		0.149
(0.335) 		0.465
(0.687) 		0.142
(0.322) 		0.32
(0.548)
8q loss 8 (12%) 58 1e-05
(0.000187) 		0.0437
(0.152) 		0.134
(0.311) 		0.071
(0.204) 		0.291
(0.516) 		0.529
(0.747) 		0.142
(0.322) 		0.322
(0.55)
16p loss 4 (6%) 62 0.685
(0.853) 		0.515
(0.737) 		0.0228
(0.0958) 		0.0373
(0.135) 		0.68
(0.853) 		0.0892
(0.238) 		0.286
(0.51) 		0.985
(1.00)
21q loss 35 (53%) 31 0.773
(0.896) 		0.00998
(0.0503) 		0.248
(0.467) 		0.196
(0.402) 		1
(1.00) 		0.128
(0.299) 		1
(1.00) 		0.0427
(0.149)
7p gain 24 (36%) 42 0.15
(0.336) 		1
(1.00) 		0.016
(0.0753) 		0.0615
(0.188) 		0.902
(0.982) 		0.117
(0.285) 		0.766
(0.896) 		0.101
(0.259)
7q gain 24 (36%) 42 0.153
(0.341) 		1
(1.00) 		0.0162
(0.0756) 		0.0623
(0.188) 		0.901
(0.982) 		0.117
(0.285) 		0.766
(0.896) 		0.0993
(0.257)
12q gain 20 (30%) 46 0.443
(0.671) 		0.596
(0.806) 		0.146
(0.33) 		0.0838
(0.23) 		0.944
(1.00) 		0.0319
(0.121) 		0.235
(0.449) 		0.132
(0.308)
15q gain 21 (32%) 45 0.107
(0.267) 		0.831
(0.933) 		0.00175
(0.0121) 		0.0618
(0.188) 		0.755
(0.896) 		0.213
(0.419) 		0.762
(0.896) 		0.475
(0.697)
xp gain 7 (11%) 59 0.808
(0.93) 		0.318
(0.547) 		0.00154
(0.0108) 		0.0508
(0.168) 		0.157
(0.348) 		0.111
(0.274) 		0.381
(0.609) 		0.119
(0.285)
xq gain 6 (9%) 60 1
(1.00) 		0.722
(0.867) 		0.00708
(0.0376) 		0.122
(0.292) 		0.265
(0.487) 		0.118
(0.285) 		0.142
(0.322) 		0.0687
(0.2)
9p loss 10 (15%) 56 1
(1.00) 		0.903
(0.982) 		0.0641
(0.19) 		0.0166
(0.076) 		0.911
(0.986) 		0.6
(0.806) 		0.695
(0.853) 		0.891
(0.982)
9q loss 10 (15%) 56 1
(1.00) 		0.904
(0.982) 		0.0637
(0.19) 		0.0164
(0.076) 		0.912
(0.986) 		0.598
(0.806) 		0.695
(0.853) 		0.892
(0.982)
3p gain 8 (12%) 58 0.268
(0.491) 		0.529
(0.747) 		0.952
(1.00) 		0.649
(0.848) 		0.515
(0.737) 		0.691
(0.853) 		0.669
(0.853) 		0.607
(0.809)
3q gain 8 (12%) 58 0.27
(0.493) 		0.531
(0.747) 		0.952
(1.00) 		0.649
(0.848) 		0.515
(0.737) 		0.693
(0.853) 		0.669
(0.853) 		0.604
(0.808)
5p gain 8 (12%) 58 0.426
(0.658) 		0.684
(0.853) 		0.448
(0.671) 		0.447
(0.671) 		0.361
(0.592) 		0.0606
(0.187) 		1
(1.00) 		0.126
(0.299)
5q gain 8 (12%) 58 0.426
(0.658) 		0.683
(0.853) 		0.449
(0.671) 		0.445
(0.671) 		0.364
(0.593) 		0.06
(0.187) 		1
(1.00) 		0.127
(0.299)
9p gain 10 (15%) 56 1
(1.00) 		1
(1.00) 		0.719
(0.867) 		0.813
(0.932) 		0.83
(0.933) 		0.601
(0.806) 		1
(1.00) 		0.265
(0.487)
9q gain 10 (15%) 56 1
(1.00) 		1
(1.00) 		0.723
(0.867) 		0.813
(0.932) 		0.831
(0.933) 		0.6
(0.806) 		1
(1.00) 		0.263
(0.487)
10p gain 4 (6%) 62 0.438
(0.669) 		0.161
(0.349) 		0.515
(0.737) 		0.203
(0.409) 		1
(1.00) 		0.166
(0.355) 		1
(1.00) 		0.458
(0.678)
12p gain 19 (29%) 47 0.481
(0.703) 		0.766
(0.896) 		0.0778
(0.219) 		0.159
(0.349) 		1
(1.00) 		0.0665
(0.196) 		0.213
(0.419) 		0.155
(0.344)
21q gain 4 (6%) 62 0.438
(0.669) 		0.161
(0.349) 		0.516
(0.737) 		0.105
(0.265) 		0.677
(0.853) 		0.165
(0.355) 		1
(1.00) 		0.409
(0.646)
11p loss 7 (11%) 59 0.627
(0.828) 		0.574
(0.788) 		0.111
(0.274) 		0.314
(0.545) 		0.199
(0.405) 		0.937
(1.00) 		0.381
(0.609) 		0.576
(0.789)
11q loss 7 (11%) 59 0.627
(0.828) 		0.573
(0.788) 		0.109
(0.27) 		0.318
(0.547) 		0.204
(0.409) 		0.938
(1.00) 		0.381
(0.609) 		0.579
(0.791)
18p loss 8 (12%) 58 0.676
(0.853) 		0.0979
(0.257) 		0.315
(0.545) 		0.21
(0.417) 		0.718
(0.867) 		0.951
(1.00) 		0.669
(0.853) 		0.773
(0.896)
18q loss 10 (15%) 56 0.618
(0.821) 		0.0791
(0.221) 		0.441
(0.671) 		0.279
(0.503) 		0.573
(0.788) 		0.864
(0.963) 		0.695
(0.853) 		0.514
(0.737)
19q loss 3 (5%) 63 0.647
(0.848) 		0.766
(0.896) 		0.764
(0.896) 		0.825
(0.933) 		0.517
(0.737) 		0.866
(0.963) 		1
(1.00) 		0.818
(0.933)
20p loss 4 (6%) 62 0.3
(0.527) 		0.805
(0.93) 		0.209
(0.417) 		0.211
(0.419) 		0.449
(0.671) 		0.653
(0.851) 		0.286
(0.51) 		0.551
(0.768)
20q loss 3 (5%) 63 1
(1.00) 		0.415
(0.651) 		0.226
(0.44) 		0.0589
(0.184) 		0.296
(0.524) 		0.827
(0.933) 		0.056
(0.177) 		0.716
(0.867)
22q loss 8 (12%) 58 0.83
(0.933) 		0.134
(0.311) 		0.247
(0.466) 		0.233
(0.447) 		0.897
(0.982) 		0.214
(0.42) 		0.687
(0.853) 		0.355
(0.585)
'4p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
4P GAIN MUTATED 4 17 2 1
4P GAIN WILD-TYPE 15 5 13 9

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

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00093

Table S2.  Gene #3: '4p gain' versus Molecular Subtype #4: '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 14 3 1 1 1 0
4P GAIN WILD-TYPE 15 2 4 5 9 3 4

Figure S2.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0086 (Fisher's exact test), Q value = 0.045

Table S3.  Gene #3: '4p gain' versus Molecular Subtype #6: '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 3 2 1
4P GAIN WILD-TYPE 16 3 7 3 2 3 8

Figure S3.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.13

Table S4.  Gene #3: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
4P GAIN MUTATED 4 16
4P GAIN WILD-TYPE 15 13

Figure S4.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.077

Table S5.  Gene #3: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S5.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S6.  Gene #4: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
4Q GAIN MUTATED 4 17 2 1
4Q GAIN WILD-TYPE 15 5 13 9

Figure S6.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00072

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

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00898 (Fisher's exact test), Q value = 0.046

Table S8.  Gene #4: '4q gain' versus Molecular Subtype #6: '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 S8.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.13

Table S9.  Gene #4: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
4Q GAIN MUTATED 4 16
4Q GAIN WILD-TYPE 15 13

Figure S9.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.077

Table S10.  Gene #4: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S10.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.075

Table S11.  Gene #7: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
7P GAIN MUTATED 4 14 4 2
7P GAIN WILD-TYPE 15 8 11 8

Figure S11.  Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.076

Table S12.  Gene #8: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
7Q GAIN MUTATED 4 14 4 2
7Q GAIN WILD-TYPE 15 8 11 8

Figure S12.  Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00372 (Fisher's exact test), Q value = 0.023

Table S13.  Gene #9: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
8P GAIN MUTATED 2 12 2 1
8P GAIN WILD-TYPE 17 10 13 9

Figure S13.  Get High-res Image Gene #9: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.12

Table S14.  Gene #9: '8p gain' versus Molecular Subtype #4: '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
8P GAIN MUTATED 2 9 3 1 2 0 0
8P GAIN WILD-TYPE 17 7 4 5 8 4 4

Figure S14.  Get High-res Image Gene #9: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.12

Table S15.  Gene #9: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S15.  Get High-res Image Gene #9: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0083

Table S16.  Gene #10: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
8Q GAIN MUTATED 2 13 2 1
8Q GAIN WILD-TYPE 17 9 13 9

Figure S16.  Get High-res Image Gene #10: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.05

Table S17.  Gene #10: '8q gain' versus Molecular Subtype #4: '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 10 3 1 2 0 0
8Q GAIN WILD-TYPE 17 6 4 5 8 4 4

Figure S17.  Get High-res Image Gene #10: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.15

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

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

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

'11p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S19.  Gene #14: '11p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
11P GAIN MUTATED 1 13 1 0
11P GAIN WILD-TYPE 18 9 14 10

Figure S19.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0035

Table S20.  Gene #14: '11p gain' versus Molecular Subtype #4: '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 S20.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.11

Table S21.  Gene #14: '11p gain' versus Molecular Subtype #6: '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 S21.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S22.  Gene #15: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
11Q GAIN MUTATED 1 14 0 0
11Q GAIN WILD-TYPE 18 8 15 10

Figure S22.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S23.  Gene #15: '11q gain' versus Molecular Subtype #4: '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 S23.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.086

Table S24.  Gene #15: '11q gain' versus Molecular Subtype #6: '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 S24.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.12

Table S25.  Gene #17: '12q gain' versus Molecular Subtype #6: '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 S25.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0059

Table S26.  Gene #18: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
14Q GAIN MUTATED 4 14 3 0
14Q GAIN WILD-TYPE 15 8 12 10

Figure S26.  Get High-res Image Gene #18: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00546 (Fisher's exact test), Q value = 0.031

Table S27.  Gene #18: '14q gain' versus Molecular Subtype #4: '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 S27.  Get High-res Image Gene #18: '14q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.12

Table S28.  Gene #18: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
14Q GAIN MUTATED 3 14
14Q GAIN WILD-TYPE 16 15

Figure S28.  Get High-res Image Gene #18: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.012

Table S29.  Gene #19: '15q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
15Q GAIN MUTATED 3 13 5 0
15Q GAIN WILD-TYPE 16 9 10 10

Figure S29.  Get High-res Image Gene #19: '15q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S30.  Gene #20: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
16P GAIN MUTATED 4 16 1 0
16P GAIN WILD-TYPE 15 6 14 10

Figure S30.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0014

Table S31.  Gene #20: '16p gain' versus Molecular Subtype #4: '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 0 1 0
16P GAIN WILD-TYPE 15 3 5 5 10 3 4

Figure S31.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00522 (Fisher's exact test), Q value = 0.031

Table S32.  Gene #20: '16p gain' versus Molecular Subtype #6: '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 1 0
16P GAIN WILD-TYPE 16 4 7 3 2 4 9

Figure S32.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.12

Table S33.  Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
16P GAIN MUTATED 3 14
16P GAIN WILD-TYPE 16 15

Figure S33.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00706 (Fisher's exact test), Q value = 0.038

Table S34.  Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 10 6 5 8 4 6 5 4
16P GAIN MUTATED 4 6 3 2 0 1 1 0
16P GAIN WILD-TYPE 6 0 2 6 4 5 4 4

Figure S34.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S35.  Gene #21: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
16Q GAIN MUTATED 4 16 1 0
16Q GAIN WILD-TYPE 15 6 14 10

Figure S35.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0012

Table S36.  Gene #21: '16q gain' versus Molecular Subtype #4: '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 S36.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0053 (Fisher's exact test), Q value = 0.031

Table S37.  Gene #21: '16q gain' versus Molecular Subtype #6: '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 S37.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.12

Table S38.  Gene #21: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
16Q GAIN MUTATED 3 14
16Q GAIN WILD-TYPE 16 15

Figure S38.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00703 (Fisher's exact test), Q value = 0.038

Table S39.  Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 10 6 5 8 4 6 5 4
16Q GAIN MUTATED 4 6 3 2 0 1 1 0
16Q GAIN WILD-TYPE 6 0 2 6 4 5 4 4

Figure S39.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.014

Table S40.  Gene #22: '18p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
18P GAIN MUTATED 1 12 2 2
18P GAIN WILD-TYPE 18 10 13 8

Figure S40.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.066

Table S41.  Gene #22: '18p gain' versus Molecular Subtype #4: '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 S41.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0488 (Fisher's exact test), Q value = 0.16

Table S42.  Gene #22: '18p gain' versus Molecular Subtype #6: '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 S42.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.048 (Fisher's exact test), Q value = 0.16

Table S43.  Gene #22: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 10 6 5 8 4 6 5 4
18P GAIN MUTATED 3 5 2 1 0 3 0 1
18P GAIN WILD-TYPE 7 1 3 7 4 3 5 3

Figure S43.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0077

Table S44.  Gene #23: '18q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
18Q GAIN MUTATED 1 12 2 1
18Q GAIN WILD-TYPE 18 10 13 9

Figure S44.  Get High-res Image Gene #23: '18q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S45.  Gene #23: '18q gain' versus Molecular Subtype #4: '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 S45.  Get High-res Image Gene #23: '18q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.096

Table S46.  Gene #24: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
19P GAIN MUTATED 2 11 5 1
19P GAIN WILD-TYPE 17 11 10 9

Figure S46.  Get High-res Image Gene #24: '19p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00893 (Fisher's exact test), Q value = 0.046

Table S47.  Gene #24: '19p gain' versus Molecular Subtype #4: '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 2 10 2 0 4 1 0
19P GAIN WILD-TYPE 17 6 5 6 6 3 4

Figure S47.  Get High-res Image Gene #24: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0387 (Fisher's exact test), Q value = 0.14

Table S48.  Gene #24: '19p gain' versus Molecular Subtype #6: '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
19P GAIN MUTATED 1 6 4 1 2 3 2
19P GAIN WILD-TYPE 17 5 8 5 3 2 7

Figure S48.  Get High-res Image Gene #24: '19p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.0092

Table S49.  Gene #25: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
19Q GAIN MUTATED 1 11 5 0
19Q GAIN WILD-TYPE 18 11 10 10

Figure S49.  Get High-res Image Gene #25: '19q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.01

Table S50.  Gene #25: '19q gain' versus Molecular Subtype #4: '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 1 10 1 0 4 1 0
19Q GAIN WILD-TYPE 18 6 6 6 6 3 4

Figure S50.  Get High-res Image Gene #25: '19q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0474 (Fisher's exact test), Q value = 0.16

Table S51.  Gene #25: '19q gain' versus Molecular Subtype #6: '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
19Q GAIN MUTATED 1 5 4 1 2 3 1
19Q GAIN WILD-TYPE 17 6 8 5 3 2 8

Figure S51.  Get High-res Image Gene #25: '19q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.12

Table S52.  Gene #26: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
20P GAIN MUTATED 4 12 3 1
20P GAIN WILD-TYPE 15 10 12 9

Figure S52.  Get High-res Image Gene #26: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S53.  Gene #26: '20p gain' versus Molecular Subtype #4: '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 3 0 2 1 0
20P GAIN WILD-TYPE 15 6 4 6 8 3 4

Figure S53.  Get High-res Image Gene #26: '20p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S54.  Gene #26: '20p gain' versus Molecular Subtype #6: '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 2 2
20P GAIN WILD-TYPE 17 5 7 5 2 3 7

Figure S54.  Get High-res Image Gene #26: '20p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S55.  Gene #27: '20q gain' versus Molecular Subtype #4: '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 2 1 0
20Q GAIN WILD-TYPE 15 6 3 6 8 3 4

Figure S55.  Get High-res Image Gene #27: '20q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 0.13

Table S56.  Gene #27: '20q gain' versus Molecular Subtype #6: '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 2 3
20Q GAIN WILD-TYPE 17 5 7 5 2 3 6

Figure S56.  Get High-res Image Gene #27: '20q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.097

Table S57.  Gene #29: '22q gain' versus Molecular Subtype #6: '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 S57.  Get High-res Image Gene #29: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0094 (Fisher's exact test), Q value = 0.048

Table S58.  Gene #29: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 10 6 5 8 4 6 5 4
22Q GAIN MUTATED 3 5 3 0 0 3 2 0
22Q GAIN WILD-TYPE 7 1 2 8 4 3 3 4

Figure S58.  Get High-res Image Gene #29: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.011

Table S59.  Gene #30: 'xp gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
XP GAIN MUTATED 0 7 0 0
XP GAIN WILD-TYPE 19 15 15 10

Figure S59.  Get High-res Image Gene #30: 'xp gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00708 (Fisher's exact test), Q value = 0.038

Table S60.  Gene #31: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
XQ GAIN MUTATED 0 6 0 0
XQ GAIN WILD-TYPE 19 16 15 10

Figure S60.  Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S61.  Gene #32: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
1P LOSS MUTATED 17 32 4
1P LOSS WILD-TYPE 1 3 9

Figure S61.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0038

Table S62.  Gene #32: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
1P LOSS MUTATED 19 16 14 4
1P LOSS WILD-TYPE 0 6 1 6

Figure S62.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0035

Table S63.  Gene #32: '1p loss' versus Molecular Subtype #4: '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 S63.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0068

Table S64.  Gene #32: '1p loss' versus Molecular Subtype #6: '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 S64.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00366 (Fisher's exact test), Q value = 0.022

Table S65.  Gene #32: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S65.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S66.  Gene #33: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
1Q LOSS MUTATED 17 32 3
1Q LOSS WILD-TYPE 1 3 10

Figure S66.  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 = 0.00031

Table S67.  Gene #33: '1q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
1Q LOSS MUTATED 19 16 14 3
1Q LOSS WILD-TYPE 0 6 1 7

Figure S67.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00084

Table S68.  Gene #33: '1q loss' versus Molecular Subtype #4: '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 11 5 3 10 4 0
1Q LOSS WILD-TYPE 0 5 2 3 0 0 4

Figure S68.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0038

Table S69.  Gene #33: '1q loss' versus Molecular Subtype #6: '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 8 11 3 4 5 3
1Q LOSS WILD-TYPE 0 3 1 3 1 0 6

Figure S69.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00449 (Fisher's exact test), Q value = 0.027

Table S70.  Gene #33: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S70.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S71.  Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
2P LOSS MUTATED 17 28 1
2P LOSS WILD-TYPE 1 7 12

Figure S71.  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 = 0.00019

Table S72.  Gene #34: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
2P LOSS MUTATED 19 14 13 0
2P LOSS WILD-TYPE 0 8 2 10

Figure S72.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S73.  Gene #34: '2p loss' versus Molecular Subtype #4: '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 S73.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S74.  Gene #34: '2p loss' versus Molecular Subtype #6: '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 S74.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.12

Table S75.  Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
2P LOSS MUTATED 9 23
2P LOSS WILD-TYPE 10 6

Figure S75.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0059

Table S76.  Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S76.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S77.  Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
2Q LOSS MUTATED 17 28 1
2Q LOSS WILD-TYPE 1 7 12

Figure S77.  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 = 0.00019

Table S78.  Gene #35: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
2Q LOSS MUTATED 19 14 13 0
2Q LOSS WILD-TYPE 0 8 2 10

Figure S78.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S79.  Gene #35: '2q loss' versus Molecular Subtype #4: '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 S79.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S80.  Gene #35: '2q loss' versus Molecular Subtype #6: '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 S80.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.12

Table S81.  Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
2Q LOSS MUTATED 9 23
2Q LOSS WILD-TYPE 10 6

Figure S81.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0057

Table S82.  Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S82.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

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

Table S83.  Gene #36: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
3P LOSS MUTATED 0 4 5
3P LOSS WILD-TYPE 5 43 9

Figure S83.  Get High-res Image Gene #36: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00328 (Fisher's exact test), Q value = 0.021

Table S84.  Gene #36: '3p loss' versus Molecular Subtype #4: '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 S84.  Get High-res Image Gene #36: '3p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.091

Table S85.  Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
3Q LOSS MUTATED 0 3 5
3Q LOSS WILD-TYPE 5 44 9

Figure S85.  Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.11

Table S86.  Gene #37: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
3Q LOSS MUTATED 0 6 2 0
3Q LOSS WILD-TYPE 19 16 13 10

Figure S86.  Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S87.  Gene #37: '3q loss' versus Molecular Subtype #4: '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 S87.  Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0057

Table S88.  Gene #38: '5p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
5P LOSS MUTATED 1 9 0 0
5P LOSS WILD-TYPE 18 13 15 10

Figure S88.  Get High-res Image Gene #38: '5p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.082

Table S89.  Gene #38: '5p loss' versus Molecular Subtype #4: '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 S89.  Get High-res Image Gene #38: '5p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.069

Table S90.  Gene #38: '5p loss' versus Molecular Subtype #6: '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 S90.  Get High-res Image Gene #38: '5p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0071

Table S91.  Gene #39: '5q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
5Q LOSS MUTATED 1 9 0 0
5Q LOSS WILD-TYPE 18 13 15 10

Figure S91.  Get High-res Image Gene #39: '5q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.084

Table S92.  Gene #39: '5q loss' versus Molecular Subtype #4: '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 S92.  Get High-res Image Gene #39: '5q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.069

Table S93.  Gene #39: '5q loss' versus Molecular Subtype #6: '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 S93.  Get High-res Image Gene #39: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.002

Table S94.  Gene #40: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
6P LOSS MUTATED 17 30 4
6P LOSS WILD-TYPE 1 5 9

Figure S94.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

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

Table S95.  Gene #40: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
6P LOSS MUTATED 19 15 14 3
6P LOSS WILD-TYPE 0 7 1 7

Figure S95.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S96.  Gene #40: '6p loss' versus Molecular Subtype #4: '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 S96.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0092

Table S97.  Gene #40: '6p loss' versus Molecular Subtype #6: '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 S97.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.003

Table S98.  Gene #40: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S98.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

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

Table S99.  Gene #41: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
6Q LOSS MUTATED 17 30 4
6Q LOSS WILD-TYPE 1 5 9

Figure S99.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00093

Table S100.  Gene #41: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
6Q LOSS MUTATED 19 15 14 3
6Q LOSS WILD-TYPE 0 7 1 7

Figure S100.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S101.  Gene #41: '6q loss' versus Molecular Subtype #4: '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 S101.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0087

Table S102.  Gene #41: '6q loss' versus Molecular Subtype #6: '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 S102.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.0029

Table S103.  Gene #41: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S103.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S104.  Gene #42: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
8P LOSS MUTATED 0 0 9
8P LOSS WILD-TYPE 5 47 5

Figure S104.  Get High-res Image Gene #42: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.14

Table S105.  Gene #42: '8p loss' versus Molecular Subtype #4: '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
8P LOSS MUTATED 6 1 0 0 0 2 0
8P LOSS WILD-TYPE 13 15 7 6 10 2 4

Figure S105.  Get High-res Image Gene #42: '8p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S106.  Gene #43: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
8Q LOSS MUTATED 0 0 8
8Q LOSS WILD-TYPE 5 47 6

Figure S106.  Get High-res Image Gene #43: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

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

Table S107.  Gene #43: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
8Q LOSS MUTATED 5 3 0
8Q LOSS WILD-TYPE 13 32 13

Figure S107.  Get High-res Image Gene #43: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.076

Table S108.  Gene #44: '9p loss' versus Molecular Subtype #4: '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 1 1 0
9P LOSS WILD-TYPE 19 13 3 5 9 3 4

Figure S108.  Get High-res Image Gene #44: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.076

Table S109.  Gene #45: '9q loss' versus Molecular Subtype #4: '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 S109.  Get High-res Image Gene #45: '9q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0029

Table S110.  Gene #46: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
10P LOSS MUTATED 17 27 4
10P LOSS WILD-TYPE 1 8 9

Figure S110.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0012

Table S111.  Gene #46: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
10P LOSS MUTATED 19 13 13 3
10P LOSS WILD-TYPE 0 9 2 7

Figure S111.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S112.  Gene #46: '10p loss' versus Molecular Subtype #4: '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 S112.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0018

Table S113.  Gene #46: '10p loss' versus Molecular Subtype #6: '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 S113.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.051

Table S114.  Gene #46: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S114.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.003

Table S115.  Gene #47: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
10Q LOSS MUTATED 17 28 4
10Q LOSS WILD-TYPE 1 7 9

Figure S115.  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 = 0.00019

Table S116.  Gene #47: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
10Q LOSS MUTATED 19 13 14 3
10Q LOSS WILD-TYPE 0 9 1 7

Figure S116.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S117.  Gene #47: '10q loss' versus Molecular Subtype #4: '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 S117.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.002

Table S118.  Gene #47: '10q loss' versus Molecular Subtype #6: '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 S118.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00292 (Fisher's exact test), Q value = 0.019

Table S119.  Gene #47: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S119.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0051

Table S120.  Gene #50: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
13Q LOSS MUTATED 11 29 3
13Q LOSS WILD-TYPE 7 6 10

Figure S120.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00381 (Fisher's exact test), Q value = 0.023

Table S121.  Gene #50: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
13Q LOSS MUTATED 15 13 13 2
13Q LOSS WILD-TYPE 4 9 2 8

Figure S121.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

Table S122.  Gene #50: '13q loss' versus Molecular Subtype #4: '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 S122.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00567 (Fisher's exact test), Q value = 0.032

Table S123.  Gene #50: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 10 6 5 8 4 6 5 4
13Q LOSS MUTATED 7 3 2 8 4 5 2 0
13Q LOSS WILD-TYPE 3 3 3 0 0 1 3 4

Figure S123.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.096

Table S124.  Gene #51: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
16P LOSS MUTATED 0 0 3 1
16P LOSS WILD-TYPE 19 22 12 9

Figure S124.  Get High-res Image Gene #51: '16p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.13

Table S125.  Gene #51: '16p loss' versus Molecular Subtype #4: '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 LOSS MUTATED 0 0 1 0 3 0 0
16P LOSS WILD-TYPE 19 16 6 6 7 4 4

Figure S125.  Get High-res Image Gene #51: '16p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00584 (Fisher's exact test), Q value = 0.033

Table S126.  Gene #52: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
16Q LOSS MUTATED 0 0 4 1
16Q LOSS WILD-TYPE 19 22 11 9

Figure S126.  Get High-res Image Gene #52: '16q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00677 (Fisher's exact test), Q value = 0.037

Table S127.  Gene #52: '16q loss' versus Molecular Subtype #4: '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 S127.  Get High-res Image Gene #52: '16q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.16

Table S128.  Gene #52: '16q loss' versus Molecular Subtype #6: '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 S128.  Get High-res Image Gene #52: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S129.  Gene #53: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
17P LOSS MUTATED 17 31 2
17P LOSS WILD-TYPE 1 4 11

Figure S129.  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 = 0.00019

Table S130.  Gene #53: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
17P LOSS MUTATED 19 16 14 1
17P LOSS WILD-TYPE 0 6 1 9

Figure S130.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S131.  Gene #53: '17p loss' versus Molecular Subtype #4: '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 S131.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S132.  Gene #53: '17p loss' versus Molecular Subtype #6: '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 S132.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.16

Table S133.  Gene #53: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
17P LOSS MUTATED 10 24
17P LOSS WILD-TYPE 9 5

Figure S133.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00226 (Fisher's exact test), Q value = 0.015

Table S134.  Gene #53: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 10 6 5 8 4 6 5 4
17P LOSS MUTATED 8 3 5 8 4 4 2 0
17P LOSS WILD-TYPE 2 3 0 0 0 2 3 4

Figure S134.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S135.  Gene #54: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
17Q LOSS MUTATED 17 31 2
17Q LOSS WILD-TYPE 1 4 11

Figure S135.  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 = 0.00019

Table S136.  Gene #54: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
17Q LOSS MUTATED 19 16 14 1
17Q LOSS WILD-TYPE 0 6 1 9

Figure S136.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S137.  Gene #54: '17q loss' versus Molecular Subtype #4: '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 S137.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00072

Table S138.  Gene #54: '17q loss' versus Molecular Subtype #6: '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 S138.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.16

Table S139.  Gene #54: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
17Q LOSS MUTATED 10 24
17Q LOSS WILD-TYPE 9 5

Figure S139.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.013

Table S140.  Gene #54: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 10 6 5 8 4 6 5 4
17Q LOSS MUTATED 8 3 5 8 4 4 2 0
17Q LOSS WILD-TYPE 2 3 0 0 0 2 3 4

Figure S140.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00998 (Fisher's exact test), Q value = 0.05

Table S141.  Gene #60: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
21Q LOSS MUTATED 12 21 2
21Q LOSS WILD-TYPE 6 14 11

Figure S141.  Get High-res Image Gene #60: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.15

Table S142.  Gene #60: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 10 6 5 8 4 6 5 4
21Q LOSS MUTATED 8 3 1 4 4 2 3 0
21Q LOSS WILD-TYPE 2 3 4 4 0 4 2 4

Figure S142.  Get High-res Image Gene #60: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.019

Table S143.  Gene #62: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
XP LOSS MUTATED 13 23 2
XP LOSS WILD-TYPE 5 12 11

Figure S143.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0026

Table S144.  Gene #62: 'xp loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
XP LOSS MUTATED 16 8 12 2
XP LOSS WILD-TYPE 3 14 3 8

Figure S144.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0036

Table S145.  Gene #62: 'xp loss' versus Molecular Subtype #4: '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 S145.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00019

Table S146.  Gene #62: 'xp loss' versus Molecular Subtype #6: '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 S146.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.061

Table S147.  Gene #62: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S147.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00654 (Fisher's exact test), Q value = 0.036

Table S148.  Gene #63: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
XQ LOSS MUTATED 15 9 12 3
XQ LOSS WILD-TYPE 4 13 3 7

Figure S148.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00341 (Fisher's exact test), Q value = 0.021

Table S149.  Gene #63: 'xq loss' versus Molecular Subtype #4: '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 6 4 2 9 3 0
XQ LOSS WILD-TYPE 4 10 3 4 1 1 4

Figure S149.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0077

Table S150.  Gene #63: 'xq loss' versus Molecular Subtype #6: '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 3 4 2
XQ LOSS WILD-TYPE 1 7 5 4 2 1 7

Figure S150.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0374 (Fisher's exact test), Q value = 0.13

Table S151.  Gene #63: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S151.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #8: '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/15084587/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/15095894/KICH-TP.transferedmergedcluster.txt

  • Number of patients = 66

  • Number of significantly arm-level cnvs = 63

  • Number of molecular subtypes = 8

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

Fisher's exact test

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

Q value calculation

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

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