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

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

Summary

Testing the association between copy number variation 80 arm-level results and 12 molecular subtypes across 504 patients, 198 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'.

  • 3p gain cnv correlated to 'CN_CNMF'.

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

  • 5p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'CN_CNMF'.

  • 6q 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'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF'.

  • 10q gain cnv correlated to 'CN_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF'.

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 15q gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 19q gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF'.

  • Xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

  • 3p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'CN_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 7p loss cnv correlated to 'CN_CNMF'.

  • 7q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 9q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 12p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 14q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 15q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 19p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'CN_CNMF'.

  • 21q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • Xq loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 198 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 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Chi-square 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
15q loss 0 (0%) 420 0.00202
(1.00) 		0.000218
(0.143) 		6.8e-35
(5.71e-32) 		9.31e-12
(7.43e-09) 		0.00259
(1.00) 		0.267
(1.00) 		2.61e-10
(2.05e-07) 		4.49e-07
(0.000338) 		1.39e-14
(1.13e-11) 		4.72e-14
(3.82e-11) 		3.26e-06
(0.00239) 		9.96e-07
(0.00074)
20q gain 0 (0%) 427 0.00809
(1.00) 		0.00105
(0.645) 		1.37e-29
(1.14e-26) 		6.66e-07
(0.000499) 		0.192
(1.00) 		0.58
(1.00) 		0.000315
(0.206) 		0.000351
(0.227) 		2.89e-08
(2.22e-05) 		4.3e-09
(3.34e-06) 		2.4e-05
(0.017) 		5.96e-07
(0.000447)
16p loss 0 (0%) 431 0.00809
(1.00) 		0.00105
(0.645) 		1.54e-30
(1.29e-27) 		1.86e-09
(1.45e-06) 		0.105
(1.00) 		0.6
(1.00) 		3.47e-08
(2.65e-05) 		9.34e-07
(0.000695) 		4.64e-12
(3.72e-09) 		6.35e-11
(5.02e-08) 		5.75e-05
(0.0393) 		7.32e-06
(0.00529)
16q loss 0 (0%) 390 0.00324
(1.00) 		0.000454
(0.291) 		7.72e-37
(6.49e-34) 		2.55e-11
(2.03e-08) 		0.237
(1.00) 		1
(1.00) 		8.89e-08
(6.77e-05) 		1.79e-06
(0.00132) 		9.45e-14
(7.64e-11) 		2.9e-10
(2.28e-07) 		2.02e-05
(0.0143) 		1.46e-07
(0.000111)
17p loss 0 (0%) 393 0.00324
(1.00) 		0.000454
(0.291) 		4.96e-54
(4.18e-51) 		2.17e-12
(1.74e-09) 		0.000571
(0.362) 		0.665
(1.00) 		7.41e-06
(0.00535) 		0.000104
(0.07) 		2.24e-18
(1.84e-15) 		3.22e-10
(2.52e-07) 		9.27e-05
(0.0628) 		2.05e-06
(0.00151)
8p loss 0 (0%) 448 0.00809
(1.00) 		0.00105
(0.645) 		4.17e-24
(3.47e-21) 		6.02e-11
(4.76e-08) 		0.165
(1.00) 		0.181
(1.00) 		0.00132
(0.797) 		1.5e-05
(0.0107) 		1.36e-13
(1.1e-10) 		2.72e-14
(2.21e-11) 		7.89e-07
(0.00059) 		1.32e-07
(0.000101)
18p gain 0 (0%) 464 0.379
(1.00) 		0.0902
(1.00) 		1.75e-13
(1.41e-10) 		0.000133
(0.0891) 		0.093
(1.00) 		0.429
(1.00) 		0.000328
(0.213) 		0.0185
(1.00) 		1.97e-06
(0.00145) 		2.07e-09
(1.62e-06) 		0.000857
(0.536) 		8.35e-05
(0.0566)
20p gain 0 (0%) 438 0.0391
(1.00) 		0.00466
(1.00) 		9.25e-25
(7.7e-22) 		4.83e-05
(0.0331) 		0.291
(1.00) 		1
(1.00) 		0.00685
(1.00) 		0.00251
(1.00) 		9.79e-06
(0.00704) 		4e-07
(0.000302) 		0.000207
(0.137) 		4.72e-05
(0.0325)
4p loss 0 (0%) 437 0.0515
(1.00) 		0.00755
(1.00) 		1.19e-24
(9.88e-22) 		3.12e-10
(2.45e-07) 		0.0339
(1.00) 		0.393
(1.00) 		0.00158
(0.943) 		0.00103
(0.637) 		6.92e-12
(5.53e-09) 		1.6e-10
(1.26e-07) 		9.82e-05
(0.0664) 		5.67e-06
(0.00411)
4q loss 0 (0%) 439 0.689
(1.00) 		0.272
(1.00) 		6.55e-25
(5.46e-22) 		3.05e-10
(2.39e-07) 		0.131
(1.00) 		0.776
(1.00) 		0.00154
(0.919) 		0.00315
(1.00) 		6.72e-07
(0.000503) 		4.34e-09
(3.37e-06) 		0.000244
(0.16) 		3.56e-05
(0.0249)
14q loss 0 (0%) 461 0.00809
(1.00) 		0.00105
(0.645) 		7.51e-17
(6.15e-14) 		8.34e-09
(6.45e-06) 		0.0847
(1.00) 		0.0052
(1.00) 		0.0356
(1.00) 		0.0277
(1.00) 		1.24e-05
(0.00889) 		1.05e-11
(8.35e-09) 		4.6e-06
(0.00336) 		1.1e-05
(0.00791)
19p loss 0 (0%) 468 5.04e-12
(4.03e-09) 		2.01e-09
(1.57e-06) 		0.285
(1.00) 		0.731
(1.00) 		0.0076
(1.00) 		0.00483
(1.00) 		1.35e-06
(0.000999) 		5.52e-07
(0.000415) 		1.42e-05
(0.0102) 		5.62e-08
(4.29e-05)
19q loss 0 (0%) 475 1.19e-08
(9.21e-06) 		7.23e-06
(0.00523) 		0.563
(1.00) 		1
(1.00) 		0.0371
(1.00) 		0.0107
(1.00) 		4.14e-05
(0.0287) 		3.57e-05
(0.0249) 		0.000325
(0.212) 		5.31e-06
(0.00386)
5q loss 0 (0%) 457 0.0515
(1.00) 		0.00755
(1.00) 		3.31e-17
(2.72e-14) 		2.94e-08
(2.25e-05) 		0.0481
(1.00) 		0.153
(1.00) 		0.0671
(1.00) 		0.128
(1.00) 		3.71e-05
(0.0258) 		5.42e-07
(0.000407) 		0.000896
(0.559) 		0.000106
(0.0713)
9q loss 0 (0%) 411 0.000567
(0.359) 		4.17e-05
(0.029) 		1.8e-37
(1.51e-34) 		1.74e-06
(0.00128) 		0.0137
(1.00) 		0.36
(1.00) 		0.00128
(0.773) 		0.111
(1.00) 		4.13e-13
(3.32e-10) 		5.36e-07
(0.000404) 		0.0303
(1.00) 		0.0109
(1.00)
12p loss 0 (0%) 478 3.45e-11
(2.74e-08) 		7e-05
(0.0477) 		0.0577
(1.00) 		1
(1.00) 		0.0151
(1.00) 		0.00763
(1.00) 		1.53e-08
(1.18e-05) 		0.000105
(0.0707) 		0.00236
(1.00) 		0.000204
(0.135)
12q loss 0 (0%) 485 1.54e-08
(1.18e-05) 		4.3e-05
(0.0298) 		0.31
(1.00) 		0.429
(1.00) 		0.00162
(0.967) 		5.88e-05
(0.0401) 		3.5e-05
(0.0245) 		1.87e-05
(0.0133) 		0.00264
(1.00) 		0.000668
(0.421)
5p gain 0 (0%) 470 0.536
(1.00) 		0.272
(1.00) 		2.39e-10
(1.88e-07) 		0.000169
(0.113) 		0.0587
(1.00) 		1
(1.00) 		0.00464
(1.00) 		0.0141
(1.00) 		0.000251
(0.164) 		1.74e-05
(0.0124) 		0.00265
(1.00) 		0.00116
(0.707)
9p loss 0 (0%) 427 0.0129
(1.00) 		0.00193
(1.00) 		4.13e-30
(3.45e-27) 		3.22e-06
(0.00236) 		0.0117
(1.00) 		0.244
(1.00) 		0.0443
(1.00) 		0.646
(1.00) 		1.14e-08
(8.78e-06) 		9.26e-07
(0.000691) 		0.0855
(1.00) 		0.00481
(1.00)
11p loss 0 (0%) 449 1.71e-22
(1.42e-19) 		1.49e-05
(0.0107) 		0.182
(1.00) 		0.75
(1.00) 		0.00973
(1.00) 		0.0685
(1.00) 		1.32e-07
(1e-04) 		0.000139
(0.0929) 		0.0123
(1.00) 		0.000578
(0.365)
13q loss 0 (0%) 443 0.689
(1.00) 		0.272
(1.00) 		3.89e-17
(3.19e-14) 		7.77e-05
(0.0527) 		0.161
(1.00) 		0.393
(1.00) 		0.193
(1.00) 		0.21
(1.00) 		2.75e-05
(0.0194) 		0.0002
(0.133) 		0.446
(1.00) 		0.243
(1.00)
17q loss 0 (0%) 430 0.00809
(1.00) 		0.00105
(0.645) 		8.27e-32
(6.93e-29) 		3.66e-05
(0.0255) 		0.0924
(1.00) 		0.612
(1.00) 		0.00419
(1.00) 		0.00893
(1.00) 		1.74e-08
(1.34e-05) 		3.33e-05
(0.0234) 		0.00308
(1.00) 		0.000952
(0.591)
18q loss 0 (0%) 454 2.7e-16
(2.2e-13) 		4.81e-05
(0.033) 		0.883
(1.00) 		0.77
(1.00) 		0.0273
(1.00) 		0.293
(1.00) 		5.35e-05
(0.0367) 		4.68e-06
(0.00341) 		0.0178
(1.00) 		0.00417
(1.00)
21q loss 0 (0%) 470 0.0391
(1.00) 		0.00466
(1.00) 		3.09e-08
(2.36e-05) 		0.0012
(0.728) 		0.095
(1.00) 		0.75
(1.00) 		0.176
(1.00) 		0.126
(1.00) 		0.000397
(0.256) 		4.33e-05
(0.0299) 		0.000334
(0.216) 		0.000211
(0.139)
22q loss 0 (0%) 414 0.00809
(1.00) 		0.00105
(0.645) 		1.02e-37
(8.58e-35) 		2.01e-07
(0.000152) 		0.0721
(1.00) 		1
(1.00) 		0.0142
(1.00) 		0.0491
(1.00) 		5.3e-11
(4.2e-08) 		1.82e-07
(0.000138) 		0.0445
(1.00) 		0.00402
(1.00)
3q gain 0 (0%) 452 0.137
(1.00) 		0.272
(1.00) 		3.89e-21
(3.23e-18) 		4.57e-05
(0.0315) 		0.388
(1.00) 		0.301
(1.00) 		0.131
(1.00) 		0.215
(1.00) 		0.00115
(0.703) 		2.4e-05
(0.017) 		0.0178
(1.00) 		0.0368
(1.00)
18q gain 0 (0%) 483 0.137
(1.00) 		0.0194
(1.00) 		1.29e-05
(0.00923) 		0.027
(1.00) 		1
(1.00) 		0.0243
(1.00) 		0.169
(1.00) 		0.00014
(0.0936) 		4.56e-05
(0.0314) 		0.0105
(1.00) 		0.00309
(1.00)
19q gain 0 (0%) 471 0.689
(1.00) 		0.272
(1.00) 		3.46e-13
(2.78e-10) 		0.00859
(1.00) 		0.0477
(1.00) 		0.367
(1.00) 		0.13
(1.00) 		0.107
(1.00) 		0.000106
(0.0715) 		7.74e-05
(0.0526) 		0.11
(1.00) 		0.026
(1.00)
3p loss 0 (0%) 471 1.22e-13
(9.83e-11) 		3.09e-05
(0.0218) 		0.00246
(1.00) 		0.0429
(1.00) 		0.0143
(1.00) 		0.0312
(1.00) 		0.000537
(0.341) 		3.22e-05
(0.0226) 		0.0436
(1.00) 		0.00465
(1.00)
7q loss 0 (0%) 476 4.6e-12
(3.69e-09) 		6.12e-05
(0.0418) 		0.197
(1.00) 		0.0121
(1.00) 		0.154
(1.00) 		0.267
(1.00) 		4.21e-06
(0.00308) 		0.000407
(0.262) 		0.0218
(1.00) 		0.0013
(0.783)
10p loss 0 (0%) 481 0.137
(1.00) 		0.0194
(1.00) 		1.5e-09
(1.17e-06) 		0.000305
(0.199) 		0.474
(1.00) 		0.633
(1.00) 		0.291
(1.00) 		0.146
(1.00) 		3.48e-06
(0.00255) 		0.00404
(1.00) 		0.118
(1.00) 		0.0129
(1.00)
19p gain 0 (0%) 469 0.151
(1.00) 		0.0272
(1.00) 		3.63e-14
(2.95e-11) 		0.0113
(1.00) 		0.255
(1.00) 		0.029
(1.00) 		0.0732
(1.00) 		0.0591
(1.00) 		0.000204
(0.135) 		0.00109
(0.665) 		0.212
(1.00) 		0.0647
(1.00)
8q loss 0 (0%) 491 1.27e-05
(0.0091) 		0.00032
(0.208) 		1
(1.00) 		0.175
(1.00) 		0.116
(1.00) 		0.0112
(1.00) 		0.00101
(0.627) 		0.000587
(0.371) 		0.00447
(1.00)
10q loss 0 (0%) 480 9.65e-09
(7.46e-06) 		0.00172
(1.00) 		0.451
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.107
(1.00) 		0.00012
(0.0808) 		0.00808
(1.00) 		0.155
(1.00) 		0.0746
(1.00)
11q loss 0 (0%) 457 1e-16
(8.2e-14) 		0.000716
(0.45) 		0.925
(1.00) 		0.713
(1.00) 		0.0374
(1.00) 		0.2
(1.00) 		1.39e-06
(0.00103) 		0.000501
(0.32) 		0.0622
(1.00) 		0.000481
(0.308)
1q gain 0 (0%) 362 0.25
(1.00) 		0.29
(1.00) 		0.000182
(0.121) 		0.00603
(1.00) 		0.00123
(0.743) 		0.000715
(0.45) 		0.901
(1.00) 		0.966
(1.00) 		0.00245
(1.00) 		0.355
(1.00) 		0.156
(1.00) 		0.721
(1.00)
2p gain 0 (0%) 451 0.425
(1.00) 		0.481
(1.00) 		2.18e-19
(1.79e-16) 		0.0596
(1.00) 		0.177
(1.00) 		0.802
(1.00) 		0.0371
(1.00) 		0.409
(1.00) 		0.466
(1.00) 		0.0754
(1.00) 		0.113
(1.00) 		0.1
(1.00)
2q gain 0 (0%) 462 0.343
(1.00) 		1
(1.00) 		1.33e-20
(1.1e-17) 		0.165
(1.00) 		0.0653
(1.00) 		0.575
(1.00) 		0.00964
(1.00) 		0.403
(1.00) 		0.477
(1.00) 		0.0227
(1.00) 		0.0727
(1.00) 		0.0621
(1.00)
3p gain 0 (0%) 474 1.95e-20
(1.61e-17) 		0.136
(1.00) 		0.525
(1.00) 		0.652
(1.00) 		0.274
(1.00) 		0.254
(1.00) 		0.187
(1.00) 		0.0319
(1.00) 		0.32
(1.00) 		0.268
(1.00)
6p gain 0 (0%) 466 0.253
(1.00) 		0.0902
(1.00) 		2.24e-20
(1.84e-17) 		0.0513
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.0673
(1.00) 		0.409
(1.00) 		0.0136
(1.00) 		0.0144
(1.00) 		0.0998
(1.00) 		0.248
(1.00)
6q gain 0 (0%) 472 0.253
(1.00) 		0.0902
(1.00) 		3.4e-17
(2.79e-14) 		0.385
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.342
(1.00) 		0.309
(1.00) 		0.0527
(1.00) 		0.0363
(1.00) 		0.56
(1.00) 		0.644
(1.00)
7p gain 0 (0%) 458 0.935
(1.00) 		0.866
(1.00) 		3.27e-14
(2.65e-11) 		0.00669
(1.00) 		0.733
(1.00) 		0.217
(1.00) 		0.0272
(1.00) 		0.559
(1.00) 		0.685
(1.00) 		0.641
(1.00) 		0.58
(1.00) 		0.199
(1.00)
7q gain 0 (0%) 458 0.855
(1.00) 		1
(1.00) 		2.96e-15
(2.41e-12) 		0.0106
(1.00) 		0.889
(1.00) 		0.0552
(1.00) 		0.141
(1.00) 		0.559
(1.00) 		0.55
(1.00) 		0.966
(1.00) 		0.892
(1.00) 		0.203
(1.00)
8p gain 0 (0%) 414 0.704
(1.00) 		0.609
(1.00) 		1.6e-19
(1.32e-16) 		0.718
(1.00) 		0.133
(1.00) 		1
(1.00) 		0.522
(1.00) 		0.445
(1.00) 		0.103
(1.00) 		0.0389
(1.00) 		0.36
(1.00) 		0.276
(1.00)
8q gain 0 (0%) 383 0.0336
(1.00) 		0.0339
(1.00) 		1.5e-20
(1.24e-17) 		0.55
(1.00) 		0.00495
(1.00) 		1
(1.00) 		0.196
(1.00) 		0.908
(1.00) 		0.00139
(0.835) 		0.000802
(0.502) 		0.165
(1.00) 		0.293
(1.00)
10p gain 0 (0%) 416 0.00714
(1.00) 		0.0476
(1.00) 		1.13e-06
(0.00084) 		0.119
(1.00) 		0.284
(1.00) 		0.136
(1.00) 		0.553
(1.00) 		0.623
(1.00) 		0.281
(1.00) 		0.00789
(1.00) 		0.0621
(1.00) 		0.0859
(1.00)
10q gain 0 (0%) 423 0.00212
(1.00) 		0.0262
(1.00) 		9.33e-07
(0.000695) 		0.28
(1.00) 		0.268
(1.00) 		0.189
(1.00) 		0.55
(1.00) 		0.346
(1.00) 		0.158
(1.00) 		0.00125
(0.754) 		0.0725
(1.00) 		0.141
(1.00)
12p gain 0 (0%) 466 0.64
(1.00) 		1
(1.00) 		6.2e-06
(0.0045) 		0.00549
(1.00) 		0.937
(1.00) 		1
(1.00) 		0.107
(1.00) 		0.0726
(1.00) 		0.0519
(1.00) 		0.0168
(1.00) 		0.109
(1.00) 		0.0404
(1.00)
12q gain 0 (0%) 475 0.64
(1.00) 		1
(1.00) 		0.000208
(0.137) 		0.0869
(1.00) 		0.901
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.27
(1.00) 		0.362
(1.00) 		0.177
(1.00) 		0.422
(1.00) 		0.334
(1.00)
13q gain 0 (0%) 483 1.59e-06
(0.00118) 		0.00317
(1.00) 		0.735
(1.00) 		0.367
(1.00) 		0.381
(1.00) 		0.383
(1.00) 		0.00232
(1.00) 		0.000563
(0.358) 		0.18
(1.00) 		0.0462
(1.00)
14q gain 0 (0%) 482 1
(1.00) 		0.769
(1.00) 		0.000135
(0.0904) 		0.355
(1.00) 		0.239
(1.00) 		0.292
(1.00) 		0.00964
(1.00) 		0.0454
(1.00) 		0.00496
(1.00) 		0.0311
(1.00) 		0.0937
(1.00) 		0.528
(1.00)
15q gain 0 (0%) 498 8.54e-06
(0.00616) 		0.847
(1.00) 		1
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.32
(1.00) 		0.292
(1.00)
17q gain 0 (0%) 491 0.000298
(0.195) 		0.0137
(1.00) 		0.0531
(1.00) 		1
(1.00) 		0.116
(1.00) 		0.11
(1.00) 		0.00571
(1.00) 		0.054
(1.00) 		0.178
(1.00) 		0.125
(1.00)
21q gain 0 (0%) 479 1.4e-07
(0.000106) 		0.216
(1.00) 		0.237
(1.00) 		0.558
(1.00) 		0.0576
(1.00) 		0.0454
(1.00) 		0.00575
(1.00) 		0.0226
(1.00) 		0.435
(1.00) 		0.136
(1.00)
22q gain 0 (0%) 495 0.000202
(0.134) 		0.000515
(0.328) 		0.376
(1.00) 		0.271
(1.00) 		0.27
(1.00) 		0.0512
(1.00) 		0.007
(1.00) 		0.0379
(1.00) 		0.0484
(1.00)
Xq gain 0 (0%) 491 0.00033
(0.214) 		0.198
(1.00) 		0.376
(1.00) 		0.0243
(1.00) 		0.0109
(1.00) 		0.0363
(1.00) 		0.147
(1.00) 		0.043
(1.00) 		0.0316
(1.00)
1p loss 0 (0%) 492 4.08e-11
(3.23e-08) 		0.00293
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.497
(1.00) 		0.647
(1.00) 		0.00173
(1.00) 		0.262
(1.00) 		0.192
(1.00)
3q loss 0 (0%) 490 3.78e-05
(0.0263) 		0.0131
(1.00) 		0.024
(1.00) 		0.558
(1.00) 		0.116
(1.00) 		0.777
(1.00) 		0.263
(1.00) 		0.255
(1.00) 		0.519
(1.00) 		0.261
(1.00)
5p loss 0 (0%) 476 0.379
(1.00) 		0.0902
(1.00) 		2.52e-09
(1.96e-06) 		0.000995
(0.617) 		0.146
(1.00) 		0.301
(1.00) 		0.25
(1.00) 		0.798
(1.00) 		0.00898
(1.00) 		0.00144
(0.865) 		0.086
(1.00) 		0.0637
(1.00)
6p loss 0 (0%) 494 4.18e-05
(0.029) 		0.0462
(1.00) 		1
(1.00) 		0.18
(1.00) 		0.0121
(1.00) 		0.156
(1.00) 		0.00586
(1.00) 		0.474
(1.00) 		0.301
(1.00)
6q loss 0 (0%) 492 0.689
(1.00) 		0.272
(1.00) 		3.1e-05
(0.0218) 		0.0356
(1.00) 		0.858
(1.00) 		0.558
(1.00) 		0.3
(1.00) 		0.0366
(1.00) 		0.0874
(1.00) 		0.00389
(1.00) 		0.282
(1.00) 		0.12
(1.00)
7p loss 0 (0%) 474 0.137
(1.00) 		0.0194
(1.00) 		2.89e-09
(2.25e-06) 		0.00318
(1.00) 		0.158
(1.00) 		0.201
(1.00) 		0.43
(1.00) 		0.169
(1.00) 		0.000511
(0.326) 		0.0282
(1.00) 		0.141
(1.00) 		0.0608
(1.00)
18p loss 0 (0%) 468 1.73e-11
(1.38e-08) 		0.000416
(0.267) 		0.326
(1.00) 		0.746
(1.00) 		0.369
(1.00) 		0.608
(1.00) 		0.0039
(1.00) 		0.000909
(0.566) 		0.0346
(1.00) 		0.0062
(1.00)
20p loss 0 (0%) 488 9.51e-06
(0.00684) 		0.083
(1.00) 		0.243
(1.00) 		0.633
(1.00) 		0.207
(1.00) 		1
(1.00) 		0.00313
(1.00) 		0.0234
(1.00) 		0.187
(1.00) 		0.187
(1.00)
Xq loss 0 (0%) 488 4.76e-06
(0.00347) 		0.00173
(1.00) 		0.617
(1.00) 		0.633
(1.00) 		0.8
(1.00) 		0.116
(1.00) 		0.0629
(1.00) 		0.00139
(0.834) 		0.0144
(1.00) 		0.00611
(1.00)
1p gain 0 (0%) 482 0.467
(1.00) 		0.491
(1.00) 		0.000788
(0.494) 		1
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.504
(1.00) 		0.0114
(1.00) 		0.0726
(1.00) 		0.0483
(1.00) 		0.203
(1.00)
4p gain 0 (0%) 497 0.00647
(1.00) 		0.462
(1.00) 		0.14
(1.00) 		0.116
(1.00) 		0.777
(1.00) 		0.132
(1.00) 		0.0194
(1.00) 		0.207
(1.00) 		0.0581
(1.00)
4q gain 0 (0%) 501 0.231
(1.00) 		0.376
(1.00) 		0.57
(1.00) 		0.0818
(1.00)
5q gain 0 (0%) 495 0.0116
(1.00) 		0.423
(1.00) 		1
(1.00) 		0.357
(1.00) 		0.0885
(1.00) 		0.171
(1.00) 		0.045
(1.00)
9p gain 0 (0%) 489 0.0626
(1.00) 		0.117
(1.00) 		1
(1.00) 		0.175
(1.00) 		0.116
(1.00) 		0.0225
(1.00) 		0.0234
(1.00) 		0.121
(1.00) 		0.397
(1.00)
9q gain 0 (0%) 499 0.319
(1.00) 		0.374
(1.00) 		0.108
(1.00) 		0.0534
(1.00) 		0.207
(1.00) 		1
(1.00)
11p gain 0 (0%) 496 0.137
(1.00) 		0.272
(1.00) 		0.0763
(1.00) 		0.207
(1.00) 		0.109
(1.00) 		1
(1.00) 		0.623
(1.00) 		0.777
(1.00) 		0.0608
(1.00) 		0.301
(1.00) 		0.612
(1.00) 		0.903
(1.00)
11q gain 0 (0%) 496 0.0668
(1.00) 		0.462
(1.00) 		0.109
(1.00) 		0.299
(1.00) 		0.368
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.903
(1.00)
16p gain 0 (0%) 493 0.000947
(0.589) 		0.0218
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.782
(1.00) 		0.777
(1.00) 		0.0634
(1.00) 		0.122
(1.00) 		0.459
(1.00) 		0.236
(1.00)
16q gain 0 (0%) 501 0.00213
(1.00) 		1
(1.00) 		1
(1.00) 		0.578
(1.00) 		0.155
(1.00)
17p gain 0 (0%) 496 0.0259
(1.00) 		0.168
(1.00) 		1
(1.00) 		0.782
(1.00) 		0.777
(1.00) 		0.0551
(1.00) 		0.148
(1.00) 		0.547
(1.00) 		0.494
(1.00)
1q loss 0 (0%) 501 0.231
(1.00) 		0.0634
(1.00) 		0.135
(1.00) 		0.367
(1.00) 		0.607
(1.00) 		0.0881
(1.00)
2p loss 0 (0%) 499 0.071
(1.00) 		0.462
(1.00) 		0.376
(1.00) 		0.674
(1.00) 		0.211
(1.00) 		1
(1.00) 		0.137
(1.00)
2q loss 0 (0%) 494 0.001
(0.619) 		0.0859
(1.00) 		0.14
(1.00) 		0.3
(1.00) 		0.0366
(1.00) 		0.124
(1.00) 		0.0524
(1.00) 		0.459
(1.00) 		0.0227
(1.00)
20q loss 0 (0%) 497 0.00813
(1.00) 		0.0146
(1.00) 		0.528
(1.00) 		0.035
(1.00) 		0.0194
(1.00) 		0.117
(1.00) 		0.0238
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 0.000182 (Chi-square test), Q value = 0.12

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
1Q GAIN CNV 87 4 27 8 9 7
1Q GAIN WILD-TYPE 207 5 127 5 13 5

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 2.18e-19 (Chi-square test), Q value = 1.8e-16

Table S2.  Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
2P GAIN CNV 8 5 24 9 3 4
2P GAIN WILD-TYPE 286 4 130 4 19 8

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1.33e-20 (Chi-square test), Q value = 1.1e-17

Table S3.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
2Q GAIN CNV 5 4 18 9 3 3
2Q GAIN WILD-TYPE 289 5 136 4 19 9

Figure S3.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1.95e-20 (Chi-square test), Q value = 1.6e-17

Table S4.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
3P GAIN CNV 2 0 16 2 2 8
3P GAIN WILD-TYPE 292 9 138 11 20 4

Figure S4.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 3.89e-21 (Chi-square test), Q value = 3.2e-18

Table S5.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
3Q GAIN CNV 3 1 34 2 3 9
3Q GAIN WILD-TYPE 291 8 120 11 19 3

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 4.57e-05 (Fisher's exact test), Q value = 0.031

Table S6.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
3Q GAIN CNV 30 7 7
3Q GAIN WILD-TYPE 116 82 148

Figure S6.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.4e-05 (Fisher's exact test), Q value = 0.017

Table S7.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
3Q GAIN CNV 6 9 37
3Q GAIN WILD-TYPE 21 213 209

Figure S7.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 2.39e-10 (Chi-square test), Q value = 1.9e-07

Table S8.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
5P GAIN CNV 3 0 29 0 2 0
5P GAIN WILD-TYPE 291 9 125 13 20 12

Figure S8.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.000169 (Fisher's exact test), Q value = 0.11

Table S9.  Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
5P GAIN CNV 20 4 3
5P GAIN WILD-TYPE 126 85 152

Figure S9.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.000251 (Chi-square test), Q value = 0.16

Table S10.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
5P GAIN CNV 21 1 3 3 5
5P GAIN WILD-TYPE 128 128 46 50 110

Figure S10.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.012

Table S11.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
5P GAIN CNV 2 3 28
5P GAIN WILD-TYPE 25 219 218

Figure S11.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 2.24e-20 (Chi-square test), Q value = 1.8e-17

Table S12.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
6P GAIN CNV 1 1 26 1 1 8
6P GAIN WILD-TYPE 293 8 128 12 21 4

Figure S12.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 3.4e-17 (Chi-square test), Q value = 2.8e-14

Table S13.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
6Q GAIN CNV 1 1 21 1 1 7
6Q GAIN WILD-TYPE 293 8 133 12 21 5

Figure S13.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 3.27e-14 (Chi-square test), Q value = 2.7e-11

Table S14.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
7P GAIN CNV 8 4 17 6 7 4
7P GAIN WILD-TYPE 286 5 137 7 15 8

Figure S14.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2.96e-15 (Chi-square test), Q value = 2.4e-12

Table S15.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
7Q GAIN CNV 11 5 13 6 7 4
7Q GAIN WILD-TYPE 283 4 141 7 15 8

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1.6e-19 (Chi-square test), Q value = 1.3e-16

Table S16.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
8P GAIN CNV 31 2 28 3 14 12
8P GAIN WILD-TYPE 263 7 126 10 8 0

Figure S16.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1.5e-20 (Chi-square test), Q value = 1.2e-17

Table S17.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
8Q GAIN CNV 32 3 56 3 15 12
8Q GAIN WILD-TYPE 262 6 98 10 7 0

Figure S17.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1.13e-06 (Chi-square test), Q value = 0.00084

Table S18.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
10P GAIN CNV 44 1 23 9 5 6
10P GAIN WILD-TYPE 250 8 131 4 17 6

Figure S18.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 9.33e-07 (Chi-square test), Q value = 7e-04

Table S19.  Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
10Q GAIN CNV 43 2 18 9 4 5
10Q GAIN WILD-TYPE 251 7 136 4 18 7

Figure S19.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 6.2e-06 (Chi-square test), Q value = 0.0045

Table S20.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
12P GAIN CNV 8 3 19 2 5 1
12P GAIN WILD-TYPE 286 6 135 11 17 11

Figure S20.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.000208 (Chi-square test), Q value = 0.14

Table S21.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
12Q GAIN CNV 8 2 11 2 5 1
12Q GAIN WILD-TYPE 286 7 143 11 17 11

Figure S21.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1.59e-06 (Chi-square test), Q value = 0.0012

Table S22.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
13Q GAIN CNV 1 0 18 1 0 1
13Q GAIN WILD-TYPE 293 9 136 12 22 11

Figure S22.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.000135 (Chi-square test), Q value = 0.09

Table S23.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
14Q GAIN CNV 3 0 15 0 2 2
14Q GAIN WILD-TYPE 291 9 139 13 20 10

Figure S23.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 8.54e-06 (Chi-square test), Q value = 0.0062

Table S24.  Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
15Q GAIN CNV 1 0 2 0 3 0
15Q GAIN WILD-TYPE 293 9 152 13 19 12

Figure S24.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.000298 (Chi-square test), Q value = 0.19

Table S25.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
17Q GAIN CNV 1 0 9 2 0 1
17Q GAIN WILD-TYPE 293 9 145 11 22 11

Figure S25.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 1.75e-13 (Chi-square test), Q value = 1.4e-10

Table S26.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
18P GAIN CNV 2 1 35 0 1 1
18P GAIN WILD-TYPE 292 8 119 13 21 11

Figure S26.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.000133 (Fisher's exact test), Q value = 0.089

Table S27.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
18P GAIN CNV 21 9 3
18P GAIN WILD-TYPE 125 80 152

Figure S27.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.000328 (Fisher's exact test), Q value = 0.21

Table S28.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
18P GAIN CNV 14 1 1
18P GAIN WILD-TYPE 35 35 32

Figure S28.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 1.97e-06 (Chi-square test), Q value = 0.0014

Table S29.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
18P GAIN CNV 26 1 5 5 3
18P GAIN WILD-TYPE 123 128 44 48 112

Figure S29.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.07e-09 (Fisher's exact test), Q value = 1.6e-06

Table S30.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
18P GAIN CNV 0 2 38
18P GAIN WILD-TYPE 27 220 208

Figure S30.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.35e-05 (Fisher's exact test), Q value = 0.057

Table S31.  Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
18P GAIN CNV 12 2 18 2
18P GAIN WILD-TYPE 87 136 92 23

Figure S31.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1.29e-05 (Chi-square test), Q value = 0.0092

Table S32.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
18Q GAIN CNV 2 1 17 0 0 1
18Q GAIN WILD-TYPE 292 8 137 13 22 11

Figure S32.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Chi-square test), Q value = 0.094

Table S33.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
18Q GAIN CNV 14 0 1 5 1
18Q GAIN WILD-TYPE 135 129 48 48 114

Figure S33.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.56e-05 (Fisher's exact test), Q value = 0.031

Table S34.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
18Q GAIN CNV 0 1 20
18Q GAIN WILD-TYPE 27 221 226

Figure S34.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 3.63e-14 (Chi-square test), Q value = 2.9e-11

Table S35.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
19P GAIN CNV 0 1 32 0 0 2
19P GAIN WILD-TYPE 294 8 122 13 22 10

Figure S35.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.000204 (Chi-square test), Q value = 0.13

Table S36.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
19P GAIN CNV 21 3 6 2 3
19P GAIN WILD-TYPE 128 126 43 51 112

Figure S36.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 3.46e-13 (Chi-square test), Q value = 2.8e-10

Table S37.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
19Q GAIN CNV 0 1 30 0 0 2
19Q GAIN WILD-TYPE 294 8 124 13 22 10

Figure S37.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.000106 (Chi-square test), Q value = 0.071

Table S38.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
19Q GAIN CNV 21 2 5 2 3
19Q GAIN WILD-TYPE 128 127 44 51 112

Figure S38.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.74e-05 (Fisher's exact test), Q value = 0.053

Table S39.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
19Q GAIN CNV 1 4 28
19Q GAIN WILD-TYPE 26 218 218

Figure S39.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 9.25e-25 (Chi-square test), Q value = 7.7e-22

Table S40.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
20P GAIN CNV 3 2 47 0 13 1
20P GAIN WILD-TYPE 291 7 107 13 9 11

Figure S40.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 4.83e-05 (Fisher's exact test), Q value = 0.033

Table S41.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
20P GAIN CNV 37 9 12
20P GAIN WILD-TYPE 109 80 143

Figure S41.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 9.79e-06 (Chi-square test), Q value = 0.007

Table S42.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
20P GAIN CNV 37 8 8 6 7
20P GAIN WILD-TYPE 112 121 41 47 108

Figure S42.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-07 (Fisher's exact test), Q value = 3e-04

Table S43.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
20P GAIN CNV 1 12 53
20P GAIN WILD-TYPE 26 210 193

Figure S43.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.14

Table S44.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
20P GAIN CNV 39 7 10
20P GAIN WILD-TYPE 130 108 78

Figure S44.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.72e-05 (Fisher's exact test), Q value = 0.032

Table S45.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
20P GAIN CNV 13 9 31 3
20P GAIN WILD-TYPE 86 129 79 22

Figure S45.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1.37e-29 (Chi-square test), Q value = 1.1e-26

Table S46.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
20Q GAIN CNV 3 2 57 0 14 1
20Q GAIN WILD-TYPE 291 7 97 13 8 11

Figure S46.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 6.66e-07 (Fisher's exact test), Q value = 5e-04

Table S47.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
20Q GAIN CNV 45 10 13
20Q GAIN WILD-TYPE 101 79 142

Figure S47.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.000315 (Fisher's exact test), Q value = 0.21

Table S48.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
20Q GAIN CNV 23 4 5
20Q GAIN WILD-TYPE 26 32 28

Figure S48.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000351 (Fisher's exact test), Q value = 0.23

Table S49.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
20Q GAIN CNV 22 6 4
20Q GAIN WILD-TYPE 24 30 32

Figure S49.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 2.89e-08 (Chi-square test), Q value = 2.2e-05

Table S50.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
20Q GAIN CNV 45 9 9 6 7
20Q GAIN WILD-TYPE 104 120 40 47 108

Figure S50.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.3e-09 (Fisher's exact test), Q value = 3.3e-06

Table S51.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
20Q GAIN CNV 1 13 62
20Q GAIN WILD-TYPE 26 209 184

Figure S51.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.4e-05 (Fisher's exact test), Q value = 0.017

Table S52.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
20Q GAIN CNV 46 8 12
20Q GAIN WILD-TYPE 123 107 76

Figure S52.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.96e-07 (Fisher's exact test), Q value = 0.00045

Table S53.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
20Q GAIN CNV 15 10 38 3
20Q GAIN WILD-TYPE 84 128 72 22

Figure S53.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1.4e-07 (Chi-square test), Q value = 0.00011

Table S54.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
21Q GAIN CNV 1 0 21 0 2 1
21Q GAIN WILD-TYPE 293 9 133 13 20 11

Figure S54.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.000202 (Chi-square test), Q value = 0.13

Table S55.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
22Q GAIN CNV 1 1 5 2 0 0
22Q GAIN WILD-TYPE 293 8 149 11 22 12

Figure S55.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'Xq gain' versus 'CN_CNMF'

P value = 0.00033 (Chi-square test), Q value = 0.21

Table S56.  Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
XQ GAIN CNV 0 0 11 0 1 1
XQ GAIN WILD-TYPE 294 9 143 13 21 11

Figure S56.  Get High-res Image Gene #40: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 4.08e-11 (Chi-square test), Q value = 3.2e-08

Table S57.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
1P LOSS CNV 0 1 6 4 1 0
1P LOSS WILD-TYPE 294 8 148 9 21 12

Figure S57.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1.22e-13 (Chi-square test), Q value = 9.8e-11

Table S58.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
3P LOSS CNV 0 0 31 0 2 0
3P LOSS WILD-TYPE 294 9 123 13 20 12

Figure S58.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 3.09e-05 (Fisher's exact test), Q value = 0.022

Table S59.  Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
3P LOSS CNV 21 6 2
3P LOSS WILD-TYPE 125 83 153

Figure S59.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.22e-05 (Fisher's exact test), Q value = 0.023

Table S60.  Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
3P LOSS CNV 1 3 27
3P LOSS WILD-TYPE 26 219 219

Figure S60.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 3.78e-05 (Chi-square test), Q value = 0.026

Table S61.  Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
3Q LOSS CNV 0 0 13 0 1 0
3Q LOSS WILD-TYPE 294 9 141 13 21 12

Figure S61.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1.19e-24 (Chi-square test), Q value = 9.9e-22

Table S62.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
4P LOSS CNV 2 2 57 4 2 0
4P LOSS WILD-TYPE 292 7 97 9 20 12

Figure S62.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 3.12e-10 (Fisher's exact test), Q value = 2.4e-07

Table S63.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
4P LOSS CNV 41 16 4
4P LOSS WILD-TYPE 105 73 151

Figure S63.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 6.92e-12 (Chi-square test), Q value = 5.5e-09

Table S64.  Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
4P LOSS CNV 45 5 4 7 4
4P LOSS WILD-TYPE 104 124 45 46 111

Figure S64.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.6e-10 (Fisher's exact test), Q value = 1.3e-07

Table S65.  Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
4P LOSS CNV 5 6 54
4P LOSS WILD-TYPE 22 216 192

Figure S65.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.82e-05 (Fisher's exact test), Q value = 0.066

Table S66.  Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
4P LOSS CNV 39 6 16
4P LOSS WILD-TYPE 130 109 72

Figure S66.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.67e-06 (Fisher's exact test), Q value = 0.0041

Table S67.  Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
4P LOSS CNV 21 7 30 3
4P LOSS WILD-TYPE 78 131 80 22

Figure S67.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 6.55e-25 (Chi-square test), Q value = 5.5e-22

Table S68.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
4Q LOSS CNV 1 2 56 4 2 0
4Q LOSS WILD-TYPE 293 7 98 9 20 12

Figure S68.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 3.05e-10 (Fisher's exact test), Q value = 2.4e-07

Table S69.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
4Q LOSS CNV 38 17 3
4Q LOSS WILD-TYPE 108 72 152

Figure S69.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 6.72e-07 (Chi-square test), Q value = 5e-04

Table S70.  Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
4Q LOSS CNV 38 7 5 7 6
4Q LOSS WILD-TYPE 111 122 44 46 109

Figure S70.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.34e-09 (Fisher's exact test), Q value = 3.4e-06

Table S71.  Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
4Q LOSS CNV 5 7 51
4Q LOSS WILD-TYPE 22 215 195

Figure S71.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000244 (Fisher's exact test), Q value = 0.16

Table S72.  Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
4Q LOSS CNV 37 6 15
4Q LOSS WILD-TYPE 132 109 73

Figure S72.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.56e-05 (Fisher's exact test), Q value = 0.025

Table S73.  Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
4Q LOSS CNV 22 7 26 3
4Q LOSS WILD-TYPE 77 131 84 22

Figure S73.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 2.52e-09 (Chi-square test), Q value = 2e-06

Table S74.  Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
5P LOSS CNV 0 2 21 1 4 0
5P LOSS WILD-TYPE 294 7 133 12 18 12

Figure S74.  Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 3.31e-17 (Chi-square test), Q value = 2.7e-14

Table S75.  Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
5Q LOSS CNV 0 1 40 1 5 0
5Q LOSS WILD-TYPE 294 8 114 12 17 12

Figure S75.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 2.94e-08 (Fisher's exact test), Q value = 2.3e-05

Table S76.  Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
5Q LOSS CNV 30 7 2
5Q LOSS WILD-TYPE 116 82 153

Figure S76.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 3.71e-05 (Chi-square test), Q value = 0.026

Table S77.  Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
5Q LOSS CNV 28 3 5 3 7
5Q LOSS WILD-TYPE 121 126 44 50 108

Figure S77.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.42e-07 (Fisher's exact test), Q value = 0.00041

Table S78.  Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
5Q LOSS CNV 2 5 39
5Q LOSS WILD-TYPE 25 217 207

Figure S78.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000106 (Fisher's exact test), Q value = 0.071

Table S79.  Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
5Q LOSS CNV 16 3 17 1
5Q LOSS WILD-TYPE 83 135 93 24

Figure S79.  Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 4.18e-05 (Chi-square test), Q value = 0.029

Table S80.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
6P LOSS CNV 0 1 7 2 0 0
6P LOSS WILD-TYPE 294 8 147 11 22 12

Figure S80.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 3.1e-05 (Chi-square test), Q value = 0.022

Table S81.  Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
6Q LOSS CNV 0 1 9 2 0 0
6Q LOSS WILD-TYPE 294 8 145 11 22 12

Figure S81.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 2.89e-09 (Chi-square test), Q value = 2.2e-06

Table S82.  Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
7P LOSS CNV 3 0 26 1 0 0
7P LOSS WILD-TYPE 291 9 128 12 22 12

Figure S82.  Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 4.6e-12 (Chi-square test), Q value = 3.7e-09

Table S83.  Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
7Q LOSS CNV 0 0 27 1 0 0
7Q LOSS WILD-TYPE 294 9 127 12 22 12

Figure S83.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 6.12e-05 (Fisher's exact test), Q value = 0.042

Table S84.  Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
7Q LOSS CNV 17 7 1
7Q LOSS WILD-TYPE 129 82 154

Figure S84.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 4.21e-06 (Chi-square test), Q value = 0.0031

Table S85.  Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
7Q LOSS CNV 21 2 3 1 1
7Q LOSS WILD-TYPE 128 127 46 52 114

Figure S85.  Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 4.17e-24 (Chi-square test), Q value = 3.5e-21

Table S86.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
8P LOSS CNV 2 2 52 0 0 0
8P LOSS WILD-TYPE 292 7 102 13 22 12

Figure S86.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 6.02e-11 (Fisher's exact test), Q value = 4.8e-08

Table S87.  Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
8P LOSS CNV 38 9 2
8P LOSS WILD-TYPE 108 80 153

Figure S87.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.5e-05 (Fisher's exact test), Q value = 0.011

Table S88.  Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
8P LOSS CNV 16 3 0
8P LOSS WILD-TYPE 30 33 36

Figure S88.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 1.36e-13 (Chi-square test), Q value = 1.1e-10

Table S89.  Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
8P LOSS CNV 41 1 5 2 4
8P LOSS WILD-TYPE 108 128 44 51 111

Figure S89.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.72e-14 (Fisher's exact test), Q value = 2.2e-11

Table S90.  Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
8P LOSS CNV 1 1 51
8P LOSS WILD-TYPE 26 221 195

Figure S90.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7.89e-07 (Fisher's exact test), Q value = 0.00059

Table S91.  Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
8P LOSS CNV 31 1 15
8P LOSS WILD-TYPE 138 114 73

Figure S91.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.32e-07 (Fisher's exact test), Q value = 1e-04

Table S92.  Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
8P LOSS CNV 19 2 24 2
8P LOSS WILD-TYPE 80 136 86 23

Figure S92.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1.27e-05 (Chi-square test), Q value = 0.0091

Table S93.  Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
8Q LOSS CNV 0 0 13 0 0 0
8Q LOSS WILD-TYPE 294 9 141 13 22 12

Figure S93.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.21

Table S94.  Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
8Q LOSS CNV 10 1 0
8Q LOSS WILD-TYPE 136 88 155

Figure S94.  Get High-res Image Gene #56: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 4.13e-30 (Chi-square test), Q value = 3.5e-27

Table S95.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
9P LOSS CNV 2 4 66 1 4 0
9P LOSS WILD-TYPE 292 5 88 12 18 12

Figure S95.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 3.22e-06 (Fisher's exact test), Q value = 0.0024

Table S96.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
9P LOSS CNV 37 19 9
9P LOSS WILD-TYPE 109 70 146

Figure S96.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1.14e-08 (Chi-square test), Q value = 8.8e-06

Table S97.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
9P LOSS CNV 46 11 6 6 6
9P LOSS WILD-TYPE 103 118 43 47 109

Figure S97.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.26e-07 (Fisher's exact test), Q value = 0.00069

Table S98.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
9P LOSS CNV 4 14 57
9P LOSS WILD-TYPE 23 208 189

Figure S98.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.029

Table S99.  Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
9Q LOSS CNV 0 0 7
9Q LOSS WILD-TYPE 19 19 8

Figure S99.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1.8e-37 (Chi-square test), Q value = 1.5e-34

Table S100.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
9Q LOSS CNV 3 4 80 1 5 0
9Q LOSS WILD-TYPE 291 5 74 12 17 12

Figure S100.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1.74e-06 (Fisher's exact test), Q value = 0.0013

Table S101.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
9Q LOSS CNV 45 22 13
9Q LOSS WILD-TYPE 101 67 142

Figure S101.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 4.13e-13 (Chi-square test), Q value = 3.3e-10

Table S102.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
9Q LOSS CNV 58 13 8 7 5
9Q LOSS WILD-TYPE 91 116 41 46 110

Figure S102.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.36e-07 (Fisher's exact test), Q value = 4e-04

Table S103.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
9Q LOSS CNV 5 19 67
9Q LOSS WILD-TYPE 22 203 179

Figure S103.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1.5e-09 (Chi-square test), Q value = 1.2e-06

Table S104.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
10P LOSS CNV 0 0 22 1 0 0
10P LOSS WILD-TYPE 294 9 132 12 22 12

Figure S104.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.000305 (Fisher's exact test), Q value = 0.2

Table S105.  Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
10P LOSS CNV 15 4 1
10P LOSS WILD-TYPE 131 85 154

Figure S105.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 3.48e-06 (Chi-square test), Q value = 0.0025

Table S106.  Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
10P LOSS CNV 18 1 2 1 0
10P LOSS WILD-TYPE 131 128 47 52 115

Figure S106.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 9.65e-09 (Chi-square test), Q value = 7.5e-06

Table S107.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
10Q LOSS CNV 1 0 22 1 0 0
10Q LOSS WILD-TYPE 293 9 132 12 22 12

Figure S107.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Chi-square test), Q value = 0.081

Table S108.  Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
10Q LOSS CNV 17 2 3 2 0
10Q LOSS WILD-TYPE 132 127 46 51 115

Figure S108.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1.71e-22 (Chi-square test), Q value = 1.4e-19

Table S109.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
11P LOSS CNV 1 0 49 4 1 0
11P LOSS WILD-TYPE 293 9 105 9 21 12

Figure S109.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1.49e-05 (Fisher's exact test), Q value = 0.011

Table S110.  Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
11P LOSS CNV 30 14 6
11P LOSS WILD-TYPE 116 75 149

Figure S110.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1.32e-07 (Chi-square test), Q value = 1e-04

Table S111.  Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
11P LOSS CNV 35 8 4 5 2
11P LOSS WILD-TYPE 114 121 45 48 113

Figure S111.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000139 (Fisher's exact test), Q value = 0.093

Table S112.  Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
11P LOSS CNV 2 11 41
11P LOSS WILD-TYPE 25 211 205

Figure S112.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-16 (Chi-square test), Q value = 8.2e-14

Table S113.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
11Q LOSS CNV 1 0 39 4 3 0
11Q LOSS WILD-TYPE 293 9 115 9 19 12

Figure S113.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 1.39e-06 (Chi-square test), Q value = 0.001

Table S114.  Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
11Q LOSS CNV 30 8 1 6 2
11Q LOSS WILD-TYPE 119 121 48 47 113

Figure S114.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 3.45e-11 (Chi-square test), Q value = 2.7e-08

Table S115.  Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
12P LOSS CNV 0 1 25 0 0 0
12P LOSS WILD-TYPE 294 8 129 13 22 12

Figure S115.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.048

Table S116.  Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
12P LOSS CNV 17 5 1
12P LOSS WILD-TYPE 129 84 154

Figure S116.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 1.53e-08 (Chi-square test), Q value = 1.2e-05

Table S117.  Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
12P LOSS CNV 22 1 1 0 1
12P LOSS WILD-TYPE 127 128 48 53 114

Figure S117.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000105 (Fisher's exact test), Q value = 0.071

Table S118.  Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
12P LOSS CNV 1 2 22
12P LOSS WILD-TYPE 26 220 224

Figure S118.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.14

Table S119.  Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
12P LOSS CNV 5 1 15 1
12P LOSS WILD-TYPE 94 137 95 24

Figure S119.  Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1.54e-08 (Chi-square test), Q value = 1.2e-05

Table S120.  Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
12Q LOSS CNV 0 0 19 0 0 0
12Q LOSS WILD-TYPE 294 9 135 13 22 12

Figure S120.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 4.3e-05 (Fisher's exact test), Q value = 0.03

Table S121.  Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
12Q LOSS CNV 14 3 0
12Q LOSS WILD-TYPE 132 86 155

Figure S121.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.04

Table S122.  Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
12Q LOSS CNV 11 0 0
12Q LOSS WILD-TYPE 35 36 36

Figure S122.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 3.5e-05 (Chi-square test), Q value = 0.025

Table S123.  Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
12Q LOSS CNV 15 0 1 1 1
12Q LOSS WILD-TYPE 134 129 48 52 114

Figure S123.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.87e-05 (Fisher's exact test), Q value = 0.013

Table S124.  Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
12Q LOSS CNV 0 0 18
12Q LOSS WILD-TYPE 27 222 228

Figure S124.  Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 3.89e-17 (Chi-square test), Q value = 3.2e-14

Table S125.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
13Q LOSS CNV 4 3 45 4 5 0
13Q LOSS WILD-TYPE 290 6 109 9 17 12

Figure S125.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 7.77e-05 (Fisher's exact test), Q value = 0.053

Table S126.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
13Q LOSS CNV 31 15 8
13Q LOSS WILD-TYPE 115 74 147

Figure S126.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 2.75e-05 (Chi-square test), Q value = 0.019

Table S127.  Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
13Q LOSS CNV 33 11 2 9 5
13Q LOSS WILD-TYPE 116 118 47 44 110

Figure S127.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.13

Table S128.  Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
13Q LOSS CNV 6 13 41
13Q LOSS WILD-TYPE 21 209 205

Figure S128.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 7.51e-17 (Chi-square test), Q value = 6.1e-14

Table S129.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
14Q LOSS CNV 0 0 37 4 2 0
14Q LOSS WILD-TYPE 294 9 117 9 20 12

Figure S129.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 8.34e-09 (Fisher's exact test), Q value = 6.5e-06

Table S130.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
14Q LOSS CNV 28 5 1
14Q LOSS WILD-TYPE 118 84 154

Figure S130.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1.24e-05 (Chi-square test), Q value = 0.0089

Table S131.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
14Q LOSS CNV 26 1 2 5 7
14Q LOSS WILD-TYPE 123 128 47 48 108

Figure S131.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.05e-11 (Fisher's exact test), Q value = 8.4e-09

Table S132.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
14Q LOSS CNV 2 0 39
14Q LOSS WILD-TYPE 25 222 207

Figure S132.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.6e-06 (Fisher's exact test), Q value = 0.0034

Table S133.  Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
14Q LOSS CNV 28 1 5
14Q LOSS WILD-TYPE 141 114 83

Figure S133.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0079

Table S134.  Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
14Q LOSS CNV 8 2 21 3
14Q LOSS WILD-TYPE 91 136 89 22

Figure S134.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000218 (Fisher's exact test), Q value = 0.14

Table S135.  Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 19 15
15Q LOSS CNV 0 0 6
15Q LOSS WILD-TYPE 19 19 9

Figure S135.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 6.8e-35 (Chi-square test), Q value = 5.7e-32

Table S136.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
15Q LOSS CNV 1 1 74 4 4 0
15Q LOSS WILD-TYPE 293 8 80 9 18 12

Figure S136.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 9.31e-12 (Fisher's exact test), Q value = 7.4e-09

Table S137.  Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
15Q LOSS CNV 50 18 6
15Q LOSS WILD-TYPE 96 71 149

Figure S137.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 2.61e-10 (Fisher's exact test), Q value = 2.1e-07

Table S138.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
15Q LOSS CNV 32 4 2
15Q LOSS WILD-TYPE 17 32 31

Figure S138.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.49e-07 (Fisher's exact test), Q value = 0.00034

Table S139.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
15Q LOSS CNV 27 9 2
15Q LOSS WILD-TYPE 19 27 34

Figure S139.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1.39e-14 (Chi-square test), Q value = 1.1e-11

Table S140.  Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
15Q LOSS CNV 55 7 9 7 4
15Q LOSS WILD-TYPE 94 122 40 46 111

Figure S140.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.72e-14 (Fisher's exact test), Q value = 3.8e-11

Table S141.  Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
15Q LOSS CNV 8 7 67
15Q LOSS WILD-TYPE 19 215 179

Figure S141.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.26e-06 (Fisher's exact test), Q value = 0.0024

Table S142.  Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
15Q LOSS CNV 49 7 17
15Q LOSS WILD-TYPE 120 108 71

Figure S142.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.96e-07 (Fisher's exact test), Q value = 0.00074

Table S143.  Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
15Q LOSS CNV 21 10 38 4
15Q LOSS WILD-TYPE 78 128 72 21

Figure S143.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1.54e-30 (Chi-square test), Q value = 1.3e-27

Table S144.  Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
16P LOSS CNV 1 1 66 2 3 0
16P LOSS WILD-TYPE 293 8 88 11 19 12

Figure S144.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1.86e-09 (Fisher's exact test), Q value = 1.5e-06

Table S145.  Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
16P LOSS CNV 40 19 5
16P LOSS WILD-TYPE 106 70 150

Figure S145.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 3.47e-08 (Fisher's exact test), Q value = 2.6e-05

Table S146.  Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
16P LOSS CNV 27 2 3
16P LOSS WILD-TYPE 22 34 30

Figure S146.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.34e-07 (Fisher's exact test), Q value = 7e-04

Table S147.  Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
16P LOSS CNV 25 4 3
16P LOSS WILD-TYPE 21 32 33

Figure S147.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 4.64e-12 (Chi-square test), Q value = 3.7e-09

Table S148.  Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
16P LOSS CNV 48 7 4 6 5
16P LOSS WILD-TYPE 101 122 45 47 110

Figure S148.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.35e-11 (Fisher's exact test), Q value = 5e-08

Table S149.  Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
16P LOSS CNV 5 7 58
16P LOSS WILD-TYPE 22 215 188

Figure S149.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.75e-05 (Fisher's exact test), Q value = 0.039

Table S150.  Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
16P LOSS CNV 40 6 17
16P LOSS WILD-TYPE 129 109 71

Figure S150.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.32e-06 (Fisher's exact test), Q value = 0.0053

Table S151.  Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
16P LOSS CNV 22 7 29 5
16P LOSS WILD-TYPE 77 131 81 20

Figure S151.  Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 7.72e-37 (Chi-square test), Q value = 6.5e-34

Table S152.  Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
16Q LOSS CNV 13 4 91 2 4 0
16Q LOSS WILD-TYPE 281 5 63 11 18 12

Figure S152.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 2.55e-11 (Fisher's exact test), Q value = 2e-08

Table S153.  Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
16Q LOSS CNV 59 27 12
16Q LOSS WILD-TYPE 87 62 143

Figure S153.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 8.89e-08 (Fisher's exact test), Q value = 6.8e-05

Table S154.  Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
16Q LOSS CNV 31 3 7
16Q LOSS WILD-TYPE 18 33 26

Figure S154.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.0013

Table S155.  Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
16Q LOSS CNV 29 6 6
16Q LOSS WILD-TYPE 17 30 30

Figure S155.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 9.45e-14 (Chi-square test), Q value = 7.6e-11

Table S156.  Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
16Q LOSS CNV 67 12 9 10 12
16Q LOSS WILD-TYPE 82 117 40 43 103

Figure S156.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.9e-10 (Fisher's exact test), Q value = 2.3e-07

Table S157.  Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
16Q LOSS CNV 5 21 84
16Q LOSS WILD-TYPE 22 201 162

Figure S157.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.014

Table S158.  Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
16Q LOSS CNV 59 13 24
16Q LOSS WILD-TYPE 110 102 64

Figure S158.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.46e-07 (Fisher's exact test), Q value = 0.00011

Table S159.  Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
16Q LOSS CNV 30 14 45 7
16Q LOSS WILD-TYPE 69 124 65 18

Figure S159.  Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 4.96e-54 (Chi-square test), Q value = 4.2e-51

Table S160.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
17P LOSS CNV 2 0 102 2 5 0
17P LOSS WILD-TYPE 292 9 52 11 17 12

Figure S160.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 2.17e-12 (Fisher's exact test), Q value = 1.7e-09

Table S161.  Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
17P LOSS CNV 63 20 12
17P LOSS WILD-TYPE 83 69 143

Figure S161.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 7.41e-06 (Fisher's exact test), Q value = 0.0053

Table S162.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 36 33
17P LOSS CNV 26 2 12
17P LOSS WILD-TYPE 23 34 21

Figure S162.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000104 (Fisher's exact test), Q value = 0.07

Table S163.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 36 36
17P LOSS CNV 26 5 9
17P LOSS WILD-TYPE 20 31 27

Figure S163.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 2.24e-18 (Chi-square test), Q value = 1.8e-15

Table S164.  Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
17P LOSS CNV 72 13 7 7 9
17P LOSS WILD-TYPE 77 116 42 46 106

Figure S164.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.22e-10 (Fisher's exact test), Q value = 2.5e-07

Table S165.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
17P LOSS CNV 6 20 82
17P LOSS WILD-TYPE 21 202 164

Figure S165.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.27e-05 (Fisher's exact test), Q value = 0.063

Table S166.  Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
17P LOSS CNV 59 15 19
17P LOSS WILD-TYPE 110 100 69

Figure S166.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.05e-06 (Fisher's exact test), Q value = 0.0015

Table S167.  Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
17P LOSS CNV 23 17 46 7
17P LOSS WILD-TYPE 76 121 64 18

Figure S167.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 8.27e-32 (Chi-square test), Q value = 6.9e-29

Table S168.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
17Q LOSS CNV 1 0 67 1 5 0
17Q LOSS WILD-TYPE 293 9 87 12 17 12

Figure S168.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 3.66e-05 (Fisher's exact test), Q value = 0.026

Table S169.  Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
17Q LOSS CNV 38 15 11
17Q LOSS WILD-TYPE 108 74 144

Figure S169.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1.74e-08 (Chi-square test), Q value = 1.3e-05

Table S170.  Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
17Q LOSS CNV 44 10 4 7 6
17Q LOSS WILD-TYPE 105 119 45 46 109

Figure S170.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.33e-05 (Fisher's exact test), Q value = 0.023

Table S171.  Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
17Q LOSS CNV 5 15 51
17Q LOSS WILD-TYPE 22 207 195

Figure S171.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1.73e-11 (Chi-square test), Q value = 1.4e-08

Table S172.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
18P LOSS CNV 1 1 25 3 6 0
18P LOSS WILD-TYPE 293 8 129 10 16 12

Figure S172.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 2.7e-16 (Chi-square test), Q value = 2.2e-13

Table S173.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
18Q LOSS CNV 1 1 39 3 6 0
18Q LOSS WILD-TYPE 293 8 115 10 16 12

Figure S173.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 4.81e-05 (Fisher's exact test), Q value = 0.033

Table S174.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
18Q LOSS CNV 29 9 6
18Q LOSS WILD-TYPE 117 80 149

Figure S174.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 5.35e-05 (Chi-square test), Q value = 0.037

Table S175.  Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
18Q LOSS CNV 29 6 4 6 4
18Q LOSS WILD-TYPE 120 123 45 47 111

Figure S175.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.68e-06 (Fisher's exact test), Q value = 0.0034

Table S176.  Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
18Q LOSS CNV 6 7 36
18Q LOSS WILD-TYPE 21 215 210

Figure S176.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 5.04e-12 (Chi-square test), Q value = 4e-09

Table S177.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
19P LOSS CNV 0 1 29 3 3 0
19P LOSS WILD-TYPE 294 8 125 10 19 12

Figure S177.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 2.01e-09 (Fisher's exact test), Q value = 1.6e-06

Table S178.  Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
19P LOSS CNV 28 3 1
19P LOSS WILD-TYPE 118 86 154

Figure S178.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1.35e-06 (Chi-square test), Q value = 0.001

Table S179.  Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
19P LOSS CNV 25 2 1 4 3
19P LOSS WILD-TYPE 124 127 48 49 112

Figure S179.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.52e-07 (Fisher's exact test), Q value = 0.00041

Table S180.  Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
19P LOSS CNV 2 2 31
19P LOSS WILD-TYPE 25 220 215

Figure S180.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.01

Table S181.  Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
19P LOSS CNV 27 2 3
19P LOSS WILD-TYPE 142 113 85

Figure S181.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.62e-08 (Fisher's exact test), Q value = 4.3e-05

Table S182.  Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
19P LOSS CNV 3 2 23 4
19P LOSS WILD-TYPE 96 136 87 21

Figure S182.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1.19e-08 (Chi-square test), Q value = 9.2e-06

Table S183.  Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
19Q LOSS CNV 1 1 22 3 2 0
19Q LOSS WILD-TYPE 293 8 132 10 20 12

Figure S183.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 7.23e-06 (Fisher's exact test), Q value = 0.0052

Table S184.  Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
19Q LOSS CNV 20 4 1
19Q LOSS WILD-TYPE 126 85 154

Figure S184.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 4.14e-05 (Chi-square test), Q value = 0.029

Table S185.  Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
19Q LOSS CNV 20 2 1 3 2
19Q LOSS WILD-TYPE 129 127 48 50 113

Figure S185.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.57e-05 (Fisher's exact test), Q value = 0.025

Table S186.  Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
19Q LOSS CNV 2 2 24
19Q LOSS WILD-TYPE 25 220 222

Figure S186.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000325 (Fisher's exact test), Q value = 0.21

Table S187.  Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
19Q LOSS CNV 21 2 2
19Q LOSS WILD-TYPE 148 113 86

Figure S187.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.31e-06 (Fisher's exact test), Q value = 0.0039

Table S188.  Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
19Q LOSS CNV 2 2 17 4
19Q LOSS WILD-TYPE 97 136 93 21

Figure S188.  Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 9.51e-06 (Chi-square test), Q value = 0.0068

Table S189.  Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
20P LOSS CNV 1 2 12 1 0 0
20P LOSS WILD-TYPE 293 7 142 12 22 12

Figure S189.  Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 3.09e-08 (Chi-square test), Q value = 2.4e-05

Table S190.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
21Q LOSS CNV 3 2 25 2 2 0
21Q LOSS WILD-TYPE 291 7 129 11 20 12

Figure S190.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.33e-05 (Fisher's exact test), Q value = 0.03

Table S191.  Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
21Q LOSS CNV 0 4 28
21Q LOSS WILD-TYPE 27 218 218

Figure S191.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000334 (Fisher's exact test), Q value = 0.22

Table S192.  Gene #78: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 169 115 88
21Q LOSS CNV 21 1 5
21Q LOSS WILD-TYPE 148 114 83

Figure S192.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000211 (Fisher's exact test), Q value = 0.14

Table S193.  Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 138 110 25
21Q LOSS CNV 9 1 14 3
21Q LOSS WILD-TYPE 90 137 96 22

Figure S193.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1.02e-37 (Chi-square test), Q value = 8.6e-35

Table S194.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
22Q LOSS CNV 1 1 79 3 6 0
22Q LOSS WILD-TYPE 293 8 75 10 16 12

Figure S194.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 2.01e-07 (Fisher's exact test), Q value = 0.00015

Table S195.  Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 89 155
22Q LOSS CNV 46 24 12
22Q LOSS WILD-TYPE 100 65 143

Figure S195.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 5.3e-11 (Chi-square test), Q value = 4.2e-08

Table S196.  Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 149 129 49 53 115
22Q LOSS CNV 53 15 9 8 3
22Q LOSS WILD-TYPE 96 114 40 45 112

Figure S196.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.82e-07 (Fisher's exact test), Q value = 0.00014

Table S197.  Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 222 246
22Q LOSS CNV 6 17 65
22Q LOSS WILD-TYPE 21 205 181

Figure S197.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Xq loss' versus 'CN_CNMF'

P value = 4.76e-06 (Chi-square test), Q value = 0.0035

Table S198.  Gene #80: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 294 9 154 13 22 12
XQ LOSS CNV 0 0 15 0 1 0
XQ LOSS WILD-TYPE 294 9 139 13 21 12

Figure S198.  Get High-res Image Gene #80: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 504

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

  • 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.

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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