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, 157 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 3p gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'RPPA_CHIERARCHICAL'.

  • 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 'RPPA_CHIERARCHICAL',  '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',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 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' and 'MRNASEQ_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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 157 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
2p loss 46 (70%) 20 0.0876
(0.275) 		1e-05
(0.000286) 		0.128
(0.34) 		0.509
(0.735) 		1e-05
(0.000286) 		1e-05
(0.000286) 		0.0815
(0.266) 		2e-05
(0.00045) 		0.0306
(0.145) 		0.00063
(0.00673)
2q loss 46 (70%) 20 0.087
(0.275) 		1e-05
(0.000286) 		0.126
(0.34) 		0.511
(0.735) 		1e-05
(0.000286) 		1e-05
(0.000286) 		0.0838
(0.27) 		2e-05
(0.00045) 		0.0306
(0.145) 		0.00066
(0.00693)
17p loss 50 (76%) 16 0.303
(0.539) 		1e-05
(0.000286) 		0.139
(0.353) 		0.0673
(0.236) 		1e-05
(0.000286) 		1e-05
(0.000286) 		0.0514
(0.202) 		8e-05
(0.0012) 		0.0491
(0.197) 		0.0019
(0.0159)
17q loss 50 (76%) 16 0.3
(0.535) 		1e-05
(0.000286) 		0.14
(0.353) 		0.0689
(0.239) 		1e-05
(0.000286) 		1e-05
(0.000286) 		0.0519
(0.202) 		7e-05
(0.00108) 		0.0491
(0.197) 		0.00214
(0.0175)
4p gain 24 (36%) 42 0.0549
(0.209) 		1
(1.00) 		0.346
(0.581) 		0.152
(0.37) 		4e-05
(0.000787) 		4e-05
(0.000787) 		0.769
(0.889) 		0.00912
(0.058) 		0.0349
(0.157) 		0.0164
(0.0927)
4q gain 24 (36%) 42 0.055
(0.209) 		1
(1.00) 		0.343
(0.579) 		0.151
(0.37) 		2e-05
(0.00045) 		6e-05
(0.00105) 		0.768
(0.889) 		0.00925
(0.0583) 		0.0349
(0.157) 		0.0173
(0.0953)
16p gain 21 (32%) 45 0.106
(0.306) 		1
(1.00) 		0.266
(0.504) 		0.367
(0.598) 		1e-05
(0.000286) 		7e-05
(0.00108) 		0.159
(0.379) 		0.00523
(0.0379) 		0.0312
(0.145) 		0.00705
(0.0472)
16q gain 21 (32%) 45 0.106
(0.306) 		1
(1.00) 		0.268
(0.505) 		0.364
(0.596) 		2e-05
(0.00045) 		0.00012
(0.00172) 		0.16
(0.379) 		0.00539
(0.0386) 		0.0312
(0.145) 		0.00696
(0.0472)
1p loss 53 (80%) 13 0.671
(0.846) 		5e-05
(0.000955) 		0.723
(0.859) 		0.595
(0.793) 		0.00046
(0.00508) 		0.00026
(0.00321) 		0.164
(0.383) 		0.00121
(0.011) 		0.176
(0.403) 		0.0037
(0.0277)
1q loss 52 (79%) 14 0.475
(0.698) 		1e-05
(0.000286) 		0.282
(0.52) 		0.405
(0.645) 		7e-05
(0.00108) 		4e-05
(0.000787) 		0.229
(0.471) 		0.00052
(0.00565) 		0.176
(0.403) 		0.00422
(0.0313)
6p loss 51 (77%) 15 0.332
(0.571) 		0.00012
(0.00172) 		0.161
(0.379) 		0.103
(0.303) 		7e-05
(0.00108) 		1e-05
(0.000286) 		0.349
(0.585) 		0.0011
(0.0103) 		0.176
(0.403) 		0.00024
(0.00315)
6q loss 51 (77%) 15 0.33
(0.569) 		0.0002
(0.00274) 		0.159
(0.379) 		0.102
(0.303) 		7e-05
(0.00108) 		1e-05
(0.000286) 		0.352
(0.587) 		0.00112
(0.0104) 		0.176
(0.403) 		0.00023
(0.00308)
10p loss 48 (73%) 18 0.343
(0.579) 		0.00031
(0.00368) 		0.0891
(0.278) 		0.107
(0.306) 		6e-05
(0.00105) 		1e-05
(0.000286) 		0.275
(0.512) 		0.00016
(0.00224) 		0.759
(0.889) 		0.0109
(0.0663)
10q loss 49 (74%) 17 0.249
(0.494) 		0.00025
(0.00315) 		0.177
(0.403) 		0.236
(0.476) 		4e-05
(0.000787) 		1e-05
(0.000286) 		0.227
(0.469) 		0.00025
(0.00315) 		0.538
(0.749) 		0.00301
(0.0237)
xp loss 38 (58%) 28 0.129
(0.34) 		0.00277
(0.0222) 		0.69
(0.846) 		0.719
(0.859) 		0.00029
(0.00351) 		0.00045
(0.00508) 		0.19
(0.425) 		1e-05
(0.000286) 		0.239
(0.48) 		0.0124
(0.0747)
18p gain 17 (26%) 49 0.522
(0.739) 		0.807
(0.924) 		0.762
(0.889) 		0.657
(0.84) 		0.00192
(0.0159) 		0.0134
(0.0796) 		0.938
(0.999) 		0.0482
(0.196) 		0.341
(0.579) 		0.0481
(0.196)
19p gain 19 (29%) 47 0.482
(0.703) 		0.274
(0.512) 		0.132
(0.343) 		0.0438
(0.184) 		0.0234
(0.121) 		0.0091
(0.058) 		0.66
(0.842) 		0.04
(0.172) 		1
(1.00) 		0.708
(0.859)
8p loss 9 (14%) 57 1e-05
(0.000286) 		0.084
(0.27) 		0.0106
(0.065) 		0.00768
(0.0504) 		0.0528
(0.203) 		0.0394
(0.171) 		0.148
(0.366) 		0.464
(0.688) 		0.142
(0.353) 		0.322
(0.558)
8q loss 8 (12%) 58 1e-05
(0.000286) 		0.0448
(0.186) 		0.0322
(0.148) 		0.0194
(0.102) 		0.134
(0.346) 		0.0732
(0.245) 		0.291
(0.529) 		0.527
(0.743) 		0.142
(0.353) 		0.319
(0.556)
13q loss 43 (65%) 23 0.26
(0.498) 		0.00046
(0.00508) 		0.297
(0.533) 		0.052
(0.202) 		0.00358
(0.0272) 		6e-05
(0.00105) 		0.851
(0.941) 		0.197
(0.434) 		0.541
(0.751) 		0.00562
(0.0393)
xq loss 39 (59%) 27 0.596
(0.793) 		0.072
(0.245) 		0.647
(0.834) 		0.538
(0.749) 		0.00674
(0.0467) 		0.00358
(0.0272) 		0.326
(0.565) 		0.00082
(0.0082) 		0.77
(0.889) 		0.037
(0.162)
8p gain 17 (26%) 49 0.411
(0.649) 		0.419
(0.657) 		0.391
(0.623) 		0.131
(0.343) 		0.00351
(0.0272) 		0.0311
(0.145) 		0.468
(0.69) 		0.0991
(0.299) 		1
(1.00) 		0.0292
(0.145)
8q gain 18 (27%) 48 0.341
(0.579) 		0.376
(0.611) 		0.255
(0.497) 		0.0727
(0.245) 		0.00109
(0.0103) 		0.0104
(0.0643) 		0.696
(0.846) 		0.0875
(0.275) 		0.751
(0.889) 		0.0416
(0.178)
11p gain 15 (23%) 51 0.282
(0.52) 		0.681
(0.846) 		0.56
(0.763) 		0.0872
(0.275) 		2e-05
(0.00045) 		0.00036
(0.0042) 		0.872
(0.959) 		0.0262
(0.131) 		0.197
(0.434) 		0.0785
(0.259)
11q gain 15 (23%) 51 0.281
(0.52) 		0.679
(0.846) 		0.212
(0.446) 		0.0876
(0.275) 		1e-05
(0.000286) 		2e-05
(0.00045) 		0.62
(0.81) 		0.0189
(0.1) 		0.197
(0.434) 		0.103
(0.303)
14q gain 21 (32%) 45 0.108
(0.307) 		0.828
(0.926) 		0.201
(0.439) 		0.293
(0.529) 		0.00071
(0.00733) 		0.00494
(0.0362) 		0.427
(0.658) 		0.0565
(0.212) 		0.0312
(0.145) 		0.0781
(0.259)
19q gain 17 (26%) 49 0.517
(0.735) 		0.312
(0.55) 		0.206
(0.44) 		0.129
(0.34) 		0.00138
(0.0124) 		0.00158
(0.0139) 		0.411
(0.649) 		0.0463
(0.191) 		1
(1.00) 		0.657
(0.84)
20p gain 20 (30%) 46 0.214
(0.446) 		0.595
(0.793) 		0.427
(0.658) 		0.139
(0.353) 		0.0294
(0.145) 		0.0312
(0.145) 		0.71
(0.859) 		0.0312
(0.145) 		0.535
(0.748) 		0.183
(0.413)
3q loss 8 (12%) 58 0.0203
(0.106) 		0.364
(0.596) 		0.895
(0.974) 		0.387
(0.621) 		0.0258
(0.13) 		0.00164
(0.0142) 		0.573
(0.775) 		0.182
(0.413) 		0.142
(0.353) 		0.687
(0.846)
5p loss 10 (15%) 56 0.0982
(0.299) 		0.253
(0.497) 		1
(1.00) 		0.821
(0.926) 		0.00084
(0.00827) 		0.0188
(0.1) 		0.425
(0.658) 		0.0137
(0.0805) 		0.451
(0.677) 		0.342
(0.579)
5q loss 10 (15%) 56 0.0996
(0.299) 		0.255
(0.497) 		1
(1.00) 		0.821
(0.926) 		0.0008
(0.00813) 		0.0189
(0.1) 		0.427
(0.658) 		0.0151
(0.088) 		0.451
(0.677) 		0.343
(0.579)
18q gain 16 (24%) 50 0.64
(0.83) 		0.927
(0.993) 		0.931
(0.996) 		0.553
(0.758) 		0.00096
(0.0093) 		0.019
(0.1) 		0.823
(0.926) 		0.0509
(0.202) 		0.119
(0.326) 		0.0629
(0.225)
20q gain 21 (32%) 45 0.228
(0.47) 		0.387
(0.621) 		0.29
(0.529) 		0.108
(0.307) 		0.0699
(0.241) 		0.0174
(0.0953) 		0.678
(0.846) 		0.036
(0.161) 		0.762
(0.889) 		0.0995
(0.299)
22q gain 19 (29%) 47 0.901
(0.974) 		0.714
(0.859) 		0.257
(0.497) 		0.242
(0.484) 		0.0687
(0.239) 		0.362
(0.596) 		0.552
(0.758) 		0.0242
(0.123) 		1
(1.00) 		0.00897
(0.058)
3p loss 9 (14%) 57 0.0362
(0.161) 		0.894
(0.974) 		0.817
(0.926) 		0.169
(0.392) 		0.0632
(0.225) 		0.00278
(0.0222) 		0.904
(0.974) 		0.203
(0.439) 		0.381
(0.613) 		0.846
(0.939)
16p loss 4 (6%) 62 0.684
(0.846) 		0.518
(0.735) 		0.675
(0.846) 		0.339
(0.579) 		0.0241
(0.123) 		0.0367
(0.162) 		0.679
(0.846) 		0.0895
(0.278) 		0.286
(0.525) 		0.985
(1.00)
16q loss 5 (8%) 61 0.72
(0.859) 		0.39
(0.623) 		0.851
(0.941) 		0.225
(0.466) 		0.00557
(0.0393) 		0.00698
(0.0472) 		0.427
(0.658) 		0.05
(0.199) 		0.0724
(0.245) 		0.69
(0.846)
21q loss 35 (53%) 31 0.775
(0.893) 		0.0101
(0.0628) 		0.126
(0.34) 		0.189
(0.425) 		0.25
(0.496) 		0.196
(0.434) 		1
(1.00) 		0.129
(0.34) 		1
(1.00) 		0.0434
(0.183)
3p gain 8 (12%) 58 0.269
(0.506) 		0.529
(0.743) 		0.459
(0.683) 		0.0449
(0.186) 		0.951
(1.00) 		0.648
(0.834) 		0.516
(0.735) 		0.692
(0.846) 		0.669
(0.846) 		0.603
(0.795)
3q gain 8 (12%) 58 0.271
(0.508) 		0.527
(0.743) 		0.458
(0.683) 		0.0433
(0.183) 		0.953
(1.00) 		0.646
(0.834) 		0.514
(0.735) 		0.693
(0.846) 		0.669
(0.846) 		0.602
(0.795)
7p gain 24 (36%) 42 0.151
(0.37) 		1
(1.00) 		0.0973
(0.299) 		0.139
(0.353) 		0.016
(0.0917) 		0.0615
(0.224) 		0.901
(0.974) 		0.118
(0.326) 		0.766
(0.889) 		0.101
(0.3)
7q gain 24 (36%) 42 0.151
(0.37) 		1
(1.00) 		0.0978
(0.299) 		0.136
(0.35) 		0.016
(0.0917) 		0.0608
(0.223) 		0.901
(0.974) 		0.116
(0.324) 		0.766
(0.889) 		0.101
(0.3)
12q gain 20 (30%) 46 0.445
(0.676) 		0.593
(0.793) 		0.787
(0.905) 		0.412
(0.649) 		0.147
(0.364) 		0.0821
(0.267) 		0.943
(1.00) 		0.0328
(0.15) 		0.235
(0.476) 		0.132
(0.343)
15q gain 21 (32%) 45 0.106
(0.306) 		0.827
(0.926) 		0.2
(0.438) 		0.293
(0.529) 		0.00167
(0.0142) 		0.0633
(0.225) 		0.754
(0.889) 		0.213
(0.446) 		0.762
(0.889) 		0.473
(0.697)
xp gain 7 (11%) 59 0.81
(0.924) 		0.317
(0.554) 		0.46
(0.683) 		0.304
(0.539) 		0.00159
(0.0139) 		0.0528
(0.203) 		0.157
(0.379) 		0.109
(0.308) 		0.381
(0.613) 		0.123
(0.335)
xq gain 6 (9%) 60 1
(1.00) 		0.722
(0.859) 		0.482
(0.703) 		0.291
(0.529) 		0.00726
(0.0481) 		0.121
(0.332) 		0.265
(0.502) 		0.119
(0.326) 		0.142
(0.353) 		0.0706
(0.242)
9p loss 10 (15%) 56 1
(1.00) 		0.902
(0.974) 		0.514
(0.735) 		0.552
(0.758) 		0.0643
(0.228) 		0.0165
(0.0927) 		0.91
(0.977) 		0.605
(0.796) 		0.695
(0.846) 		0.891
(0.974)
9q loss 10 (15%) 56 1
(1.00) 		0.904
(0.974) 		0.511
(0.735) 		0.555
(0.759) 		0.0631
(0.225) 		0.0171
(0.0952) 		0.91
(0.977) 		0.6
(0.794) 		0.695
(0.846) 		0.891
(0.974)
5p gain 8 (12%) 58 0.424
(0.658) 		0.682
(0.846) 		0.709
(0.859) 		0.198
(0.434) 		0.448
(0.676) 		0.447
(0.676) 		0.362
(0.596) 		0.0607
(0.223) 		1
(1.00) 		0.127
(0.34)
5q gain 8 (12%) 58 0.423
(0.658) 		0.681
(0.846) 		0.712
(0.859) 		0.196
(0.434) 		0.447
(0.676) 		0.446
(0.676) 		0.364
(0.596) 		0.0597
(0.221) 		1
(1.00) 		0.127
(0.34)
9p gain 10 (15%) 56 1
(1.00) 		1
(1.00) 		0.258
(0.497) 		0.235
(0.476) 		0.724
(0.859) 		0.813
(0.925) 		0.833
(0.927) 		0.6
(0.794) 		1
(1.00) 		0.264
(0.502)
9q gain 10 (15%) 56 1
(1.00) 		1
(1.00) 		0.256
(0.497) 		0.235
(0.476) 		0.722
(0.859) 		0.813
(0.925) 		0.832
(0.927) 		0.6
(0.794) 		1
(1.00) 		0.261
(0.499)
10p gain 4 (6%) 62 0.438
(0.671) 		0.16
(0.379) 		1
(1.00) 		0.552
(0.758) 		0.512
(0.735) 		0.205
(0.44) 		1
(1.00) 		0.167
(0.388) 		1
(1.00) 		0.459
(0.683)
12p gain 19 (29%) 47 0.479
(0.702) 		0.764
(0.889) 		0.836
(0.929) 		0.467
(0.69) 		0.0785
(0.259) 		0.157
(0.379) 		1
(1.00) 		0.0668
(0.235) 		0.213
(0.446) 		0.155
(0.375)
21q gain 4 (6%) 62 0.437
(0.671) 		0.162
(0.38) 		0.555
(0.759) 		0.809
(0.924) 		0.517
(0.735) 		0.106
(0.306) 		0.679
(0.846) 		0.165
(0.386) 		1
(1.00) 		0.41
(0.649)
11p loss 7 (11%) 59 0.627
(0.816) 		0.574
(0.775) 		0.529
(0.743) 		0.253
(0.497) 		0.11
(0.31) 		0.317
(0.554) 		0.202
(0.439) 		0.937
(0.999) 		0.381
(0.613) 		0.575
(0.775)
11q loss 7 (11%) 59 0.629
(0.817) 		0.572
(0.775) 		0.533
(0.746) 		0.253
(0.497) 		0.112
(0.313) 		0.317
(0.554) 		0.205
(0.44) 		0.938
(0.999) 		0.381
(0.613) 		0.576
(0.775)
18p loss 8 (12%) 58 0.677
(0.846) 		0.0969
(0.299) 		0.352
(0.587) 		0.26
(0.498) 		0.315
(0.554) 		0.211
(0.446) 		0.716
(0.859) 		0.95
(1.00) 		0.669
(0.846) 		0.77
(0.889)
18q loss 10 (15%) 56 0.622
(0.812) 		0.0802
(0.263) 		0.257
(0.497) 		0.236
(0.476) 		0.446
(0.676) 		0.279
(0.518) 		0.574
(0.775) 		0.863
(0.952) 		0.695
(0.846) 		0.514
(0.735)
19q loss 3 (5%) 63 0.646
(0.834) 		0.765
(0.889) 		0.613
(0.804) 		0.31
(0.549) 		0.767
(0.889) 		0.824
(0.926) 		0.514
(0.735) 		0.865
(0.953) 		1
(1.00) 		0.82
(0.926)
20p loss 4 (6%) 62 0.3
(0.535) 		0.806
(0.924) 		0.365
(0.596) 		0.337
(0.579) 		0.204
(0.44) 		0.212
(0.446) 		0.451
(0.677) 		0.655
(0.84) 		0.286
(0.525) 		0.55
(0.758)
20q loss 3 (5%) 63 1
(1.00) 		0.419
(0.657) 		0.614
(0.804) 		0.592
(0.793) 		0.225
(0.466) 		0.0587
(0.219) 		0.294
(0.529) 		0.825
(0.926) 		0.056
(0.211) 		0.716
(0.859)
22q loss 8 (12%) 58 0.829
(0.926) 		0.132
(0.343) 		0.879
(0.965) 		1
(1.00) 		0.247
(0.493) 		0.234
(0.476) 		0.898
(0.974) 		0.214
(0.446) 		0.687
(0.846) 		0.354
(0.588)
'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 0.19

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'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.18

Table S2.  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 S2.  Get High-res Image Gene #2: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00079

Table S3.  Gene #3: '4p gain' versus Molecular Subtype #5: '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 S3.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00079

Table S4.  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 14 3 1 1 1 0
4P GAIN WILD-TYPE 15 2 4 5 9 3 4

Figure S4.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00912 (Fisher's exact test), Q value = 0.058

Table S5.  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 3 2 1
4P GAIN WILD-TYPE 16 3 7 3 2 3 8

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

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.16

Table S6.  Gene #3: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

Figure S6.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.093

Table S7.  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
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 S7.  Get High-res Image Gene #3: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00045

Table S8.  Gene #4: '4q gain' versus Molecular Subtype #5: '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 S8.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.001

Table S9.  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 S9.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00925 (Fisher's exact test), Q value = 0.058

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

'4q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.16

Table S11.  Gene #4: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

Figure S11.  Get High-res Image Gene #4: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.095

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

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.092

Table S13.  Gene #7: '7p gain' versus Molecular Subtype #5: '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 S13.  Get High-res Image Gene #7: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.092

Table S14.  Gene #8: '7q gain' versus Molecular Subtype #5: '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 S14.  Get High-res Image Gene #8: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00351 (Fisher's exact test), Q value = 0.027

Table S15.  Gene #9: '8p gain' versus Molecular Subtype #5: '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 S15.  Get High-res Image Gene #9: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.14

Table S16.  Gene #9: '8p 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
8P GAIN MUTATED 2 9 3 1 2 0 0
8P GAIN WILD-TYPE 17 7 4 5 8 4 4

Figure S16.  Get High-res Image Gene #9: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.14

Table S17.  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
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 S17.  Get High-res Image Gene #9: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.01

Table S18.  Gene #10: '8q gain' versus Molecular Subtype #5: '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 S18.  Get High-res Image Gene #10: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.064

Table S19.  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 10 3 1 2 0 0
8Q GAIN WILD-TYPE 17 6 4 5 8 4 4

Figure S19.  Get High-res Image Gene #10: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0416 (Fisher's exact test), Q value = 0.18

Table S20.  Gene #10: '8q 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
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 S20.  Get High-res Image Gene #10: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00045

Table S21.  Gene #14: '11p gain' versus Molecular Subtype #5: '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 S21.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0042

Table S22.  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 S22.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.13

Table S23.  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 S23.  Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S24.  Gene #15: '11q gain' versus Molecular Subtype #5: '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 S24.  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 = 0.00045

Table S25.  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 S25.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.1

Table S26.  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 S26.  Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S27.  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 S27.  Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0073

Table S28.  Gene #18: '14q gain' versus Molecular Subtype #5: '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 S28.  Get High-res Image Gene #18: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00494 (Fisher's exact test), Q value = 0.036

Table S29.  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 S29.  Get High-res Image Gene #18: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.14

Table S30.  Gene #18: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

Figure S30.  Get High-res Image Gene #18: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.014

Table S31.  Gene #19: '15q gain' versus Molecular Subtype #5: '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 S31.  Get High-res Image Gene #19: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S32.  Gene #20: '16p gain' versus Molecular Subtype #5: '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 S32.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S33.  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 0 1 0
16P GAIN WILD-TYPE 15 3 5 5 10 3 4

Figure S33.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00523 (Fisher's exact test), Q value = 0.038

Table S34.  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 1 0
16P GAIN WILD-TYPE 16 4 7 3 2 4 9

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

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.14

Table S35.  Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

Figure S35.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00705 (Fisher's exact test), Q value = 0.047

Table S36.  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
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 S36.  Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00045

Table S37.  Gene #21: '16q gain' versus Molecular Subtype #5: '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 S37.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0017

Table S38.  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 S38.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00539 (Fisher's exact test), Q value = 0.039

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

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.14

Table S40.  Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

Figure S40.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00696 (Fisher's exact test), Q value = 0.047

Table S41.  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
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 S41.  Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00192 (Fisher's exact test), Q value = 0.016

Table S42.  Gene #22: '18p gain' versus Molecular Subtype #5: '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 S42.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.08

Table S43.  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 S43.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0482 (Fisher's exact test), Q value = 0.2

Table S44.  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 S44.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0481 (Fisher's exact test), Q value = 0.2

Table S45.  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
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 S45.  Get High-res Image Gene #22: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0093

Table S46.  Gene #23: '18q gain' versus Molecular Subtype #5: '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 S46.  Get High-res Image Gene #23: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.1

Table S47.  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 S47.  Get High-res Image Gene #23: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.18

Table S48.  Gene #24: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
19P GAIN MUTATED 12 2 5
19P GAIN WILD-TYPE 17 18 9

Figure S48.  Get High-res Image Gene #24: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.12

Table S49.  Gene #24: '19p gain' versus Molecular Subtype #5: '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 S49.  Get High-res Image Gene #24: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0091 (Fisher's exact test), Q value = 0.058

Table S50.  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 2 10 2 0 4 1 0
19P GAIN WILD-TYPE 17 6 5 6 6 3 4

Figure S50.  Get High-res Image Gene #24: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.17

Table S51.  Gene #24: '19p 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
19P GAIN MUTATED 1 6 4 1 2 3 2
19P GAIN WILD-TYPE 17 5 8 5 3 2 7

Figure S51.  Get High-res Image Gene #24: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.012

Table S52.  Gene #25: '19q gain' versus Molecular Subtype #5: '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 S52.  Get High-res Image Gene #25: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00158 (Fisher's exact test), Q value = 0.014

Table S53.  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 1 10 1 0 4 1 0
19Q GAIN WILD-TYPE 18 6 6 6 6 3 4

Figure S53.  Get High-res Image Gene #25: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.19

Table S54.  Gene #25: '19q 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
19Q GAIN MUTATED 1 5 4 1 2 3 1
19Q GAIN WILD-TYPE 17 6 8 5 3 2 8

Figure S54.  Get High-res Image Gene #25: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.14

Table S55.  Gene #26: '20p gain' versus Molecular Subtype #5: '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 S55.  Get High-res Image Gene #26: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.14

Table S56.  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 3 0 2 1 0
20P GAIN WILD-TYPE 15 6 4 6 8 3 4

Figure S56.  Get High-res Image Gene #26: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.14

Table S57.  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 2 2
20P GAIN WILD-TYPE 17 5 7 5 2 3 7

Figure S57.  Get High-res Image Gene #26: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.095

Table S58.  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 2 1 0
20Q GAIN WILD-TYPE 15 6 3 6 8 3 4

Figure S58.  Get High-res Image Gene #27: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.16

Table S59.  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 2 3
20Q GAIN WILD-TYPE 17 5 7 5 2 3 6

Figure S59.  Get High-res Image Gene #27: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.12

Table S60.  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 S60.  Get High-res Image Gene #29: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00897 (Fisher's exact test), Q value = 0.058

Table S61.  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
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 S61.  Get High-res Image Gene #29: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.014

Table S62.  Gene #30: 'xp gain' versus Molecular Subtype #5: '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 S62.  Get High-res Image Gene #30: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00726 (Fisher's exact test), Q value = 0.048

Table S63.  Gene #31: 'xq gain' versus Molecular Subtype #5: '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 S63.  Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00095

Table S64.  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 S64.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0051

Table S65.  Gene #32: '1p loss' versus Molecular Subtype #5: '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 S65.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0032

Table S66.  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 S66.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.011

Table S67.  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 S67.  Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0037 (Fisher's exact test), Q value = 0.028

Table S68.  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
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 S68.  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 = 0.00029

Table S69.  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 S69.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

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

Table S70.  Gene #33: '1q loss' versus Molecular Subtype #5: '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 S70.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00079

Table S71.  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 11 5 3 10 4 0
1Q LOSS WILD-TYPE 0 5 2 3 0 0 4

Figure S71.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0056

Table S72.  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 8 11 3 4 5 3
1Q LOSS WILD-TYPE 0 3 1 3 1 0 6

Figure S72.  Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00422 (Fisher's exact test), Q value = 0.031

Table S73.  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
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 S73.  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 = 0.00029

Table S74.  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 S74.  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 = 0.00029

Table S75.  Gene #34: '2p loss' versus Molecular Subtype #5: '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 S75.  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 = 0.00029

Table S76.  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 S76.  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 = 0.00045

Table S77.  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 S77.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.14

Table S78.  Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

Figure S78.  Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0067

Table S79.  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
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 S79.  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 = 0.00029

Table S80.  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 S80.  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 = 0.00029

Table S81.  Gene #35: '2q loss' versus Molecular Subtype #5: '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 S81.  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 = 0.00029

Table S82.  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 S82.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00045

Table S83.  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 S83.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.14

Table S84.  Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

Figure S84.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0069

Table S85.  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
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 S85.  Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.16

Table S86.  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 S86.  Get High-res Image Gene #36: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00278 (Fisher's exact test), Q value = 0.022

Table S87.  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 S87.  Get High-res Image Gene #36: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.11

Table S88.  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 S88.  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 = 0.13

Table S89.  Gene #37: '3q loss' versus Molecular Subtype #5: '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 S89.  Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00164 (Fisher's exact test), Q value = 0.014

Table S90.  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 S90.  Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0083

Table S91.  Gene #38: '5p loss' versus Molecular Subtype #5: '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 S91.  Get High-res Image Gene #38: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.1

Table S92.  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 S92.  Get High-res Image Gene #38: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.08

Table S93.  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 S93.  Get High-res Image Gene #38: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0081

Table S94.  Gene #39: '5q loss' versus Molecular Subtype #5: '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 S94.  Get High-res Image Gene #39: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.1

Table S95.  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 S95.  Get High-res Image Gene #39: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.088

Table S96.  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 S96.  Get High-res Image Gene #39: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0017

Table S97.  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 S97.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

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

Table S98.  Gene #40: '6p loss' versus Molecular Subtype #5: '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 S98.  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 = 0.00029

Table S99.  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 S99.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.01

Table S100.  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 S100.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0031

Table S101.  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
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 S101.  Get High-res Image Gene #40: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0027

Table S102.  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 S102.  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 = 0.0011

Table S103.  Gene #41: '6q loss' versus Molecular Subtype #5: '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 S103.  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 = 0.00029

Table S104.  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 S104.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.01

Table S105.  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 S105.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0031

Table S106.  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
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 S106.  Get High-res Image Gene #41: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S107.  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 S107.  Get High-res Image Gene #42: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.065

Table S108.  Gene #42: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 17 20
8P LOSS MUTATED 1 1 7
8P LOSS WILD-TYPE 25 16 13

Figure S108.  Get High-res Image Gene #42: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00768 (Fisher's exact test), Q value = 0.05

Table S109.  Gene #42: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
8P LOSS MUTATED 1 7 1
8P LOSS WILD-TYPE 28 13 13

Figure S109.  Get High-res Image Gene #42: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 0.17

Table S110.  Gene #42: '8p 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
8P LOSS MUTATED 6 1 0 0 0 2 0
8P LOSS WILD-TYPE 13 15 7 6 10 2 4

Figure S110.  Get High-res Image Gene #42: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S111.  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 S111.  Get High-res Image Gene #43: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.19

Table S112.  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 S112.  Get High-res Image Gene #43: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'RPPA_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.15

Table S113.  Gene #43: '8q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 17 20
8Q LOSS MUTATED 1 1 6
8Q LOSS WILD-TYPE 25 16 14

Figure S113.  Get High-res Image Gene #43: '8q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.1

Table S114.  Gene #43: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
8Q LOSS MUTATED 1 6 1
8Q LOSS WILD-TYPE 28 14 13

Figure S114.  Get High-res Image Gene #43: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.093

Table S115.  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 1 1 0
9P LOSS WILD-TYPE 19 13 3 5 9 3 4

Figure S115.  Get High-res Image Gene #44: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.095

Table S116.  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 S116.  Get High-res Image Gene #45: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0037

Table S117.  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 S117.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.001

Table S118.  Gene #46: '10p loss' versus Molecular Subtype #5: '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 S118.  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 = 0.00029

Table S119.  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 S119.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0022

Table S120.  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 S120.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.066

Table S121.  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
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 S121.  Get High-res Image Gene #46: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0031

Table S122.  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 S122.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00079

Table S123.  Gene #47: '10q loss' versus Molecular Subtype #5: '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 S123.  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 = 0.00029

Table S124.  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 S124.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0031

Table S125.  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 S125.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00301 (Fisher's exact test), Q value = 0.024

Table S126.  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
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 S126.  Get High-res Image Gene #47: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0051

Table S127.  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 S127.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.027

Table S128.  Gene #50: '13q loss' versus Molecular Subtype #5: '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 S128.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.001

Table S129.  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 S129.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00562 (Fisher's exact test), Q value = 0.039

Table S130.  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
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 S130.  Get High-res Image Gene #50: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.12

Table S131.  Gene #51: '16p loss' versus Molecular Subtype #5: '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 S131.  Get High-res Image Gene #51: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0367 (Fisher's exact test), Q value = 0.16

Table S132.  Gene #51: '16p 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
16P LOSS MUTATED 0 0 1 0 3 0 0
16P LOSS WILD-TYPE 19 16 6 6 7 4 4

Figure S132.  Get High-res Image Gene #51: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00557 (Fisher's exact test), Q value = 0.039

Table S133.  Gene #52: '16q loss' versus Molecular Subtype #5: '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 S133.  Get High-res Image Gene #52: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00698 (Fisher's exact test), Q value = 0.047

Table S134.  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 S134.  Get High-res Image Gene #52: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S135.  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 S135.  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 = 0.00029

Table S136.  Gene #53: '17p loss' versus Molecular Subtype #5: '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 S136.  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 = 0.00029

Table S137.  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 S137.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S138.  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 S138.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.2

Table S139.  Gene #53: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

Figure S139.  Get High-res Image Gene #53: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.016

Table S140.  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
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 S140.  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 = 0.00029

Table S141.  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 S141.  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 = 0.00029

Table S142.  Gene #54: '17q loss' versus Molecular Subtype #5: '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 S142.  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 = 0.00029

Table S143.  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 S143.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S144.  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 S144.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.2

Table S145.  Gene #54: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

Figure S145.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00214 (Fisher's exact test), Q value = 0.018

Table S146.  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
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 S146.  Get High-res Image Gene #54: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.063

Table S147.  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 S147.  Get High-res Image Gene #60: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.18

Table S148.  Gene #60: '21q 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
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 S148.  Get High-res Image Gene #60: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.022

Table S149.  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 S149.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0035

Table S150.  Gene #62: 'xp loss' versus Molecular Subtype #5: '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 S150.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0051

Table S151.  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 S151.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S152.  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 S152.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.075

Table S153.  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
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 S153.  Get High-res Image Gene #62: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.00674 (Fisher's exact test), Q value = 0.047

Table S154.  Gene #63: 'xq loss' versus Molecular Subtype #5: '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 S154.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.027

Table S155.  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 6 4 2 9 3 0
XQ LOSS WILD-TYPE 4 10 3 4 1 1 4

Figure S155.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0082

Table S156.  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 3 4 2
XQ LOSS WILD-TYPE 1 7 5 4 2 1 7

Figure S156.  Get High-res Image Gene #63: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.16

Table S157.  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
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 S157.  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/20146430/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/20147307/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)
Made with Nozzle