Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1B56GX2
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1B56GX2
Overview
Introduction

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

Summary

Testing the association between copy number variation 71 arm-level results and 10 molecular subtypes across 493 patients, 126 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

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

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 2p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 6p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 9p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 17p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 71 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 126 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
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
2q loss 11 (2%) 482 0.000249
(0.137) 		0.000374
(0.205) 		4.75e-06
(0.00288) 		1
(1.00) 		0.15
(1.00) 		3.15e-05
(0.0183) 		8.96e-08
(5.69e-05) 		7.91e-08
(5.04e-05) 		0.000238
(0.132) 		8.83e-10
(5.72e-07)
17p loss 25 (5%) 468 0.000117
(0.0656) 		0.000178
(0.0996) 		4.3e-06
(0.00263) 		0.908
(1.00) 		0.00789
(1.00) 		3.06e-05
(0.0178) 		1.9e-06
(0.00118) 		1.5e-08
(9.65e-06) 		1.63e-08
(1.04e-05) 		8.35e-09
(5.38e-06)
2p loss 10 (2%) 483 0.000249
(0.137) 		0.000374
(0.205) 		1.52e-05
(0.00899) 		0.456
(1.00) 		0.226
(1.00) 		0.000142
(0.0793) 		4.72e-07
(0.000296) 		1.87e-08
(1.2e-05) 		0.000575
(0.309) 		8.72e-11
(5.69e-08)
3p loss 304 (62%) 189 0.013
(1.00) 		0.0102
(1.00) 		6.37e-24
(4.24e-21) 		0.000521
(0.282) 		4.7e-06
(0.00285) 		3.95e-05
(0.0228) 		3.85e-11
(2.52e-08) 		7.09e-10
(4.6e-07) 		4.4e-06
(0.00268) 		6.96e-08
(4.44e-05)
14q loss 158 (32%) 335 0.00179
(0.916) 		0.000956
(0.502) 		2.02e-10
(1.32e-07) 		3.06e-05
(0.0178) 		3.07e-06
(0.00189) 		4.36e-05
(0.0252) 		6.97e-11
(4.56e-08) 		2.8e-07
(0.000177) 		2.87e-06
(0.00178) 		0.00273
(1.00)
17q loss 12 (2%) 481 0.000668
(0.359) 		0.00077
(0.408) 		0.000224
(0.124) 		0.456
(1.00) 		0.105
(1.00) 		6.94e-06
(0.00416) 		1.91e-06
(0.00119) 		7.91e-08
(5.04e-05) 		7.66e-05
(0.0432) 		8.5e-11
(5.55e-08)
8q gain 34 (7%) 459 0.0536
(1.00) 		0.0581
(1.00) 		2.75e-07
(0.000174) 		0.00105
(0.544) 		6.42e-06
(0.00386) 		0.0588
(1.00) 		1.15e-07
(7.27e-05) 		4.88e-05
(0.028) 		1.88e-05
(0.0111) 		0.00404
(1.00)
12p gain 78 (16%) 415 0.194
(1.00) 		0.165
(1.00) 		7.99e-07
(0.000499) 		0.00104
(0.543) 		4.58e-05
(0.0264) 		0.0319
(1.00) 		1.1e-05
(0.00658) 		1.89e-05
(0.0111) 		3.72e-07
(0.000234) 		0.324
(1.00)
12q gain 78 (16%) 415 0.194
(1.00) 		0.165
(1.00) 		7.99e-07
(0.000499) 		0.00104
(0.543) 		4.58e-05
(0.0264) 		0.0371
(1.00) 		1.1e-05
(0.00658) 		1.89e-05
(0.0111) 		3.72e-07
(0.000234) 		0.324
(1.00)
20p gain 66 (13%) 427 0.102
(1.00) 		0.11
(1.00) 		1.05e-12
(6.91e-10) 		0.000674
(0.361) 		5.04e-05
(0.0288) 		0.00756
(1.00) 		3.59e-06
(0.0022) 		5.29e-06
(0.00319) 		4.47e-06
(0.00272) 		0.00806
(1.00)
20q gain 68 (14%) 425 0.0753
(1.00) 		0.092
(1.00) 		6.23e-14
(4.13e-11) 		0.000674
(0.361) 		3.03e-05
(0.0177) 		0.00831
(1.00) 		3.3e-07
(0.000208) 		1.47e-06
(0.000913) 		2.09e-07
(0.000132) 		0.00551
(1.00)
6p loss 58 (12%) 435 0.0139
(1.00) 		0.0029
(1.00) 		4.27e-12
(2.8e-09) 		0.00899
(1.00) 		3.44e-08
(2.2e-05) 		3.53e-06
(0.00216) 		0.000722
(0.384) 		0.00105
(0.545) 		6.4e-09
(4.14e-06) 		0.000191
(0.107)
9p loss 87 (18%) 406 0.378
(1.00) 		0.0694
(1.00) 		9.23e-25
(6.15e-22) 		3.57e-12
(2.35e-09) 		0.00081
(0.428) 		0.0915
(1.00) 		1.39e-11
(9.11e-09) 		2.71e-12
(1.79e-09) 		7.47e-09
(4.83e-06) 		0.125
(1.00)
9q loss 92 (19%) 401 0.378
(1.00) 		0.0694
(1.00) 		4.43e-26
(2.96e-23) 		4.3e-13
(2.85e-10) 		0.000738
(0.392) 		0.0264
(1.00) 		1.31e-12
(8.68e-10) 		3.94e-14
(2.62e-11) 		4.67e-10
(3.04e-07) 		0.118
(1.00)
18p loss 46 (9%) 447 0.194
(1.00) 		0.433
(1.00) 		3.02e-06
(0.00186) 		0.0194
(1.00) 		8.04e-06
(0.00482) 		0.0129
(1.00) 		6.06e-06
(0.00365) 		0.000196
(0.109) 		4.63e-06
(0.00281) 		0.00887
(1.00)
1q loss 21 (4%) 472 0.0217
(1.00) 		0.00286
(1.00) 		2.09e-05
(0.0122) 		0.904
(1.00) 		0.642
(1.00) 		0.0178
(1.00) 		6.65e-05
(0.0377) 		6.27e-07
(0.000392) 		0.0197
(1.00) 		7.54e-09
(4.86e-06)
6q loss 82 (17%) 411 0.0393
(1.00) 		0.0125
(1.00) 		6.34e-17
(4.21e-14) 		0.121
(1.00) 		2.91e-06
(0.0018) 		0.000779
(0.412) 		0.204
(1.00) 		0.478
(1.00) 		1.43e-05
(0.00849) 		0.00031
(0.17)
18q loss 48 (10%) 445 0.259
(1.00) 		0.238
(1.00) 		3.61e-06
(0.00221) 		0.0324
(1.00) 		2.14e-05
(0.0125) 		0.064
(1.00) 		2.87e-05
(0.0167) 		0.000574
(0.309) 		1.51e-05
(0.00896) 		0.00138
(0.71)
1p loss 32 (6%) 461 0.000836
(0.441) 		6.2e-05
(0.0353) 		0.00395
(1.00) 		0.198
(1.00) 		0.516
(1.00) 		0.00474
(1.00) 		0.0123
(1.00) 		4.64e-06
(0.00282) 		0.004
(1.00) 		1.36e-08
(8.75e-06)
13q loss 31 (6%) 462 0.0253
(1.00) 		0.0281
(1.00) 		6.36e-05
(0.0361) 		0.247
(1.00) 		0.00194
(0.986) 		0.0041
(1.00) 		0.0025
(1.00) 		0.00046
(0.25) 		7.43e-05
(0.042) 		0.00105
(0.544)
3q gain 27 (5%) 466 0.0823
(1.00) 		0.0851
(1.00) 		6.58e-05
(0.0373) 		0.0804
(1.00) 		0.0206
(1.00) 		0.00178
(0.913) 		0.000395
(0.215) 		0.00931
(1.00) 		0.00104
(0.543) 		0.00298
(1.00)
8p gain 14 (3%) 479 5.42e-05
(0.0309) 		0.0796
(1.00) 		9.12e-05
(0.0513) 		0.204
(1.00) 		0.000978
(0.513) 		0.000683
(0.365) 		0.0105
(1.00) 		0.0107
(1.00)
21q loss 32 (6%) 461 0.0145
(1.00) 		0.0219
(1.00) 		0.000367
(0.201) 		0.479
(1.00) 		0.905
(1.00) 		0.0288
(1.00) 		0.00192
(0.979) 		1.72e-05
(0.0101) 		0.0322
(1.00) 		0.00057
(0.308)
1q gain 32 (6%) 461 0.611
(1.00) 		1
(1.00) 		1.05e-05
(0.00625) 		0.452
(1.00) 		0.14
(1.00) 		0.122
(1.00) 		0.00972
(1.00) 		0.15
(1.00) 		0.0196
(1.00) 		0.858
(1.00)
2p gain 48 (10%) 445 0.561
(1.00) 		0.472
(1.00) 		1.08e-06
(0.000676) 		0.653
(1.00) 		0.898
(1.00) 		0.934
(1.00) 		0.144
(1.00) 		0.0785
(1.00) 		0.491
(1.00) 		0.348
(1.00)
2q gain 49 (10%) 444 0.561
(1.00) 		0.472
(1.00) 		4.9e-05
(0.0281) 		0.824
(1.00) 		0.96
(1.00) 		0.838
(1.00) 		0.0519
(1.00) 		0.0498
(1.00) 		0.442
(1.00) 		0.348
(1.00)
5p gain 141 (29%) 352 0.593
(1.00) 		0.592
(1.00) 		1.25e-05
(0.00745) 		0.441
(1.00) 		0.473
(1.00) 		0.257
(1.00) 		0.0458
(1.00) 		0.00844
(1.00) 		0.0216
(1.00) 		0.0544
(1.00)
5q gain 156 (32%) 337 0.105
(1.00) 		0.121
(1.00) 		5.87e-05
(0.0335) 		0.375
(1.00) 		0.489
(1.00) 		0.399
(1.00) 		0.0381
(1.00) 		0.00512
(1.00) 		0.0451
(1.00) 		0.0115
(1.00)
7p gain 127 (26%) 366 0.877
(1.00) 		0.939
(1.00) 		5.05e-06
(0.00305) 		0.0543
(1.00) 		0.0512
(1.00) 		0.0109
(1.00) 		0.068
(1.00) 		0.0824
(1.00) 		0.0017
(0.87) 		0.641
(1.00)
7q gain 129 (26%) 364 0.877
(1.00) 		0.939
(1.00) 		1.36e-05
(0.00809) 		0.0417
(1.00) 		0.00861
(1.00) 		0.00131
(0.678) 		0.0581
(1.00) 		0.131
(1.00) 		0.000705
(0.376) 		0.888
(1.00)
17p gain 16 (3%) 477 0.00522
(1.00) 		0.00665
(1.00) 		0.000357
(0.196) 		0.42
(1.00) 		0.553
(1.00) 		0.169
(1.00) 		0.191
(1.00) 		0.0327
(1.00) 		0.404
(1.00) 		0.0464
(1.00)
19p gain 25 (5%) 468 0.189
(1.00) 		0.197
(1.00) 		3.37e-05
(0.0195) 		0.34
(1.00) 		0.0934
(1.00) 		0.31
(1.00) 		0.0428
(1.00) 		0.0115
(1.00) 		0.0254
(1.00) 		0.068
(1.00)
19q gain 28 (6%) 465 0.0536
(1.00) 		0.0581
(1.00) 		3e-06
(0.00185) 		0.201
(1.00) 		0.0419
(1.00) 		0.117
(1.00) 		0.0185
(1.00) 		0.00414
(1.00) 		0.00828
(1.00) 		0.0283
(1.00)
21q gain 33 (7%) 460 0.82
(1.00) 		0.815
(1.00) 		0.000117
(0.0658) 		0.0986
(1.00) 		0.665
(1.00) 		0.691
(1.00) 		0.0709
(1.00) 		0.08
(1.00) 		0.307
(1.00) 		1
(1.00)
22q gain 25 (5%) 468 0.58
(1.00) 		0.039
(1.00) 		0.000399
(0.217) 		0.0756
(1.00) 		0.664
(1.00) 		0.253
(1.00) 		0.826
(1.00) 		0.846
(1.00) 		0.823
(1.00) 		0.649
(1.00)
4q loss 28 (6%) 465 1
(1.00) 		1
(1.00) 		0.000221
(0.123) 		0.255
(1.00) 		0.857
(1.00) 		0.29
(1.00) 		0.0631
(1.00) 		0.0573
(1.00) 		0.782
(1.00) 		0.512
(1.00)
10p loss 32 (6%) 461 0.026
(1.00) 		0.0287
(1.00) 		0.000201
(0.112) 		0.382
(1.00) 		0.432
(1.00) 		0.0588
(1.00) 		0.0123
(1.00) 		0.0197
(1.00) 		0.569
(1.00) 		0.0101
(1.00)
1p gain 5 (1%) 488 0.627
(1.00) 		1
(1.00) 		0.0248
(1.00) 		0.846
(1.00) 		0.85
(1.00) 		0.519
(1.00) 		1
(1.00)
3p gain 7 (1%) 486 0.386
(1.00) 		1
(1.00) 		0.172
(1.00) 		0.00189
(0.962) 		0.294
(1.00) 		0.161
(1.00) 		0.0111
(1.00) 		0.136
(1.00)
4p gain 8 (2%) 485 0.206
(1.00) 		0.608
(1.00) 		0.172
(1.00) 		0.061
(1.00) 		0.0257
(1.00) 		0.378
(1.00) 		0.0155
(1.00) 		0.264
(1.00)
4q gain 8 (2%) 485 0.67
(1.00) 		0.795
(1.00) 		0.226
(1.00) 		0.371
(1.00) 		0.0112
(1.00) 		0.509
(1.00) 		0.0411
(1.00) 		0.264
(1.00)
6p gain 6 (1%) 487 0.77
(1.00) 		0.555
(1.00) 		0.226
(1.00) 		0.666
(1.00) 		0.215
(1.00) 		0.449
(1.00) 		0.441
(1.00) 		0.192
(1.00)
6q gain 5 (1%) 488 0.532
(1.00) 		0.795
(1.00) 		0.288
(1.00) 		0.445
(1.00) 		0.442
(1.00) 		0.571
(1.00) 		0.833
(1.00) 		0.104
(1.00)
9p gain 8 (2%) 485 0.741
(1.00) 		0.249
(1.00) 		0.0857
(1.00) 		0.28
(1.00) 		0.103
(1.00) 		0.0571
(1.00) 		0.734
(1.00) 		0.0424
(1.00)
9q gain 8 (2%) 485 0.283
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.061
(1.00) 		0.523
(1.00) 		0.636
(1.00) 		0.619
(1.00) 		0.362
(1.00)
10p gain 6 (1%) 487 0.39
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.267
(1.00) 		0.311
(1.00) 		0.387
(1.00) 		0.576
(1.00)
10q gain 4 (1%) 489 0.184
(1.00) 		1
(1.00) 		0.532
(1.00) 		1
(1.00) 		0.688
(1.00) 		0.508
(1.00) 		0.325
(1.00) 		0.559
(1.00)
11p gain 17 (3%) 476 0.769
(1.00) 		0.778
(1.00) 		0.000529
(0.286) 		0.771
(1.00) 		0.205
(1.00) 		0.89
(1.00) 		0.491
(1.00) 		0.265
(1.00) 		0.699
(1.00) 		0.478
(1.00)
11q gain 15 (3%) 478 0.769
(1.00) 		0.778
(1.00) 		0.00118
(0.61) 		0.698
(1.00) 		0.358
(1.00) 		0.819
(1.00) 		0.586
(1.00) 		0.505
(1.00) 		0.647
(1.00) 		0.478
(1.00)
13q gain 14 (3%) 479 0.742
(1.00) 		0.077
(1.00) 		0.358
(1.00) 		0.388
(1.00) 		0.0685
(1.00) 		0.636
(1.00) 		0.157
(1.00) 		0.493
(1.00)
14q gain 5 (1%) 488 0.0496
(1.00) 		0.608
(1.00) 		0.273
(1.00) 		0.0482
(1.00) 		0.00354
(1.00) 		0.0477
(1.00) 		0.122
(1.00) 		0.0685
(1.00)
15q gain 14 (3%) 479 0.0947
(1.00) 		0.578
(1.00) 		0.931
(1.00) 		0.73
(1.00) 		0.116
(1.00) 		0.379
(1.00) 		0.88
(1.00) 		0.726
(1.00)
16p gain 65 (13%) 428 0.1
(1.00) 		0.212
(1.00) 		0.153
(1.00) 		0.689
(1.00) 		0.634
(1.00) 		0.211
(1.00) 		0.635
(1.00) 		0.113
(1.00) 		0.318
(1.00) 		0.357
(1.00)
16q gain 58 (12%) 435 0.0706
(1.00) 		0.171
(1.00) 		0.175
(1.00) 		0.909
(1.00) 		0.475
(1.00) 		0.434
(1.00) 		0.696
(1.00) 		0.336
(1.00) 		0.433
(1.00) 		0.594
(1.00)
17q gain 22 (4%) 471 0.00827
(1.00) 		0.0102
(1.00) 		0.00481
(1.00) 		0.119
(1.00) 		0.448
(1.00) 		0.73
(1.00) 		0.253
(1.00) 		0.00949
(1.00) 		0.249
(1.00) 		0.00595
(1.00)
18p gain 18 (4%) 475 0.0764
(1.00) 		0.039
(1.00) 		0.238
(1.00) 		0.153
(1.00) 		0.347
(1.00) 		0.159
(1.00) 		0.0977
(1.00) 		0.41
(1.00) 		0.288
(1.00) 		0.641
(1.00)
18q gain 18 (4%) 475 0.0764
(1.00) 		0.039
(1.00) 		0.238
(1.00) 		0.153
(1.00) 		0.347
(1.00) 		0.159
(1.00) 		0.0977
(1.00) 		0.41
(1.00) 		0.288
(1.00) 		0.641
(1.00)
Xq gain 11 (2%) 482 0.414
(1.00) 		0.432
(1.00) 		0.639
(1.00) 		0.578
(1.00) 		1
(1.00) 		0.816
(1.00) 		0.198
(1.00) 		0.277
(1.00) 		0.153
(1.00) 		0.17
(1.00)
3q loss 73 (15%) 420 0.701
(1.00) 		0.7
(1.00) 		0.00144
(0.738) 		0.192
(1.00) 		0.236
(1.00) 		0.00364
(1.00) 		0.518
(1.00) 		0.804
(1.00) 		0.0122
(1.00) 		0.338
(1.00)
4p loss 35 (7%) 458 0.289
(1.00) 		0.296
(1.00) 		0.0658
(1.00) 		0.274
(1.00) 		0.58
(1.00) 		0.947
(1.00) 		0.0888
(1.00) 		0.366
(1.00) 		0.393
(1.00) 		0.707
(1.00)
8p loss 94 (19%) 399 0.777
(1.00) 		0.781
(1.00) 		0.047
(1.00) 		0.706
(1.00) 		0.778
(1.00) 		0.7
(1.00) 		0.185
(1.00) 		0.633
(1.00) 		0.215
(1.00) 		0.863
(1.00)
8q loss 37 (8%) 456 0.49
(1.00) 		0.586
(1.00) 		0.747
(1.00) 		0.255
(1.00) 		0.55
(1.00) 		0.606
(1.00) 		0.112
(1.00) 		0.0266
(1.00) 		0.288
(1.00) 		0.908
(1.00)
10q loss 48 (10%) 445 0.0972
(1.00) 		0.119
(1.00) 		0.00263
(1.00) 		0.0409
(1.00) 		0.565
(1.00) 		0.0182
(1.00) 		0.095
(1.00) 		0.126
(1.00) 		0.357
(1.00) 		0.171
(1.00)
11p loss 5 (1%) 488 0.121
(1.00) 		0.608
(1.00) 		0.332
(1.00) 		0.0482
(1.00) 		0.359
(1.00) 		0.462
(1.00) 		0.608
(1.00) 		0.404
(1.00)
11q loss 7 (1%) 486 0.0527
(1.00) 		0.826
(1.00) 		0.381
(1.00) 		0.115
(1.00) 		0.377
(1.00) 		0.311
(1.00) 		0.334
(1.00) 		0.301
(1.00)
15q loss 12 (2%) 481 0.58
(1.00) 		0.584
(1.00) 		0.0213
(1.00) 		0.373
(1.00) 		0.441
(1.00) 		0.522
(1.00) 		0.0733
(1.00) 		0.136
(1.00) 		0.211
(1.00) 		0.228
(1.00)
16q loss 5 (1%) 488 0.0135
(1.00) 		0.869
(1.00) 		0.854
(1.00) 		1
(1.00) 		0.292
(1.00) 		0.569
(1.00) 		0.424
(1.00)
19p loss 4 (1%) 489 0.184
(1.00) 		0.332
(1.00) 		0.0366
(1.00) 		0.0248
(1.00) 		0.341
(1.00) 		0.379
(1.00) 		0.88
(1.00) 		0.775
(1.00)
20p loss 6 (1%) 487 0.0475
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.666
(1.00) 		0.267
(1.00) 		0.747
(1.00) 		0.0921
(1.00) 		0.192
(1.00)
22q loss 11 (2%) 482 0.00501
(1.00) 		0.161
(1.00) 		0.133
(1.00) 		0.193
(1.00) 		0.000888
(0.467) 		0.0191
(1.00) 		0.373
(1.00) 		0.816
(1.00)
Xq loss 7 (1%) 486 0.0394
(1.00) 		0.0772
(1.00) 		0.308
(1.00) 		0.826
(1.00) 		0.695
(1.00) 		0.36
(1.00) 		0.0676
(1.00) 		0.00763
(1.00) 		0.0279
(1.00) 		0.00685
(1.00)
'1q gain mutation analysis' versus 'CN_CNMF'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0063

Table S1.  Gene #2: '1q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
1Q GAIN MUTATED 21 6 5
1Q GAIN WILD-TYPE 111 191 159

Figure S1.  Get High-res Image Gene #2: '1q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2p gain mutation analysis' versus 'CN_CNMF'

P value = 1.08e-06 (Fisher's exact test), Q value = 0.00068

Table S2.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
2P GAIN MUTATED 29 9 10
2P GAIN WILD-TYPE 103 188 154

Figure S2.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2q gain mutation analysis' versus 'CN_CNMF'

P value = 4.9e-05 (Fisher's exact test), Q value = 0.028

Table S3.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
2Q GAIN MUTATED 27 12 10
2Q GAIN WILD-TYPE 105 185 154

Figure S3.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'3q gain mutation analysis' versus 'CN_CNMF'

P value = 6.58e-05 (Fisher's exact test), Q value = 0.037

Table S4.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
3Q GAIN MUTATED 16 2 9
3Q GAIN WILD-TYPE 116 195 155

Figure S4.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'3q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000395 (Fisher's exact test), Q value = 0.22

Table S5.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
3Q GAIN MUTATED 4 20 3
3Q GAIN WILD-TYPE 193 159 94

Figure S5.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'5p gain mutation analysis' versus 'CN_CNMF'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.0075

Table S6.  Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
5P GAIN MUTATED 58 52 31
5P GAIN WILD-TYPE 74 145 133

Figure S6.  Get High-res Image Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q gain mutation analysis' versus 'CN_CNMF'

P value = 5.87e-05 (Fisher's exact test), Q value = 0.033

Table S7.  Gene #10: '5q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
5Q GAIN MUTATED 59 63 34
5Q GAIN WILD-TYPE 73 134 130

Figure S7.  Get High-res Image Gene #10: '5q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 5.05e-06 (Fisher's exact test), Q value = 0.0031

Table S8.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
7P GAIN MUTATED 55 34 38
7P GAIN WILD-TYPE 77 163 126

Figure S8.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 1.36e-05 (Fisher's exact test), Q value = 0.0081

Table S9.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
7Q GAIN MUTATED 54 34 41
7Q GAIN WILD-TYPE 78 163 123

Figure S9.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p gain mutation analysis' versus 'CN_CNMF'

P value = 5.42e-05 (Fisher's exact test), Q value = 0.031

Table S10.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
8P GAIN MUTATED 10 0 4
8P GAIN WILD-TYPE 122 197 160

Figure S10.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p gain mutation analysis' versus 'RPPA_CNMF'

P value = 9.12e-05 (Fisher's exact test), Q value = 0.051

Table S11.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
8P GAIN MUTATED 11 0 1
8P GAIN WILD-TYPE 148 147 140

Figure S11.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'8q gain mutation analysis' versus 'CN_CNMF'

P value = 2.75e-07 (Fisher's exact test), Q value = 0.00017

Table S12.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
8Q GAIN MUTATED 19 1 14
8Q GAIN WILD-TYPE 113 196 150

Figure S12.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8q gain mutation analysis' versus 'RPPA_CNMF'

P value = 6.42e-06 (Fisher's exact test), Q value = 0.0039

Table S13.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
8Q GAIN MUTATED 24 2 6
8Q GAIN WILD-TYPE 135 145 135

Figure S13.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'8q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.15e-07 (Fisher's exact test), Q value = 7.3e-05

Table S14.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
8Q GAIN MUTATED 1 25 5
8Q GAIN WILD-TYPE 196 154 92

Figure S14.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'8q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.88e-05 (Fisher's exact test), Q value = 0.028

Table S15.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
8Q GAIN MUTATED 3 4 24
8Q GAIN WILD-TYPE 66 210 166

Figure S15.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.011

Table S16.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
8Q GAIN MUTATED 5 3 22 3
8Q GAIN WILD-TYPE 99 181 121 41

Figure S16.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'12p gain mutation analysis' versus 'CN_CNMF'

P value = 7.99e-07 (Fisher's exact test), Q value = 5e-04

Table S17.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
12P GAIN MUTATED 37 13 28
12P GAIN WILD-TYPE 95 184 136

Figure S17.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12p gain mutation analysis' versus 'RPPA_CNMF'

P value = 4.58e-05 (Fisher's exact test), Q value = 0.026

Table S18.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
12P GAIN MUTATED 41 12 16
12P GAIN WILD-TYPE 118 135 125

Figure S18.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'12p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0066

Table S19.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
12P GAIN MUTATED 15 45 12
12P GAIN WILD-TYPE 182 134 85

Figure S19.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'12p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.011

Table S20.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
12P GAIN MUTATED 7 18 47
12P GAIN WILD-TYPE 62 196 143

Figure S20.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.72e-07 (Fisher's exact test), Q value = 0.00023

Table S21.  Gene #23: '12p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
12P GAIN MUTATED 8 17 43 10
12P GAIN WILD-TYPE 96 167 100 34

Figure S21.  Get High-res Image Gene #23: '12p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'12q gain mutation analysis' versus 'CN_CNMF'

P value = 7.99e-07 (Fisher's exact test), Q value = 5e-04

Table S22.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
12Q GAIN MUTATED 37 13 28
12Q GAIN WILD-TYPE 95 184 136

Figure S22.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12q gain mutation analysis' versus 'RPPA_CNMF'

P value = 4.58e-05 (Fisher's exact test), Q value = 0.026

Table S23.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
12Q GAIN MUTATED 41 12 16
12Q GAIN WILD-TYPE 118 135 125

Figure S23.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'12q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0066

Table S24.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
12Q GAIN MUTATED 15 45 12
12Q GAIN WILD-TYPE 182 134 85

Figure S24.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'12q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.011

Table S25.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
12Q GAIN MUTATED 7 18 47
12Q GAIN WILD-TYPE 62 196 143

Figure S25.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.72e-07 (Fisher's exact test), Q value = 0.00023

Table S26.  Gene #24: '12q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
12Q GAIN MUTATED 8 17 43 10
12Q GAIN WILD-TYPE 96 167 100 34

Figure S26.  Get High-res Image Gene #24: '12q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'17p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000357 (Fisher's exact test), Q value = 0.2

Table S27.  Gene #30: '17p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
17P GAIN MUTATED 6 0 10
17P GAIN WILD-TYPE 126 197 154

Figure S27.  Get High-res Image Gene #30: '17p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.02

Table S28.  Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
19P GAIN MUTATED 14 1 10
19P GAIN WILD-TYPE 118 196 154

Figure S28.  Get High-res Image Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q gain mutation analysis' versus 'CN_CNMF'

P value = 3e-06 (Fisher's exact test), Q value = 0.0019

Table S29.  Gene #35: '19q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
19Q GAIN MUTATED 17 1 10
19Q GAIN WILD-TYPE 115 196 154

Figure S29.  Get High-res Image Gene #35: '19q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 1.05e-12 (Fisher's exact test), Q value = 6.9e-10

Table S30.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
20P GAIN MUTATED 36 3 27
20P GAIN WILD-TYPE 96 194 137

Figure S30.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'RPPA_CNMF'

P value = 5.04e-05 (Fisher's exact test), Q value = 0.029

Table S31.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
20P GAIN MUTATED 36 8 17
20P GAIN WILD-TYPE 123 139 124

Figure S31.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.59e-06 (Fisher's exact test), Q value = 0.0022

Table S32.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
20P GAIN MUTATED 12 42 10
20P GAIN WILD-TYPE 185 137 87

Figure S32.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.29e-06 (Fisher's exact test), Q value = 0.0032

Table S33.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
20P GAIN MUTATED 8 13 43
20P GAIN WILD-TYPE 61 201 147

Figure S33.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.47e-06 (Fisher's exact test), Q value = 0.0027

Table S34.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
20P GAIN MUTATED 8 13 37 8
20P GAIN WILD-TYPE 96 171 106 36

Figure S34.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 6.23e-14 (Fisher's exact test), Q value = 4.1e-11

Table S35.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
20Q GAIN MUTATED 39 3 26
20Q GAIN WILD-TYPE 93 194 138

Figure S35.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'RPPA_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.018

Table S36.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
20Q GAIN MUTATED 37 8 18
20Q GAIN WILD-TYPE 122 139 123

Figure S36.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.3e-07 (Fisher's exact test), Q value = 0.00021

Table S37.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
20Q GAIN MUTATED 12 45 9
20Q GAIN WILD-TYPE 185 134 88

Figure S37.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.47e-06 (Fisher's exact test), Q value = 0.00091

Table S38.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
20Q GAIN MUTATED 8 13 45
20Q GAIN WILD-TYPE 61 201 145

Figure S38.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.09e-07 (Fisher's exact test), Q value = 0.00013

Table S39.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
20Q GAIN MUTATED 7 13 40 8
20Q GAIN WILD-TYPE 97 171 103 36

Figure S39.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'21q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.066

Table S40.  Gene #38: '21q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
21Q GAIN MUTATED 20 6 7
21Q GAIN WILD-TYPE 112 191 157

Figure S40.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000399 (Fisher's exact test), Q value = 0.22

Table S41.  Gene #39: '22q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
22Q GAIN MUTATED 15 3 7
22Q GAIN WILD-TYPE 117 194 157

Figure S41.  Get High-res Image Gene #39: '22q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.2e-05 (Fisher's exact test), Q value = 0.035

Table S42.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
1P LOSS MUTATED 8 1 2
1P LOSS WILD-TYPE 6 22 31

Figure S42.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'1p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.64e-06 (Fisher's exact test), Q value = 0.0028

Table S43.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
1P LOSS MUTATED 15 9 6
1P LOSS WILD-TYPE 54 205 184

Figure S43.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.36e-08 (Fisher's exact test), Q value = 8.8e-06

Table S44.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 259 51
1P LOSS MUTATED 6 10 16
1P LOSS WILD-TYPE 159 249 35

Figure S44.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss mutation analysis' versus 'CN_CNMF'

P value = 2.09e-05 (Fisher's exact test), Q value = 0.012

Table S45.  Gene #42: '1q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
1Q LOSS MUTATED 2 2 17
1Q LOSS WILD-TYPE 130 195 147

Figure S45.  Get High-res Image Gene #42: '1q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.65e-05 (Fisher's exact test), Q value = 0.038

Table S46.  Gene #42: '1q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
1Q LOSS MUTATED 5 3 13
1Q LOSS WILD-TYPE 192 176 84

Figure S46.  Get High-res Image Gene #42: '1q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'1q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.27e-07 (Fisher's exact test), Q value = 0.00039

Table S47.  Gene #42: '1q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
1Q LOSS MUTATED 13 5 3
1Q LOSS WILD-TYPE 56 209 187

Figure S47.  Get High-res Image Gene #42: '1q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.54e-09 (Fisher's exact test), Q value = 4.9e-06

Table S48.  Gene #42: '1q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 259 51
1Q LOSS MUTATED 2 6 13
1Q LOSS WILD-TYPE 163 253 38

Figure S48.  Get High-res Image Gene #42: '1q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.14

Table S49.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
2P LOSS MUTATED 0 1 5
2P LOSS WILD-TYPE 33 23 8

Figure S49.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'2p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000374 (Fisher's exact test), Q value = 0.2

Table S50.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
2P LOSS MUTATED 5 1 0
2P LOSS WILD-TYPE 9 22 33

Figure S50.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'2p loss mutation analysis' versus 'CN_CNMF'

P value = 1.52e-05 (Fisher's exact test), Q value = 0.009

Table S51.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
2P LOSS MUTATED 0 0 10
2P LOSS WILD-TYPE 132 197 154

Figure S51.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2p loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 0.000142 (Fisher's exact test), Q value = 0.079

Table S52.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 211 104
2P LOSS MUTATED 0 0 6
2P LOSS WILD-TYPE 132 211 98

Figure S52.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'2p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.72e-07 (Fisher's exact test), Q value = 3e-04

Table S53.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
2P LOSS MUTATED 0 0 9
2P LOSS WILD-TYPE 197 179 88

Figure S53.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'2p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.87e-08 (Fisher's exact test), Q value = 1.2e-05

Table S54.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
2P LOSS MUTATED 9 0 0
2P LOSS WILD-TYPE 60 214 190

Figure S54.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.72e-11 (Fisher's exact test), Q value = 5.7e-08

Table S55.  Gene #43: '2p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 259 51
2P LOSS MUTATED 0 0 10
2P LOSS WILD-TYPE 165 259 41

Figure S55.  Get High-res Image Gene #43: '2p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.14

Table S56.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
2Q LOSS MUTATED 0 1 5
2Q LOSS WILD-TYPE 33 23 8

Figure S56.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'2q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000374 (Fisher's exact test), Q value = 0.2

Table S57.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
2Q LOSS MUTATED 5 1 0
2Q LOSS WILD-TYPE 9 22 33

Figure S57.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'2q loss mutation analysis' versus 'CN_CNMF'

P value = 4.75e-06 (Fisher's exact test), Q value = 0.0029

Table S58.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
2Q LOSS MUTATED 0 0 11
2Q LOSS WILD-TYPE 132 197 153

Figure S58.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'2q loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 3.15e-05 (Fisher's exact test), Q value = 0.018

Table S59.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 211 104
2Q LOSS MUTATED 0 0 7
2Q LOSS WILD-TYPE 132 211 97

Figure S59.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'2q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.96e-08 (Fisher's exact test), Q value = 5.7e-05

Table S60.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
2Q LOSS MUTATED 0 0 10
2Q LOSS WILD-TYPE 197 179 87

Figure S60.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'2q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.91e-08 (Fisher's exact test), Q value = 5e-05

Table S61.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
2Q LOSS MUTATED 9 0 1
2Q LOSS WILD-TYPE 60 214 189

Figure S61.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000238 (Fisher's exact test), Q value = 0.13

Table S62.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
2Q LOSS MUTATED 1 0 10 0
2Q LOSS WILD-TYPE 103 184 133 44

Figure S62.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'2q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.83e-10 (Fisher's exact test), Q value = 5.7e-07

Table S63.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 259 51
2Q LOSS MUTATED 0 1 10
2Q LOSS WILD-TYPE 165 258 41

Figure S63.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss mutation analysis' versus 'CN_CNMF'

P value = 6.37e-24 (Fisher's exact test), Q value = 4.2e-21

Table S64.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
3P LOSS MUTATED 107 148 49
3P LOSS WILD-TYPE 25 49 115

Figure S64.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'3p loss mutation analysis' versus 'RPPA_CNMF'

P value = 4.7e-06 (Fisher's exact test), Q value = 0.0029

Table S65.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
3P LOSS MUTATED 82 114 81
3P LOSS WILD-TYPE 77 33 60

Figure S65.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'3p loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 3.95e-05 (Fisher's exact test), Q value = 0.023

Table S66.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 211 104
3P LOSS MUTATED 86 146 45
3P LOSS WILD-TYPE 46 65 59

Figure S66.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'3p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.85e-11 (Fisher's exact test), Q value = 2.5e-08

Table S67.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
3P LOSS MUTATED 154 95 39
3P LOSS WILD-TYPE 43 84 58

Figure S67.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'3p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.09e-10 (Fisher's exact test), Q value = 4.6e-07

Table S68.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
3P LOSS MUTATED 23 160 105
3P LOSS WILD-TYPE 46 54 85

Figure S68.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.4e-06 (Fisher's exact test), Q value = 0.0027

Table S69.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
3P LOSS MUTATED 55 136 69 31
3P LOSS WILD-TYPE 49 48 74 13

Figure S69.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'3p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.96e-08 (Fisher's exact test), Q value = 4.4e-05

Table S70.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 259 51
3P LOSS MUTATED 83 188 20
3P LOSS WILD-TYPE 82 71 31

Figure S70.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000221 (Fisher's exact test), Q value = 0.12

Table S71.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
4Q LOSS MUTATED 16 3 9
4Q LOSS WILD-TYPE 116 194 155

Figure S71.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6p loss mutation analysis' versus 'CN_CNMF'

P value = 4.27e-12 (Fisher's exact test), Q value = 2.8e-09

Table S72.  Gene #49: '6p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
6P LOSS MUTATED 37 4 17
6P LOSS WILD-TYPE 95 193 147

Figure S72.  Get High-res Image Gene #49: '6p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6p loss mutation analysis' versus 'RPPA_CNMF'

P value = 3.44e-08 (Fisher's exact test), Q value = 2.2e-05

Table S73.  Gene #49: '6p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
6P LOSS MUTATED 37 4 11
6P LOSS WILD-TYPE 122 143 130

Figure S73.  Get High-res Image Gene #49: '6p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'6p loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 3.53e-06 (Fisher's exact test), Q value = 0.0022

Table S74.  Gene #49: '6p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 211 104
6P LOSS MUTATED 17 10 25
6P LOSS WILD-TYPE 115 201 79

Figure S74.  Get High-res Image Gene #49: '6p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'6p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.4e-09 (Fisher's exact test), Q value = 4.1e-06

Table S75.  Gene #49: '6p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
6P LOSS MUTATED 3 13 38 2
6P LOSS WILD-TYPE 101 171 105 42

Figure S75.  Get High-res Image Gene #49: '6p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'6p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000191 (Fisher's exact test), Q value = 0.11

Table S76.  Gene #49: '6p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 259 51
6P LOSS MUTATED 16 24 16
6P LOSS WILD-TYPE 149 235 35

Figure S76.  Get High-res Image Gene #49: '6p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss mutation analysis' versus 'CN_CNMF'

P value = 6.34e-17 (Fisher's exact test), Q value = 4.2e-14

Table S77.  Gene #50: '6q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
6Q LOSS MUTATED 54 9 19
6Q LOSS WILD-TYPE 78 188 145

Figure S77.  Get High-res Image Gene #50: '6q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6q loss mutation analysis' versus 'RPPA_CNMF'

P value = 2.91e-06 (Fisher's exact test), Q value = 0.0018

Table S78.  Gene #50: '6q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
6Q LOSS MUTATED 46 17 12
6Q LOSS WILD-TYPE 113 130 129

Figure S78.  Get High-res Image Gene #50: '6q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'6q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.0085

Table S79.  Gene #50: '6q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
6Q LOSS MUTATED 8 27 42 3
6Q LOSS WILD-TYPE 96 157 101 41

Figure S79.  Get High-res Image Gene #50: '6q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'6q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.17

Table S80.  Gene #50: '6q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 259 51
6Q LOSS MUTATED 19 42 19
6Q LOSS WILD-TYPE 146 217 32

Figure S80.  Get High-res Image Gene #50: '6q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 9.23e-25 (Fisher's exact test), Q value = 6.2e-22

Table S81.  Gene #53: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
9P LOSS MUTATED 60 3 24
9P LOSS WILD-TYPE 72 194 140

Figure S81.  Get High-res Image Gene #53: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.57e-12 (Fisher's exact test), Q value = 2.3e-09

Table S82.  Gene #53: '9p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
9P LOSS MUTATED 38 3 10
9P LOSS WILD-TYPE 58 115 54

Figure S82.  Get High-res Image Gene #53: '9p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'9p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.39e-11 (Fisher's exact test), Q value = 9.1e-09

Table S83.  Gene #53: '9p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
9P LOSS MUTATED 14 60 9
9P LOSS WILD-TYPE 183 119 88

Figure S83.  Get High-res Image Gene #53: '9p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'9p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.71e-12 (Fisher's exact test), Q value = 1.8e-09

Table S84.  Gene #53: '9p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
9P LOSS MUTATED 5 15 63
9P LOSS WILD-TYPE 64 199 127

Figure S84.  Get High-res Image Gene #53: '9p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.47e-09 (Fisher's exact test), Q value = 4.8e-06

Table S85.  Gene #53: '9p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
9P LOSS MUTATED 11 16 50 8
9P LOSS WILD-TYPE 93 168 93 36

Figure S85.  Get High-res Image Gene #53: '9p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 4.43e-26 (Fisher's exact test), Q value = 3e-23

Table S86.  Gene #54: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
9Q LOSS MUTATED 64 4 24
9Q LOSS WILD-TYPE 68 193 140

Figure S86.  Get High-res Image Gene #54: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.3e-13 (Fisher's exact test), Q value = 2.8e-10

Table S87.  Gene #54: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
9Q LOSS MUTATED 40 3 10
9Q LOSS WILD-TYPE 56 115 54

Figure S87.  Get High-res Image Gene #54: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'9q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.31e-12 (Fisher's exact test), Q value = 8.7e-10

Table S88.  Gene #54: '9q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
9Q LOSS MUTATED 15 64 9
9Q LOSS WILD-TYPE 182 115 88

Figure S88.  Get High-res Image Gene #54: '9q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'9q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.94e-14 (Fisher's exact test), Q value = 2.6e-11

Table S89.  Gene #54: '9q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
9Q LOSS MUTATED 5 15 68
9Q LOSS WILD-TYPE 64 199 122

Figure S89.  Get High-res Image Gene #54: '9q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.67e-10 (Fisher's exact test), Q value = 3e-07

Table S90.  Gene #54: '9q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
9Q LOSS MUTATED 11 16 53 9
9Q LOSS WILD-TYPE 93 168 90 35

Figure S90.  Get High-res Image Gene #54: '9q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'10p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000201 (Fisher's exact test), Q value = 0.11

Table S91.  Gene #55: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
10P LOSS MUTATED 10 3 19
10P LOSS WILD-TYPE 122 194 145

Figure S91.  Get High-res Image Gene #55: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q loss mutation analysis' versus 'CN_CNMF'

P value = 6.36e-05 (Fisher's exact test), Q value = 0.036

Table S92.  Gene #59: '13q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
13Q LOSS MUTATED 14 2 15
13Q LOSS WILD-TYPE 118 195 149

Figure S92.  Get High-res Image Gene #59: '13q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.25

Table S93.  Gene #59: '13q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
13Q LOSS MUTATED 7 4 19
13Q LOSS WILD-TYPE 62 210 171

Figure S93.  Get High-res Image Gene #59: '13q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.43e-05 (Fisher's exact test), Q value = 0.042

Table S94.  Gene #59: '13q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
13Q LOSS MUTATED 7 3 20 1
13Q LOSS WILD-TYPE 97 181 123 43

Figure S94.  Get High-res Image Gene #59: '13q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'14q loss mutation analysis' versus 'CN_CNMF'

P value = 2.02e-10 (Fisher's exact test), Q value = 1.3e-07

Table S95.  Gene #60: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
14Q LOSS MUTATED 73 41 44
14Q LOSS WILD-TYPE 59 156 120

Figure S95.  Get High-res Image Gene #60: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.06e-05 (Fisher's exact test), Q value = 0.018

Table S96.  Gene #60: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 96 118 64
14Q LOSS MUTATED 43 20 23
14Q LOSS WILD-TYPE 53 98 41

Figure S96.  Get High-res Image Gene #60: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'14q loss mutation analysis' versus 'RPPA_CNMF'

P value = 3.07e-06 (Fisher's exact test), Q value = 0.0019

Table S97.  Gene #60: '14q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
14Q LOSS MUTATED 77 40 32
14Q LOSS WILD-TYPE 82 107 109

Figure S97.  Get High-res Image Gene #60: '14q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'14q loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 4.36e-05 (Fisher's exact test), Q value = 0.025

Table S98.  Gene #60: '14q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 211 104
14Q LOSS MUTATED 62 50 37
14Q LOSS WILD-TYPE 70 161 67

Figure S98.  Get High-res Image Gene #60: '14q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'14q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.97e-11 (Fisher's exact test), Q value = 4.6e-08

Table S99.  Gene #60: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
14Q LOSS MUTATED 54 88 11
14Q LOSS WILD-TYPE 143 91 86

Figure S99.  Get High-res Image Gene #60: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.8e-07 (Fisher's exact test), Q value = 0.00018

Table S100.  Gene #60: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
14Q LOSS MUTATED 8 60 85
14Q LOSS WILD-TYPE 61 154 105

Figure S100.  Get High-res Image Gene #60: '14q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.0018

Table S101.  Gene #60: '14q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
14Q LOSS MUTATED 27 51 70 6
14Q LOSS WILD-TYPE 77 133 73 38

Figure S101.  Get High-res Image Gene #60: '14q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'17p loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.066

Table S102.  Gene #63: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
17P LOSS MUTATED 0 3 6
17P LOSS WILD-TYPE 33 21 7

Figure S102.  Get High-res Image Gene #63: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'17p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 0.000178 (Fisher's exact test), Q value = 0.1

Table S103.  Gene #63: '17p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 23 33
17P LOSS MUTATED 6 3 0
17P LOSS WILD-TYPE 8 20 33

Figure S103.  Get High-res Image Gene #63: '17p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'17p loss mutation analysis' versus 'CN_CNMF'

P value = 4.3e-06 (Fisher's exact test), Q value = 0.0026

Table S104.  Gene #63: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
17P LOSS MUTATED 12 0 13
17P LOSS WILD-TYPE 120 197 151

Figure S104.  Get High-res Image Gene #63: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 3.06e-05 (Fisher's exact test), Q value = 0.018

Table S105.  Gene #63: '17p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 211 104
17P LOSS MUTATED 4 3 14
17P LOSS WILD-TYPE 128 208 90

Figure S105.  Get High-res Image Gene #63: '17p loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'17p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.9e-06 (Fisher's exact test), Q value = 0.0012

Table S106.  Gene #63: '17p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
17P LOSS MUTATED 0 12 11
17P LOSS WILD-TYPE 197 167 86

Figure S106.  Get High-res Image Gene #63: '17p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'17p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.5e-08 (Fisher's exact test), Q value = 9.7e-06

Table S107.  Gene #63: '17p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
17P LOSS MUTATED 12 0 11
17P LOSS WILD-TYPE 57 214 179

Figure S107.  Get High-res Image Gene #63: '17p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.63e-08 (Fisher's exact test), Q value = 1e-05

Table S108.  Gene #63: '17p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
17P LOSS MUTATED 3 0 21 1
17P LOSS WILD-TYPE 101 184 122 43

Figure S108.  Get High-res Image Gene #63: '17p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'17p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.35e-09 (Fisher's exact test), Q value = 5.4e-06

Table S109.  Gene #63: '17p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 259 51
17P LOSS MUTATED 9 3 13
17P LOSS WILD-TYPE 156 256 38

Figure S109.  Get High-res Image Gene #63: '17p loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.12

Table S110.  Gene #64: '17q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
17Q LOSS MUTATED 2 0 10
17Q LOSS WILD-TYPE 130 197 154

Figure S110.  Get High-res Image Gene #64: '17q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q loss mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 6.94e-06 (Fisher's exact test), Q value = 0.0042

Table S111.  Gene #64: '17q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 211 104
17Q LOSS MUTATED 0 0 8
17Q LOSS WILD-TYPE 132 211 96

Figure S111.  Get High-res Image Gene #64: '17q loss mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'17q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.91e-06 (Fisher's exact test), Q value = 0.0012

Table S112.  Gene #64: '17q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
17Q LOSS MUTATED 0 1 9
17Q LOSS WILD-TYPE 197 178 88

Figure S112.  Get High-res Image Gene #64: '17q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'17q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.91e-08 (Fisher's exact test), Q value = 5e-05

Table S113.  Gene #64: '17q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
17Q LOSS MUTATED 9 0 1
17Q LOSS WILD-TYPE 60 214 189

Figure S113.  Get High-res Image Gene #64: '17q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 7.66e-05 (Fisher's exact test), Q value = 0.043

Table S114.  Gene #64: '17q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
17Q LOSS MUTATED 1 0 11 0
17Q LOSS WILD-TYPE 103 184 132 44

Figure S114.  Get High-res Image Gene #64: '17q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'17q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.5e-11 (Fisher's exact test), Q value = 5.6e-08

Table S115.  Gene #64: '17q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 165 259 51
17Q LOSS MUTATED 0 1 11
17Q LOSS WILD-TYPE 165 258 40

Figure S115.  Get High-res Image Gene #64: '17q loss mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 3.02e-06 (Fisher's exact test), Q value = 0.0019

Table S116.  Gene #65: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
18P LOSS MUTATED 26 6 14
18P LOSS WILD-TYPE 106 191 150

Figure S116.  Get High-res Image Gene #65: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p loss mutation analysis' versus 'RPPA_CNMF'

P value = 8.04e-06 (Fisher's exact test), Q value = 0.0048

Table S117.  Gene #65: '18p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
18P LOSS MUTATED 28 3 11
18P LOSS WILD-TYPE 131 144 130

Figure S117.  Get High-res Image Gene #65: '18p loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'18p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.06e-06 (Fisher's exact test), Q value = 0.0036

Table S118.  Gene #65: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
18P LOSS MUTATED 8 32 4
18P LOSS WILD-TYPE 189 147 93

Figure S118.  Get High-res Image Gene #65: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000196 (Fisher's exact test), Q value = 0.11

Table S119.  Gene #65: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
18P LOSS MUTATED 7 8 29
18P LOSS WILD-TYPE 62 206 161

Figure S119.  Get High-res Image Gene #65: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.63e-06 (Fisher's exact test), Q value = 0.0028

Table S120.  Gene #65: '18p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
18P LOSS MUTATED 9 6 29 2
18P LOSS WILD-TYPE 95 178 114 42

Figure S120.  Get High-res Image Gene #65: '18p loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 3.61e-06 (Fisher's exact test), Q value = 0.0022

Table S121.  Gene #66: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
18Q LOSS MUTATED 27 7 14
18Q LOSS WILD-TYPE 105 190 150

Figure S121.  Get High-res Image Gene #66: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18q loss mutation analysis' versus 'RPPA_CNMF'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.013

Table S122.  Gene #66: '18q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 147 141
18Q LOSS MUTATED 29 4 12
18Q LOSS WILD-TYPE 130 143 129

Figure S122.  Get High-res Image Gene #66: '18q loss mutation analysis' versus Clinical Feature #5: 'RPPA_CNMF'

'18q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.017

Table S123.  Gene #66: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 197 179 97
18Q LOSS MUTATED 9 32 5
18Q LOSS WILD-TYPE 188 147 92

Figure S123.  Get High-res Image Gene #66: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.51e-05 (Fisher's exact test), Q value = 0.009

Table S124.  Gene #66: '18q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 104 184 143 44
18Q LOSS MUTATED 10 7 29 2
18Q LOSS WILD-TYPE 94 177 114 42

Figure S124.  Get High-res Image Gene #66: '18q loss mutation analysis' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000367 (Fisher's exact test), Q value = 0.2

Table S125.  Gene #69: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 132 197 164
21Q LOSS MUTATED 6 5 21
21Q LOSS WILD-TYPE 126 192 143

Figure S125.  Get High-res Image Gene #69: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'21q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.72e-05 (Fisher's exact test), Q value = 0.01

Table S126.  Gene #69: '21q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 214 190
21Q LOSS MUTATED 14 6 9
21Q LOSS WILD-TYPE 55 208 181

Figure S126.  Get High-res Image Gene #69: '21q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Molecular subtypes file = KIRC-TP.transferedmergedcluster.txt

  • Number of patients = 493

  • Number of significantly arm-level cnvs = 71

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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