Correlation between copy number variations of arm-level result and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C13F4MMH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Uterine Corpus Endometrioid Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13F4MMH
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 79 arm-level results and 10 molecular subtypes across 492 patients, 236 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 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',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

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

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

  • 19p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

  • 22q gain cnv correlated to 'METHLYATION_CNMF'.

  • Xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'CN_CNMF'.

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

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 6q loss cnv correlated to 'CN_CNMF'.

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

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

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

  • 8q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

  • 11q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

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

  • 19p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 20p loss cnv correlated to 'CN_CNMF'.

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

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

  • Xq loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 236 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
3p loss 0 (0%) 461 1.34e-14
(8.84e-12) 		0.000141
(0.0699) 		0.000526
(0.244) 		0.028
(1.00) 		1.79e-07
(0.000103) 		8.63e-08
(5.04e-05) 		4.21e-05
(0.0216) 		2.37e-05
(0.0124)
9q loss 0 (0%) 399 0.0015
(0.657) 		0.000248
(0.119) 		1.53e-37
(1.07e-34) 		5.86e-07
(0.000332) 		0.00601
(1.00) 		0.378
(1.00) 		2.56e-13
(1.68e-10) 		2.82e-16
(1.88e-13) 		2.09e-12
(1.36e-09) 		3.83e-10
(2.38e-07)
3q gain 0 (0%) 442 0.176
(1.00) 		0.0543
(1.00) 		3.41e-22
(2.34e-19) 		2.49e-05
(0.013) 		0.388
(1.00) 		0.301
(1.00) 		1.19e-06
(0.000666) 		5.14e-05
(0.0261) 		2.07e-05
(0.0109) 		0.000263
(0.126)
5p gain 0 (0%) 460 0.86
(1.00) 		0.623
(1.00) 		3.01e-09
(1.83e-06) 		0.000136
(0.0674) 		0.0311
(1.00) 		0.712
(1.00) 		3.95e-06
(0.00215) 		0.00042
(0.197) 		1.66e-05
(0.00884) 		5.29e-05
(0.0268)
18p gain 0 (0%) 455 0.0591
(1.00) 		0.133
(1.00) 		4.94e-14
(3.26e-11) 		6.64e-05
(0.0336) 		0.093
(1.00) 		0.429
(1.00) 		3.34e-05
(0.0173) 		7.28e-07
(0.000411) 		4.26e-09
(2.58e-06) 		6.47e-09
(3.9e-06)
4p loss 0 (0%) 426 0.0729
(1.00) 		0.0133
(1.00) 		4.79e-25
(3.3e-22) 		7.08e-11
(4.47e-08) 		0.0339
(1.00) 		0.393
(1.00) 		2.45e-09
(1.49e-06) 		1.29e-07
(7.48e-05) 		1.88e-13
(1.23e-10) 		4.44e-12
(2.88e-09)
4q loss 0 (0%) 428 0.683
(1.00) 		0.371
(1.00) 		1.36e-26
(9.39e-24) 		2.66e-11
(1.69e-08) 		0.131
(1.00) 		0.776
(1.00) 		2.64e-08
(1.57e-05) 		2.45e-08
(1.45e-05) 		1.04e-10
(6.55e-08) 		1.39e-10
(8.69e-08)
5q loss 0 (0%) 447 0.0729
(1.00) 		0.0133
(1.00) 		1.18e-18
(7.99e-16) 		7.26e-09
(4.37e-06) 		0.0481
(1.00) 		0.153
(1.00) 		6.28e-08
(3.69e-05) 		2.96e-08
(1.76e-05) 		2.83e-09
(1.72e-06) 		7.58e-08
(4.44e-05)
7q loss 0 (0%) 465 4.91e-14
(3.24e-11) 		0.00018
(0.0884) 		0.197
(1.00) 		0.0121
(1.00) 		1.32e-07
(7.64e-05) 		1.59e-06
(0.000886) 		1.77e-05
(0.00942) 		1.25e-05
(0.0067)
8p loss 0 (0%) 439 0.0191
(1.00) 		0.00403
(1.00) 		4.01e-24
(2.75e-21) 		1.08e-11
(6.92e-09) 		0.165
(1.00) 		0.181
(1.00) 		4.84e-12
(3.13e-09) 		6.9e-10
(4.28e-07) 		4.01e-15
(2.67e-12) 		7.17e-17
(4.82e-14)
9p loss 0 (0%) 416 0.0227
(1.00) 		0.00379
(1.00) 		2.63e-29
(1.82e-26) 		2.34e-06
(0.00129) 		0.0117
(1.00) 		0.244
(1.00) 		2.12e-12
(1.38e-09) 		7.6e-15
(5.04e-12) 		1.37e-09
(8.42e-07) 		1.19e-08
(7.13e-06)
11p loss 0 (0%) 439 1.44e-21
(9.89e-19) 		7.44e-07
(0.000419) 		0.182
(1.00) 		0.75
(1.00) 		4.46e-08
(2.63e-05) 		2.6e-07
(0.000149) 		1.99e-08
(1.18e-05) 		1.99e-06
(0.0011)
11q loss 0 (0%) 447 1.15e-15
(7.67e-13) 		7.53e-05
(0.0379) 		0.925
(1.00) 		0.713
(1.00) 		0.000397
(0.187) 		8.07e-06
(0.00436) 		2.54e-06
(0.0014) 		0.000184
(0.09)
13q loss 0 (0%) 432 0.683
(1.00) 		0.371
(1.00) 		2.43e-18
(1.64e-15) 		0.000113
(0.056) 		0.161
(1.00) 		0.393
(1.00) 		0.000395
(0.187) 		3.89e-06
(0.00212) 		7.27e-05
(0.0366) 		0.000188
(0.0919)
14q loss 0 (0%) 450 0.0191
(1.00) 		0.00403
(1.00) 		8.94e-17
(6e-14) 		1.48e-09
(9.03e-07) 		0.0847
(1.00) 		0.0052
(1.00) 		3.38e-08
(2e-05) 		1.95e-07
(0.000112) 		3.34e-09
(2.02e-06) 		9.82e-12
(6.33e-09)
15q loss 0 (0%) 411 0.00677
(1.00) 		0.00103
(0.456) 		4.68e-35
(3.25e-32) 		1.61e-13
(1.06e-10) 		0.00259
(1.00) 		0.267
(1.00) 		7.92e-10
(4.9e-07) 		1.07e-10
(6.71e-08) 		5.22e-15
(3.46e-12) 		1.07e-16
(7.19e-14)
16p loss 0 (0%) 423 0.0191
(1.00) 		0.00403
(1.00) 		2.82e-31
(1.95e-28) 		2.77e-09
(1.69e-06) 		0.193
(1.00) 		0.796
(1.00) 		7.52e-10
(4.65e-07) 		1.47e-09
(9.03e-07) 		1.47e-09
(9.03e-07) 		1.36e-10
(8.51e-08)
16q loss 0 (0%) 382 0.00686
(1.00) 		0.00173
(0.751) 		5.94e-40
(4.14e-37) 		2.86e-11
(1.82e-08) 		0.237
(1.00) 		1
(1.00) 		1.01e-11
(6.48e-09) 		2.34e-10
(1.46e-07) 		1.07e-11
(6.87e-09) 		1.9e-11
(1.22e-08)
17p loss 0 (0%) 387 0.00686
(1.00) 		0.00173
(0.751) 		8.66e-53
(6.05e-50) 		8.14e-13
(5.31e-10) 		0.000571
(0.263) 		0.665
(1.00) 		1.6e-20
(1.09e-17) 		2.15e-21
(1.47e-18) 		4.87e-17
(3.28e-14) 		2.92e-15
(1.95e-12)
17q loss 0 (0%) 424 0.0191
(1.00) 		0.00403
(1.00) 		1.48e-29
(1.02e-26) 		3.41e-05
(0.0176) 		0.0924
(1.00) 		0.612
(1.00) 		4.28e-09
(2.58e-06) 		1.95e-11
(1.24e-08) 		2.71e-07
(0.000156) 		5.5e-07
(0.000313)
18q loss 0 (0%) 443 9.75e-18
(6.57e-15) 		1.98e-06
(0.00109) 		0.725
(1.00) 		1
(1.00) 		3.87e-06
(0.00212) 		5.65e-07
(0.00032) 		3.04e-06
(0.00167) 		2.59e-07
(0.000149)
19p loss 0 (0%) 458 4.63e-12
(3e-09) 		1.07e-07
(6.19e-05) 		0.331
(1.00) 		1
(1.00) 		1.84e-05
(0.00979) 		7.84e-06
(0.00424) 		1.01e-05
(0.00546) 		6.41e-07
(0.000362)
22q loss 0 (0%) 405 0.0191
(1.00) 		0.00403
(1.00) 		1.41e-36
(9.78e-34) 		4.23e-08
(2.5e-05) 		0.0721
(1.00) 		1
(1.00) 		4.88e-11
(3.09e-08) 		3.29e-14
(2.17e-11) 		9.64e-11
(6.08e-08) 		1.01e-09
(6.24e-07)
13q gain 0 (0%) 472 9.55e-08
(5.56e-05) 		0.00556
(1.00) 		0.735
(1.00) 		0.367
(1.00) 		7.14e-05
(0.036) 		0.000462
(0.216) 		3.45e-05
(0.0178) 		4.23e-05
(0.0217)
19p gain 0 (0%) 461 0.0591
(1.00) 		0.0151
(1.00) 		2.4e-13
(1.57e-10) 		0.00429
(1.00) 		0.528
(1.00) 		0.151
(1.00) 		4.73e-06
(0.00257) 		1.84e-05
(0.00979) 		9.18e-07
(0.000515) 		3.24e-05
(0.0168)
19q gain 0 (0%) 464 4.28e-13
(2.8e-10) 		0.00147
(0.644) 		0.085
(1.00) 		1
(1.00) 		4.73e-06
(0.00257) 		1.59e-06
(0.000886) 		8.12e-07
(0.000456) 		2.17e-05
(0.0114)
20p gain 0 (0%) 427 0.176
(1.00) 		0.0543
(1.00) 		2.28e-18
(1.54e-15) 		3.47e-05
(0.0179) 		0.291
(1.00) 		1
(1.00) 		9.04e-05
(0.0454) 		0.0119
(1.00) 		1.84e-08
(1.1e-05) 		4.4e-07
(0.00025)
20q gain 0 (0%) 414 0.0591
(1.00) 		0.0151
(1.00) 		3.62e-24
(2.49e-21) 		8.6e-08
(5.03e-05) 		0.192
(1.00) 		0.58
(1.00) 		1.75e-06
(0.000967) 		0.000621
(0.285) 		1.63e-11
(1.05e-08) 		3.65e-10
(2.27e-07)
12p loss 0 (0%) 467 3.86e-11
(2.46e-08) 		0.000192
(0.0939) 		0.0577
(1.00) 		1
(1.00) 		3.62e-05
(0.0186) 		0.0057
(1.00) 		9.52e-08
(5.55e-05) 		4.34e-06
(0.00236)
1q gain 0 (0%) 354 0.111
(1.00) 		0.637
(1.00) 		3.04e-07
(0.000174) 		0.00534
(1.00) 		0.00123
(0.54) 		0.000715
(0.325) 		3.31e-06
(0.00182) 		9.23e-07
(0.000517) 		3.74e-07
(0.000213) 		0.0178
(1.00)
21q gain 0 (0%) 467 1.13e-08
(6.82e-06) 		0.0794
(1.00) 		0.237
(1.00) 		0.558
(1.00) 		0.000204
(0.0992) 		0.0095
(1.00) 		0.000414
(0.195) 		0.000375
(0.178)
10p loss 0 (0%) 469 0.176
(1.00) 		0.0543
(1.00) 		4e-11
(2.54e-08) 		0.000334
(0.159) 		0.474
(1.00) 		0.633
(1.00) 		0.000469
(0.218) 		0.0016
(0.696) 		1.25e-05
(0.0067) 		0.00108
(0.477)
10q loss 0 (0%) 468 2.94e-10
(1.83e-07) 		0.000192
(0.0939) 		0.451
(1.00) 		1
(1.00) 		0.000469
(0.218) 		0.0057
(1.00) 		0.000214
(0.104) 		0.00195
(0.841)
12q loss 0 (0%) 474 1.23e-09
(7.56e-07) 		0.0001
(0.0501) 		0.31
(1.00) 		0.429
(1.00) 		0.00106
(0.467) 		0.0067
(1.00) 		1.25e-06
(0.000698) 		1.67e-06
(0.000925)
8q gain 0 (0%) 374 0.00461
(1.00) 		0.0424
(1.00) 		1.65e-21
(1.13e-18) 		0.368
(1.00) 		0.00495
(1.00) 		1
(1.00) 		0.00591
(1.00) 		0.000299
(0.143) 		0.0018
(0.778) 		3.27e-05
(0.017)
18q gain 0 (0%) 472 0.176
(1.00) 		0.0543
(1.00) 		8.26e-06
(0.00445) 		0.00562
(1.00) 		1
(1.00) 		0.0173
(1.00) 		0.00565
(1.00) 		0.000111
(0.0553) 		0.000436
(0.205)
5p loss 0 (0%) 465 0.352
(1.00) 		0.133
(1.00) 		1.16e-10
(7.29e-08) 		0.000334
(0.159) 		0.162
(1.00) 		0.181
(1.00) 		0.000782
(0.353) 		0.000672
(0.307) 		0.000216
(0.105) 		0.00281
(1.00)
7p loss 0 (0%) 463 0.176
(1.00) 		0.0543
(1.00) 		9.88e-10
(6.09e-07) 		0.00656
(1.00) 		0.158
(1.00) 		0.201
(1.00) 		0.000162
(0.0798) 		2.27e-05
(0.0119) 		0.000783
(0.353) 		0.00338
(1.00)
8q loss 0 (0%) 480 2.23e-05
(0.0117) 		0.000955
(0.427) 		1
(1.00) 		0.0396
(1.00) 		0.154
(1.00) 		0.000302
(0.144) 		0.000443
(0.207)
18p loss 0 (0%) 456 3.15e-12
(2.05e-09) 		2.09e-05
(0.0111) 		0.326
(1.00) 		0.746
(1.00) 		0.00066
(0.302) 		0.000172
(0.0844) 		0.00472
(1.00) 		0.000594
(0.273)
19q loss 0 (0%) 464 1.79e-08
(1.07e-05) 		4.65e-05
(0.0237) 		0.734
(1.00) 		0.713
(1.00) 		0.000719
(0.326) 		0.00283
(1.00) 		0.000676
(0.308) 		1.46e-05
(0.00783)
21q loss 0 (0%) 460 0.0591
(1.00) 		0.0151
(1.00) 		6.47e-08
(3.8e-05) 		0.00252
(1.00) 		0.095
(1.00) 		0.75
(1.00) 		0.000148
(0.0732) 		0.00136
(0.598) 		0.00097
(0.432) 		4.43e-05
(0.0226)
Xq loss 0 (0%) 474 2.97e-07
(0.00017) 		0.000569
(0.263) 		0.617
(1.00) 		0.633
(1.00) 		0.016
(1.00) 		0.0067
(1.00) 		0.000233
(0.113) 		2.27e-05
(0.0119)
2p gain 0 (0%) 441 0.233
(1.00) 		0.298
(1.00) 		5.41e-11
(3.42e-08) 		0.0588
(1.00) 		0.177
(1.00) 		0.802
(1.00) 		0.238
(1.00) 		0.434
(1.00) 		0.0184
(1.00) 		0.162
(1.00)
2q gain 0 (0%) 452 0.518
(1.00) 		0.769
(1.00) 		4.83e-11
(3.06e-08) 		0.175
(1.00) 		0.0653
(1.00) 		0.575
(1.00) 		0.3
(1.00) 		0.624
(1.00) 		0.015
(1.00) 		0.117
(1.00)
3p gain 0 (0%) 464 4.15e-19
(2.82e-16) 		0.121
(1.00) 		0.525
(1.00) 		0.652
(1.00) 		0.0149
(1.00) 		0.0429
(1.00) 		0.338
(1.00) 		0.225
(1.00)
6p gain 0 (0%) 454 0.43
(1.00) 		0.243
(1.00) 		1.52e-16
(1.02e-13) 		0.0347
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.00665
(1.00) 		0.0075
(1.00) 		0.0121
(1.00) 		0.0302
(1.00)
6q gain 0 (0%) 462 0.43
(1.00) 		0.243
(1.00) 		1.58e-13
(1.04e-10) 		0.331
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.00839
(1.00) 		0.00793
(1.00) 		0.168
(1.00) 		0.278
(1.00)
7p gain 0 (0%) 449 1
(1.00) 		0.867
(1.00) 		8.62e-19
(5.85e-16) 		0.0118
(1.00) 		0.733
(1.00) 		0.217
(1.00) 		1
(1.00) 		0.475
(1.00) 		0.244
(1.00) 		0.609
(1.00)
7q gain 0 (0%) 449 0.944
(1.00) 		0.776
(1.00) 		2.4e-19
(1.63e-16) 		0.0244
(1.00) 		0.889
(1.00) 		0.0552
(1.00) 		0.385
(1.00) 		0.0331
(1.00) 		0.44
(1.00) 		0.425
(1.00)
8p gain 0 (0%) 406 0.395
(1.00) 		1
(1.00) 		7.48e-18
(5.05e-15) 		0.913
(1.00) 		0.133
(1.00) 		1
(1.00) 		0.474
(1.00) 		0.434
(1.00) 		0.38
(1.00) 		0.0022
(0.947)
10q gain 0 (0%) 413 0.0015
(0.657) 		0.0303
(1.00) 		9.34e-05
(0.0468) 		0.176
(1.00) 		0.388
(1.00) 		0.252
(1.00) 		0.0262
(1.00) 		0.256
(1.00) 		0.0128
(1.00) 		0.00257
(1.00)
12p gain 0 (0%) 455 0.815
(1.00) 		0.825
(1.00) 		4.78e-08
(2.82e-05) 		0.00909
(1.00) 		0.937
(1.00) 		1
(1.00) 		0.0455
(1.00) 		0.0906
(1.00) 		0.0241
(1.00) 		0.0169
(1.00)
12q gain 0 (0%) 464 0.815
(1.00) 		0.825
(1.00) 		3.68e-07
(0.00021) 		0.121
(1.00) 		0.901
(1.00) 		1
(1.00) 		0.0811
(1.00) 		0.227
(1.00) 		0.126
(1.00) 		0.311
(1.00)
14q gain 0 (0%) 472 1
(1.00) 		1
(1.00) 		2.16e-05
(0.0114) 		0.227
(1.00) 		0.239
(1.00) 		0.292
(1.00) 		0.401
(1.00) 		0.0737
(1.00) 		0.0486
(1.00) 		0.0281
(1.00)
17p gain 0 (0%) 485 2.6e-05
(0.0136) 		0.244
(1.00) 		1
(1.00) 		0.316
(1.00) 		0.315
(1.00) 		0.0701
(1.00) 		0.145
(1.00)
22q gain 0 (0%) 483 0.00473
(1.00) 		0.000537
(0.249) 		0.376
(1.00) 		0.115
(1.00) 		0.361
(1.00) 		0.00132
(0.581) 		0.00259
(1.00)
Xq gain 0 (0%) 480 0.000257
(0.123) 		0.322
(1.00) 		0.376
(1.00) 		0.157
(1.00) 		0.447
(1.00) 		0.00871
(1.00) 		0.0888
(1.00)
1p loss 0 (0%) 479 1.82e-08
(1.09e-05) 		0.000955
(0.427) 		1
(1.00) 		0.0403
(1.00) 		0.0884
(1.00) 		0.0517
(1.00) 		0.00318
(1.00)
3q loss 0 (0%) 480 4.31e-05
(0.022) 		0.0584
(1.00) 		0.024
(1.00) 		0.558
(1.00) 		0.00479
(1.00) 		0.00274
(1.00) 		0.0347
(1.00) 		0.0739
(1.00)
6q loss 0 (0%) 480 0.683
(1.00) 		0.371
(1.00) 		0.000236
(0.114) 		0.0354
(1.00) 		0.858
(1.00) 		0.558
(1.00) 		0.016
(1.00) 		0.0384
(1.00) 		0.133
(1.00) 		0.0103
(1.00)
20p loss 0 (0%) 477 0.000122
(0.0608) 		0.107
(1.00) 		0.243
(1.00) 		0.633
(1.00) 		0.0368
(1.00) 		0.0465
(1.00) 		0.00635
(1.00) 		0.0702
(1.00)
1p gain 0 (0%) 471 0.683
(1.00) 		0.184
(1.00) 		0.035
(1.00) 		0.661
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.182
(1.00) 		0.29
(1.00) 		0.00743
(1.00) 		0.0758
(1.00)
4p gain 0 (0%) 486 0.0039
(1.00) 		0.125
(1.00) 		0.14
(1.00) 		0.0396
(1.00) 		0.154
(1.00) 		0.0229
(1.00) 		0.0281
(1.00)
5q gain 0 (0%) 483 0.00286
(1.00) 		0.423
(1.00) 		1
(1.00) 		0.0679
(1.00) 		0.286
(1.00) 		0.052
(1.00) 		0.203
(1.00)
9p gain 0 (0%) 478 0.0484
(1.00) 		0.0786
(1.00) 		1
(1.00) 		0.822
(1.00) 		0.0787
(1.00) 		0.0699
(1.00) 		0.0294
(1.00)
9q gain 0 (0%) 488 0.352
(1.00) 		0.363
(1.00) 		0.781
(1.00) 		0.361
(1.00) 		0.387
(1.00) 		0.127
(1.00)
10p gain 0 (0%) 405 0.00355
(1.00) 		0.064
(1.00) 		0.0007
(0.318) 		0.204
(1.00) 		0.284
(1.00) 		0.136
(1.00) 		0.0155
(1.00) 		0.255
(1.00) 		0.0639
(1.00) 		0.0178
(1.00)
11p gain 0 (0%) 484 0.176
(1.00) 		0.0543
(1.00) 		0.0099
(1.00) 		0.0373
(1.00) 		0.109
(1.00) 		1
(1.00) 		0.157
(1.00) 		0.447
(1.00) 		0.13
(1.00) 		0.238
(1.00)
11q gain 0 (0%) 484 0.0111
(1.00) 		0.462
(1.00) 		0.109
(1.00) 		0.299
(1.00) 		0.194
(1.00) 		0.396
(1.00) 		0.242
(1.00) 		0.361
(1.00)
15q gain 0 (0%) 486 0.00416
(1.00) 		0.846
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.699
(1.00) 		0.884
(1.00) 		1
(1.00)
16p gain 0 (0%) 480 0.000794
(0.357) 		0.0313
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.0679
(1.00) 		0.0787
(1.00) 		0.0831
(1.00) 		0.336
(1.00)
16q gain 0 (0%) 488 0.046
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.861
(1.00)
17q gain 0 (0%) 479 0.000727
(0.329) 		0.00357
(1.00) 		0.0531
(1.00) 		1
(1.00) 		0.0276
(1.00) 		0.284
(1.00) 		0.00887
(1.00) 		0.011
(1.00)
1q loss 0 (0%) 488 0.0365
(1.00) 		0.0574
(1.00) 		0.115
(1.00) 		0.361
(1.00) 		0.0991
(1.00) 		0.127
(1.00)
2p loss 0 (0%) 486 0.019
(1.00) 		0.518
(1.00) 		0.14
(1.00) 		0.157
(1.00) 		0.0878
(1.00) 		0.773
(1.00) 		0.199
(1.00)
2q loss 0 (0%) 484 0.00637
(1.00) 		0.199
(1.00) 		0.14
(1.00) 		0.157
(1.00) 		0.0878
(1.00) 		0.493
(1.00) 		0.192
(1.00)
6p loss 0 (0%) 482 0.683
(1.00) 		0.371
(1.00) 		0.000862
(0.386) 		0.0962
(1.00) 		0.858
(1.00) 		0.558
(1.00) 		0.194
(1.00) 		0.249
(1.00) 		0.172
(1.00) 		0.0171
(1.00)
20q loss 0 (0%) 485 0.0106
(1.00) 		0.054
(1.00) 		0.528
(1.00) 		0.391
(1.00) 		0.474
(1.00) 		0.164
(1.00) 		0.078
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 3.04e-07 (Chi-square test), Q value = 0.00017

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
1Q GAIN CNV 85 18 21 8 6
1Q GAIN WILD-TYPE 205 22 118 9 0

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 3.31e-06 (Fisher's exact test), Q value = 0.0018

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
1Q GAIN CNV 24 26 51
1Q GAIN WILD-TYPE 118 81 62

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.23e-07 (Fisher's exact test), Q value = 0.00052

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
1Q GAIN CNV 26 24 31 20
1Q GAIN WILD-TYPE 39 68 34 120

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 3.74e-07 (Fisher's exact test), Q value = 0.00021

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
1Q GAIN CNV 41 35 62
1Q GAIN WILD-TYPE 166 109 70

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

'2p gain' versus 'CN_CNMF'

P value = 5.41e-11 (Chi-square test), Q value = 3.4e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
2P GAIN CNV 9 14 22 5 1
2P GAIN WILD-TYPE 281 26 117 12 5

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

'2q gain' versus 'CN_CNMF'

P value = 4.83e-11 (Chi-square test), Q value = 3.1e-08

Table S6.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
2Q GAIN CNV 6 13 16 4 1
2Q GAIN WILD-TYPE 284 27 123 13 5

Figure S6.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 4.15e-19 (Chi-square test), Q value = 2.8e-16

Table S7.  Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
3P GAIN CNV 1 4 13 9 1
3P GAIN WILD-TYPE 289 36 126 8 5

Figure S7.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 3.41e-22 (Chi-square test), Q value = 2.3e-19

Table S8.  Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
3Q GAIN CNV 2 5 31 11 1
3Q GAIN WILD-TYPE 288 35 108 6 5

Figure S8.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 2.49e-05 (Fisher's exact test), Q value = 0.013

Table S9.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
3Q GAIN CNV 29 6 6
3Q GAIN WILD-TYPE 114 79 143

Figure S9.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00067

Table S10.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
3Q GAIN CNV 26 6 1
3Q GAIN WILD-TYPE 116 101 112

Figure S10.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.14e-05 (Fisher's exact test), Q value = 0.026

Table S11.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
3Q GAIN CNV 0 3 7 23
3Q GAIN WILD-TYPE 65 89 58 117

Figure S11.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 2.07e-05 (Fisher's exact test), Q value = 0.011

Table S12.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
3Q GAIN CNV 37 7 6
3Q GAIN WILD-TYPE 170 137 126

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000263 (Fisher's exact test), Q value = 0.13

Table S13.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
3Q GAIN CNV 9 5 4 32
3Q GAIN WILD-TYPE 184 74 23 152

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 3.01e-09 (Chi-square test), Q value = 1.8e-06

Table S14.  Gene #8: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
5P GAIN CNV 3 2 25 1 1
5P GAIN WILD-TYPE 287 38 114 16 5

Figure S14.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.000136 (Fisher's exact test), Q value = 0.067

Table S15.  Gene #8: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
5P GAIN CNV 20 3 3
5P GAIN WILD-TYPE 123 82 146

Figure S15.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 3.95e-06 (Fisher's exact test), Q value = 0.0022

Table S16.  Gene #8: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
5P GAIN CNV 19 0 3
5P GAIN WILD-TYPE 123 107 110

Figure S16.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.2

Table S17.  Gene #8: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
5P GAIN CNV 2 0 3 17
5P GAIN WILD-TYPE 63 92 62 123

Figure S17.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.0088

Table S18.  Gene #8: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
5P GAIN CNV 25 1 5
5P GAIN WILD-TYPE 182 143 127

Figure S18.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.29e-05 (Fisher's exact test), Q value = 0.027

Table S19.  Gene #8: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
5P GAIN CNV 3 3 1 24
5P GAIN WILD-TYPE 190 76 26 160

Figure S19.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1.52e-16 (Chi-square test), Q value = 1e-13

Table S20.  Gene #10: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
6P GAIN CNV 1 3 25 8 1
6P GAIN WILD-TYPE 289 37 114 9 5

Figure S20.  Get High-res Image Gene #10: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 1.58e-13 (Chi-square test), Q value = 1e-10

Table S21.  Gene #11: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
6Q GAIN CNV 1 3 18 7 1
6Q GAIN WILD-TYPE 289 37 121 10 5

Figure S21.  Get High-res Image Gene #11: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 8.62e-19 (Chi-square test), Q value = 5.9e-16

Table S22.  Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
7P GAIN CNV 5 17 14 6 1
7P GAIN WILD-TYPE 285 23 125 11 5

Figure S22.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 2.4e-19 (Chi-square test), Q value = 1.6e-16

Table S23.  Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
7Q GAIN CNV 8 17 10 7 1
7Q GAIN WILD-TYPE 282 23 129 10 5

Figure S23.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 7.48e-18 (Chi-square test), Q value = 5.1e-15

Table S24.  Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
8P GAIN CNV 28 16 25 15 2
8P GAIN WILD-TYPE 262 24 114 2 4

Figure S24.  Get High-res Image Gene #14: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1.65e-21 (Chi-square test), Q value = 1.1e-18

Table S25.  Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
8Q GAIN CNV 29 19 51 16 3
8Q GAIN WILD-TYPE 261 21 88 1 3

Figure S25.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000299 (Fisher's exact test), Q value = 0.14

Table S26.  Gene #15: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
8Q GAIN CNV 10 12 9 47
8Q GAIN WILD-TYPE 55 80 56 93

Figure S26.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.27e-05 (Fisher's exact test), Q value = 0.017

Table S27.  Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
8Q GAIN CNV 28 17 13 57
8Q GAIN WILD-TYPE 165 62 14 127

Figure S27.  Get High-res Image Gene #15: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 9.34e-05 (Chi-square test), Q value = 0.047

Table S28.  Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
10Q GAIN CNV 44 12 13 7 3
10Q GAIN WILD-TYPE 246 28 126 10 3

Figure S28.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 4.78e-08 (Chi-square test), Q value = 2.8e-05

Table S29.  Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
12P GAIN CNV 7 7 19 1 3
12P GAIN WILD-TYPE 283 33 120 16 3

Figure S29.  Get High-res Image Gene #22: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 3.68e-07 (Chi-square test), Q value = 0.00021

Table S30.  Gene #23: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
12Q GAIN CNV 7 6 11 1 3
12Q GAIN WILD-TYPE 283 34 128 16 3

Figure S30.  Get High-res Image Gene #23: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 9.55e-08 (Chi-square test), Q value = 5.6e-05

Table S31.  Gene #24: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
13Q GAIN CNV 1 0 17 1 1
13Q GAIN WILD-TYPE 289 40 122 16 5

Figure S31.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 7.14e-05 (Fisher's exact test), Q value = 0.036

Table S32.  Gene #24: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
13Q GAIN CNV 13 1 0
13Q GAIN WILD-TYPE 129 106 113

Figure S32.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000462 (Fisher's exact test), Q value = 0.22

Table S33.  Gene #24: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
13Q GAIN CNV 0 1 0 13
13Q GAIN WILD-TYPE 65 91 65 127

Figure S33.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 3.45e-05 (Fisher's exact test), Q value = 0.018

Table S34.  Gene #24: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
13Q GAIN CNV 18 2 0
13Q GAIN WILD-TYPE 189 142 132

Figure S34.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.23e-05 (Fisher's exact test), Q value = 0.022

Table S35.  Gene #24: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
13Q GAIN CNV 2 0 0 18
13Q GAIN WILD-TYPE 191 79 27 166

Figure S35.  Get High-res Image Gene #24: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 2.16e-05 (Chi-square test), Q value = 0.011

Table S36.  Gene #25: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
14Q GAIN CNV 2 2 13 3 0
14Q GAIN WILD-TYPE 288 38 126 14 6

Figure S36.  Get High-res Image Gene #25: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 2.6e-05 (Chi-square test), Q value = 0.014

Table S37.  Gene #29: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
17P GAIN CNV 1 0 3 2 1
17P GAIN WILD-TYPE 289 40 136 15 5

Figure S37.  Get High-res Image Gene #29: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 4.94e-14 (Chi-square test), Q value = 3.3e-11

Table S38.  Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
18P GAIN CNV 2 2 32 1 0
18P GAIN WILD-TYPE 288 38 107 16 6

Figure S38.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 6.64e-05 (Fisher's exact test), Q value = 0.034

Table S39.  Gene #31: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
18P GAIN CNV 20 8 2
18P GAIN WILD-TYPE 123 77 147

Figure S39.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.017

Table S40.  Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
18P GAIN CNV 18 2 1
18P GAIN WILD-TYPE 124 105 112

Figure S40.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.28e-07 (Fisher's exact test), Q value = 0.00041

Table S41.  Gene #31: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
18P GAIN CNV 0 1 0 20
18P GAIN WILD-TYPE 65 91 65 120

Figure S41.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 4.26e-09 (Fisher's exact test), Q value = 2.6e-06

Table S42.  Gene #31: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
18P GAIN CNV 33 1 3
18P GAIN WILD-TYPE 174 143 129

Figure S42.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.47e-09 (Fisher's exact test), Q value = 3.9e-06

Table S43.  Gene #31: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
18P GAIN CNV 2 3 0 32
18P GAIN WILD-TYPE 191 76 27 152

Figure S43.  Get High-res Image Gene #31: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 8.26e-06 (Chi-square test), Q value = 0.0045

Table S44.  Gene #32: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
18Q GAIN CNV 2 1 16 1 0
18Q GAIN WILD-TYPE 288 39 123 16 6

Figure S44.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.055

Table S45.  Gene #32: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
18Q GAIN CNV 17 0 3
18Q GAIN WILD-TYPE 190 144 129

Figure S45.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000436 (Fisher's exact test), Q value = 0.2

Table S46.  Gene #32: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
18Q GAIN CNV 1 3 0 16
18Q GAIN WILD-TYPE 192 76 27 168

Figure S46.  Get High-res Image Gene #32: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 2.4e-13 (Chi-square test), Q value = 1.6e-10

Table S47.  Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
19P GAIN CNV 0 1 27 3 0
19P GAIN WILD-TYPE 290 39 112 14 6

Figure S47.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 4.73e-06 (Fisher's exact test), Q value = 0.0026

Table S48.  Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
19P GAIN CNV 16 1 0
19P GAIN WILD-TYPE 126 106 113

Figure S48.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.84e-05 (Fisher's exact test), Q value = 0.0098

Table S49.  Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
19P GAIN CNV 0 0 1 16
19P GAIN WILD-TYPE 65 92 64 124

Figure S49.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 9.18e-07 (Fisher's exact test), Q value = 0.00052

Table S50.  Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
19P GAIN CNV 27 3 1
19P GAIN WILD-TYPE 180 141 131

Figure S50.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.017

Table S51.  Gene #33: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
19P GAIN CNV 4 1 2 24
19P GAIN WILD-TYPE 189 78 25 160

Figure S51.  Get High-res Image Gene #33: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 4.28e-13 (Chi-square test), Q value = 2.8e-10

Table S52.  Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
19Q GAIN CNV 0 0 25 3 0
19Q GAIN WILD-TYPE 290 40 114 14 6

Figure S52.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 4.73e-06 (Fisher's exact test), Q value = 0.0026

Table S53.  Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
19Q GAIN CNV 16 1 0
19Q GAIN WILD-TYPE 126 106 113

Figure S53.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.59e-06 (Fisher's exact test), Q value = 0.00089

Table S54.  Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
19Q GAIN CNV 0 0 0 17
19Q GAIN WILD-TYPE 65 92 65 123

Figure S54.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 8.12e-07 (Fisher's exact test), Q value = 0.00046

Table S55.  Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
19Q GAIN CNV 25 2 1
19Q GAIN WILD-TYPE 182 142 131

Figure S55.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.011

Table S56.  Gene #34: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
19Q GAIN CNV 3 1 1 23
19Q GAIN WILD-TYPE 190 78 26 161

Figure S56.  Get High-res Image Gene #34: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 2.28e-18 (Chi-square test), Q value = 1.5e-15

Table S57.  Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
20P GAIN CNV 4 13 43 3 2
20P GAIN WILD-TYPE 286 27 96 14 4

Figure S57.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 3.47e-05 (Fisher's exact test), Q value = 0.018

Table S58.  Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
20P GAIN CNV 37 9 11
20P GAIN WILD-TYPE 106 76 138

Figure S58.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 9.04e-05 (Fisher's exact test), Q value = 0.045

Table S59.  Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
20P GAIN CNV 27 5 5
20P GAIN WILD-TYPE 115 102 108

Figure S59.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1.84e-08 (Fisher's exact test), Q value = 1.1e-05

Table S60.  Gene #35: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
20P GAIN CNV 50 7 8
20P GAIN WILD-TYPE 157 137 124

Figure S60.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.4e-07 (Fisher's exact test), Q value = 0.00025

Table S61.  Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
20P GAIN CNV 11 10 0 44
20P GAIN WILD-TYPE 182 69 27 140

Figure S61.  Get High-res Image Gene #35: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 3.62e-24 (Chi-square test), Q value = 2.5e-21

Table S62.  Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
20Q GAIN CNV 4 15 54 3 2
20Q GAIN WILD-TYPE 286 25 85 14 4

Figure S62.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 8.6e-08 (Fisher's exact test), Q value = 5e-05

Table S63.  Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
20Q GAIN CNV 47 10 12
20Q GAIN WILD-TYPE 96 75 137

Figure S63.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.75e-06 (Fisher's exact test), Q value = 0.00097

Table S64.  Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
20Q GAIN CNV 32 5 5
20Q GAIN WILD-TYPE 110 102 108

Figure S64.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1.63e-11 (Fisher's exact test), Q value = 1e-08

Table S65.  Gene #36: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
20Q GAIN CNV 61 8 8
20Q GAIN WILD-TYPE 146 136 124

Figure S65.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.65e-10 (Fisher's exact test), Q value = 2.3e-07

Table S66.  Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
20Q GAIN CNV 12 10 0 55
20Q GAIN WILD-TYPE 181 69 27 129

Figure S66.  Get High-res Image Gene #36: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1.13e-08 (Chi-square test), Q value = 6.8e-06

Table S67.  Gene #37: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
21Q GAIN CNV 1 2 21 1 0
21Q GAIN WILD-TYPE 289 38 118 16 6

Figure S67.  Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.099

Table S68.  Gene #37: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
21Q GAIN CNV 12 1 0
21Q GAIN WILD-TYPE 130 106 113

Figure S68.  Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.000414 (Fisher's exact test), Q value = 0.19

Table S69.  Gene #37: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
21Q GAIN CNV 20 4 1
21Q GAIN WILD-TYPE 187 140 131

Figure S69.  Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000375 (Fisher's exact test), Q value = 0.18

Table S70.  Gene #37: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
21Q GAIN CNV 4 1 0 20
21Q GAIN WILD-TYPE 189 78 27 164

Figure S70.  Get High-res Image Gene #37: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.000537 (Fisher's exact test), Q value = 0.25

Table S71.  Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
22Q GAIN CNV 8 0 0
22Q GAIN WILD-TYPE 135 85 149

Figure S71.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Xq gain' versus 'CN_CNMF'

P value = 0.000257 (Chi-square test), Q value = 0.12

Table S72.  Gene #39: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
XQ GAIN CNV 0 1 10 1 0
XQ GAIN WILD-TYPE 290 39 129 16 6

Figure S72.  Get High-res Image Gene #39: 'Xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1.82e-08 (Chi-square test), Q value = 1.1e-05

Table S73.  Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
1P LOSS CNV 0 4 7 0 2
1P LOSS WILD-TYPE 290 36 132 17 4

Figure S73.  Get High-res Image Gene #40: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1.34e-14 (Chi-square test), Q value = 8.8e-12

Table S74.  Gene #44: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
3P LOSS CNV 0 2 29 0 0
3P LOSS WILD-TYPE 290 38 110 17 6

Figure S74.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.000141 (Fisher's exact test), Q value = 0.07

Table S75.  Gene #44: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
3P LOSS CNV 19 6 2
3P LOSS WILD-TYPE 124 79 147

Figure S75.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.000526 (Chi-square test), Q value = 0.24

Table S76.  Gene #44: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 37 39 12 41 24
3P LOSS CNV 1 7 0 0 0 1
3P LOSS WILD-TYPE 40 30 39 12 41 23

Figure S76.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1.79e-07 (Fisher's exact test), Q value = 1e-04

Table S77.  Gene #44: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
3P LOSS CNV 19 1 0
3P LOSS WILD-TYPE 123 106 113

Figure S77.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.63e-08 (Fisher's exact test), Q value = 5e-05

Table S78.  Gene #44: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
3P LOSS CNV 0 0 0 20
3P LOSS WILD-TYPE 65 92 65 120

Figure S78.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 4.21e-05 (Fisher's exact test), Q value = 0.022

Table S79.  Gene #44: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
3P LOSS CNV 24 2 3
3P LOSS WILD-TYPE 183 142 129

Figure S79.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.37e-05 (Fisher's exact test), Q value = 0.012

Table S80.  Gene #44: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
3P LOSS CNV 2 3 1 23
3P LOSS WILD-TYPE 191 76 26 161

Figure S80.  Get High-res Image Gene #44: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 4.31e-05 (Chi-square test), Q value = 0.022

Table S81.  Gene #45: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
3Q LOSS CNV 0 1 11 0 0
3Q LOSS WILD-TYPE 290 39 128 17 6

Figure S81.  Get High-res Image Gene #45: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 4.79e-25 (Chi-square test), Q value = 3.3e-22

Table S82.  Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
4P LOSS CNV 2 8 54 1 1
4P LOSS WILD-TYPE 288 32 85 16 5

Figure S82.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 7.08e-11 (Fisher's exact test), Q value = 4.5e-08

Table S83.  Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
4P LOSS CNV 41 15 3
4P LOSS WILD-TYPE 102 70 146

Figure S83.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 2.45e-09 (Fisher's exact test), Q value = 1.5e-06

Table S84.  Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
4P LOSS CNV 30 1 3
4P LOSS WILD-TYPE 112 106 110

Figure S84.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.29e-07 (Fisher's exact test), Q value = 7.5e-05

Table S85.  Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
4P LOSS CNV 2 1 2 29
4P LOSS WILD-TYPE 63 91 63 111

Figure S85.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1.88e-13 (Fisher's exact test), Q value = 1.2e-10

Table S86.  Gene #46: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
4P LOSS CNV 55 4 5
4P LOSS WILD-TYPE 152 140 127

Figure S86.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.44e-12 (Fisher's exact test), Q value = 2.9e-09

Table S87.  Gene #46: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
4P LOSS CNV 4 7 4 49
4P LOSS WILD-TYPE 189 72 23 135

Figure S87.  Get High-res Image Gene #46: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1.36e-26 (Chi-square test), Q value = 9.4e-24

Table S88.  Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
4Q LOSS CNV 1 8 54 0 1
4Q LOSS WILD-TYPE 289 32 85 17 5

Figure S88.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 2.66e-11 (Fisher's exact test), Q value = 1.7e-08

Table S89.  Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
4Q LOSS CNV 39 16 2
4Q LOSS WILD-TYPE 104 69 147

Figure S89.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 2.64e-08 (Fisher's exact test), Q value = 1.6e-05

Table S90.  Gene #47: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
4Q LOSS CNV 27 0 5
4Q LOSS WILD-TYPE 115 107 108

Figure S90.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.45e-08 (Fisher's exact test), Q value = 1.5e-05

Table S91.  Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
4Q LOSS CNV 2 0 2 28
4Q LOSS WILD-TYPE 63 92 63 112

Figure S91.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.04e-10 (Fisher's exact test), Q value = 6.6e-08

Table S92.  Gene #47: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
4Q LOSS CNV 51 6 5
4Q LOSS WILD-TYPE 156 138 127

Figure S92.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.39e-10 (Fisher's exact test), Q value = 8.7e-08

Table S93.  Gene #47: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
4Q LOSS CNV 5 6 5 46
4Q LOSS WILD-TYPE 188 73 22 138

Figure S93.  Get High-res Image Gene #47: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1.16e-10 (Chi-square test), Q value = 7.3e-08

Table S94.  Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
5P LOSS CNV 0 8 19 0 0
5P LOSS WILD-TYPE 290 32 120 17 6

Figure S94.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.000334 (Fisher's exact test), Q value = 0.16

Table S95.  Gene #48: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
5P LOSS CNV 15 4 1
5P LOSS WILD-TYPE 128 81 148

Figure S95.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.000216 (Fisher's exact test), Q value = 0.1

Table S96.  Gene #48: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
5P LOSS CNV 22 3 2
5P LOSS WILD-TYPE 185 141 130

Figure S96.  Get High-res Image Gene #48: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 1.18e-18 (Chi-square test), Q value = 8e-16

Table S97.  Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
5Q LOSS CNV 0 7 38 0 0
5Q LOSS WILD-TYPE 290 33 101 17 6

Figure S97.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 7.26e-09 (Fisher's exact test), Q value = 4.4e-06

Table S98.  Gene #49: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
5Q LOSS CNV 29 6 1
5Q LOSS WILD-TYPE 114 79 148

Figure S98.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 6.28e-08 (Fisher's exact test), Q value = 3.7e-05

Table S99.  Gene #49: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
5Q LOSS CNV 25 1 2
5Q LOSS WILD-TYPE 117 106 111

Figure S99.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.96e-08 (Fisher's exact test), Q value = 1.8e-05

Table S100.  Gene #49: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
5Q LOSS CNV 0 0 3 25
5Q LOSS WILD-TYPE 65 92 62 115

Figure S100.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 2.83e-09 (Fisher's exact test), Q value = 1.7e-06

Table S101.  Gene #49: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
5Q LOSS CNV 38 4 2
5Q LOSS WILD-TYPE 169 140 130

Figure S101.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.58e-08 (Fisher's exact test), Q value = 4.4e-05

Table S102.  Gene #49: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
5Q LOSS CNV 4 4 1 35
5Q LOSS WILD-TYPE 189 75 26 149

Figure S102.  Get High-res Image Gene #49: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.000236 (Chi-square test), Q value = 0.11

Table S103.  Gene #51: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
6Q LOSS CNV 0 3 9 0 0
6Q LOSS WILD-TYPE 290 37 130 17 6

Figure S103.  Get High-res Image Gene #51: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 9.88e-10 (Chi-square test), Q value = 6.1e-07

Table S104.  Gene #52: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
7P LOSS CNV 3 1 24 0 1
7P LOSS WILD-TYPE 287 39 115 17 5

Figure S104.  Get High-res Image Gene #52: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.08

Table S105.  Gene #52: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
7P LOSS CNV 18 2 2
7P LOSS WILD-TYPE 124 105 111

Figure S105.  Get High-res Image Gene #52: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.012

Table S106.  Gene #52: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
7P LOSS CNV 2 0 1 19
7P LOSS WILD-TYPE 63 92 64 121

Figure S106.  Get High-res Image Gene #52: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 4.91e-14 (Chi-square test), Q value = 3.2e-11

Table S107.  Gene #53: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
7Q LOSS CNV 0 0 26 0 1
7Q LOSS WILD-TYPE 290 40 113 17 5

Figure S107.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.088

Table S108.  Gene #53: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
7Q LOSS CNV 16 6 1
7Q LOSS WILD-TYPE 127 79 148

Figure S108.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 1.32e-07 (Fisher's exact test), Q value = 7.6e-05

Table S109.  Gene #53: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
7Q LOSS CNV 17 0 0
7Q LOSS WILD-TYPE 125 107 113

Figure S109.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.59e-06 (Fisher's exact test), Q value = 0.00089

Table S110.  Gene #53: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
7Q LOSS CNV 0 0 0 17
7Q LOSS WILD-TYPE 65 92 65 123

Figure S110.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 1.77e-05 (Fisher's exact test), Q value = 0.0094

Table S111.  Gene #53: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
7Q LOSS CNV 23 3 1
7Q LOSS WILD-TYPE 184 141 131

Figure S111.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.0067

Table S112.  Gene #53: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
7Q LOSS CNV 3 1 0 23
7Q LOSS WILD-TYPE 190 78 27 161

Figure S112.  Get High-res Image Gene #53: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 4.01e-24 (Chi-square test), Q value = 2.8e-21

Table S113.  Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
8P LOSS CNV 2 1 48 2 0
8P LOSS WILD-TYPE 288 39 91 15 6

Figure S113.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1.08e-11 (Fisher's exact test), Q value = 6.9e-09

Table S114.  Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
8P LOSS CNV 37 8 1
8P LOSS WILD-TYPE 106 77 148

Figure S114.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 4.84e-12 (Fisher's exact test), Q value = 3.1e-09

Table S115.  Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
8P LOSS CNV 30 0 1
8P LOSS WILD-TYPE 112 107 112

Figure S115.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.9e-10 (Fisher's exact test), Q value = 4.3e-07

Table S116.  Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
8P LOSS CNV 1 0 1 29
8P LOSS WILD-TYPE 64 92 64 111

Figure S116.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 4.01e-15 (Fisher's exact test), Q value = 2.7e-12

Table S117.  Gene #54: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
8P LOSS CNV 47 1 2
8P LOSS WILD-TYPE 160 143 130

Figure S117.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.17e-17 (Fisher's exact test), Q value = 4.8e-14

Table S118.  Gene #54: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
8P LOSS CNV 1 2 0 47
8P LOSS WILD-TYPE 192 77 27 137

Figure S118.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 2.23e-05 (Chi-square test), Q value = 0.012

Table S119.  Gene #55: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
8Q LOSS CNV 0 0 11 1 0
8Q LOSS WILD-TYPE 290 40 128 16 6

Figure S119.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.000302 (Fisher's exact test), Q value = 0.14

Table S120.  Gene #55: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
8Q LOSS CNV 11 0 0
8Q LOSS WILD-TYPE 196 144 132

Figure S120.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000443 (Fisher's exact test), Q value = 0.21

Table S121.  Gene #55: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
8Q LOSS CNV 0 0 0 11
8Q LOSS WILD-TYPE 193 79 27 173

Figure S121.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 2.63e-29 (Chi-square test), Q value = 1.8e-26

Table S122.  Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
9P LOSS CNV 2 11 61 2 0
9P LOSS WILD-TYPE 288 29 78 15 6

Figure S122.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 2.34e-06 (Fisher's exact test), Q value = 0.0013

Table S123.  Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
9P LOSS CNV 36 19 8
9P LOSS WILD-TYPE 107 66 141

Figure S123.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 2.12e-12 (Fisher's exact test), Q value = 1.4e-09

Table S124.  Gene #56: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
9P LOSS CNV 41 3 3
9P LOSS WILD-TYPE 101 104 110

Figure S124.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.6e-15 (Fisher's exact test), Q value = 5e-12

Table S125.  Gene #56: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
9P LOSS CNV 0 1 3 43
9P LOSS WILD-TYPE 65 91 62 97

Figure S125.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1.37e-09 (Fisher's exact test), Q value = 8.4e-07

Table S126.  Gene #56: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
9P LOSS CNV 55 15 4
9P LOSS WILD-TYPE 152 129 128

Figure S126.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.19e-08 (Fisher's exact test), Q value = 7.1e-06

Table S127.  Gene #56: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
9P LOSS CNV 14 4 4 52
9P LOSS WILD-TYPE 179 75 23 132

Figure S127.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.000248 (Fisher's exact test), Q value = 0.12

Table S128.  Gene #57: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 15 18
9Q LOSS CNV 0 0 7
9Q LOSS WILD-TYPE 20 15 11

Figure S128.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1.53e-37 (Chi-square test), Q value = 1.1e-34

Table S129.  Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
9Q LOSS CNV 3 13 75 1 1
9Q LOSS WILD-TYPE 287 27 64 16 5

Figure S129.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 5.86e-07 (Fisher's exact test), Q value = 0.00033

Table S130.  Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
9Q LOSS CNV 46 21 12
9Q LOSS WILD-TYPE 97 64 137

Figure S130.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 2.56e-13 (Fisher's exact test), Q value = 1.7e-10

Table S131.  Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
9Q LOSS CNV 48 4 5
9Q LOSS WILD-TYPE 94 103 108

Figure S131.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.82e-16 (Fisher's exact test), Q value = 1.9e-13

Table S132.  Gene #57: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
9Q LOSS CNV 0 2 5 50
9Q LOSS WILD-TYPE 65 90 60 90

Figure S132.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 2.09e-12 (Fisher's exact test), Q value = 1.4e-09

Table S133.  Gene #57: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
9Q LOSS CNV 69 16 6
9Q LOSS WILD-TYPE 138 128 126

Figure S133.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.83e-10 (Fisher's exact test), Q value = 2.4e-07

Table S134.  Gene #57: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
9Q LOSS CNV 15 8 6 62
9Q LOSS WILD-TYPE 178 71 21 122

Figure S134.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 4e-11 (Chi-square test), Q value = 2.5e-08

Table S135.  Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
10P LOSS CNV 0 1 22 0 0
10P LOSS WILD-TYPE 290 39 117 17 6

Figure S135.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.000334 (Fisher's exact test), Q value = 0.16

Table S136.  Gene #58: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
10P LOSS CNV 15 4 1
10P LOSS WILD-TYPE 128 81 148

Figure S136.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.000469 (Fisher's exact test), Q value = 0.22

Table S137.  Gene #58: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
10P LOSS CNV 11 1 0
10P LOSS WILD-TYPE 131 106 113

Figure S137.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 1.25e-05 (Fisher's exact test), Q value = 0.0067

Table S138.  Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
10P LOSS CNV 20 1 1
10P LOSS WILD-TYPE 187 143 131

Figure S138.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 2.94e-10 (Chi-square test), Q value = 1.8e-07

Table S139.  Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
10Q LOSS CNV 1 1 22 0 0
10Q LOSS WILD-TYPE 289 39 117 17 6

Figure S139.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.094

Table S140.  Gene #59: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
10Q LOSS CNV 16 5 1
10Q LOSS WILD-TYPE 127 80 148

Figure S140.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.000469 (Fisher's exact test), Q value = 0.22

Table S141.  Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
10Q LOSS CNV 11 1 0
10Q LOSS WILD-TYPE 131 106 113

Figure S141.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.1

Table S142.  Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
10Q LOSS CNV 20 2 2
10Q LOSS WILD-TYPE 187 142 130

Figure S142.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1.44e-21 (Chi-square test), Q value = 9.9e-19

Table S143.  Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
11P LOSS CNV 1 4 45 1 2
11P LOSS WILD-TYPE 289 36 94 16 4

Figure S143.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 7.44e-07 (Fisher's exact test), Q value = 0.00042

Table S144.  Gene #60: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
11P LOSS CNV 31 13 4
11P LOSS WILD-TYPE 112 72 145

Figure S144.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 4.46e-08 (Fisher's exact test), Q value = 2.6e-05

Table S145.  Gene #60: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
11P LOSS CNV 24 0 3
11P LOSS WILD-TYPE 118 107 110

Figure S145.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.6e-07 (Fisher's exact test), Q value = 0.00015

Table S146.  Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
11P LOSS CNV 1 0 2 24
11P LOSS WILD-TYPE 64 92 63 116

Figure S146.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1.99e-08 (Fisher's exact test), Q value = 1.2e-05

Table S147.  Gene #60: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
11P LOSS CNV 42 7 3
11P LOSS WILD-TYPE 165 137 129

Figure S147.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-06 (Fisher's exact test), Q value = 0.0011

Table S148.  Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
11P LOSS CNV 7 5 3 37
11P LOSS WILD-TYPE 186 74 24 147

Figure S148.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1.15e-15 (Chi-square test), Q value = 7.7e-13

Table S149.  Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
11Q LOSS CNV 1 6 35 1 2
11Q LOSS WILD-TYPE 289 34 104 16 4

Figure S149.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 7.53e-05 (Fisher's exact test), Q value = 0.038

Table S150.  Gene #61: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
11Q LOSS CNV 26 12 5
11Q LOSS WILD-TYPE 117 73 144

Figure S150.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.000397 (Fisher's exact test), Q value = 0.19

Table S151.  Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
11Q LOSS CNV 17 2 2
11Q LOSS WILD-TYPE 125 105 111

Figure S151.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.07e-06 (Fisher's exact test), Q value = 0.0044

Table S152.  Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
11Q LOSS CNV 1 0 1 19
11Q LOSS WILD-TYPE 64 92 64 121

Figure S152.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 2.54e-06 (Fisher's exact test), Q value = 0.0014

Table S153.  Gene #61: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
11Q LOSS CNV 35 7 3
11Q LOSS WILD-TYPE 172 137 129

Figure S153.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.09

Table S154.  Gene #61: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
11Q LOSS CNV 8 4 2 31
11Q LOSS WILD-TYPE 185 75 25 153

Figure S154.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 3.86e-11 (Chi-square test), Q value = 2.5e-08

Table S155.  Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
12P LOSS CNV 0 2 23 0 0
12P LOSS WILD-TYPE 290 38 116 17 6

Figure S155.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.094

Table S156.  Gene #62: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
12P LOSS CNV 16 5 1
12P LOSS WILD-TYPE 127 80 148

Figure S156.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 3.62e-05 (Fisher's exact test), Q value = 0.019

Table S157.  Gene #62: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
12P LOSS CNV 12 0 0
12P LOSS WILD-TYPE 130 107 113

Figure S157.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 9.52e-08 (Fisher's exact test), Q value = 5.6e-05

Table S158.  Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
12P LOSS CNV 23 1 0
12P LOSS WILD-TYPE 184 143 132

Figure S158.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.34e-06 (Fisher's exact test), Q value = 0.0024

Table S159.  Gene #62: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
12P LOSS CNV 1 1 1 21
12P LOSS WILD-TYPE 192 78 26 163

Figure S159.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1.23e-09 (Chi-square test), Q value = 7.6e-07

Table S160.  Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
12Q LOSS CNV 0 0 18 0 0
12Q LOSS WILD-TYPE 290 40 121 17 6

Figure S160.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.05

Table S161.  Gene #63: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
12Q LOSS CNV 13 3 0
12Q LOSS WILD-TYPE 130 82 149

Figure S161.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 1.25e-06 (Fisher's exact test), Q value = 7e-04

Table S162.  Gene #63: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
12Q LOSS CNV 17 0 0
12Q LOSS WILD-TYPE 190 144 132

Figure S162.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.67e-06 (Fisher's exact test), Q value = 0.00092

Table S163.  Gene #63: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
12Q LOSS CNV 0 0 0 17
12Q LOSS WILD-TYPE 193 79 27 167

Figure S163.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 2.43e-18 (Chi-square test), Q value = 1.6e-15

Table S164.  Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
13Q LOSS CNV 5 15 39 0 1
13Q LOSS WILD-TYPE 285 25 100 17 5

Figure S164.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.056

Table S165.  Gene #64: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
13Q LOSS CNV 31 14 8
13Q LOSS WILD-TYPE 112 71 141

Figure S165.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.000395 (Fisher's exact test), Q value = 0.19

Table S166.  Gene #64: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
13Q LOSS CNV 23 3 6
13Q LOSS WILD-TYPE 119 104 107

Figure S166.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.89e-06 (Fisher's exact test), Q value = 0.0021

Table S167.  Gene #64: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
13Q LOSS CNV 3 1 2 26
13Q LOSS WILD-TYPE 62 91 63 114

Figure S167.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 7.27e-05 (Fisher's exact test), Q value = 0.037

Table S168.  Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
13Q LOSS CNV 41 10 8
13Q LOSS WILD-TYPE 166 134 124

Figure S168.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000188 (Fisher's exact test), Q value = 0.092

Table S169.  Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
13Q LOSS CNV 11 7 6 35
13Q LOSS WILD-TYPE 182 72 21 149

Figure S169.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 8.94e-17 (Chi-square test), Q value = 6e-14

Table S170.  Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
14Q LOSS CNV 0 4 35 1 2
14Q LOSS WILD-TYPE 290 36 104 16 4

Figure S170.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1.48e-09 (Fisher's exact test), Q value = 9e-07

Table S171.  Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
14Q LOSS CNV 27 5 0
14Q LOSS WILD-TYPE 116 80 149

Figure S171.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 3.38e-08 (Fisher's exact test), Q value = 2e-05

Table S172.  Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
14Q LOSS CNV 23 0 2
14Q LOSS WILD-TYPE 119 107 111

Figure S172.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.95e-07 (Fisher's exact test), Q value = 0.00011

Table S173.  Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
14Q LOSS CNV 1 0 1 23
14Q LOSS WILD-TYPE 64 92 64 117

Figure S173.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 3.34e-09 (Fisher's exact test), Q value = 2e-06

Table S174.  Gene #65: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
14Q LOSS CNV 35 1 4
14Q LOSS WILD-TYPE 172 143 128

Figure S174.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.82e-12 (Fisher's exact test), Q value = 6.3e-09

Table S175.  Gene #65: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
14Q LOSS CNV 0 4 1 35
14Q LOSS WILD-TYPE 193 75 26 149

Figure S175.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 4.68e-35 (Chi-square test), Q value = 3.2e-32

Table S176.  Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
15Q LOSS CNV 1 10 67 0 3
15Q LOSS WILD-TYPE 289 30 72 17 3

Figure S176.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1.61e-13 (Fisher's exact test), Q value = 1.1e-10

Table S177.  Gene #66: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
15Q LOSS CNV 51 16 4
15Q LOSS WILD-TYPE 92 69 145

Figure S177.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 7.92e-10 (Fisher's exact test), Q value = 4.9e-07

Table S178.  Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
15Q LOSS CNV 36 2 5
15Q LOSS WILD-TYPE 106 105 108

Figure S178.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-10 (Fisher's exact test), Q value = 6.7e-08

Table S179.  Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
15Q LOSS CNV 1 1 4 37
15Q LOSS WILD-TYPE 64 91 61 103

Figure S179.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 5.22e-15 (Fisher's exact test), Q value = 3.5e-12

Table S180.  Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
15Q LOSS CNV 66 7 6
15Q LOSS WILD-TYPE 141 137 126

Figure S180.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.07e-16 (Fisher's exact test), Q value = 7.2e-14

Table S181.  Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
15Q LOSS CNV 4 8 6 61
15Q LOSS WILD-TYPE 189 71 21 123

Figure S181.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 2.82e-31 (Chi-square test), Q value = 2e-28

Table S182.  Gene #67: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
16P LOSS CNV 2 6 61 0 0
16P LOSS WILD-TYPE 288 34 78 17 6

Figure S182.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 2.77e-09 (Fisher's exact test), Q value = 1.7e-06

Table S183.  Gene #67: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
16P LOSS CNV 38 17 4
16P LOSS WILD-TYPE 105 68 145

Figure S183.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 7.52e-10 (Fisher's exact test), Q value = 4.7e-07

Table S184.  Gene #67: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
16P LOSS CNV 35 2 4
16P LOSS WILD-TYPE 107 105 109

Figure S184.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.47e-09 (Fisher's exact test), Q value = 9e-07

Table S185.  Gene #67: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
16P LOSS CNV 3 1 2 35
16P LOSS WILD-TYPE 62 91 63 105

Figure S185.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1.47e-09 (Fisher's exact test), Q value = 9e-07

Table S186.  Gene #67: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
16P LOSS CNV 52 6 8
16P LOSS WILD-TYPE 155 138 124

Figure S186.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.36e-10 (Fisher's exact test), Q value = 8.5e-08

Table S187.  Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
16P LOSS CNV 6 7 4 49
16P LOSS WILD-TYPE 187 72 23 135

Figure S187.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 5.94e-40 (Chi-square test), Q value = 4.1e-37

Table S188.  Gene #68: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
16Q LOSS CNV 13 10 87 0 0
16Q LOSS WILD-TYPE 277 30 52 17 6

Figure S188.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 2.86e-11 (Fisher's exact test), Q value = 1.8e-08

Table S189.  Gene #68: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
16Q LOSS CNV 58 25 11
16Q LOSS WILD-TYPE 85 60 138

Figure S189.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1.01e-11 (Fisher's exact test), Q value = 6.5e-09

Table S190.  Gene #68: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
16Q LOSS CNV 54 6 11
16Q LOSS WILD-TYPE 88 101 102

Figure S190.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.34e-10 (Fisher's exact test), Q value = 1.5e-07

Table S191.  Gene #68: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
16Q LOSS CNV 9 4 6 52
16Q LOSS WILD-TYPE 56 88 59 88

Figure S191.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1.07e-11 (Fisher's exact test), Q value = 6.9e-09

Table S192.  Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
16Q LOSS CNV 77 12 17
16Q LOSS WILD-TYPE 130 132 115

Figure S192.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.9e-11 (Fisher's exact test), Q value = 1.2e-08

Table S193.  Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
16Q LOSS CNV 18 11 5 72
16Q LOSS WILD-TYPE 175 68 22 112

Figure S193.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 8.66e-53 (Chi-square test), Q value = 6e-50

Table S194.  Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
17P LOSS CNV 3 9 93 0 0
17P LOSS WILD-TYPE 287 31 46 17 6

Figure S194.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 8.14e-13 (Fisher's exact test), Q value = 5.3e-10

Table S195.  Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
17P LOSS CNV 61 18 10
17P LOSS WILD-TYPE 82 67 139

Figure S195.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1.6e-20 (Fisher's exact test), Q value = 1.1e-17

Table S196.  Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
17P LOSS CNV 58 2 4
17P LOSS WILD-TYPE 84 105 109

Figure S196.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.15e-21 (Fisher's exact test), Q value = 1.5e-18

Table S197.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
17P LOSS CNV 1 0 5 58
17P LOSS WILD-TYPE 64 92 60 82

Figure S197.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 4.87e-17 (Fisher's exact test), Q value = 3.3e-14

Table S198.  Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
17P LOSS CNV 81 15 6
17P LOSS WILD-TYPE 126 129 126

Figure S198.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.92e-15 (Fisher's exact test), Q value = 1.9e-12

Table S199.  Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
17P LOSS CNV 15 7 5 75
17P LOSS WILD-TYPE 178 72 22 109

Figure S199.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1.48e-29 (Chi-square test), Q value = 1e-26

Table S200.  Gene #70: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
17Q LOSS CNV 1 9 58 0 0
17Q LOSS WILD-TYPE 289 31 81 17 6

Figure S200.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 3.41e-05 (Fisher's exact test), Q value = 0.018

Table S201.  Gene #70: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
17Q LOSS CNV 35 14 9
17Q LOSS WILD-TYPE 108 71 140

Figure S201.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 4.28e-09 (Fisher's exact test), Q value = 2.6e-06

Table S202.  Gene #70: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
17Q LOSS CNV 33 2 4
17Q LOSS WILD-TYPE 109 105 109

Figure S202.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.95e-11 (Fisher's exact test), Q value = 1.2e-08

Table S203.  Gene #70: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
17Q LOSS CNV 1 0 3 35
17Q LOSS WILD-TYPE 64 92 62 105

Figure S203.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 2.71e-07 (Fisher's exact test), Q value = 0.00016

Table S204.  Gene #70: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
17Q LOSS CNV 48 11 6
17Q LOSS WILD-TYPE 159 133 126

Figure S204.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.5e-07 (Fisher's exact test), Q value = 0.00031

Table S205.  Gene #70: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
17Q LOSS CNV 11 5 5 44
17Q LOSS WILD-TYPE 182 74 22 140

Figure S205.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 3.15e-12 (Chi-square test), Q value = 2e-09

Table S206.  Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
18P LOSS CNV 1 9 25 0 1
18P LOSS WILD-TYPE 289 31 114 17 5

Figure S206.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 2.09e-05 (Fisher's exact test), Q value = 0.011

Table S207.  Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
18P LOSS CNV 22 6 2
18P LOSS WILD-TYPE 121 79 147

Figure S207.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000172 (Fisher's exact test), Q value = 0.084

Table S208.  Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
18P LOSS CNV 1 0 4 17
18P LOSS WILD-TYPE 64 92 61 123

Figure S208.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 9.75e-18 (Chi-square test), Q value = 6.6e-15

Table S209.  Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
18Q LOSS CNV 1 9 38 0 1
18Q LOSS WILD-TYPE 289 31 101 17 5

Figure S209.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1.98e-06 (Fisher's exact test), Q value = 0.0011

Table S210.  Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
18Q LOSS CNV 30 10 4
18Q LOSS WILD-TYPE 113 75 145

Figure S210.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 3.87e-06 (Fisher's exact test), Q value = 0.0021

Table S211.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
18Q LOSS CNV 23 1 4
18Q LOSS WILD-TYPE 119 106 109

Figure S211.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.65e-07 (Fisher's exact test), Q value = 0.00032

Table S212.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
18Q LOSS CNV 1 0 3 24
18Q LOSS WILD-TYPE 64 92 62 116

Figure S212.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 3.04e-06 (Fisher's exact test), Q value = 0.0017

Table S213.  Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
18Q LOSS CNV 37 5 6
18Q LOSS WILD-TYPE 170 139 126

Figure S213.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.59e-07 (Fisher's exact test), Q value = 0.00015

Table S214.  Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
18Q LOSS CNV 4 6 6 32
18Q LOSS WILD-TYPE 189 73 21 152

Figure S214.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 4.63e-12 (Chi-square test), Q value = 3e-09

Table S215.  Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
19P LOSS CNV 0 7 26 1 0
19P LOSS WILD-TYPE 290 33 113 16 6

Figure S215.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1.07e-07 (Fisher's exact test), Q value = 6.2e-05

Table S216.  Gene #73: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
19P LOSS CNV 25 4 1
19P LOSS WILD-TYPE 118 81 148

Figure S216.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1.84e-05 (Fisher's exact test), Q value = 0.0098

Table S217.  Gene #73: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
19P LOSS CNV 16 0 2
19P LOSS WILD-TYPE 126 107 111

Figure S217.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.84e-06 (Fisher's exact test), Q value = 0.0042

Table S218.  Gene #73: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
19P LOSS CNV 1 0 0 17
19P LOSS WILD-TYPE 64 92 65 123

Figure S218.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0055

Table S219.  Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
19P LOSS CNV 27 2 4
19P LOSS WILD-TYPE 180 142 128

Figure S219.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6.41e-07 (Fisher's exact test), Q value = 0.00036

Table S220.  Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
19P LOSS CNV 1 4 3 25
19P LOSS WILD-TYPE 192 75 24 159

Figure S220.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1.79e-08 (Chi-square test), Q value = 1.1e-05

Table S221.  Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
19Q LOSS CNV 1 6 20 1 0
19Q LOSS WILD-TYPE 289 34 119 16 6

Figure S221.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 4.65e-05 (Fisher's exact test), Q value = 0.024

Table S222.  Gene #74: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
19Q LOSS CNV 18 5 1
19Q LOSS WILD-TYPE 125 80 148

Figure S222.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.0078

Table S223.  Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
19Q LOSS CNV 1 3 3 20
19Q LOSS WILD-TYPE 192 76 24 164

Figure S223.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.000122 (Chi-square test), Q value = 0.061

Table S224.  Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
20P LOSS CNV 1 2 12 0 0
20P LOSS WILD-TYPE 289 38 127 17 6

Figure S224.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 6.47e-08 (Chi-square test), Q value = 3.8e-05

Table S225.  Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
21Q LOSS CNV 3 4 23 1 1
21Q LOSS WILD-TYPE 287 36 116 16 5

Figure S225.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.073

Table S226.  Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
21Q LOSS CNV 15 0 3
21Q LOSS WILD-TYPE 127 107 110

Figure S226.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.43e-05 (Fisher's exact test), Q value = 0.023

Table S227.  Gene #77: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
21Q LOSS CNV 2 7 0 21
21Q LOSS WILD-TYPE 191 72 27 163

Figure S227.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1.41e-36 (Chi-square test), Q value = 9.8e-34

Table S228.  Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
22Q LOSS CNV 1 13 71 1 1
22Q LOSS WILD-TYPE 289 27 68 16 5

Figure S228.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 4.23e-08 (Fisher's exact test), Q value = 2.5e-05

Table S229.  Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 143 85 149
22Q LOSS CNV 46 22 10
22Q LOSS WILD-TYPE 97 63 139

Figure S229.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 4.88e-11 (Fisher's exact test), Q value = 3.1e-08

Table S230.  Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 107 113
22Q LOSS CNV 41 3 5
22Q LOSS WILD-TYPE 101 104 108

Figure S230.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.29e-14 (Fisher's exact test), Q value = 2.2e-11

Table S231.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 92 65 140
22Q LOSS CNV 1 1 3 44
22Q LOSS WILD-TYPE 64 91 62 96

Figure S231.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 9.64e-11 (Fisher's exact test), Q value = 6.1e-08

Table S232.  Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
22Q LOSS CNV 64 14 7
22Q LOSS WILD-TYPE 143 130 125

Figure S232.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.01e-09 (Fisher's exact test), Q value = 6.2e-07

Table S233.  Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
22Q LOSS CNV 13 8 6 58
22Q LOSS WILD-TYPE 180 71 21 126

Figure S233.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'Xq loss' versus 'CN_CNMF'

P value = 2.97e-07 (Chi-square test), Q value = 0.00017

Table S234.  Gene #79: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 290 40 139 17 6
XQ LOSS CNV 0 1 16 1 0
XQ LOSS WILD-TYPE 290 39 123 16 6

Figure S234.  Get High-res Image Gene #79: 'Xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'Xq loss' versus 'MIRSEQ_CNMF'

P value = 0.000233 (Fisher's exact test), Q value = 0.11

Table S235.  Gene #79: 'Xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 207 144 132
XQ LOSS CNV 16 1 1
XQ LOSS WILD-TYPE 191 143 131

Figure S235.  Get High-res Image Gene #79: 'Xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'Xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.012

Table S236.  Gene #79: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 193 79 27 184
XQ LOSS CNV 0 1 1 16
XQ LOSS WILD-TYPE 193 78 26 168

Figure S236.  Get High-res Image Gene #79: 'Xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 492

  • Number of significantly arm-level cnvs = 79

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

Download Results

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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