Correlation between copy number variations of arm-level result and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 82 arm-level events and 14 molecular subtypes across 579 patients, 252 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

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

  • 2p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 4p gain cnv correlated to 'MIR_CNMF',  'CN_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 7q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 8p gain cnv correlated to 'MRNA_CHIERARCHICAL'.

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

  • 9p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 10p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CNMF'.

  • 11p gain cnv correlated to 'METHLYATION_CNMF' and 'RPPA_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 12p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'MRNA_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 16p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 16q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 17q gain cnv correlated to 'MRNA_CHIERARCHICAL' and 'MIR_CHIERARCHICAL'.

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

  • 18q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 21q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • xp gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 2p loss cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF'.

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

  • 5q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'MRNA_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • 8q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • 9q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'MIR_CNMF',  'CN_CNMF', and 'METHLYATION_CNMF'.

  • 11p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'METHLYATION_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CHIERARCHICAL',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

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

  • 15q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 16p loss cnv correlated to 'MIR_CNMF' and 'MIRSEQ_CNMF'.

  • 16q loss cnv correlated to 'MIR_CNMF' and 'CN_CNMF'.

  • 17q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • 18p loss cnv correlated to 'MIR_CHIERARCHICAL' and 'METHLYATION_CNMF'.

  • 18q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 19q loss cnv correlated to 'MIR_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 20p loss cnv correlated to 'MIRSEQ_CNMF'.

  • 20q loss cnv correlated to 'MIR_CNMF'.

  • 22q loss cnv correlated to 'MRNA_CNMF',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • xp loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • xq loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 252 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
15q loss 280 (48%) 299 0.00056
(0.0102) 		0.017
(0.106) 		0.00011
(0.00301) 		0.00031
(0.00684) 		1e-05
(0.000383) 		1e-05
(0.000383) 		0.147
(0.412) 		0.918
(1) 		0.00601
(0.0527) 		0.272
(0.559) 		0.00832
(0.0636) 		0.00062
(0.0108) 		0.0427
(0.199) 		0.624
(0.849)
2p gain 186 (32%) 393 1e-05
(0.000383) 		1e-05
(0.000383) 		0.887
(0.987) 		0.00061
(0.0108) 		1e-05
(0.000383) 		1e-05
(0.000383) 		0.00414
(0.0417) 		0.431
(0.727) 		1e-05
(0.000383) 		1e-05
(0.000383) 		0.821
(0.951) 		0.0256
(0.142) 		0.675
(0.873) 		0.612
(0.844)
2q gain 155 (27%) 424 0.00053
(0.00981) 		4e-05
(0.00135) 		1
(1.00) 		0.00791
(0.0622) 		1e-05
(0.000383) 		0.00022
(0.00515) 		0.046
(0.211) 		0.9
(0.991) 		0.0001
(0.00287) 		0.00017
(0.00434) 		0.609
(0.842) 		0.00601
(0.0527) 		1
(1.00) 		0.747
(0.909)
12p gain 255 (44%) 324 3e-05
(0.00104) 		0.00151
(0.0197) 		0.741
(0.904) 		0.00115
(0.0161) 		1e-05
(0.000383) 		1e-05
(0.000383) 		0.108
(0.354) 		0.76
(0.916) 		0.00046
(0.0088) 		0.0007
(0.0115) 		0.229
(0.523) 		0.0002
(0.00489) 		0.415
(0.712) 		0.254
(0.544)
5q loss 223 (39%) 356 0.00033
(0.00715) 		0.00172
(0.0212) 		0.709
(0.89) 		0.0131
(0.0894) 		0.00044
(0.00856) 		1e-05
(0.000383) 		0.0808
(0.299) 		0.462
(0.758) 		0.00102
(0.0148) 		0.00165
(0.0206) 		0.621
(0.849) 		0.00742
(0.06) 		0.378
(0.686) 		0.718
(0.893)
12q gain 177 (31%) 402 0.00448
(0.0429) 		0.0554
(0.242) 		0.626
(0.849) 		0.034
(0.17) 		1e-05
(0.000383) 		1e-05
(0.000383) 		0.0724
(0.282) 		0.599
(0.837) 		0.0221
(0.128) 		0.0219
(0.128) 		0.103
(0.346) 		0.011
(0.0806) 		0.0743
(0.285) 		0.291
(0.584)
20p gain 289 (50%) 290 0.00129
(0.0176) 		0.00111
(0.0157) 		0.724
(0.897) 		0.00042
(0.00846) 		1e-05
(0.000383) 		1e-05
(0.000383) 		0.353
(0.659) 		0.356
(0.662) 		0.0131
(0.0894) 		0.0705
(0.28) 		0.224
(0.522) 		0.00366
(0.0382) 		0.391
(0.692) 		0.522
(0.789)
20q gain 328 (57%) 251 1e-05
(0.000383) 		0.00044
(0.00856) 		0.672
(0.871) 		0.00013
(0.00347) 		1e-05
(0.000383) 		1e-05
(0.000383) 		0.504
(0.773) 		0.129
(0.384) 		0.0743
(0.285) 		0.00638
(0.0535) 		0.257
(0.547) 		0.0048
(0.0444) 		1
(1.00) 		0.495
(0.769)
3p loss 95 (16%) 484 0.0226
(0.131) 		0.00088
(0.0137) 		0.816
(0.951) 		0.00538
(0.0483) 		0.00038
(0.00793) 		0.00268
(0.0304) 		0.13
(0.386) 		0.0296
(0.157) 		0.0921
(0.323) 		0.00144
(0.019) 		0.123
(0.373) 		0.0896
(0.315) 		1
(1.00) 		0.123
(0.373)
3q loss 43 (7%) 536 0.013
(0.0894) 		0.0389
(0.185) 		0.286
(0.578) 		0.056
(0.242) 		0.0304
(0.159) 		0.00325
(0.0349) 		0.264
(0.555) 		0.126
(0.376) 		0.0643
(0.263) 		0.035
(0.173) 		0.307
(0.6) 		0.00102
(0.0148) 		0.594
(0.833) 		0.033
(0.168)
9q loss 286 (49%) 293 0.00689
(0.0567) 		0.0138
(0.0938) 		0.22
(0.519) 		0.034
(0.17) 		1e-05
(0.000383) 		0.00612
(0.0528) 		0.689
(0.881) 		0.56
(0.82) 		0.00723
(0.0589) 		0.00087
(0.0137) 		0.223
(0.521) 		0.0579
(0.246) 		1
(1.00) 		0.623
(0.849)
22q loss 430 (74%) 149 0.00227
(0.0269) 		0.0926
(0.323) 		0.036
(0.177) 		0.128
(0.38) 		5e-05
(0.00159) 		0.00183
(0.0223) 		0.0154
(0.0998) 		0.0622
(0.258) 		0.054
(0.237) 		0.0144
(0.0958) 		0.041
(0.194) 		0.575
(0.827) 		0.135
(0.394) 		0.105
(0.35)
10p gain 188 (32%) 391 0.00435
(0.0424) 		0.0206
(0.123) 		0.677
(0.874) 		0.375
(0.684) 		1e-05
(0.000383) 		0.00015
(0.00391) 		0.775
(0.927) 		0.884
(0.985) 		0.0016
(0.0203) 		0.113
(0.36) 		0.563
(0.823) 		0.00057
(0.0102) 		1
(1.00) 		0.94
(1.00)
13q gain 60 (10%) 519 0.00782
(0.0619) 		0.00029
(0.00653) 		0.587
(0.833) 		0.0246
(0.137) 		8e-05
(0.00242) 		1e-05
(0.000383) 		0.285
(0.578) 		0.904
(0.991) 		0.0338
(0.17) 		0.114
(0.363) 		0.149
(0.413) 		0.0994
(0.339) 		0.455
(0.748)
8q loss 90 (16%) 489 0.00771
(0.0618) 		0.00549
(0.0489) 		0.52
(0.787) 		0.261
(0.55) 		0.00101
(0.0148) 		0.0347
(0.173) 		0.151
(0.414) 		0.388
(0.69) 		0.00273
(0.0304) 		0.00092
(0.0141) 		0.664
(0.867) 		0.125
(0.376) 		1
(1.00) 		0.901
(0.991)
12p loss 79 (14%) 500 0.0028
(0.0309) 		0.0107
(0.0786) 		0.658
(0.862) 		0.00691
(0.0567) 		0.00101
(0.0148) 		0.252
(0.544) 		0.705
(0.889) 		0.552
(0.817) 		0.472
(0.758) 		0.166
(0.444) 		0.00958
(0.071) 		0.00637
(0.0535) 		0.293
(0.587) 		0.725
(0.897)
13q loss 310 (54%) 269 0.029
(0.156) 		0.00842
(0.0636) 		0.803
(0.945) 		0.0166
(0.104) 		0.0513
(0.23) 		2e-05
(0.000717) 		0.0111
(0.0809) 		0.0139
(0.0938) 		0.165
(0.442) 		0.277
(0.566) 		0.217
(0.519) 		0.532
(0.799) 		0.666
(0.867) 		0.151
(0.414)
6p gain 170 (29%) 409 0.513
(0.781) 		0.00425
(0.0424) 		0.903
(0.991) 		0.0127
(0.0886) 		1e-05
(0.000383) 		0.00011
(0.00301) 		0.968
(1.00) 		0.627
(0.849) 		0.15
(0.414) 		0.00079
(0.0128) 		0.36
(0.668) 		0.0659
(0.268) 		0.415
(0.712) 		0.762
(0.918)
6q gain 97 (17%) 482 0.656
(0.861) 		0.0512
(0.23) 		0.823
(0.951) 		0.0211
(0.125) 		1e-05
(0.000383) 		1e-05
(0.000383) 		0.818
(0.951) 		0.6
(0.837) 		0.125
(0.376) 		0.0342
(0.171) 		0.199
(0.493) 		0.0297
(0.157) 		0.381
(0.686) 		0.576
(0.827)
8q gain 242 (42%) 337 0.0212
(0.125) 		0.00068
(0.0113) 		0.08
(0.297) 		0.142
(0.406) 		0.26
(0.549) 		0.447
(0.745) 		0.802
(0.945) 		0.651
(0.861) 		0.00622
(0.0532) 		0.0151
(0.0989) 		0.56
(0.82) 		0.864
(0.975) 		0.031
(0.16) 		0.691
(0.881)
5p loss 133 (23%) 446 0.0746
(0.285) 		0.0314
(0.162) 		0.543
(0.809) 		0.0889
(0.315) 		0.0121
(0.085) 		0.00661
(0.055) 		0.101
(0.343) 		0.232
(0.524) 		0.00065
(0.0111) 		0.00161
(0.0203) 		0.574
(0.827) 		0.0504
(0.229) 		1
(1.00) 		0.907
(0.991)
12q loss 105 (18%) 474 0.0824
(0.302) 		0.0836
(0.303) 		0.729
(0.897) 		0.171
(0.453) 		0.023
(0.132) 		0.228
(0.523) 		0.0951
(0.33) 		0.653
(0.861) 		0.172
(0.454) 		0.0266
(0.145) 		0.0265
(0.145) 		0.0305
(0.159) 		0.135
(0.394) 		0.0398
(0.189)
19p loss 185 (32%) 394 0.979
(1.00) 		0.452
(0.748) 		0.331
(0.632) 		0.0437
(0.203) 		0.00525
(0.0478) 		0.019
(0.116) 		0.0149
(0.0982) 		0.061
(0.255) 		0.759
(0.916) 		0.254
(0.544) 		0.679
(0.874) 		0.118
(0.369) 		0.0115
(0.083) 		0.125
(0.376)
10q gain 111 (19%) 468 0.00392
(0.0398) 		0.00939
(0.0705) 		0.241
(0.535) 		0.118
(0.369) 		0.00387
(0.0397) 		0.0922
(0.323) 		0.621
(0.849) 		0.313
(0.606) 		0.016
(0.102) 		0.0564
(0.242) 		0.729
(0.897) 		0.246
(0.539) 		0.646
(0.86) 		0.657
(0.861)
16p gain 59 (10%) 520 0.00253
(0.029) 		0.00433
(0.0424) 		0.406
(0.706) 		0.177
(0.465) 		0.0299
(0.157) 		0.0174
(0.108) 		0.631
(0.853) 		0.144
(0.408) 		0.166
(0.444) 		0.862
(0.974) 		0.125
(0.376) 		0.0795
(0.296) 		0.481
(0.758)
16q gain 31 (5%) 548 0.00066
(0.0111) 		0.0444
(0.205) 		0.158
(0.428) 		0.22
(0.519) 		0.268
(0.559) 		0.00346
(0.0368) 		0.858
(0.972) 		0.171
(0.454) 		0.064
(0.262) 		0.339
(0.641) 		0.00084
(0.0134) 		0.106
(0.352) 		1
(1.00)
21q gain 109 (19%) 470 0.29
(0.583) 		0.881
(0.985) 		0.96
(1.00) 		0.581
(0.83) 		0.00139
(0.0188) 		0.0163
(0.104) 		0.179
(0.467) 		0.383
(0.688) 		0.207
(0.506) 		0.148
(0.412) 		0.024
(0.135) 		0.0441
(0.204) 		1
(1.00)
14q loss 215 (37%) 364 0.251
(0.544) 		0.191
(0.483) 		0.968
(1.00) 		0.399
(0.701) 		1e-05
(0.000383) 		0.0036
(0.0379) 		0.857
(0.972) 		0.77
(0.923) 		0.00775
(0.0618) 		0.0001
(0.00287) 		0.857
(0.972) 		0.399
(0.701) 		0.381
(0.686) 		0.225
(0.522)
17q loss 383 (66%) 196 0.0845
(0.305) 		0.0282
(0.152) 		0.0153
(0.0997) 		0.0118
(0.084) 		0.943
(1.00) 		0.559
(0.82) 		0.691
(0.881) 		0.277
(0.566) 		0.031
(0.16) 		0.142
(0.406) 		0.0782
(0.294) 		0.715
(0.892) 		0.624
(0.849) 		0.276
(0.566)
19q loss 178 (31%) 401 0.696
(0.884) 		0.252
(0.544) 		0.253
(0.544) 		0.0164
(0.104) 		0.00461
(0.0431) 		0.0737
(0.285) 		0.0192
(0.116) 		0.227
(0.523) 		0.729
(0.897) 		0.396
(0.7) 		0.301
(0.593) 		0.053
(0.235) 		0.00535
(0.0483) 		0.426
(0.723)
1q gain 221 (38%) 358 0.833
(0.959) 		0.271
(0.559) 		0.706
(0.89) 		0.224
(0.522) 		1e-05
(0.000383) 		0.00842
(0.0636) 		0.406
(0.706) 		0.668
(0.869) 		0.047
(0.215) 		0.075
(0.285) 		0.229
(0.523) 		0.108
(0.354) 		0.198
(0.493) 		0.56
(0.82)
4p gain 60 (10%) 519 0.246
(0.539) 		0.19
(0.483) 		0.0049
(0.045) 		0.0601
(0.253) 		0.016
(0.102) 		0.12
(0.37) 		0.538
(0.806) 		0.467
(0.758) 		0.78
(0.928) 		0.44
(0.737) 		0.324
(0.621) 		0.0179
(0.11) 		1
(1.00) 		0.575
(0.827)
4q gain 32 (6%) 547 0.496
(0.769) 		0.765
(0.919) 		0.212
(0.514) 		0.0783
(0.294) 		0.00436
(0.0424) 		0.00818
(0.0636) 		0.711
(0.89) 		0.0252
(0.14) 		0.703
(0.888) 		0.466
(0.758) 		0.229
(0.523) 		0.0636
(0.262)
9p loss 262 (45%) 317 0.00285
(0.0309) 		0.00607
(0.0528) 		0.509
(0.777) 		0.185
(0.475) 		0.016
(0.102) 		0.072
(0.281) 		0.905
(0.991) 		0.298
(0.588) 		0.106
(0.352) 		0.0597
(0.252) 		0.0557
(0.242) 		0.257
(0.548) 		0.391
(0.692) 		0.152
(0.416)
10q loss 124 (21%) 455 0.938
(1.00) 		0.826
(0.953) 		0.00462
(0.0431) 		0.297
(0.588) 		0.0232
(0.132) 		0.00197
(0.0236) 		0.644
(0.86) 		0.727
(0.897) 		0.652
(0.861) 		0.842
(0.963) 		0.696
(0.884) 		0.371
(0.678) 		0.381
(0.686) 		0.698
(0.886)
xp loss 325 (56%) 254 0.143
(0.408) 		0.251
(0.544) 		0.204
(0.502) 		0.664
(0.867) 		0.00626
(0.0532) 		0.0424
(0.198) 		0.464
(0.758) 		0.021
(0.125) 		0.754
(0.916) 		0.976
(1.00) 		0.212
(0.514) 		0.457
(0.75) 		1
(1.00) 		0.306
(0.599)
3q gain 275 (47%) 304 0.935
(1.00) 		0.868
(0.976) 		0.345
(0.651) 		0.432
(0.728) 		1e-05
(0.000383) 		0.0172
(0.107) 		0.991
(1.00) 		0.209
(0.51) 		0.271
(0.559) 		0.477
(0.758) 		0.255
(0.546) 		0.0891
(0.315) 		1
(1.00) 		0.633
(0.853)
7p gain 181 (31%) 398 0.59
(0.833) 		0.475
(0.758) 		0.0832
(0.302) 		0.107
(0.354) 		1e-05
(0.000383) 		0.0002
(0.00489) 		0.9
(0.991) 		0.155
(0.422) 		0.906
(0.991) 		0.824
(0.952) 		0.965
(1.00) 		0.12
(0.37) 		1
(1.00) 		0.765
(0.919)
7q gain 203 (35%) 376 0.649
(0.861) 		0.0827
(0.302) 		0.297
(0.588) 		0.38
(0.686) 		1e-05
(0.000383) 		0.00141
(0.0188) 		0.553
(0.817) 		0.26
(0.549) 		0.729
(0.897) 		0.986
(1.00) 		0.151
(0.414) 		0.632
(0.853) 		0.646
(0.86) 		0.369
(0.678)
9p gain 92 (16%) 487 0.113
(0.36) 		0.423
(0.719) 		0.235
(0.528) 		0.865
(0.976) 		0.00273
(0.0304) 		0.00829
(0.0636) 		0.541
(0.807) 		0.576
(0.827) 		0.733
(0.9) 		0.714
(0.892) 		0.187
(0.478) 		0.187
(0.478) 		0.624
(0.849) 		0.607
(0.842)
11p gain 77 (13%) 502 0.713
(0.891) 		0.101
(0.343) 		0.638
(0.857) 		0.47
(0.758) 		0.134
(0.394) 		0.014
(0.0938) 		0.00823
(0.0636) 		0.286
(0.578) 		0.603
(0.84) 		0.277
(0.566) 		0.561
(0.82) 		0.836
(0.959) 		1
(1.00)
11q gain 115 (20%) 464 0.391
(0.692) 		0.25
(0.544) 		0.884
(0.985) 		0.18
(0.467) 		0.00441
(0.0425) 		0.00197
(0.0236) 		0.192
(0.485) 		0.245
(0.539) 		0.523
(0.789) 		0.247
(0.54) 		0.41
(0.709) 		0.78
(0.928) 		0.323
(0.621) 		0.105
(0.35)
17q gain 47 (8%) 532 0.42
(0.716) 		0.0369
(0.178) 		0.759
(0.916) 		0.0371
(0.178) 		0.526
(0.793) 		0.388
(0.69) 		0.779
(0.928) 		0.814
(0.951) 		1
(1.00) 		0.268
(0.559) 		0.827
(0.953) 		0.878
(0.983) 		1
(1.00)
18p gain 120 (21%) 459 0.182
(0.468) 		0.0999
(0.34) 		0.872
(0.979) 		0.386
(0.689) 		0.00127
(0.0176) 		0.00029
(0.00653) 		0.0708
(0.28) 		0.932
(1.00) 		0.0874
(0.312) 		0.835
(0.959) 		0.354
(0.66) 		0.235
(0.528) 		0.646
(0.86) 		0.814
(0.951)
18q gain 72 (12%) 507 0.646
(0.86) 		0.163
(0.438) 		0.227
(0.523) 		0.387
(0.69) 		0.0232
(0.132) 		0.0243
(0.136) 		1
(1.00) 		0.916
(0.999) 		0.621
(0.849) 		0.585
(0.833) 		0.108
(0.354) 		0.194
(0.49) 		1
(1.00) 		1
(1.00)
19p gain 171 (30%) 408 0.0767
(0.291) 		0.454
(0.748) 		0.52
(0.787) 		0.116
(0.367) 		2e-05
(0.000717) 		0.026
(0.143) 		0.266
(0.559) 		0.802
(0.945) 		0.247
(0.54) 		0.178
(0.465) 		0.27
(0.559) 		0.313
(0.606) 		1
(1.00) 		0.746
(0.909)
xp gain 78 (13%) 501 0.45
(0.746) 		0.636
(0.856) 		0.901
(0.991) 		0.594
(0.833) 		0.0294
(0.157) 		0.492
(0.767) 		0.766
(0.919) 		0.317
(0.611) 		0.93
(1.00) 		0.974
(1.00) 		0.0388
(0.185) 		0.0675
(0.274) 		1
(1.00)
1p loss 65 (11%) 514 0.0324
(0.166) 		0.00034
(0.00723) 		0.465
(0.758) 		0.197
(0.492) 		0.469
(0.758) 		0.286
(0.578) 		0.0718
(0.281) 		0.468
(0.758) 		0.86
(0.973) 		0.259
(0.549) 		0.448
(0.745) 		0.309
(0.601) 		1
(1.00)
4p loss 316 (55%) 263 0.368
(0.677) 		0.022
(0.128) 		0.282
(0.573) 		0.613
(0.845) 		0.00454
(0.0431) 		0.485
(0.763) 		0.144
(0.408) 		0.83
(0.956) 		0.447
(0.745) 		0.919
(1) 		0.118
(0.369) 		0.196
(0.491) 		1
(1.00) 		0.625
(0.849)
6q loss 242 (42%) 337 0.963
(1.00) 		0.0748
(0.285) 		0.435
(0.732) 		0.0975
(0.336) 		0.0339
(0.17) 		0.0713
(0.281) 		0.679
(0.874) 		0.802
(0.945) 		0.0976
(0.336) 		0.0118
(0.084) 		0.791
(0.938) 		0.57
(0.827) 		0.594
(0.833) 		0.904
(0.991)
8p loss 277 (48%) 302 0.74
(0.904) 		0.893
(0.991) 		0.237
(0.529) 		0.947
(1.00) 		0.00246
(0.0288) 		0.11
(0.358) 		0.051
(0.23) 		0.475
(0.758) 		0.809
(0.949) 		0.707
(0.89) 		0.701
(0.886) 		0.0371
(0.178) 		1
(1.00) 		0.94
(1.00)
11p loss 198 (34%) 381 0.237
(0.529) 		0.0117
(0.084) 		0.546
(0.811) 		0.311
(0.603) 		0.199
(0.493) 		0.036
(0.177) 		0.43
(0.726) 		0.884
(0.985) 		0.146
(0.409) 		0.0737
(0.285) 		0.475
(0.758) 		0.146
(0.409) 		0.323
(0.621) 		0.801
(0.945)
16p loss 334 (58%) 245 0.379
(0.686) 		0.845
(0.964) 		0.0415
(0.195) 		0.347
(0.653) 		0.218
(0.519) 		0.113
(0.36) 		0.144
(0.408) 		0.947
(1.00) 		0.135
(0.394) 		0.847
(0.965) 		0.0481
(0.219) 		0.0698
(0.279) 		0.675
(0.873) 		0.367
(0.677)
16q loss 413 (71%) 166 0.578
(0.829) 		0.871
(0.978) 		0.00283
(0.0309) 		0.0779
(0.294) 		0.0278
(0.15) 		0.064
(0.262) 		0.412
(0.71) 		0.433
(0.729) 		0.155
(0.422) 		0.785
(0.932) 		0.0541
(0.237) 		0.127
(0.379) 		0.624
(0.849) 		0.608
(0.842)
18p loss 235 (41%) 344 0.408
(0.708) 		0.949
(1.00) 		0.472
(0.758) 		0.0204
(0.123) 		0.546
(0.811) 		0.00251
(0.029) 		0.295
(0.588) 		0.498
(0.769) 		0.576
(0.827) 		0.0535
(0.236) 		0.839
(0.961) 		0.54
(0.806) 		0.666
(0.867) 		0.582
(0.83)
1p gain 168 (29%) 411 0.0792
(0.296) 		0.349
(0.654) 		0.121
(0.371) 		0.735
(0.9) 		0.00051
(0.0096) 		0.182
(0.468) 		0.241
(0.535) 		0.898
(0.991) 		0.412
(0.71) 		0.614
(0.845) 		0.254
(0.544) 		0.683
(0.877) 		0.231
(0.524) 		0.522
(0.789)
3p gain 160 (28%) 419 0.438
(0.735) 		0.449
(0.745) 		0.0715
(0.281) 		0.527
(0.793) 		0.0121
(0.0849) 		0.783
(0.931) 		0.875
(0.981) 		0.709
(0.89) 		0.48
(0.758) 		0.901
(0.991) 		0.99
(1.00) 		0.82
(0.951) 		1
(1.00) 		0.812
(0.95)
5p gain 199 (34%) 380 0.565
(0.823) 		0.711
(0.89) 		0.858
(0.972) 		0.759
(0.916) 		0.0004
(0.0082) 		0.193
(0.488) 		0.444
(0.742) 		0.231
(0.524) 		0.512
(0.781) 		0.27
(0.559) 		0.181
(0.468) 		0.573
(0.827) 		0.666
(0.867) 		0.215
(0.517)
8p gain 119 (21%) 460 0.0704
(0.28) 		0.00373
(0.0386) 		0.399
(0.701) 		0.417
(0.715) 		0.694
(0.884) 		0.809
(0.949) 		0.142
(0.406) 		0.296
(0.588) 		0.145
(0.409) 		0.0565
(0.242) 		0.131
(0.387) 		0.495
(0.769) 		0.221
(0.519) 		0.101
(0.343)
19q gain 161 (28%) 418 0.26
(0.549) 		0.755
(0.916) 		0.907
(0.991) 		0.17
(0.453) 		5e-05
(0.00159) 		0.132
(0.389) 		0.54
(0.806) 		0.304
(0.596) 		0.313
(0.606) 		0.236
(0.528) 		0.27
(0.559) 		0.676
(0.873) 		0.594
(0.833) 		0.724
(0.897)
xq gain 108 (19%) 471 0.655
(0.861) 		0.911
(0.994) 		0.651
(0.861) 		0.216
(0.518) 		6e-05
(0.00186) 		0.866
(0.976) 		0.217
(0.519) 		0.0862
(0.309) 		0.982
(1.00) 		0.822
(0.951) 		0.492
(0.767) 		0.489
(0.766) 		0.594
(0.833) 		0.517
(0.786)
1q loss 43 (7%) 536 0.117
(0.368) 		0.0141
(0.0942) 		0.0578
(0.246) 		0.599
(0.837) 		0.689
(0.881) 		0.382
(0.687) 		0.88
(0.984) 		0.984
(1.00) 		0.454
(0.748) 		0.361
(0.668) 		0.97
(1.00) 		0.933
(1.00)
2p loss 53 (9%) 526 0.931
(1.00) 		0.0237
(0.134) 		0.619
(0.849) 		0.49
(0.767) 		0.579
(0.829) 		0.774
(0.926) 		0.898
(0.991) 		0.728
(0.897) 		0.47
(0.758) 		0.901
(0.991) 		0.721
(0.897) 		0.402
(0.703) 		0.481
(0.758)
4q loss 362 (63%) 217 0.206
(0.504) 		0.0818
(0.302) 		0.501
(0.771) 		0.718
(0.893) 		0.00153
(0.0197) 		0.559
(0.82) 		0.213
(0.516) 		0.262
(0.551) 		0.689
(0.881) 		0.475
(0.758) 		0.215
(0.517) 		0.18
(0.467) 		1
(1.00) 		0.37
(0.678)
6p loss 165 (28%) 414 0.97
(1.00) 		0.02
(0.121) 		0.449
(0.745) 		0.508
(0.777) 		0.149
(0.413) 		0.119
(0.37) 		0.552
(0.817) 		0.593
(0.833) 		0.501
(0.771) 		0.0678
(0.274) 		0.479
(0.758) 		0.103
(0.345) 		0.571
(0.827) 		0.573
(0.827)
11q loss 148 (26%) 431 0.297
(0.588) 		0.903
(0.991) 		0.214
(0.517) 		0.565
(0.823) 		0.00955
(0.071) 		0.0687
(0.276) 		0.401
(0.703) 		0.41
(0.709) 		0.181
(0.468) 		0.419
(0.716) 		0.498
(0.769) 		0.177
(0.465) 		0.594
(0.833) 		0.385
(0.689)
18q loss 293 (51%) 286 0.338
(0.641) 		0.973
(1.00) 		0.296
(0.588) 		0.958
(1.00) 		0.857
(0.972) 		0.105
(0.35) 		0.941
(1.00) 		0.3
(0.591) 		0.233
(0.525) 		0.0372
(0.178) 		0.978
(1.00) 		0.779
(0.928) 		0.67
(0.87) 		0.245
(0.539)
20p loss 50 (9%) 529 0.352
(0.658) 		0.725
(0.897) 		0.221
(0.519) 		0.624
(0.849) 		0.111
(0.359) 		0.468
(0.758) 		0.12
(0.37) 		0.205
(0.502) 		0.281
(0.571) 		0.36
(0.668) 		0.00108
(0.0155) 		0.271
(0.559) 		0.481
(0.758)
20q loss 32 (6%) 547 0.116
(0.366) 		0.5
(0.771) 		0.0369
(0.178) 		0.504
(0.773) 		0.441
(0.737) 		0.64
(0.859) 		0.0683
(0.275) 		0.271
(0.559) 		0.228
(0.523) 		0.419
(0.716) 		0.133
(0.392) 		0.379
(0.686) 		0.481
(0.758)
xq loss 280 (48%) 299 0.196
(0.491) 		0.352
(0.658) 		0.405
(0.706) 		0.961
(1.00) 		0.00022
(0.00515) 		0.113
(0.36) 		0.398
(0.701) 		0.083
(0.302) 		0.654
(0.861) 		0.678
(0.874) 		0.646
(0.86) 		0.668
(0.869) 		1
(1.00) 		0.289
(0.583)
5q gain 60 (10%) 519 0.0588
(0.249) 		0.197
(0.492) 		0.822
(0.951) 		0.894
(0.991) 		0.844
(0.964) 		0.495
(0.769) 		0.646
(0.86) 		0.75
(0.912) 		0.594
(0.833) 		0.241
(0.535) 		0.379
(0.686) 		0.792
(0.938) 		0.481
(0.758)
9q gain 45 (8%) 534 0.251
(0.544) 		0.305
(0.597) 		0.0932
(0.324) 		0.533
(0.8) 		0.141
(0.406) 		0.221
(0.519) 		0.42
(0.716) 		0.329
(0.63) 		0.244
(0.539) 		0.308
(0.6) 		0.498
(0.769) 		0.756
(0.916) 		0.455
(0.748)
14q gain 59 (10%) 520 0.14
(0.406) 		0.191
(0.483) 		0.405
(0.706) 		0.7
(0.886) 		0.411
(0.709) 		0.74
(0.904) 		0.628
(0.85) 		0.65
(0.861) 		0.818
(0.951) 		0.803
(0.945) 		0.655
(0.861) 		0.633
(0.853) 		1
(1.00)
15q gain 40 (7%) 539 0.844
(0.964) 		0.486
(0.764) 		0.0873
(0.312) 		0.755
(0.916) 		0.0971
(0.336) 		0.605
(0.84) 		0.609
(0.842) 		0.061
(0.255) 		0.558
(0.82) 		0.467
(0.758) 		0.314
(0.606) 		0.201
(0.497) 		1
(1.00)
17p gain 22 (4%) 557 0.429
(0.726) 		0.114
(0.363) 		0.0564
(0.242) 		0.0526
(0.235) 		0.151
(0.414) 		0.235
(0.528) 		0.502
(0.771) 		0.653
(0.861) 		0.511
(0.781) 		0.123
(0.373) 		0.175
(0.459) 		0.841
(0.963)
22q gain 24 (4%) 555 0.366
(0.675) 		0.596
(0.835) 		0.931
(1.00) 		0.605
(0.84) 		0.37
(0.678) 		0.174
(0.458) 		0.592
(0.833) 		0.118
(0.369) 		0.0862
(0.309) 		0.278
(0.566) 		0.0991
(0.339) 		0.0829
(0.302) 		0.571
(0.827) 		0.385
(0.689)
2q loss 59 (10%) 520 0.92
(1.00) 		0.272
(0.559) 		0.695
(0.884) 		0.15
(0.414) 		0.858
(0.972) 		0.682
(0.877) 		0.71
(0.89) 		0.144
(0.408) 		0.331
(0.632) 		0.735
(0.9) 		0.558
(0.82) 		0.227
(0.523) 		0.481
(0.758)
7p loss 121 (21%) 458 0.99
(1.00) 		0.403
(0.704) 		0.477
(0.758) 		0.699
(0.886) 		0.111
(0.358) 		0.149
(0.413) 		0.517
(0.786) 		0.899
(0.991) 		0.11
(0.358) 		0.23
(0.523) 		0.54
(0.806) 		0.794
(0.939) 		0.594
(0.833) 		0.202
(0.498)
7q loss 81 (14%) 498 0.334
(0.635) 		0.0888
(0.315) 		0.346
(0.651) 		0.303
(0.595) 		0.733
(0.9) 		0.109
(0.357) 		1
(1.00) 		0.426
(0.723) 		0.295
(0.588) 		0.0615
(0.256) 		0.121
(0.372) 		0.82
(0.951) 		1
(1.00) 		0.34
(0.642)
10p loss 97 (17%) 482 0.221
(0.519) 		0.963
(1.00) 		0.219
(0.519) 		0.334
(0.635) 		0.646
(0.86) 		0.229
(0.523) 		0.896
(0.991) 		0.87
(0.978) 		0.811
(0.95) 		0.78
(0.928) 		0.362
(0.669) 		0.834
(0.959) 		1
(1.00) 		0.22
(0.519)
17p loss 478 (83%) 101 0.339
(0.641) 		0.231
(0.524) 		0.136
(0.394) 		0.204
(0.502) 		0.587
(0.833) 		0.245
(0.539) 		0.55
(0.816) 		0.575
(0.827) 		0.157
(0.426) 		0.221
(0.519) 		0.474
(0.758) 		0.476
(0.758) 		1
(1.00)
21q loss 199 (34%) 380 0.82
(0.951) 		0.053
(0.235) 		0.384
(0.689) 		0.181
(0.468) 		0.491
(0.767) 		0.141
(0.406) 		0.6
(0.837) 		0.808
(0.949) 		0.764
(0.919) 		0.487
(0.765) 		0.687
(0.881) 		0.73
(0.897) 		0.162
(0.436) 		0.582
(0.83)
'1p gain' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0096

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
1P GAIN MUTATED 37 52 79
1P GAIN WILD-TYPE 134 154 123

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'CN_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
1Q GAIN MUTATED 56 55 110
1Q GAIN WILD-TYPE 115 151 92

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00842 (Fisher's exact test), Q value = 0.064

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
1Q GAIN MUTATED 82 57 78
1Q GAIN WILD-TYPE 90 118 143

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.22

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
1Q GAIN MUTATED 27 53 39
1Q GAIN WILD-TYPE 52 55 74

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
2P GAIN MUTATED 93 45 36
2P GAIN WILD-TYPE 122 171 90

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
2P GAIN MUTATED 77 48 49
2P GAIN WILD-TYPE 233 110 40

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.011

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
2P GAIN MUTATED 21 16 22 21 10 20 17 9 30 8
2P GAIN WILD-TYPE 64 41 36 61 24 55 17 27 22 34

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
2P GAIN MUTATED 37 47 102
2P GAIN WILD-TYPE 134 159 100

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
2P GAIN MUTATED 83 44 52
2P GAIN WILD-TYPE 89 131 169

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.042

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
2P GAIN MUTATED 46 74 14
2P GAIN WILD-TYPE 100 115 62

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
2P GAIN MUTATED 13 54 39
2P GAIN WILD-TYPE 66 54 74

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
2P GAIN MUTATED 33 37 36
2P GAIN WILD-TYPE 113 22 59

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.14

Table S13.  Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
2P GAIN MUTATED 23 27 63 32
2P GAIN WILD-TYPE 82 44 102 74

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0098

Table S14.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
2Q GAIN MUTATED 76 42 29
2Q GAIN WILD-TYPE 139 174 97

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0014

Table S15.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
2Q GAIN MUTATED 70 36 41
2Q GAIN WILD-TYPE 240 122 48

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00791 (Fisher's exact test), Q value = 0.062

Table S16.  Gene #4: '2q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
2Q GAIN MUTATED 16 12 18 18 9 20 15 6 24 8
2Q GAIN WILD-TYPE 69 45 40 64 25 55 19 30 28 34

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S17.  Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
2Q GAIN MUTATED 31 40 84
2Q GAIN WILD-TYPE 140 166 118

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0052

Table S18.  Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
2Q GAIN MUTATED 66 36 49
2Q GAIN WILD-TYPE 106 139 172

Figure S18.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'2q gain' versus 'RPPA_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.21

Table S19.  Gene #4: '2q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
2Q GAIN MUTATED 35 59 13
2Q GAIN WILD-TYPE 111 130 63

Figure S19.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0029

Table S20.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
2Q GAIN MUTATED 10 44 30
2Q GAIN WILD-TYPE 69 64 83

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0043

Table S21.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
2Q GAIN MUTATED 29 29 26
2Q GAIN WILD-TYPE 117 30 69

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00601 (Fisher's exact test), Q value = 0.053

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
2Q GAIN MUTATED 16 23 55 28
2Q GAIN WILD-TYPE 89 48 110 78

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.085

Table S23.  Gene #5: '3p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
3P GAIN MUTATED 38 51 71
3P GAIN WILD-TYPE 133 155 131

Figure S23.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S24.  Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
3Q GAIN MUTATED 58 90 127
3Q GAIN WILD-TYPE 113 116 75

Figure S24.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.11

Table S25.  Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
3Q GAIN MUTATED 96 72 99
3Q GAIN WILD-TYPE 76 103 122

Figure S25.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4p gain' versus 'MIR_CNMF'

P value = 0.0049 (Fisher's exact test), Q value = 0.045

Table S26.  Gene #7: '4p gain' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
4P GAIN MUTATED 7 16 33
4P GAIN WILD-TYPE 152 148 199

Figure S26.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'MIR_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.1

Table S27.  Gene #7: '4p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
4P GAIN MUTATED 9 23 28
4P GAIN WILD-TYPE 162 183 174

Figure S27.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'CN_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.11

Table S28.  Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
4P GAIN MUTATED 8 13 24 6
4P GAIN WILD-TYPE 97 58 141 100

Figure S28.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.042

Table S29.  Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
4Q GAIN MUTATED 2 15 15
4Q GAIN WILD-TYPE 169 191 187

Figure S29.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.00818 (Fisher's exact test), Q value = 0.064

Table S30.  Gene #8: '4q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
4Q GAIN MUTATED 17 8 6
4Q GAIN WILD-TYPE 155 167 215

Figure S30.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.14

Table S31.  Gene #8: '4q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
4Q GAIN MUTATED 9 4 8 4
4Q GAIN WILD-TYPE 134 50 52 150

Figure S31.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0082

Table S32.  Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
5P GAIN MUTATED 39 77 83
5P GAIN WILD-TYPE 132 129 119

Figure S32.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'CN_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00425 (Fisher's exact test), Q value = 0.042

Table S33.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
6P GAIN MUTATED 79 44 39
6P GAIN WILD-TYPE 231 114 50

Figure S33.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.089

Table S34.  Gene #11: '6p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
6P GAIN MUTATED 20 13 14 20 11 28 11 13 25 6
6P GAIN WILD-TYPE 65 44 44 62 23 47 23 23 27 36

Figure S34.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S35.  Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
6P GAIN MUTATED 29 56 85
6P GAIN WILD-TYPE 142 150 117

Figure S35.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.003

Table S36.  Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
6P GAIN MUTATED 72 39 55
6P GAIN WILD-TYPE 100 136 166

Figure S36.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.013

Table S37.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
6P GAIN MUTATED 36 31 31
6P GAIN WILD-TYPE 110 28 64

Figure S37.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.12

Table S38.  Gene #12: '6q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
6Q GAIN MUTATED 11 5 9 14 7 9 10 8 16 3
6Q GAIN WILD-TYPE 74 52 49 68 27 66 24 28 36 39

Figure S38.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S39.  Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
6Q GAIN MUTATED 12 30 55
6Q GAIN WILD-TYPE 159 176 147

Figure S39.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S40.  Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
6Q GAIN MUTATED 48 16 32
6Q GAIN WILD-TYPE 124 159 189

Figure S40.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.17

Table S41.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
6Q GAIN MUTATED 23 18 14
6Q GAIN WILD-TYPE 123 41 81

Figure S41.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.16

Table S42.  Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
6Q GAIN MUTATED 15 19 35 12
6Q GAIN WILD-TYPE 90 52 130 94

Figure S42.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S43.  Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
7P GAIN MUTATED 43 44 94
7P GAIN WILD-TYPE 128 162 108

Figure S43.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0049

Table S44.  Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
7P GAIN MUTATED 75 41 63
7P GAIN WILD-TYPE 97 134 158

Figure S44.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S45.  Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
7Q GAIN MUTATED 46 57 100
7Q GAIN WILD-TYPE 125 149 102

Figure S45.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.019

Table S46.  Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
7Q GAIN MUTATED 76 45 77
7Q GAIN WILD-TYPE 96 130 144

Figure S46.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00373 (Fisher's exact test), Q value = 0.039

Table S47.  Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
8P GAIN MUTATED 49 45 22
8P GAIN WILD-TYPE 261 113 67

Figure S47.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'MRNA_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.12

Table S48.  Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
8Q GAIN MUTATED 83 86 67
8Q GAIN WILD-TYPE 132 130 59

Figure S48.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.011

Table S49.  Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
8Q GAIN MUTATED 115 87 34
8Q GAIN WILD-TYPE 195 71 55

Figure S49.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00622 (Fisher's exact test), Q value = 0.053

Table S50.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
8Q GAIN MUTATED 39 36 61
8Q GAIN WILD-TYPE 40 72 52

Figure S50.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.099

Table S51.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
8Q GAIN MUTATED 64 19 53
8Q GAIN WILD-TYPE 82 40 42

Figure S51.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.16

Table S52.  Gene #16: '8q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 12 10
8Q GAIN MUTATED 7 1
8Q GAIN WILD-TYPE 5 9

Figure S52.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.03

Table S53.  Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
9P GAIN MUTATED 17 29 46
9P GAIN WILD-TYPE 154 177 156

Figure S53.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.00829 (Fisher's exact test), Q value = 0.064

Table S54.  Gene #17: '9p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
9P GAIN MUTATED 33 16 42
9P GAIN WILD-TYPE 139 159 179

Figure S54.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 0.00435 (Fisher's exact test), Q value = 0.042

Table S55.  Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
10P GAIN MUTATED 81 53 48
10P GAIN WILD-TYPE 134 163 78

Figure S55.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0206 (Fisher's exact test), Q value = 0.12

Table S56.  Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
10P GAIN MUTATED 90 52 40
10P GAIN WILD-TYPE 220 106 49

Figure S56.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S57.  Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
10P GAIN MUTATED 41 45 102
10P GAIN WILD-TYPE 130 161 100

Figure S57.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0039

Table S58.  Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
10P GAIN MUTATED 77 44 63
10P GAIN WILD-TYPE 95 131 158

Figure S58.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.02

Table S59.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
10P GAIN MUTATED 14 45 40
10P GAIN WILD-TYPE 65 63 73

Figure S59.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.01

Table S60.  Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
10P GAIN MUTATED 22 27 70 27
10P GAIN WILD-TYPE 83 44 95 79

Figure S60.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MRNA_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.04

Table S61.  Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
10Q GAIN MUTATED 55 28 24
10Q GAIN WILD-TYPE 160 188 102

Figure S61.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00939 (Fisher's exact test), Q value = 0.07

Table S62.  Gene #20: '10q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
10Q GAIN MUTATED 52 27 28
10Q GAIN WILD-TYPE 258 131 61

Figure S62.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.04

Table S63.  Gene #20: '10q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
10Q GAIN MUTATED 24 33 54
10Q GAIN WILD-TYPE 147 173 148

Figure S63.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.1

Table S64.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
10Q GAIN MUTATED 7 27 20
10Q GAIN WILD-TYPE 72 81 93

Figure S64.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.094

Table S65.  Gene #21: '11p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
11P GAIN MUTATED 26 13 37
11P GAIN WILD-TYPE 146 162 184

Figure S65.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11p gain' versus 'RPPA_CNMF'

P value = 0.00823 (Fisher's exact test), Q value = 0.064

Table S66.  Gene #21: '11p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
11P GAIN MUTATED 9 32 11
11P GAIN WILD-TYPE 137 157 65

Figure S66.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'RPPA_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.00441 (Fisher's exact test), Q value = 0.043

Table S67.  Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
11Q GAIN MUTATED 20 48 47
11Q GAIN WILD-TYPE 151 158 155

Figure S67.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.024

Table S68.  Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
11Q GAIN MUTATED 38 20 55
11Q GAIN WILD-TYPE 134 155 166

Figure S68.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p gain' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.001

Table S69.  Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
12P GAIN MUTATED 118 75 49
12P GAIN WILD-TYPE 97 141 77

Figure S69.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.02

Table S70.  Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
12P GAIN MUTATED 132 57 53
12P GAIN WILD-TYPE 178 101 36

Figure S70.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.016

Table S71.  Gene #23: '12p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
12P GAIN MUTATED 33 20 28 36 15 30 19 11 37 12
12P GAIN WILD-TYPE 52 37 30 46 19 45 15 25 15 30

Figure S71.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S72.  Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
12P GAIN MUTATED 54 68 133
12P GAIN WILD-TYPE 117 138 69

Figure S72.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S73.  Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
12P GAIN MUTATED 104 71 74
12P GAIN WILD-TYPE 68 104 147

Figure S73.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0088

Table S74.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
12P GAIN MUTATED 22 61 45
12P GAIN WILD-TYPE 57 47 68

Figure S74.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.011

Table S75.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
12P GAIN MUTATED 53 38 37
12P GAIN WILD-TYPE 93 21 58

Figure S75.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0049

Table S76.  Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
12P GAIN MUTATED 27 38 81 46
12P GAIN WILD-TYPE 78 33 84 60

Figure S76.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MRNA_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.043

Table S77.  Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
12Q GAIN MUTATED 81 50 38
12Q GAIN WILD-TYPE 134 166 88

Figure S77.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.17

Table S78.  Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
12Q GAIN MUTATED 27 16 21 21 11 20 15 9 23 5
12Q GAIN WILD-TYPE 58 41 37 61 23 55 19 27 29 37

Figure S78.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S79.  Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
12Q GAIN MUTATED 40 38 99
12Q GAIN WILD-TYPE 131 168 103

Figure S79.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S80.  Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
12Q GAIN MUTATED 78 43 54
12Q GAIN WILD-TYPE 94 132 167

Figure S80.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.13

Table S81.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
12Q GAIN MUTATED 21 45 29
12Q GAIN WILD-TYPE 58 63 84

Figure S81.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.13

Table S82.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
12Q GAIN MUTATED 45 27 23
12Q GAIN WILD-TYPE 101 32 72

Figure S82.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.081

Table S83.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
12Q GAIN MUTATED 19 28 53 34
12Q GAIN WILD-TYPE 86 43 112 72

Figure S83.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MRNA_CNMF'

P value = 0.00782 (Fisher's exact test), Q value = 0.062

Table S84.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
13Q GAIN MUTATED 26 12 19
13Q GAIN WILD-TYPE 189 204 107

Figure S84.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0065

Table S85.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
13Q GAIN MUTATED 19 20 18
13Q GAIN WILD-TYPE 291 138 71

Figure S85.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.14

Table S86.  Gene #25: '13q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
13Q GAIN MUTATED 6 8 5 6 2 10 9 1 8 1
13Q GAIN WILD-TYPE 79 49 53 76 32 65 25 35 44 41

Figure S86.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0024

Table S87.  Gene #25: '13q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
13Q GAIN MUTATED 22 7 31
13Q GAIN WILD-TYPE 149 199 171

Figure S87.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S88.  Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
13Q GAIN MUTATED 31 20 8
13Q GAIN WILD-TYPE 141 155 213

Figure S88.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.17

Table S89.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
13Q GAIN MUTATED 3 15 16
13Q GAIN WILD-TYPE 76 93 97

Figure S89.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.029

Table S90.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
16P GAIN MUTATED 34 18 6
16P GAIN WILD-TYPE 181 198 120

Figure S90.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00433 (Fisher's exact test), Q value = 0.042

Table S91.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
16P GAIN MUTATED 34 8 16
16P GAIN WILD-TYPE 276 150 73

Figure S91.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.16

Table S92.  Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
16P GAIN MUTATED 14 15 30
16P GAIN WILD-TYPE 157 191 172

Figure S92.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.11

Table S93.  Gene #28: '16p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
16P GAIN MUTATED 23 9 26
16P GAIN WILD-TYPE 149 166 195

Figure S93.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16q gain' versus 'MRNA_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.011

Table S94.  Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
16Q GAIN MUTATED 18 12 0
16Q GAIN WILD-TYPE 197 204 126

Figure S94.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0444 (Fisher's exact test), Q value = 0.2

Table S95.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
16Q GAIN MUTATED 20 3 7
16Q GAIN WILD-TYPE 290 155 82

Figure S95.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00346 (Fisher's exact test), Q value = 0.037

Table S96.  Gene #29: '16q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
16Q GAIN MUTATED 10 2 18
16Q GAIN WILD-TYPE 162 173 203

Figure S96.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.013

Table S97.  Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
16Q GAIN MUTATED 0 9 13
16Q GAIN WILD-TYPE 121 173 131

Figure S97.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.18

Table S98.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
17Q GAIN MUTATED 18 16 12
17Q GAIN WILD-TYPE 292 142 77

Figure S98.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.18

Table S99.  Gene #31: '17q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
17Q GAIN MUTATED 8 5 5 4 1 3 0 4 10 6
17Q GAIN WILD-TYPE 77 52 53 78 33 72 34 32 42 36

Figure S99.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.018

Table S100.  Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
18P GAIN MUTATED 26 35 59
18P GAIN WILD-TYPE 145 171 143

Figure S100.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0065

Table S101.  Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
18P GAIN MUTATED 54 26 38
18P GAIN WILD-TYPE 118 149 183

Figure S101.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.13

Table S102.  Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
18Q GAIN MUTATED 14 23 35
18Q GAIN WILD-TYPE 157 183 167

Figure S102.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.14

Table S103.  Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
18Q GAIN MUTATED 32 17 23
18Q GAIN WILD-TYPE 140 158 198

Figure S103.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00072

Table S104.  Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
19P GAIN MUTATED 33 55 83
19P GAIN WILD-TYPE 138 151 119

Figure S104.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.14

Table S105.  Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
19P GAIN MUTATED 60 39 69
19P GAIN WILD-TYPE 112 136 152

Figure S105.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0016

Table S106.  Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
19Q GAIN MUTATED 33 49 79
19Q GAIN WILD-TYPE 138 157 123

Figure S106.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.018

Table S107.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
20P GAIN MUTATED 125 88 64
20P GAIN WILD-TYPE 90 128 62

Figure S107.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.016

Table S108.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
20P GAIN MUTATED 147 70 60
20P GAIN WILD-TYPE 163 88 29

Figure S108.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0085

Table S109.  Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
20P GAIN MUTATED 31 27 33 36 21 41 26 16 32 13
20P GAIN WILD-TYPE 54 30 25 46 13 34 8 20 20 29

Figure S109.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S110.  Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
20P GAIN MUTATED 66 79 144
20P GAIN WILD-TYPE 105 127 58

Figure S110.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S111.  Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
20P GAIN MUTATED 117 79 86
20P GAIN WILD-TYPE 55 96 135

Figure S111.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.089

Table S112.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
20P GAIN MUTATED 32 67 57
20P GAIN WILD-TYPE 47 41 56

Figure S112.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00366 (Fisher's exact test), Q value = 0.038

Table S113.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
20P GAIN MUTATED 40 41 98 50
20P GAIN WILD-TYPE 65 30 67 56

Figure S113.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S114.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
20Q GAIN MUTATED 143 95 76
20Q GAIN WILD-TYPE 72 121 50

Figure S114.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0086

Table S115.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
20Q GAIN MUTATED 164 83 67
20Q GAIN WILD-TYPE 146 75 22

Figure S115.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'MIR_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0035

Table S116.  Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
20Q GAIN MUTATED 35 30 35 40 24 41 26 21 42 19
20Q GAIN WILD-TYPE 50 27 23 42 10 34 8 15 10 23

Figure S116.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S117.  Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
20Q GAIN MUTATED 69 98 161
20Q GAIN WILD-TYPE 102 108 41

Figure S117.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S118.  Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
20Q GAIN MUTATED 132 87 101
20Q GAIN WILD-TYPE 40 88 120

Figure S118.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00638 (Fisher's exact test), Q value = 0.053

Table S119.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
20Q GAIN MUTATED 74 44 57
20Q GAIN WILD-TYPE 72 15 38

Figure S119.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0048 (Fisher's exact test), Q value = 0.044

Table S120.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
20Q GAIN MUTATED 48 47 108 57
20Q GAIN WILD-TYPE 57 24 57 49

Figure S120.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.019

Table S121.  Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
21Q GAIN MUTATED 22 33 54
21Q GAIN WILD-TYPE 149 173 148

Figure S121.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.1

Table S122.  Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
21Q GAIN MUTATED 45 25 39
21Q GAIN WILD-TYPE 127 150 182

Figure S122.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.14

Table S123.  Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
21Q GAIN MUTATED 34 30 23
21Q GAIN WILD-TYPE 87 152 121

Figure S123.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.2

Table S124.  Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
21Q GAIN MUTATED 16 20 37 14
21Q GAIN WILD-TYPE 89 51 128 92

Figure S124.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.16

Table S125.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
XP GAIN MUTATED 14 29 35
XP GAIN WILD-TYPE 157 177 167

Figure S125.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'CN_CNMF'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.19

Table S126.  Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
XP GAIN MUTATED 17 31 11
XP GAIN WILD-TYPE 104 151 133

Figure S126.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0019

Table S127.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
XQ GAIN MUTATED 17 35 56
XQ GAIN WILD-TYPE 154 171 146

Figure S127.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'CN_CNMF'

'1p loss' versus 'MRNA_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.17

Table S128.  Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
1P LOSS MUTATED 33 16 13
1P LOSS WILD-TYPE 182 200 113

Figure S128.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0072

Table S129.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
1P LOSS MUTATED 31 10 21
1P LOSS WILD-TYPE 279 148 68

Figure S129.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.094

Table S130.  Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
1Q LOSS MUTATED 20 7 13
1Q LOSS WILD-TYPE 290 151 76

Figure S130.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.13

Table S131.  Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
2P LOSS MUTATED 39 10 4
2P LOSS WILD-TYPE 271 148 85

Figure S131.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.13

Table S132.  Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
3P LOSS MUTATED 45 25 24
3P LOSS WILD-TYPE 170 191 102

Figure S132.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.014

Table S133.  Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
3P LOSS MUTATED 38 30 26
3P LOSS WILD-TYPE 272 128 63

Figure S133.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00538 (Fisher's exact test), Q value = 0.048

Table S134.  Gene #46: '3p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
3P LOSS MUTATED 16 4 4 12 5 13 12 8 15 5
3P LOSS WILD-TYPE 69 53 54 70 29 62 22 28 37 37

Figure S134.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0079

Table S135.  Gene #46: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
3P LOSS MUTATED 23 22 50
3P LOSS WILD-TYPE 148 184 152

Figure S135.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.03

Table S136.  Gene #46: '3p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
3P LOSS MUTATED 42 27 25
3P LOSS WILD-TYPE 130 148 196

Figure S136.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.16

Table S137.  Gene #46: '3p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
3P LOSS MUTATED 19 8 17 18
3P LOSS WILD-TYPE 124 46 43 136

Figure S137.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.019

Table S138.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
3P LOSS MUTATED 15 18 21
3P LOSS WILD-TYPE 131 41 74

Figure S138.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MRNA_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.089

Table S139.  Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
3Q LOSS MUTATED 22 8 13
3Q LOSS WILD-TYPE 193 208 113

Figure S139.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.19

Table S140.  Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
3Q LOSS MUTATED 17 14 12
3Q LOSS WILD-TYPE 293 144 77

Figure S140.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.16

Table S141.  Gene #47: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
3Q LOSS MUTATED 14 8 21
3Q LOSS WILD-TYPE 157 198 181

Figure S141.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.035

Table S142.  Gene #47: '3q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
3Q LOSS MUTATED 22 13 8
3Q LOSS WILD-TYPE 150 162 213

Figure S142.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.17

Table S143.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
3Q LOSS MUTATED 6 8 10
3Q LOSS WILD-TYPE 140 51 85

Figure S143.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.015

Table S144.  Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
3Q LOSS MUTATED 3 7 21 2
3Q LOSS WILD-TYPE 102 64 144 104

Figure S144.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.17

Table S145.  Gene #47: '3q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S145.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.13

Table S146.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
4P LOSS MUTATED 176 72 55
4P LOSS WILD-TYPE 134 86 34

Figure S146.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.00454 (Fisher's exact test), Q value = 0.043

Table S147.  Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
4P LOSS MUTATED 93 96 127
4P LOSS WILD-TYPE 78 110 75

Figure S147.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'CN_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.02

Table S148.  Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
4Q LOSS MUTATED 107 111 144
4Q LOSS WILD-TYPE 64 95 58

Figure S148.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'CN_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 0.16

Table S149.  Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
5P LOSS MUTATED 69 30 30
5P LOSS WILD-TYPE 241 128 59

Figure S149.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.085

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
5P LOSS MUTATED 33 39 61
5P LOSS WILD-TYPE 138 167 141

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

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.00661 (Fisher's exact test), Q value = 0.055

Table S151.  Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
5P LOSS MUTATED 52 28 50
5P LOSS WILD-TYPE 120 147 171

Figure S151.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.011

Table S152.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
5P LOSS MUTATED 13 42 23
5P LOSS WILD-TYPE 66 66 90

Figure S152.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00161 (Fisher's exact test), Q value = 0.02

Table S153.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
5P LOSS MUTATED 35 26 17
5P LOSS WILD-TYPE 111 33 78

Figure S153.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0071

Table S154.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
5Q LOSS MUTATED 105 68 41
5Q LOSS WILD-TYPE 110 148 85

Figure S154.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00172 (Fisher's exact test), Q value = 0.021

Table S155.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
5Q LOSS MUTATED 113 52 49
5Q LOSS WILD-TYPE 197 106 40

Figure S155.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.089

Table S156.  Gene #51: '5q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
5Q LOSS MUTATED 27 20 23 28 14 24 22 14 29 13
5Q LOSS WILD-TYPE 58 37 35 54 20 51 12 22 23 29

Figure S156.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0086

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
5Q LOSS MUTATED 54 69 100
5Q LOSS WILD-TYPE 117 137 102

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

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S158.  Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
5Q LOSS MUTATED 96 51 72
5Q LOSS WILD-TYPE 76 124 149

Figure S158.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.015

Table S159.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
5Q LOSS MUTATED 24 58 37
5Q LOSS WILD-TYPE 55 50 76

Figure S159.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00165 (Fisher's exact test), Q value = 0.021

Table S160.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
5Q LOSS MUTATED 55 35 29
5Q LOSS WILD-TYPE 91 24 66

Figure S160.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00742 (Fisher's exact test), Q value = 0.06

Table S161.  Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
5Q LOSS MUTATED 37 36 76 31
5Q LOSS WILD-TYPE 68 35 89 75

Figure S161.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.12

Table S162.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
6P LOSS MUTATED 98 46 15
6P LOSS WILD-TYPE 212 112 74

Figure S162.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.17

Table S163.  Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
6Q LOSS MUTATED 80 92 70
6Q LOSS WILD-TYPE 91 114 132

Figure S163.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'CN_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.084

Table S164.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
6Q LOSS MUTATED 60 15 47
6Q LOSS WILD-TYPE 86 44 48

Figure S164.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.029

Table S165.  Gene #56: '8p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
8P LOSS MUTATED 66 97 114
8P LOSS WILD-TYPE 105 109 88

Figure S165.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'CN_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.18

Table S166.  Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
8P LOSS MUTATED 37 39 83 51
8P LOSS WILD-TYPE 68 32 82 55

Figure S166.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MRNA_CNMF'

P value = 0.00771 (Fisher's exact test), Q value = 0.062

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
8Q LOSS MUTATED 46 25 14
8Q LOSS WILD-TYPE 169 191 112

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

'8q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00549 (Fisher's exact test), Q value = 0.049

Table S168.  Gene #57: '8q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
8Q LOSS MUTATED 43 18 24
8Q LOSS WILD-TYPE 267 140 65

Figure S168.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.015

Table S169.  Gene #57: '8q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
8Q LOSS MUTATED 18 25 47
8Q LOSS WILD-TYPE 153 181 155

Figure S169.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.17

Table S170.  Gene #57: '8q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
8Q LOSS MUTATED 37 24 27
8Q LOSS WILD-TYPE 135 151 194

Figure S170.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.03

Table S171.  Gene #57: '8q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
8Q LOSS MUTATED 8 29 13
8Q LOSS WILD-TYPE 71 79 100

Figure S171.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.014

Table S172.  Gene #57: '8q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
8Q LOSS MUTATED 19 20 11
8Q LOSS WILD-TYPE 127 39 84

Figure S172.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.031

Table S173.  Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
9P LOSS MUTATED 106 77 65
9P LOSS WILD-TYPE 109 139 61

Figure S173.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00607 (Fisher's exact test), Q value = 0.053

Table S174.  Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
9P LOSS MUTATED 125 70 53
9P LOSS WILD-TYPE 185 88 36

Figure S174.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.1

Table S175.  Gene #58: '9p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
9P LOSS MUTATED 79 78 105
9P LOSS WILD-TYPE 92 128 97

Figure S175.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'CN_CNMF'

'9q loss' versus 'MRNA_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.057

Table S176.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
9Q LOSS MUTATED 120 88 63
9Q LOSS WILD-TYPE 95 128 63

Figure S176.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.094

Table S177.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
9Q LOSS MUTATED 143 72 56
9Q LOSS WILD-TYPE 167 86 33

Figure S177.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.17

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

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
9Q LOSS MUTATED 31 30 34 33 21 33 21 18 31 19
9Q LOSS WILD-TYPE 54 27 24 49 13 42 13 18 21 23

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

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S179.  Gene #59: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
9Q LOSS MUTATED 81 68 137
9Q LOSS WILD-TYPE 90 138 65

Figure S179.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00612 (Fisher's exact test), Q value = 0.053

Table S180.  Gene #59: '9q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
9Q LOSS MUTATED 102 80 97
9Q LOSS WILD-TYPE 70 95 124

Figure S180.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.00723 (Fisher's exact test), Q value = 0.059

Table S181.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
9Q LOSS MUTATED 27 62 52
9Q LOSS WILD-TYPE 52 46 61

Figure S181.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.014

Table S182.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
9Q LOSS MUTATED 57 40 44
9Q LOSS WILD-TYPE 89 19 51

Figure S182.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIR_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.043

Table S183.  Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
10Q LOSS MUTATED 32 23 64
10Q LOSS WILD-TYPE 127 141 168

Figure S183.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.13

Table S184.  Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
10Q LOSS MUTATED 33 35 56
10Q LOSS WILD-TYPE 138 171 146

Figure S184.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.024

Table S185.  Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
10Q LOSS MUTATED 53 27 43
10Q LOSS WILD-TYPE 119 148 178

Figure S185.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.084

Table S186.  Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
11P LOSS MUTATED 91 57 41
11P LOSS WILD-TYPE 219 101 48

Figure S186.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.18

Table S187.  Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
11P LOSS MUTATED 72 54 67
11P LOSS WILD-TYPE 100 121 154

Figure S187.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.00955 (Fisher's exact test), Q value = 0.071

Table S188.  Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
11Q LOSS MUTATED 38 43 67
11Q LOSS WILD-TYPE 133 163 135

Figure S188.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'CN_CNMF'

'12p loss' versus 'MRNA_CNMF'

P value = 0.0028 (Fisher's exact test), Q value = 0.031

Table S189.  Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
12P LOSS MUTATED 18 32 27
12P LOSS WILD-TYPE 197 184 99

Figure S189.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.079

Table S190.  Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
12P LOSS MUTATED 42 30 5
12P LOSS WILD-TYPE 268 128 84

Figure S190.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00691 (Fisher's exact test), Q value = 0.057

Table S191.  Gene #64: '12p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
12P LOSS MUTATED 12 12 6 11 4 12 1 11 1 7
12P LOSS WILD-TYPE 73 45 52 71 30 63 33 25 51 35

Figure S191.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.015

Table S192.  Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
12P LOSS MUTATED 26 39 14
12P LOSS WILD-TYPE 145 167 188

Figure S192.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'CN_CNMF'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 0.00958 (Fisher's exact test), Q value = 0.071

Table S193.  Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
12P LOSS MUTATED 18 35 11
12P LOSS WILD-TYPE 103 147 133

Figure S193.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.053

Table S194.  Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
12P LOSS MUTATED 24 5 26 9
12P LOSS WILD-TYPE 81 66 139 97

Figure S194.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.13

Table S195.  Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
12Q LOSS MUTATED 29 49 27
12Q LOSS WILD-TYPE 142 157 175

Figure S195.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.14

Table S196.  Gene #65: '12q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
12Q LOSS MUTATED 21 5 23
12Q LOSS WILD-TYPE 125 54 72

Figure S196.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.14

Table S197.  Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
12Q LOSS MUTATED 24 40 16
12Q LOSS WILD-TYPE 97 142 128

Figure S197.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.16

Table S198.  Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
12Q LOSS MUTATED 27 9 32 12
12Q LOSS WILD-TYPE 78 62 133 94

Figure S198.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0398 (Fisher's exact test), Q value = 0.19

Table S199.  Gene #65: '12q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 2 2 6 4 2
12Q LOSS MUTATED 0 0 1 4 0 0
12Q LOSS WILD-TYPE 6 2 1 2 4 2

Figure S199.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.16

Table S200.  Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
13Q LOSS MUTATED 111 129 57
13Q LOSS WILD-TYPE 104 87 69

Figure S200.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00842 (Fisher's exact test), Q value = 0.064

Table S201.  Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
13Q LOSS MUTATED 182 78 37
13Q LOSS WILD-TYPE 128 80 52

Figure S201.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.1

Table S202.  Gene #66: '13q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
13Q LOSS MUTATED 46 29 38 50 17 30 13 26 25 24
13Q LOSS WILD-TYPE 39 28 20 32 17 45 21 10 27 18

Figure S202.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'13q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00072

Table S203.  Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
13Q LOSS MUTATED 89 72 144
13Q LOSS WILD-TYPE 83 103 77

Figure S203.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.081

Table S204.  Gene #66: '13q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
13Q LOSS MUTATED 64 114 40
13Q LOSS WILD-TYPE 82 75 36

Figure S204.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.094

Table S205.  Gene #66: '13q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
13Q LOSS MUTATED 63 30 41 84
13Q LOSS WILD-TYPE 80 24 19 70

Figure S205.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S206.  Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
14Q LOSS MUTATED 52 58 105
14Q LOSS WILD-TYPE 119 148 97

Figure S206.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0036 (Fisher's exact test), Q value = 0.038

Table S207.  Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
14Q LOSS MUTATED 81 58 70
14Q LOSS WILD-TYPE 91 117 151

Figure S207.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.00775 (Fisher's exact test), Q value = 0.062

Table S208.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
14Q LOSS MUTATED 19 49 36
14Q LOSS WILD-TYPE 60 59 77

Figure S208.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0029

Table S209.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
14Q LOSS MUTATED 36 34 34
14Q LOSS WILD-TYPE 110 25 61

Figure S209.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.01

Table S210.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
15Q LOSS MUTATED 126 87 57
15Q LOSS WILD-TYPE 89 129 69

Figure S210.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.11

Table S211.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
15Q LOSS MUTATED 150 66 54
15Q LOSS WILD-TYPE 160 92 35

Figure S211.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'MIR_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.003

Table S212.  Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
15Q LOSS MUTATED 62 70 138
15Q LOSS WILD-TYPE 97 94 94

Figure S212.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'15q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0068

Table S213.  Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
15Q LOSS MUTATED 26 27 34 41 18 42 23 18 30 11
15Q LOSS WILD-TYPE 59 30 24 41 16 33 11 18 22 31

Figure S213.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S214.  Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
15Q LOSS MUTATED 65 74 141
15Q LOSS WILD-TYPE 106 132 61

Figure S214.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S215.  Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
15Q LOSS MUTATED 114 69 94
15Q LOSS WILD-TYPE 58 106 127

Figure S215.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00601 (Fisher's exact test), Q value = 0.053

Table S216.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
15Q LOSS MUTATED 27 62 51
15Q LOSS WILD-TYPE 52 46 62

Figure S216.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00832 (Fisher's exact test), Q value = 0.064

Table S217.  Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
15Q LOSS MUTATED 55 108 63
15Q LOSS WILD-TYPE 66 74 81

Figure S217.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.011

Table S218.  Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 105 71 165 106
15Q LOSS MUTATED 43 37 103 43
15Q LOSS WILD-TYPE 62 34 62 63

Figure S218.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.2

Table S219.  Gene #68: '15q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 12 10
15Q LOSS MUTATED 4 8
15Q LOSS WILD-TYPE 8 2

Figure S219.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIR_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.2

Table S220.  Gene #69: '16p loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
16P LOSS MUTATED 97 81 142
16P LOSS WILD-TYPE 62 83 90

Figure S220.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'MIR_CNMF'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.22

Table S221.  Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
16P LOSS MUTATED 67 120 77
16P LOSS WILD-TYPE 54 62 67

Figure S221.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'16q loss' versus 'MIR_CNMF'

P value = 0.00283 (Fisher's exact test), Q value = 0.031

Table S222.  Gene #70: '16q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
16Q LOSS MUTATED 117 100 178
16Q LOSS WILD-TYPE 42 64 54

Figure S222.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.15

Table S223.  Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
16Q LOSS MUTATED 112 144 157
16Q LOSS WILD-TYPE 59 62 45

Figure S223.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'CN_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.15

Table S224.  Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 310 158 89
17Q LOSS MUTATED 220 94 55
17Q LOSS WILD-TYPE 90 64 34

Figure S224.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'MIR_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.1

Table S225.  Gene #72: '17q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
17Q LOSS MUTATED 104 96 168
17Q LOSS WILD-TYPE 55 68 64

Figure S225.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'17q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.084

Table S226.  Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
17Q LOSS MUTATED 50 37 43 59 19 50 30 26 26 28
17Q LOSS WILD-TYPE 35 20 15 23 15 25 4 10 26 14

Figure S226.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.16

Table S227.  Gene #72: '17q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 108 113
17Q LOSS MUTATED 61 70 67
17Q LOSS WILD-TYPE 18 38 46

Figure S227.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'18p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.12

Table S228.  Gene #73: '18p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
18P LOSS MUTATED 37 16 20 27 21 40 12 17 20 19
18P LOSS WILD-TYPE 48 41 38 55 13 35 22 19 32 23

Figure S228.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.029

Table S229.  Gene #73: '18p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
18P LOSS MUTATED 59 90 83
18P LOSS WILD-TYPE 113 85 138

Figure S229.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.18

Table S230.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
18Q LOSS MUTATED 64 37 52
18Q LOSS WILD-TYPE 82 22 43

Figure S230.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.2

Table S231.  Gene #75: '19p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
19P LOSS MUTATED 26 16 20 31 8 20 18 9 11 19
19P LOSS WILD-TYPE 59 41 38 51 26 55 16 27 41 23

Figure S231.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.00525 (Fisher's exact test), Q value = 0.048

Table S232.  Gene #75: '19p loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
19P LOSS MUTATED 56 50 79
19P LOSS WILD-TYPE 115 156 123

Figure S232.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.12

Table S233.  Gene #75: '19p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
19P LOSS MUTATED 69 49 62
19P LOSS WILD-TYPE 103 126 159

Figure S233.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.098

Table S234.  Gene #75: '19p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
19P LOSS MUTATED 36 54 33
19P LOSS WILD-TYPE 110 135 43

Figure S234.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.083

Table S235.  Gene #75: '19p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 12 10
19P LOSS MUTATED 8 1
19P LOSS WILD-TYPE 4 9

Figure S235.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIR_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.1

Table S236.  Gene #76: '19q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 85 57 58 82 34 75 34 36 52 42
19Q LOSS MUTATED 29 16 16 31 7 18 18 9 9 17
19Q LOSS WILD-TYPE 56 41 42 51 27 57 16 27 43 25

Figure S236.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00461 (Fisher's exact test), Q value = 0.043

Table S237.  Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
19Q LOSS MUTATED 61 46 71
19Q LOSS WILD-TYPE 110 160 131

Figure S237.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'CN_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.12

Table S238.  Gene #76: '19q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
19Q LOSS MUTATED 34 49 31
19Q LOSS WILD-TYPE 112 140 45

Figure S238.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00535 (Fisher's exact test), Q value = 0.048

Table S239.  Gene #76: '19q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 12 10
19Q LOSS MUTATED 7 0
19Q LOSS WILD-TYPE 5 10

Figure S239.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.015

Table S240.  Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
20P LOSS MUTATED 2 23 15
20P LOSS WILD-TYPE 119 159 129

Figure S240.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'20q loss' versus 'MIR_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.18

Table S241.  Gene #78: '20q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
20Q LOSS MUTATED 11 3 16
20Q LOSS WILD-TYPE 148 161 216

Figure S241.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.027

Table S242.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 216 126
22Q LOSS MUTATED 175 144 93
22Q LOSS WILD-TYPE 40 72 33

Figure S242.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MIR_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.18

Table S243.  Gene #80: '22q loss' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 164 232
22Q LOSS MUTATED 110 117 185
22Q LOSS WILD-TYPE 49 47 47

Figure S243.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'MIR_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0016

Table S244.  Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
22Q LOSS MUTATED 120 139 171
22Q LOSS WILD-TYPE 51 67 31

Figure S244.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.022

Table S245.  Gene #80: '22q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
22Q LOSS MUTATED 140 134 146
22Q LOSS WILD-TYPE 32 41 75

Figure S245.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.1

Table S246.  Gene #80: '22q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 189 76
22Q LOSS MUTATED 105 151 48
22Q LOSS WILD-TYPE 41 38 28

Figure S246.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'RPPA_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.096

Table S247.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 59 95
22Q LOSS MUTATED 101 52 70
22Q LOSS WILD-TYPE 45 7 25

Figure S247.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.19

Table S248.  Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 182 144
22Q LOSS MUTATED 83 148 110
22Q LOSS WILD-TYPE 38 34 34

Figure S248.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 0.00626 (Fisher's exact test), Q value = 0.053

Table S249.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
XP LOSS MUTATED 97 131 97
XP LOSS WILD-TYPE 74 75 105

Figure S249.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.0424 (Fisher's exact test), Q value = 0.2

Table S250.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 172 175 221
XP LOSS MUTATED 84 101 136
XP LOSS WILD-TYPE 88 74 85

Figure S250.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.12

Table S251.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 54 60 154
XP LOSS MUTATED 65 33 39 92
XP LOSS WILD-TYPE 78 21 21 62

Figure S251.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0052

Table S252.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 206 202
XQ LOSS MUTATED 92 114 74
XQ LOSS WILD-TYPE 79 92 128

Figure S252.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/19783384/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/20141012/OV-TP.transferedmergedcluster.txt

  • Number of patients = 579

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 14

  • 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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