Colon/Rectal Adenocarcinoma: Correlation between copy number variations of arm-level result and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 78 arm-level results and 10 molecular subtypes across 575 patients, 87 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF'.

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

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'CN_CNMF'.

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

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

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

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

  • 1p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF'.

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF'.

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

  • 15q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 17p loss cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 18p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'CN_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF'.

  • 22q 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 78 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 87 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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
20q gain 403 (70%) 172 1.23e-18
(9.18e-16) 		2.68e-17
(1.99e-14) 		2.22e-46
(1.68e-43) 		9.04e-13
(6.64e-10) 		0.011
(1.00) 		2.28e-05
(0.0158) 		9.03e-18
(6.72e-15) 		1.13e-13
(8.32e-11) 		0.463
(1.00) 		0.101
(1.00)
13q gain 314 (55%) 261 1e-07
(7.24e-05) 		2.44e-05
(0.0168) 		1.62e-37
(1.23e-34) 		1.71e-08
(1.24e-05) 		0.0855
(1.00) 		0.026
(1.00) 		8.54e-09
(6.2e-06) 		6.4e-07
(0.000455) 		0.01
(1.00) 		0.45
(1.00)
20p gain 288 (50%) 287 6.06e-05
(0.0415) 		6.71e-09
(4.88e-06) 		4.25e-22
(3.19e-19) 		7.67e-05
(0.0525) 		0.0297
(1.00) 		0.0403
(1.00) 		3.2e-07
(0.000229) 		3.2e-07
(0.000229) 		0.625
(1.00) 		0.472
(1.00)
18p loss 324 (56%) 251 9.87e-15
(7.29e-12) 		8.51e-12
(6.23e-09) 		4.26e-47
(3.23e-44) 		4.33e-19
(3.24e-16) 		0.0877
(1.00) 		0.00123
(0.809) 		5.39e-16
(3.99e-13) 		2.73e-11
(2e-08) 		0.065
(1.00) 		0.787
(1.00)
18q loss 352 (61%) 223 1.42e-12
(1.04e-09) 		1.96e-11
(1.44e-08) 		6.8e-51
(5.16e-48) 		8.03e-21
(6.02e-18) 		0.139
(1.00) 		0.0128
(1.00) 		3.96e-16
(2.93e-13) 		3.68e-09
(2.68e-06) 		0.00938
(1.00) 		0.378
(1.00)
14q loss 143 (25%) 432 4.76e-06
(0.00334) 		2.49e-07
(0.000178) 		1.12e-31
(8.43e-29) 		1.97e-07
(0.000142) 		0.00124
(0.813) 		0.0104
(1.00) 		1.73e-07
(0.000124) 		0.000705
(0.469) 		0.114
(1.00) 		0.709
(1.00)
7p gain 290 (50%) 285 0.000443
(0.298) 		0.00887
(1.00) 		1.89e-21
(1.42e-18) 		7.29e-07
(0.000518) 		0.247
(1.00) 		0.00872
(1.00) 		3.72e-08
(2.69e-05) 		9.54e-05
(0.0652) 		0.0703
(1.00) 		0.0304
(1.00)
7q gain 255 (44%) 320 0.000644
(0.43) 		0.0134
(1.00) 		6.95e-16
(5.14e-13) 		8.61e-06
(0.00601) 		0.29
(1.00) 		0.0785
(1.00) 		8.79e-07
(0.000623) 		1.24e-05
(0.00862) 		0.245
(1.00) 		0.155
(1.00)
17p loss 252 (44%) 323 0.000242
(0.164) 		0.00165
(1.00) 		5.49e-22
(4.12e-19) 		2.44e-07
(0.000175) 		0.769
(1.00) 		0.367
(1.00) 		3.25e-06
(0.00228) 		0.000795
(0.529) 		0.027
(1.00) 		0.497
(1.00)
2p gain 60 (10%) 515 0.0169
(1.00) 		0.00499
(1.00) 		0.00816
(1.00) 		0.000256
(0.172) 		0.0702
(1.00) 		0.596
(1.00) 		0.000224
(0.152) 		0.000137
(0.0937) 		0.216
(1.00) 		0.0209
(1.00)
11p gain 39 (7%) 536 0.063
(1.00) 		0.654
(1.00) 		1.71e-05
(0.0119) 		0.000214
(0.146) 		0.781
(1.00) 		0.733
(1.00) 		0.0491
(1.00) 		0.000153
(0.104) 		0.246
(1.00) 		0.882
(1.00)
2q gain 59 (10%) 516 0.00368
(1.00) 		0.00391
(1.00) 		0.00101
(0.666) 		5.82e-06
(0.00407) 		0.363
(1.00) 		0.795
(1.00) 		0.000234
(0.158) 		0.000824
(0.547) 		0.251
(1.00) 		0.0504
(1.00)
17q gain 67 (12%) 508 0.0455
(1.00) 		0.0639
(1.00) 		0.000269
(0.181) 		0.00143
(0.938) 		0.175
(1.00) 		0.142
(1.00) 		1.47e-05
(0.0102) 		0.00195
(1.00) 		0.0785
(1.00) 		0.354
(1.00)
1p loss 68 (12%) 507 0.0784
(1.00) 		0.00327
(1.00) 		7.55e-06
(0.00528) 		3.84e-05
(0.0264) 		0.481
(1.00) 		0.828
(1.00) 		0.0764
(1.00) 		0.00823
(1.00) 		0.193
(1.00) 		0.62
(1.00)
9q loss 37 (6%) 538 0.0484
(1.00) 		0.0135
(1.00) 		1.95e-06
(0.00138) 		3.42e-05
(0.0235) 		0.094
(1.00) 		0.399
(1.00) 		0.0214
(1.00) 		0.0167
(1.00) 		0.0491
(1.00) 		0.82
(1.00)
15q loss 156 (27%) 419 0.0144
(1.00) 		0.0117
(1.00) 		2.09e-24
(1.57e-21) 		0.0158
(1.00) 		0.861
(1.00) 		0.612
(1.00) 		1.19e-05
(0.00829) 		0.000572
(0.383) 		0.368
(1.00) 		0.246
(1.00)
3p gain 36 (6%) 539 0.126
(1.00) 		0.433
(1.00) 		0.000181
(0.123) 		0.257
(1.00) 		0.292
(1.00) 		0.346
(1.00) 		0.26
(1.00) 		0.885
(1.00) 		0.208
(1.00) 		0.366
(1.00)
3q gain 53 (9%) 522 0.22
(1.00) 		0.0947
(1.00) 		2.49e-06
(0.00175) 		0.0353
(1.00) 		0.0168
(1.00) 		0.417
(1.00) 		0.075
(1.00) 		0.588
(1.00) 		0.111
(1.00) 		0.544
(1.00)
6p gain 77 (13%) 498 0.246
(1.00) 		0.00492
(1.00) 		1.55e-06
(0.00109) 		0.401
(1.00) 		0.222
(1.00) 		0.539
(1.00) 		0.0227
(1.00) 		0.227
(1.00) 		0.848
(1.00) 		0.392
(1.00)
6q gain 71 (12%) 504 0.375
(1.00) 		0.0199
(1.00) 		7.47e-07
(0.000531) 		0.159
(1.00) 		0.347
(1.00) 		0.383
(1.00) 		0.0607
(1.00) 		0.575
(1.00) 		0.749
(1.00) 		0.251
(1.00)
8p gain 108 (19%) 467 0.946
(1.00) 		0.746
(1.00) 		1e-08
(7.27e-06) 		0.433
(1.00) 		0.581
(1.00) 		0.101
(1.00) 		0.181
(1.00) 		0.44
(1.00) 		0.49
(1.00) 		0.891
(1.00)
8q gain 235 (41%) 340 0.0693
(1.00) 		0.621
(1.00) 		1.06e-33
(7.98e-31) 		0.00942
(1.00) 		0.217
(1.00) 		0.413
(1.00) 		0.0011
(0.724) 		0.0265
(1.00) 		0.459
(1.00) 		0.633
(1.00)
11q gain 39 (7%) 536 0.102
(1.00) 		0.0316
(1.00) 		1.33e-06
(0.000939) 		0.000911
(0.603) 		0.765
(1.00) 		0.503
(1.00) 		0.0356
(1.00) 		0.00526
(1.00) 		0.559
(1.00) 		0.406
(1.00)
16p gain 96 (17%) 479 0.0975
(1.00) 		0.0844
(1.00) 		1.26e-16
(9.37e-14) 		0.0108
(1.00) 		0.297
(1.00) 		0.0858
(1.00) 		0.0228
(1.00) 		0.136
(1.00) 		0.577
(1.00) 		0.347
(1.00)
16q gain 96 (17%) 479 0.0433
(1.00) 		0.0683
(1.00) 		3.02e-18
(2.25e-15) 		0.00391
(1.00) 		0.351
(1.00) 		0.069
(1.00) 		0.0198
(1.00) 		0.0602
(1.00) 		0.465
(1.00) 		0.277
(1.00)
19p gain 52 (9%) 523 0.167
(1.00) 		0.228
(1.00) 		5.84e-05
(0.0401) 		0.0236
(1.00) 		0.215
(1.00) 		0.258
(1.00) 		0.423
(1.00) 		0.474
(1.00) 		0.718
(1.00) 		0.745
(1.00)
4p loss 122 (21%) 453 0.106
(1.00) 		0.105
(1.00) 		5.5e-11
(4.01e-08) 		0.0036
(1.00) 		0.274
(1.00) 		0.729
(1.00) 		0.0062
(1.00) 		0.0572
(1.00) 		0.045
(1.00) 		0.769
(1.00)
4q loss 113 (20%) 462 0.0962
(1.00) 		0.0638
(1.00) 		3.18e-12
(2.33e-09) 		0.00168
(1.00) 		0.589
(1.00) 		0.441
(1.00) 		0.00213
(1.00) 		0.0535
(1.00) 		0.0122
(1.00) 		0.564
(1.00)
5q loss 60 (10%) 515 0.0163
(1.00) 		0.0917
(1.00) 		5.53e-07
(0.000394) 		0.0816
(1.00) 		0.735
(1.00) 		0.539
(1.00) 		0.0211
(1.00) 		0.0985
(1.00) 		0.963
(1.00) 		0.579
(1.00)
8p loss 145 (25%) 430 0.0117
(1.00) 		0.00463
(1.00) 		1.14e-18
(8.53e-16) 		0.000373
(0.251) 		0.479
(1.00) 		0.0984
(1.00) 		0.11
(1.00) 		0.152
(1.00) 		0.515
(1.00) 		0.73
(1.00)
9p loss 39 (7%) 536 0.564
(1.00) 		0.12
(1.00) 		2.9e-05
(0.02) 		0.00158
(1.00) 		0.0635
(1.00) 		0.157
(1.00) 		0.102
(1.00) 		0.0221
(1.00) 		0.127
(1.00) 		1
(1.00)
10q loss 46 (8%) 529 0.34
(1.00) 		0.568
(1.00) 		1.44e-06
(0.00101) 		0.153
(1.00) 		0.609
(1.00) 		0.279
(1.00) 		0.102
(1.00) 		0.231
(1.00) 		0.714
(1.00) 		0.811
(1.00)
12p loss 33 (6%) 542 0.114
(1.00) 		0.264
(1.00) 		5.42e-07
(0.000387) 		0.258
(1.00) 		0.702
(1.00) 		0.685
(1.00) 		0.201
(1.00) 		0.46
(1.00) 		0.541
(1.00) 		0.222
(1.00)
12q loss 28 (5%) 547 0.131
(1.00) 		0.0524
(1.00) 		1.11e-06
(0.000784) 		0.522
(1.00) 		0.648
(1.00) 		0.697
(1.00) 		0.143
(1.00) 		0.189
(1.00) 		0.616
(1.00) 		0.681
(1.00)
19p loss 20 (3%) 555 0.49
(1.00) 		0.598
(1.00) 		1.46e-05
(0.0102) 		0.0244
(1.00) 		1
(1.00) 		0.182
(1.00) 		0.00155
(1.00) 		0.00289
(1.00) 		0.235
(1.00) 		0.371
(1.00)
19q loss 18 (3%) 557 0.49
(1.00) 		0.598
(1.00) 		0.000235
(0.159) 		0.0965
(1.00) 		0.778
(1.00) 		0.859
(1.00) 		0.00155
(1.00) 		0.00289
(1.00) 		0.424
(1.00) 		0.0976
(1.00)
20p loss 47 (8%) 528 0.169
(1.00) 		0.18
(1.00) 		4.56e-07
(0.000326) 		0.039
(1.00) 		0.925
(1.00) 		0.172
(1.00) 		0.577
(1.00) 		0.391
(1.00) 		0.554
(1.00) 		0.486
(1.00)
21q loss 114 (20%) 461 0.0588
(1.00) 		0.319
(1.00) 		3.64e-05
(0.025) 		0.0555
(1.00) 		0.0841
(1.00) 		0.479
(1.00) 		0.235
(1.00) 		0.392
(1.00) 		0.118
(1.00) 		0.342
(1.00)
22q loss 122 (21%) 453 0.0679
(1.00) 		0.0038
(1.00) 		7.8e-14
(5.75e-11) 		0.352
(1.00) 		0.257
(1.00) 		0.409
(1.00) 		0.0676
(1.00) 		0.0646
(1.00) 		0.0662
(1.00) 		0.1
(1.00)
1p gain 15 (3%) 560 0.406
(1.00) 		0.102
(1.00) 		0.932
(1.00) 		0.497
(1.00) 		0.26
(1.00) 		0.118
(1.00) 		0.178
(1.00) 		0.33
(1.00) 		0.111
(1.00) 		0.911
(1.00)
1q gain 80 (14%) 495 0.484
(1.00) 		0.855
(1.00) 		0.0158
(1.00) 		0.926
(1.00) 		0.625
(1.00) 		0.736
(1.00) 		0.128
(1.00) 		0.0758
(1.00) 		0.0729
(1.00) 		0.978
(1.00)
4p gain 6 (1%) 569 0.0622
(1.00) 		0.226
(1.00) 		0.206
(1.00) 		0.485
(1.00) 		0.137
(1.00) 		0.0525
(1.00)
4q gain 7 (1%) 568 0.704
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.787
(1.00) 		1
(1.00) 		0.619
(1.00) 		0.383
(1.00) 		0.809
(1.00)
5p gain 60 (10%) 515 0.113
(1.00) 		0.708
(1.00) 		0.0015
(0.985) 		0.178
(1.00) 		0.274
(1.00) 		0.99
(1.00) 		0.401
(1.00) 		0.4
(1.00) 		0.784
(1.00) 		0.354
(1.00)
5q gain 33 (6%) 542 0.457
(1.00) 		0.534
(1.00) 		0.00356
(1.00) 		0.356
(1.00) 		0.367
(1.00) 		0.764
(1.00) 		0.73
(1.00) 		0.446
(1.00) 		0.818
(1.00) 		0.483
(1.00)
9p gain 79 (14%) 496 0.42
(1.00) 		0.843
(1.00) 		0.178
(1.00) 		0.79
(1.00) 		0.706
(1.00) 		0.73
(1.00) 		0.539
(1.00) 		0.855
(1.00) 		0.78
(1.00) 		0.781
(1.00)
9q gain 64 (11%) 511 0.476
(1.00) 		0.923
(1.00) 		0.214
(1.00) 		0.433
(1.00) 		0.262
(1.00) 		0.496
(1.00) 		0.989
(1.00) 		0.691
(1.00) 		0.408
(1.00) 		0.739
(1.00)
10p gain 28 (5%) 547 0.137
(1.00) 		0.846
(1.00) 		0.00981
(1.00) 		0.0125
(1.00) 		0.962
(1.00) 		0.97
(1.00) 		0.617
(1.00) 		0.0446
(1.00) 		0.616
(1.00) 		0.496
(1.00)
10q gain 13 (2%) 562 0.691
(1.00) 		0.589
(1.00) 		0.193
(1.00) 		0.0437
(1.00) 		0.434
(1.00) 		0.0889
(1.00) 		0.448
(1.00) 		0.0762
(1.00) 		0.694
(1.00) 		0.902
(1.00)
12p gain 93 (16%) 482 0.362
(1.00) 		0.818
(1.00) 		0.256
(1.00) 		0.0171
(1.00) 		0.636
(1.00) 		0.292
(1.00) 		0.0232
(1.00) 		0.0134
(1.00) 		0.22
(1.00) 		0.112
(1.00)
12q gain 78 (14%) 497 0.315
(1.00) 		0.721
(1.00) 		0.0986
(1.00) 		0.00193
(1.00) 		0.812
(1.00) 		0.288
(1.00) 		0.0353
(1.00) 		0.0154
(1.00) 		0.222
(1.00) 		0.166
(1.00)
14q gain 19 (3%) 556 0.495
(1.00) 		0.55
(1.00) 		0.0301
(1.00) 		0.709
(1.00) 		0.313
(1.00) 		0.517
(1.00) 		0.0605
(1.00) 		0.048
(1.00) 		1
(1.00) 		0.371
(1.00)
15q gain 7 (1%) 568 0.515
(1.00) 		0.882
(1.00) 		1
(1.00) 		0.144
(1.00) 		1
(1.00) 		0.244
(1.00) 		0.87
(1.00) 		0.374
(1.00)
17p gain 13 (2%) 562 0.78
(1.00) 		0.00605
(1.00) 		1
(1.00) 		0.85
(1.00) 		0.715
(1.00) 		0.673
(1.00) 		0.0157
(1.00) 		0.009
(1.00) 		0.694
(1.00) 		0.902
(1.00)
18p gain 21 (4%) 554 0.192
(1.00) 		0.0168
(1.00) 		0.00061
(0.408) 		0.00955
(1.00) 		0.949
(1.00) 		0.795
(1.00) 		0.133
(1.00) 		0.391
(1.00) 		0.568
(1.00) 		0.397
(1.00)
18q gain 12 (2%) 563 0.172
(1.00) 		0.00729
(1.00) 		0.327
(1.00) 		0.711
(1.00) 		0.122
(1.00) 		0.858
(1.00) 		0.105
(1.00) 		0.134
(1.00)
19q gain 61 (11%) 514 0.0123
(1.00) 		0.0249
(1.00) 		0.0122
(1.00) 		0.0715
(1.00) 		0.0155
(1.00) 		0.0496
(1.00) 		0.507
(1.00) 		0.512
(1.00) 		0.832
(1.00) 		0.495
(1.00)
21q gain 19 (3%) 556 0.436
(1.00) 		0.381
(1.00) 		0.00268
(1.00) 		0.709
(1.00) 		0.558
(1.00) 		0.0523
(1.00) 		0.619
(1.00) 		0.834
(1.00) 		0.686
(1.00) 		0.143
(1.00)
22q gain 7 (1%) 568 0.691
(1.00) 		0.00605
(1.00) 		0.234
(1.00) 		0.466
(1.00) 		0.669
(1.00) 		0.033
(1.00) 		0.689
(1.00) 		0.499
(1.00) 		0.459
(1.00) 		0.596
(1.00)
Xq gain 17 (3%) 558 0.147
(1.00) 		0.735
(1.00) 		0.0167
(1.00) 		0.338
(1.00) 		0.00404
(1.00) 		0.477
(1.00) 		0.846
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.705
(1.00)
1q loss 25 (4%) 550 0.558
(1.00) 		0.0215
(1.00) 		0.0823
(1.00) 		0.0315
(1.00) 		0.603
(1.00) 		0.498
(1.00) 		0.158
(1.00) 		0.324
(1.00) 		0.425
(1.00) 		0.725
(1.00)
2p loss 10 (2%) 565 1
(1.00) 		0.435
(1.00) 		0.0735
(1.00) 		0.448
(1.00) 		0.585
(1.00) 		0.0151
(1.00) 		0.0133
(1.00)
2q loss 8 (1%) 567 0.741
(1.00) 		0.444
(1.00) 		0.548
(1.00) 		0.57
(1.00) 		0.582
(1.00) 		0.0584
(1.00) 		0.0455
(1.00)
3p loss 35 (6%) 540 0.938
(1.00) 		0.53
(1.00) 		0.831
(1.00) 		0.835
(1.00) 		0.758
(1.00) 		0.792
(1.00) 		0.441
(1.00) 		0.157
(1.00) 		0.105
(1.00) 		0.729
(1.00)
3q loss 17 (3%) 558 0.618
(1.00) 		0.816
(1.00) 		0.757
(1.00) 		0.0157
(1.00) 		0.395
(1.00) 		0.595
(1.00) 		0.385
(1.00) 		0.184
(1.00) 		0.74
(1.00) 		0.772
(1.00)
5p loss 34 (6%) 541 0.291
(1.00) 		0.433
(1.00) 		0.000544
(0.365) 		0.0341
(1.00) 		1
(1.00) 		0.63
(1.00) 		0.234
(1.00) 		0.0352
(1.00) 		0.969
(1.00) 		0.829
(1.00)
6p loss 18 (3%) 557 0.117
(1.00) 		0.0742
(1.00) 		0.026
(1.00) 		0.277
(1.00) 		0.764
(1.00) 		0.836
(1.00) 		0.89
(1.00) 		0.601
(1.00) 		0.602
(1.00) 		0.923
(1.00)
6q loss 33 (6%) 542 0.457
(1.00) 		0.338
(1.00) 		0.0983
(1.00) 		1
(1.00) 		0.0252
(1.00) 		0.47
(1.00) 		0.737
(1.00) 		0.677
(1.00) 		0.262
(1.00) 		0.298
(1.00)
7q loss 3 (1%) 572 0.212
(1.00) 		0.787
(1.00) 		0.737
(1.00) 		0.764
(1.00) 		1
(1.00)
8q loss 12 (2%) 563 0.603
(1.00) 		0.639
(1.00) 		0.0828
(1.00) 		0.58
(1.00) 		0.0521
(1.00) 		0.33
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.159
(1.00) 		0.271
(1.00)
10p loss 40 (7%) 535 0.704
(1.00) 		0.401
(1.00) 		0.000862
(0.572) 		0.419
(1.00) 		0.151
(1.00) 		0.16
(1.00) 		0.409
(1.00) 		0.532
(1.00) 		0.132
(1.00) 		0.591
(1.00)
11p loss 40 (7%) 535 0.797
(1.00) 		1
(1.00) 		0.00977
(1.00) 		0.706
(1.00) 		0.867
(1.00) 		0.562
(1.00) 		0.0716
(1.00) 		0.0838
(1.00) 		0.113
(1.00) 		0.359
(1.00)
11q loss 51 (9%) 524 0.975
(1.00) 		0.858
(1.00) 		0.00166
(1.00) 		0.232
(1.00) 		0.835
(1.00) 		0.453
(1.00) 		0.0997
(1.00) 		0.509
(1.00) 		0.129
(1.00) 		0.835
(1.00)
13q loss 12 (2%) 563 0.324
(1.00) 		0.108
(1.00) 		0.0495
(1.00) 		0.226
(1.00) 		0.0915
(1.00) 		0.164
(1.00) 		0.236
(1.00) 		0.668
(1.00) 		0.726
(1.00) 		0.403
(1.00)
16p loss 15 (3%) 560 0.256
(1.00) 		0.598
(1.00) 		0.0995
(1.00) 		0.226
(1.00) 		0.517
(1.00) 		0.91
(1.00) 		0.589
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.911
(1.00)
16q loss 17 (3%) 558 0.0131
(1.00) 		0.506
(1.00) 		0.00221
(1.00) 		0.492
(1.00) 		0.715
(1.00) 		0.852
(1.00) 		0.0911
(1.00) 		0.121
(1.00) 		0.134
(1.00) 		0.257
(1.00)
17q loss 45 (8%) 530 0.762
(1.00) 		0.558
(1.00) 		0.0023
(1.00) 		0.857
(1.00) 		0.921
(1.00) 		0.751
(1.00) 		0.101
(1.00) 		0.105
(1.00) 		0.116
(1.00) 		0.635
(1.00)
Xq loss 11 (2%) 564 0.765
(1.00) 		0.839
(1.00) 		0.339
(1.00) 		0.446
(1.00) 		0.817
(1.00) 		0.41
(1.00) 		0.0157
(1.00) 		0.0674
(1.00) 		0.515
(1.00) 		0.652
(1.00)
'2p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000256 (Fisher's exact test), Q value = 0.17

Table S1.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
2P GAIN MUTATED 28 9 3
2P GAIN WILD-TYPE 115 104 88

Figure S1.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'2p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.15

Table S2.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
2P GAIN MUTATED 1 20 4 3
2P GAIN WILD-TYPE 37 61 52 63

Figure S2.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'2p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000137 (Fisher's exact test), Q value = 0.094

Table S3.  Gene #3: '2p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
2P GAIN MUTATED 9 1 18
2P GAIN WILD-TYPE 86 66 61

Figure S3.  Get High-res Image Gene #3: '2p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.82e-06 (Fisher's exact test), Q value = 0.0041

Table S4.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
2Q GAIN MUTATED 28 8 1
2Q GAIN WILD-TYPE 115 105 90

Figure S4.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'2q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000234 (Fisher's exact test), Q value = 0.16

Table S5.  Gene #4: '2q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
2Q GAIN MUTATED 2 19 3 2
2Q GAIN WILD-TYPE 36 62 53 64

Figure S5.  Get High-res Image Gene #4: '2q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'3p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000181 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
3P GAIN MUTATED 25 7 4 0
3P GAIN WILD-TYPE 175 227 96 41

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

'3q gain mutation analysis' versus 'CN_CNMF'

P value = 2.49e-06 (Fisher's exact test), Q value = 0.0018

Table S7.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
3Q GAIN MUTATED 35 7 9 2
3Q GAIN WILD-TYPE 165 227 91 39

Figure S7.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6p gain mutation analysis' versus 'CN_CNMF'

P value = 1.55e-06 (Fisher's exact test), Q value = 0.0011

Table S8.  Gene #11: '6p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
6P GAIN MUTATED 46 15 8 8
6P GAIN WILD-TYPE 154 219 92 33

Figure S8.  Get High-res Image Gene #11: '6p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'6q gain mutation analysis' versus 'CN_CNMF'

P value = 7.47e-07 (Fisher's exact test), Q value = 0.00053

Table S9.  Gene #12: '6q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
6Q GAIN MUTATED 43 12 8 8
6Q GAIN WILD-TYPE 157 222 92 33

Figure S9.  Get High-res Image Gene #12: '6q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 1.89e-21 (Fisher's exact test), Q value = 1.4e-18

Table S10.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
7P GAIN MUTATED 144 62 59 25
7P GAIN WILD-TYPE 56 172 41 16

Figure S10.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.29e-07 (Fisher's exact test), Q value = 0.00052

Table S11.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
7P GAIN MUTATED 102 52 36
7P GAIN WILD-TYPE 41 61 55

Figure S11.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.72e-08 (Fisher's exact test), Q value = 2.7e-05

Table S12.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
7P GAIN MUTATED 22 61 31 17
7P GAIN WILD-TYPE 16 20 25 49

Figure S12.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.54e-05 (Fisher's exact test), Q value = 0.065

Table S13.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
7P GAIN MUTATED 53 23 55
7P GAIN WILD-TYPE 42 44 24

Figure S13.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 6.95e-16 (Fisher's exact test), Q value = 5.1e-13

Table S14.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
7Q GAIN MUTATED 126 56 52 21
7Q GAIN WILD-TYPE 74 178 48 20

Figure S14.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.61e-06 (Fisher's exact test), Q value = 0.006

Table S15.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
7Q GAIN MUTATED 88 47 28
7Q GAIN WILD-TYPE 55 66 63

Figure S15.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.79e-07 (Fisher's exact test), Q value = 0.00062

Table S16.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
7Q GAIN MUTATED 17 56 24 16
7Q GAIN WILD-TYPE 21 25 32 50

Figure S16.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0086

Table S17.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
7Q GAIN MUTATED 43 18 52
7Q GAIN WILD-TYPE 52 49 27

Figure S17.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain mutation analysis' versus 'CN_CNMF'

P value = 1e-08 (Fisher's exact test), Q value = 7.3e-06

Table S18.  Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
8P GAIN MUTATED 26 29 39 14
8P GAIN WILD-TYPE 174 205 61 27

Figure S18.  Get High-res Image Gene #15: '8p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8q gain mutation analysis' versus 'CN_CNMF'

P value = 1.06e-33 (Fisher's exact test), Q value = 8e-31

Table S19.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
8Q GAIN MUTATED 78 44 88 25
8Q GAIN WILD-TYPE 122 190 12 16

Figure S19.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p gain mutation analysis' versus 'CN_CNMF'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.012

Table S20.  Gene #21: '11p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
11P GAIN MUTATED 26 4 5 4
11P GAIN WILD-TYPE 174 230 95 37

Figure S20.  Get High-res Image Gene #21: '11p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'11p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.15

Table S21.  Gene #21: '11p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
11P GAIN MUTATED 20 2 3
11P GAIN WILD-TYPE 123 111 88

Figure S21.  Get High-res Image Gene #21: '11p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'11p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000153 (Fisher's exact test), Q value = 0.1

Table S22.  Gene #21: '11p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
11P GAIN MUTATED 3 0 12
11P GAIN WILD-TYPE 92 67 67

Figure S22.  Get High-res Image Gene #21: '11p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain mutation analysis' versus 'CN_CNMF'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00094

Table S23.  Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
11Q GAIN MUTATED 24 3 5 7
11Q GAIN WILD-TYPE 176 231 95 34

Figure S23.  Get High-res Image Gene #22: '11q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q gain mutation analysis' versus 'MRNA_CNMF'

P value = 1e-07 (Fisher's exact test), Q value = 7.2e-05

Table S24.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
13Q GAIN MUTATED 13 46 48 13
13Q GAIN WILD-TYPE 32 16 21 26

Figure S24.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'13q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.44e-05 (Fisher's exact test), Q value = 0.017

Table S25.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
13Q GAIN MUTATED 19 76 25
13Q GAIN WILD-TYPE 42 38 15

Figure S25.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'13q gain mutation analysis' versus 'CN_CNMF'

P value = 1.62e-37 (Fisher's exact test), Q value = 1.2e-34

Table S26.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
13Q GAIN MUTATED 175 64 56 19
13Q GAIN WILD-TYPE 25 170 44 22

Figure S26.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'13q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.71e-08 (Fisher's exact test), Q value = 1.2e-05

Table S27.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
13Q GAIN MUTATED 106 46 40
13Q GAIN WILD-TYPE 37 67 51

Figure S27.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'13q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.54e-09 (Fisher's exact test), Q value = 6.2e-06

Table S28.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
13Q GAIN MUTATED 25 57 28 14
13Q GAIN WILD-TYPE 13 24 28 52

Figure S28.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'13q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.4e-07 (Fisher's exact test), Q value = 0.00046

Table S29.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
13Q GAIN MUTATED 53 17 54
13Q GAIN WILD-TYPE 42 50 25

Figure S29.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain mutation analysis' versus 'CN_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 9.4e-14

Table S30.  Gene #28: '16p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
16P GAIN MUTATED 66 7 16 7
16P GAIN WILD-TYPE 134 227 84 34

Figure S30.  Get High-res Image Gene #28: '16p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'16q gain mutation analysis' versus 'CN_CNMF'

P value = 3.02e-18 (Fisher's exact test), Q value = 2.3e-15

Table S31.  Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
16Q GAIN MUTATED 68 6 16 6
16Q GAIN WILD-TYPE 132 228 84 35

Figure S31.  Get High-res Image Gene #29: '16q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000269 (Fisher's exact test), Q value = 0.18

Table S32.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
17Q GAIN MUTATED 36 13 15 3
17Q GAIN WILD-TYPE 164 221 85 38

Figure S32.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.01

Table S33.  Gene #31: '17q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
17Q GAIN MUTATED 5 22 2 2
17Q GAIN WILD-TYPE 33 59 54 64

Figure S33.  Get High-res Image Gene #31: '17q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 5.84e-05 (Fisher's exact test), Q value = 0.04

Table S34.  Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
19P GAIN MUTATED 29 7 10 6
19P GAIN WILD-TYPE 171 227 90 35

Figure S34.  Get High-res Image Gene #34: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'MRNA_CNMF'

P value = 6.06e-05 (Fisher's exact test), Q value = 0.042

Table S35.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
20P GAIN MUTATED 14 39 47 14
20P GAIN WILD-TYPE 31 23 22 25

Figure S35.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'20p gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 6.71e-09 (Fisher's exact test), Q value = 4.9e-06

Table S36.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
20P GAIN MUTATED 13 71 30
20P GAIN WILD-TYPE 48 43 10

Figure S36.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 4.25e-22 (Fisher's exact test), Q value = 3.2e-19

Table S37.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
20P GAIN MUTATED 130 67 52 39
20P GAIN WILD-TYPE 70 167 48 2

Figure S37.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.67e-05 (Fisher's exact test), Q value = 0.052

Table S38.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
20P GAIN MUTATED 89 42 37
20P GAIN WILD-TYPE 54 71 54

Figure S38.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.2e-07 (Fisher's exact test), Q value = 0.00023

Table S39.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
20P GAIN MUTATED 19 48 26 10
20P GAIN WILD-TYPE 19 33 30 56

Figure S39.  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 = 3.2e-07 (Fisher's exact test), Q value = 0.00023

Table S40.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
20P GAIN MUTATED 46 11 46
20P GAIN WILD-TYPE 49 56 33

Figure S40.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MRNA_CNMF'

P value = 1.23e-18 (Fisher's exact test), Q value = 9.2e-16

Table S41.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
20Q GAIN MUTATED 15 61 62 18
20Q GAIN WILD-TYPE 30 1 7 21

Figure S41.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'20q gain mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.68e-17 (Fisher's exact test), Q value = 2e-14

Table S42.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
20Q GAIN MUTATED 18 102 36
20Q GAIN WILD-TYPE 43 12 4

Figure S42.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 2.22e-46 (Fisher's exact test), Q value = 1.7e-43

Table S43.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
20Q GAIN MUTATED 193 91 79 40
20Q GAIN WILD-TYPE 7 143 21 1

Figure S43.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 9.04e-13 (Fisher's exact test), Q value = 6.6e-10

Table S44.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
20Q GAIN MUTATED 128 57 53
20Q GAIN WILD-TYPE 15 56 38

Figure S44.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'RPPA_CHIERARCHICAL'

P value = 2.28e-05 (Chi-square test), Q value = 0.016

Table S45.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 66 44 30 123
20Q GAIN MUTATED 28 46 55 30 15 99
20Q GAIN WILD-TYPE 13 40 11 14 15 24

Figure S45.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.03e-18 (Fisher's exact test), Q value = 6.7e-15

Table S46.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
20Q GAIN MUTATED 27 74 41 15
20Q GAIN WILD-TYPE 11 7 15 51

Figure S46.  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 = 1.13e-13 (Fisher's exact test), Q value = 8.3e-11

Table S47.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
20Q GAIN MUTATED 69 19 69
20Q GAIN WILD-TYPE 26 48 10

Figure S47.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 7.55e-06 (Fisher's exact test), Q value = 0.0053

Table S48.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
1P LOSS MUTATED 39 14 6 9
1P LOSS WILD-TYPE 161 220 94 32

Figure S48.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.84e-05 (Fisher's exact test), Q value = 0.026

Table S49.  Gene #41: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
1P LOSS MUTATED 29 4 6
1P LOSS WILD-TYPE 114 109 85

Figure S49.  Get High-res Image Gene #41: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4p loss mutation analysis' versus 'CN_CNMF'

P value = 5.5e-11 (Fisher's exact test), Q value = 4e-08

Table S50.  Gene #47: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
4P LOSS MUTATED 70 21 17 14
4P LOSS WILD-TYPE 130 213 83 27

Figure S50.  Get High-res Image Gene #47: '4p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'4q loss mutation analysis' versus 'CN_CNMF'

P value = 3.18e-12 (Fisher's exact test), Q value = 2.3e-09

Table S51.  Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
4Q LOSS MUTATED 68 16 17 12
4Q LOSS WILD-TYPE 132 218 83 29

Figure S51.  Get High-res Image Gene #48: '4q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'5q loss mutation analysis' versus 'CN_CNMF'

P value = 5.53e-07 (Fisher's exact test), Q value = 0.00039

Table S52.  Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
5Q LOSS MUTATED 31 6 17 6
5Q LOSS WILD-TYPE 169 228 83 35

Figure S52.  Get High-res Image Gene #50: '5q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 1.14e-18 (Fisher's exact test), Q value = 8.5e-16

Table S53.  Gene #54: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
8P LOSS MUTATED 88 17 31 9
8P LOSS WILD-TYPE 112 217 69 32

Figure S53.  Get High-res Image Gene #54: '8p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 2.9e-05 (Fisher's exact test), Q value = 0.02

Table S54.  Gene #56: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
9P LOSS MUTATED 26 4 7 2
9P LOSS WILD-TYPE 174 230 93 39

Figure S54.  Get High-res Image Gene #56: '9p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.0014

Table S55.  Gene #57: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
9Q LOSS MUTATED 28 4 3 2
9Q LOSS WILD-TYPE 172 230 97 39

Figure S55.  Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'9q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.42e-05 (Fisher's exact test), Q value = 0.024

Table S56.  Gene #57: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
9Q LOSS MUTATED 19 1 2
9Q LOSS WILD-TYPE 124 112 89

Figure S56.  Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.001

Table S57.  Gene #59: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
10Q LOSS MUTATED 16 6 13 11
10Q LOSS WILD-TYPE 184 228 87 30

Figure S57.  Get High-res Image Gene #59: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12p loss mutation analysis' versus 'CN_CNMF'

P value = 5.42e-07 (Fisher's exact test), Q value = 0.00039

Table S58.  Gene #62: '12p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
12P LOSS MUTATED 21 2 3 7
12P LOSS WILD-TYPE 179 232 97 34

Figure S58.  Get High-res Image Gene #62: '12p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'12q loss mutation analysis' versus 'CN_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00078

Table S59.  Gene #63: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
12Q LOSS MUTATED 19 2 1 6
12Q LOSS WILD-TYPE 181 232 99 35

Figure S59.  Get High-res Image Gene #63: '12q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'MRNA_CNMF'

P value = 4.76e-06 (Fisher's exact test), Q value = 0.0033

Table S60.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
14Q LOSS MUTATED 7 28 26 2
14Q LOSS WILD-TYPE 38 34 43 37

Figure S60.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'14q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 2.49e-07 (Fisher's exact test), Q value = 0.00018

Table S61.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
14Q LOSS MUTATED 3 42 18
14Q LOSS WILD-TYPE 58 72 22

Figure S61.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'14q loss mutation analysis' versus 'CN_CNMF'

P value = 1.12e-31 (Fisher's exact test), Q value = 8.4e-29

Table S62.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
14Q LOSS MUTATED 109 20 6 8
14Q LOSS WILD-TYPE 91 214 94 33

Figure S62.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'14q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.97e-07 (Fisher's exact test), Q value = 0.00014

Table S63.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
14Q LOSS MUTATED 53 12 12
14Q LOSS WILD-TYPE 90 101 79

Figure S63.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'14q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.73e-07 (Fisher's exact test), Q value = 0.00012

Table S64.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
14Q LOSS MUTATED 9 33 10 2
14Q LOSS WILD-TYPE 29 48 46 64

Figure S64.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 2.09e-24 (Fisher's exact test), Q value = 1.6e-21

Table S65.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
15Q LOSS MUTATED 88 16 26 26
15Q LOSS WILD-TYPE 112 218 74 15

Figure S65.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'15q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0083

Table S66.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
15Q LOSS MUTATED 11 30 13 3
15Q LOSS WILD-TYPE 27 51 43 63

Figure S66.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'17p loss mutation analysis' versus 'MRNA_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.16

Table S67.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
17P LOSS MUTATED 14 36 41 10
17P LOSS WILD-TYPE 31 26 28 29

Figure S67.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'17p loss mutation analysis' versus 'CN_CNMF'

P value = 5.49e-22 (Fisher's exact test), Q value = 4.1e-19

Table S68.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
17P LOSS MUTATED 128 46 57 21
17P LOSS WILD-TYPE 72 188 43 20

Figure S68.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'17p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.44e-07 (Fisher's exact test), Q value = 0.00018

Table S69.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
17P LOSS MUTATED 86 35 27
17P LOSS WILD-TYPE 57 78 64

Figure S69.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'17p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.25e-06 (Fisher's exact test), Q value = 0.0023

Table S70.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
17P LOSS MUTATED 21 45 21 11
17P LOSS WILD-TYPE 17 36 35 55

Figure S70.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18p loss mutation analysis' versus 'MRNA_CNMF'

P value = 9.87e-15 (Fisher's exact test), Q value = 7.3e-12

Table S71.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
18P LOSS MUTATED 11 53 52 10
18P LOSS WILD-TYPE 34 9 17 29

Figure S71.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'18p loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 8.51e-12 (Fisher's exact test), Q value = 6.2e-09

Table S72.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
18P LOSS MUTATED 13 81 32
18P LOSS WILD-TYPE 48 33 8

Figure S72.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 4.26e-47 (Fisher's exact test), Q value = 3.2e-44

Table S73.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
18P LOSS MUTATED 176 53 62 33
18P LOSS WILD-TYPE 24 181 38 8

Figure S73.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.33e-19 (Fisher's exact test), Q value = 3.2e-16

Table S74.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
18P LOSS MUTATED 120 38 35
18P LOSS WILD-TYPE 23 75 56

Figure S74.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 5.39e-16 (Fisher's exact test), Q value = 4e-13

Table S75.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
18P LOSS MUTATED 20 66 33 9
18P LOSS WILD-TYPE 18 15 23 57

Figure S75.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.73e-11 (Fisher's exact test), Q value = 2e-08

Table S76.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
18P LOSS MUTATED 56 13 59
18P LOSS WILD-TYPE 39 54 20

Figure S76.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss mutation analysis' versus 'MRNA_CNMF'

P value = 1.42e-12 (Fisher's exact test), Q value = 1e-09

Table S77.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 62 69 39
18Q LOSS MUTATED 15 54 54 12
18Q LOSS WILD-TYPE 30 8 15 27

Figure S77.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

'18q loss mutation analysis' versus 'MRNA_CHIERARCHICAL'

P value = 1.96e-11 (Fisher's exact test), Q value = 1.4e-08

Table S78.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 114 40
18Q LOSS MUTATED 16 86 33
18Q LOSS WILD-TYPE 45 28 7

Figure S78.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 6.8e-51 (Fisher's exact test), Q value = 5.2e-48

Table S79.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
18Q LOSS MUTATED 180 59 77 36
18Q LOSS WILD-TYPE 20 175 23 5

Figure S79.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'18q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.03e-21 (Fisher's exact test), Q value = 6e-18

Table S80.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 113 91
18Q LOSS MUTATED 128 45 38
18Q LOSS WILD-TYPE 15 68 53

Figure S80.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'18q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.96e-16 (Fisher's exact test), Q value = 2.9e-13

Table S81.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 81 56 66
18Q LOSS MUTATED 26 68 34 11
18Q LOSS WILD-TYPE 12 13 22 55

Figure S81.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'18q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.68e-09 (Fisher's exact test), Q value = 2.7e-06

Table S82.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 67 79
18Q LOSS MUTATED 58 19 62
18Q LOSS WILD-TYPE 37 48 17

Figure S82.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss mutation analysis' versus 'CN_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.01

Table S83.  Gene #73: '19p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
19P LOSS MUTATED 7 1 5 7
19P LOSS WILD-TYPE 193 233 95 34

Figure S83.  Get High-res Image Gene #73: '19p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000235 (Fisher's exact test), Q value = 0.16

Table S84.  Gene #74: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
19Q LOSS MUTATED 6 1 6 5
19Q LOSS WILD-TYPE 194 233 94 36

Figure S84.  Get High-res Image Gene #74: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p loss mutation analysis' versus 'CN_CNMF'

P value = 4.56e-07 (Fisher's exact test), Q value = 0.00033

Table S85.  Gene #75: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
20P LOSS MUTATED 27 5 15 0
20P LOSS WILD-TYPE 173 229 85 41

Figure S85.  Get High-res Image Gene #75: '20p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 3.64e-05 (Fisher's exact test), Q value = 0.025

Table S86.  Gene #76: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
21Q LOSS MUTATED 58 28 16 12
21Q LOSS WILD-TYPE 142 206 84 29

Figure S86.  Get High-res Image Gene #76: '21q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 7.8e-14 (Fisher's exact test), Q value = 5.7e-11

Table S87.  Gene #77: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 200 234 100 41
22Q LOSS MUTATED 76 20 13 13
22Q LOSS WILD-TYPE 124 214 87 28

Figure S87.  Get High-res Image Gene #77: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 575

  • Number of significantly arm-level cnvs = 78

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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