Correlation between copy number variations of arm-level result and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1KP81N6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1KP81N6
Overview
Introduction

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

Summary

Testing the association between copy number variation 80 arm-level events and 10 molecular subtypes across 492 patients, 330 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 3p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 6q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 9q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

  • 12p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'METHLYATION_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 16q gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'CN_CNMF'.

  • 18p gain cnv correlated to 'CN_CNMF'.

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

  • 19q gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

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

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

  • 21q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 1p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

  • 2p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 3p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

  • 3q loss cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

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

  • 4q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 6p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 9p loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'RPPA_CNMF'.

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

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

  • 13q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 16p loss cnv correlated to 'CN_CNMF'.

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

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

  • 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',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 19q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 20p loss cnv correlated to 'METHLYATION_CNMF'.

  • 20q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 330 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
8p gain 68 (14%) 424 1e-05
(0.000163) 		1e-05
(0.000163) 		1e-05
(0.000163) 		0.00031
(0.00256) 		2e-05
(0.000281) 		0.0003
(0.00255) 		0.00039
(0.003) 		0.00518
(0.0222) 		6e-05
(0.000696) 		0.00619
(0.0248)
8q gain 126 (26%) 366 1e-05
(0.000163) 		1e-05
(0.000163) 		0.00024
(0.00216) 		0.00017
(0.0016) 		1e-05
(0.000163) 		3e-05
(0.000387) 		8e-05
(0.000877) 		1e-05
(0.000163) 		2e-05
(0.000281) 		0.00018
(0.00167)
18q loss 100 (20%) 392 1e-05
(0.000163) 		0.00157
(0.00916) 		0.0368
(0.0988) 		0.00097
(0.00636) 		0.00311
(0.0152) 		0.0304
(0.0874) 		0.00137
(0.00837) 		0.00304
(0.015) 		0.00077
(0.00522) 		0.00125
(0.00775)
7p gain 101 (21%) 391 1e-05
(0.000163) 		1e-05
(0.000163) 		0.00293
(0.0147) 		0.404
(0.508) 		1e-05
(0.000163) 		3e-05
(0.000387) 		0.00036
(0.00282) 		6e-05
(0.000696) 		0.00109
(0.00692) 		0.00025
(0.0022)
7q gain 94 (19%) 398 1e-05
(0.000163) 		1e-05
(0.000163) 		0.00954
(0.0357) 		0.754
(0.814) 		1e-05
(0.000163) 		8e-05
(0.000877) 		0.00031
(0.00256) 		6e-05
(0.000696) 		0.00056
(0.00411) 		0.00029
(0.00249)
15q loss 35 (7%) 457 1e-05
(0.000163) 		0.0035
(0.0163) 		0.00183
(0.0102) 		0.41
(0.511) 		0.00187
(0.0104) 		0.0107
(0.039) 		0.00486
(0.021) 		0.0124
(0.0434) 		0.00315
(0.0152) 		0.034
(0.0945)
3p gain 40 (8%) 452 1e-05
(0.000163) 		0.0129
(0.045) 		0.159
(0.265) 		0.0273
(0.0809) 		3e-05
(0.000387) 		0.00033
(0.00267) 		0.0532
(0.125) 		0.00496
(0.0213) 		0.00458
(0.02) 		0.00082
(0.00551)
3q gain 54 (11%) 438 1e-05
(0.000163) 		0.00261
(0.0136) 		0.101
(0.192) 		0.0204
(0.0633) 		6e-05
(0.000696) 		0.00192
(0.0105) 		0.105
(0.197) 		0.0111
(0.04) 		0.00286
(0.0145) 		0.00063
(0.00458)
1p loss 22 (4%) 470 1e-05
(0.000163) 		0.00094
(0.00621) 		0.35
(0.46) 		0.868
(0.91) 		0.0121
(0.0427) 		0.0002
(0.00184) 		0.00973
(0.0362) 		0.00355
(0.0164) 		0.028
(0.0825) 		0.00304
(0.015)
4p loss 23 (5%) 469 1e-05
(0.000163) 		0.0427
(0.109) 		0.0806
(0.167) 		0.187
(0.296) 		0.00108
(0.00692) 		0.0404
(0.105) 		2e-05
(0.000281) 		0.00287
(0.0145) 		0.00377
(0.0169) 		0.00015
(0.00148)
10p loss 41 (8%) 451 1e-05
(0.000163) 		1e-05
(0.000163) 		0.18
(0.291) 		0.314
(0.425) 		7e-05
(0.000789) 		0.00013
(0.00135) 		1e-05
(0.000163) 		5e-05
(0.000625) 		0.0115
(0.041) 		0.00124
(0.00775)
10q loss 43 (9%) 449 1e-05
(0.000163) 		3e-05
(0.000387) 		0.0692
(0.151) 		0.162
(0.267) 		0.00071
(0.00498) 		0.00046
(0.00347) 		3e-05
(0.000387) 		0.00124
(0.00775) 		0.00246
(0.013) 		0.00395
(0.0177)
13q loss 78 (16%) 414 1e-05
(0.000163) 		0.0166
(0.0535) 		0.00251
(0.0131) 		0.0102
(0.0376) 		0.236
(0.349) 		0.0555
(0.129) 		0.0134
(0.0461) 		0.0263
(0.0784) 		0.0297
(0.086) 		0.00342
(0.0161)
xp loss 38 (8%) 454 1e-05
(0.000163) 		0.00017
(0.0016) 		0.375
(0.482) 		0.0563
(0.13) 		2e-05
(0.000281) 		4e-05
(0.000508) 		1e-05
(0.000163) 		0.0352
(0.0959) 		0.00575
(0.0235) 		0.00483
(0.021)
xq loss 38 (8%) 454 1e-05
(0.000163) 		0.00017
(0.0016) 		0.375
(0.482) 		0.0571
(0.132) 		1e-05
(0.000163) 		7e-05
(0.000789) 		1e-05
(0.000163) 		0.0352
(0.0959) 		0.00575
(0.0235) 		0.00533
(0.0226)
5p gain 23 (5%) 469 6e-05
(0.000696) 		0.00051
(0.00381) 		0.0375
(0.0999) 		0.192
(0.301) 		0.00285
(0.0145) 		0.0607
(0.137) 		0.228
(0.343) 		0.0018
(0.0101) 		0.0075
(0.0296) 		0.00179
(0.0101)
6q loss 41 (8%) 451 1e-05
(0.000163) 		0.0143
(0.0487) 		0.0853
(0.174) 		0.028
(0.0825) 		0.00952
(0.0357) 		0.0007
(0.00496) 		0.0521
(0.124) 		0.0957
(0.185) 		0.0153
(0.0504) 		0.00612
(0.0246)
16q loss 107 (22%) 385 1e-05
(0.000163) 		1e-05
(0.000163) 		0.0952
(0.185) 		0.978
(0.991) 		0.0036
(0.0165) 		0.0292
(0.085) 		0.00546
(0.0227) 		0.00041
(0.00312) 		0.00233
(0.0125) 		0.418
(0.517)
18p loss 67 (14%) 425 1e-05
(0.000163) 		0.00914
(0.0346) 		0.256
(0.369) 		0.00212
(0.0115) 		0.00107
(0.00692) 		0.0518
(0.124) 		0.0639
(0.143) 		0.0349
(0.0959) 		0.00076
(0.00522) 		0.0396
(0.103)
20p gain 26 (5%) 466 1e-05
(0.000163) 		0.0385
(0.101) 		0.317
(0.427) 		0.147
(0.249) 		0.00148
(0.00877) 		0.036
(0.0975) 		0.0148
(0.0496) 		0.00434
(0.0192) 		0.12
(0.214) 		0.118
(0.211)
21q gain 21 (4%) 471 1e-05
(0.000163) 		0.00862
(0.033) 		0.68
(0.75) 		0.842
(0.89) 		0.0675
(0.148) 		0.027
(0.0802) 		0.0569
(0.131) 		0.00318
(0.0152) 		0.0184
(0.0585) 		0.0205
(0.0634)
5q loss 23 (5%) 469 1e-05
(0.000163) 		0.018
(0.0578) 		0.183
(0.293) 		0.253
(0.367) 		0.0311
(0.0892) 		0.00191
(0.0105) 		0.0112
(0.0403) 		0.00053
(0.00393) 		0.654
(0.73) 		0.277
(0.39)
17p loss 76 (15%) 416 1e-05
(0.000163) 		1e-05
(0.000163) 		0.24
(0.353) 		0.155
(0.262) 		0.00017
(0.0016) 		0.00145
(0.00866) 		0.294
(0.406) 		0.0329
(0.0927) 		0.015
(0.0497) 		0.233
(0.346)
17q loss 20 (4%) 472 0.00037
(0.00287) 		0.00164
(0.00937) 		0.497
(0.59) 		0.526
(0.617) 		0.00194
(0.0106) 		0.0361
(0.0975) 		0.00985
(0.0365) 		0.0457
(0.114) 		0.0557
(0.13) 		0.473
(0.568)
9q gain 48 (10%) 444 1e-05
(0.000163) 		0.00015
(0.00148) 		0.00782
(0.0305) 		0.107
(0.199) 		0.00031
(0.00256) 		0.246
(0.359) 		0.405
(0.508) 		0.0139
(0.0477) 		0.127
(0.221) 		0.317
(0.427)
10p gain 15 (3%) 477 0.00246
(0.013) 		0.0009
(0.006) 		0.599
(0.676) 		0.806
(0.859) 		0.123
(0.216) 		0.0343
(0.0945) 		0.00433
(0.0192) 		0.0131
(0.0455) 		0.163
(0.268) 		0.143
(0.244)
11p gain 27 (5%) 465 1e-05
(0.000163) 		0.0164
(0.0532) 		0.139
(0.237) 		0.405
(0.508) 		0.121
(0.214) 		0.0207
(0.0636) 		0.192
(0.301) 		0.0341
(0.0945) 		0.0232
(0.0699) 		0.202
(0.315)
12q gain 18 (4%) 474 0.00144
(0.00866) 		0.0032
(0.0152) 		0.00898
(0.0342) 		0.427
(0.524) 		0.103
(0.193) 		0.0602
(0.137) 		0.871
(0.912) 		0.0321
(0.0915) 		0.113
(0.205) 		0.00437
(0.0192)
20q gain 29 (6%) 463 1e-05
(0.000163) 		0.00776
(0.0304) 		0.00917
(0.0346) 		0.0763
(0.162) 		0.0394
(0.103) 		0.0873
(0.175) 		0.0789
(0.165) 		0.00664
(0.0264) 		0.261
(0.374) 		0.204
(0.316)
6p loss 26 (5%) 466 1e-05
(0.000163) 		0.012
(0.0427) 		0.0864
(0.174) 		0.0619
(0.139) 		0.117
(0.21) 		0.0028
(0.0145) 		0.192
(0.301) 		0.0838
(0.172) 		0.0435
(0.11) 		0.0164
(0.0532)
8p loss 171 (35%) 321 1e-05
(0.000163) 		1e-05
(0.000163) 		0.918
(0.945) 		0.345
(0.456) 		2e-05
(0.000281) 		2e-05
(0.000281) 		0.0129
(0.045) 		0.0672
(0.148) 		0.187
(0.296) 		0.338
(0.448)
12p loss 47 (10%) 445 0.0001
(0.00108) 		0.17
(0.278) 		0.744
(0.807) 		0.699
(0.765) 		0.0336
(0.0942) 		0.436
(0.535) 		0.041
(0.106) 		0.0145
(0.0493) 		0.0147
(0.0495) 		0.304
(0.415)
22q loss 47 (10%) 445 1e-05
(0.000163) 		0.244
(0.357) 		0.471
(0.566) 		0.371
(0.481) 		0.0149
(0.0496) 		0.0479
(0.118) 		0.256
(0.369) 		0.0285
(0.0833) 		0.0769
(0.163) 		0.0377
(0.1)
2p gain 11 (2%) 481 0.00596
(0.0242) 		0.0342
(0.0945) 		0.0795
(0.166) 		0.445
(0.542) 		0.00348
(0.0163) 		0.0925
(0.183) 		0.159
(0.265) 		0.0203
(0.0632) 		0.189
(0.298) 		0.25
(0.363)
9p gain 34 (7%) 458 1e-05
(0.000163) 		0.00014
(0.00142) 		0.0496
(0.121) 		0.126
(0.219) 		0.00612
(0.0246) 		0.0952
(0.185) 		0.646
(0.723) 		0.112
(0.205) 		0.35
(0.46) 		0.232
(0.346)
10q gain 14 (3%) 478 0.00546
(0.0227) 		0.00576
(0.0235) 		0.132
(0.229) 		0.0928
(0.183) 		0.0716
(0.155) 		0.0328
(0.0927) 		0.0118
(0.0419) 		0.087
(0.174) 		0.352
(0.462) 		0.216
(0.329)
11q gain 30 (6%) 462 1e-05
(0.000163) 		0.0368
(0.0988) 		0.0826
(0.17) 		0.341
(0.452) 		0.134
(0.23) 		0.0531
(0.125) 		0.216
(0.329) 		0.0325
(0.0923) 		0.0433
(0.11) 		0.273
(0.386)
12p gain 15 (3%) 477 0.00251
(0.0131) 		0.00298
(0.0149) 		0.0112
(0.0403) 		0.832
(0.884) 		0.124
(0.218) 		0.0643
(0.143) 		0.883
(0.92) 		0.00376
(0.0169) 		0.238
(0.352) 		0.0604
(0.137)
2q loss 18 (4%) 474 0.00013
(0.00135) 		0.0219
(0.0671) 		0.763
(0.823) 		0.885
(0.921) 		0.363
(0.473) 		0.484
(0.577) 		0.0639
(0.143) 		0.0352
(0.0959) 		0.00708
(0.028) 		0.18
(0.291)
4q loss 16 (3%) 476 0.00013
(0.00135) 		0.125
(0.219) 		0.541
(0.629) 		0.865
(0.908) 		0.00161
(0.00927) 		0.133
(0.229) 		0.0694
(0.151) 		0.0468
(0.116) 		0.0814
(0.168) 		0.0422
(0.108)
5p loss 12 (2%) 480 0.0037
(0.0168) 		0.201
(0.314) 		0.555
(0.64) 		0.549
(0.636) 		0.416
(0.516) 		0.00575
(0.0235) 		0.318
(0.427) 		0.00329
(0.0156) 		0.481
(0.575) 		0.0491
(0.12)
1q gain 26 (5%) 466 0.00014
(0.00142) 		0.145
(0.246) 		0.0704
(0.153) 		0.214
(0.328) 		0.102
(0.193) 		0.00067
(0.00483) 		0.0994
(0.189) 		0.0337
(0.0944) 		0.688
(0.757) 		0.13
(0.226)
16p gain 32 (7%) 460 1e-05
(0.000163) 		0.256
(0.369) 		0.119
(0.212) 		0.862
(0.906) 		0.175
(0.284) 		0.231
(0.346) 		0.469
(0.565) 		0.00531
(0.0226) 		0.0409
(0.106) 		0.0784
(0.165)
xp gain 7 (1%) 485 0.0184
(0.0585) 		0.00848
(0.0327) 		0.156
(0.262) 		0.84
(0.889) 		0.0835
(0.172) 		0.0922
(0.182) 		0.121
(0.214) 		0.0456
(0.114) 		0.283
(0.397) 		0.369
(0.479)
xq gain 7 (1%) 485 0.0199
(0.0621) 		0.00849
(0.0327) 		0.156
(0.262) 		0.84
(0.889) 		0.0841
(0.172) 		0.0933
(0.183) 		0.123
(0.216) 		0.0455
(0.114) 		0.283
(0.397) 		0.374
(0.482)
2p loss 14 (3%) 478 0.0007
(0.00496) 		0.00839
(0.0326) 		0.589
(0.666) 		0.577
(0.659) 		0.494
(0.587) 		0.611
(0.687) 		0.0501
(0.121) 		0.264
(0.375) 		0.0153
(0.0504) 		0.406
(0.508)
8q loss 21 (4%) 471 0.0514
(0.123) 		0.00022
(0.002) 		0.718
(0.783) 		0.634
(0.712) 		0.00036
(0.00282) 		0.00073
(0.00508) 		0.0538
(0.126) 		0.397
(0.504) 		0.444
(0.541) 		0.0861
(0.174)
9p loss 21 (4%) 471 0.00025
(0.0022) 		0.312
(0.424) 		0.089
(0.178) 		0.00541
(0.0227) 		0.42
(0.518) 		0.0221
(0.0671) 		0.18
(0.291) 		0.246
(0.359) 		0.0753
(0.161) 		0.527
(0.617)
20q loss 8 (2%) 484 0.0489
(0.12) 		0.00158
(0.00916) 		0.78
(0.836) 		0.373
(0.482) 		0.351
(0.46) 		0.0428
(0.109) 		0.232
(0.346) 		0.0785
(0.165) 		0.726
(0.789) 		0.912
(0.941)
1p gain 15 (3%) 477 0.00109
(0.00692) 		0.514
(0.605) 		0.0733
(0.158) 		0.464
(0.562) 		0.112
(0.205) 		0.00151
(0.00888) 		0.33
(0.441) 		0.0775
(0.164) 		0.72
(0.783) 		0.501
(0.594)
2q gain 7 (1%) 485 0.0188
(0.0592) 		0.418
(0.517) 		0.227
(0.342) 		0.689
(0.757) 		0.0189
(0.0592) 		0.554
(0.64) 		0.123
(0.216) 		0.063
(0.141) 		0.444
(0.541) 		0.513
(0.604)
6p gain 10 (2%) 482 0.0148
(0.0496) 		0.222
(0.337) 		0.303
(0.415) 		0.405
(0.508) 		0.353
(0.462) 		0.274
(0.387) 		0.581
(0.659) 		0.104
(0.195) 		0.037
(0.0991) 		0.317
(0.427)
6q gain 6 (1%) 486 0.0493
(0.12) 		0.461
(0.559) 		0.478
(0.573) 		0.913
(0.941) 		0.944
(0.967) 		0.581
(0.659) 		0.51
(0.602) 		0.0382
(0.101) 		0.16
(0.266) 		0.208
(0.32)
14q gain 10 (2%) 482 0.0014
(0.00848) 		0.0907
(0.18) 		0.522
(0.614) 		0.778
(0.835) 		0.0103
(0.0377) 		0.229
(0.344) 		0.0994
(0.189) 		0.257
(0.369) 		0.289
(0.4) 		0.0547
(0.128)
16q gain 7 (1%) 485 0.109
(0.202) 		0.0251
(0.0751) 		0.883
(0.92) 		0.928
(0.952) 		0.561
(0.643) 		1
(1.00) 		0.862
(0.906) 		0.0303
(0.0874) 		0.285
(0.398) 		0.365
(0.474)
17p gain 8 (2%) 484 0.29
(0.401) 		0.922
(0.948) 		0.358
(0.468) 		1
(1.00) 		0.383
(0.489) 		0.661
(0.734) 		0.511
(0.603) 		0.0158
(0.0516) 		1
(1.00) 		0.0107
(0.039)
19p gain 12 (2%) 480 0.00032
(0.00261) 		0.103
(0.193) 		0.00362
(0.0165) 		0.302
(0.413) 		0.637
(0.714) 		0.342
(0.452) 		0.112
(0.205) 		0.0848
(0.173) 		0.375
(0.482) 		0.361
(0.471)
19q gain 12 (2%) 480 0.00036
(0.00282) 		0.111
(0.205) 		0.0411
(0.106) 		0.108
(0.201) 		0.581
(0.659) 		0.367
(0.476) 		0.0955
(0.185) 		0.0613
(0.139) 		0.405
(0.508) 		0.284
(0.397)
3p loss 9 (2%) 483 0.114
(0.206) 		0.134
(0.23) 		0.468
(0.565) 		0.205
(0.317) 		0.192
(0.301) 		0.038
(0.101) 		0.0184
(0.0585) 		0.408
(0.509) 		0.117
(0.21) 		0.181
(0.292)
3q loss 5 (1%) 487 0.423
(0.521) 		0.66
(0.734) 		0.491
(0.584) 		0.25
(0.363) 		0.0221
(0.0671) 		0.032
(0.0915)
9q loss 11 (2%) 481 0.0476
(0.118) 		0.264
(0.375) 		0.0154
(0.0504) 		0.232
(0.346) 		0.175
(0.285) 		0.187
(0.296) 		0.116
(0.21) 		0.507
(0.599) 		0.332
(0.442) 		0.604
(0.682)
12q loss 20 (4%) 472 0.00137
(0.00837) 		0.296
(0.407) 		0.287
(0.399) 		0.331
(0.441) 		0.294
(0.406) 		0.262
(0.374) 		0.0738
(0.158) 		0.05
(0.121) 		0.0779
(0.164) 		0.555
(0.64)
14q loss 25 (5%) 467 0.00028
(0.00243) 		0.0239
(0.0718) 		0.241
(0.354) 		0.84
(0.889) 		0.196
(0.306) 		0.0983
(0.189) 		0.067
(0.148) 		0.0646
(0.143) 		0.0506
(0.121) 		0.306
(0.417)
19p loss 19 (4%) 473 2e-05
(0.000281) 		0.318
(0.427) 		0.387
(0.492) 		0.121
(0.214) 		0.0956
(0.185) 		0.113
(0.205) 		0.0143
(0.0487) 		0.13
(0.226) 		0.0808
(0.167) 		0.277
(0.391)
19q loss 18 (4%) 474 2e-05
(0.000281) 		0.308
(0.419) 		0.482
(0.576) 		0.252
(0.365) 		0.0657
(0.145) 		0.0957
(0.185) 		0.0221
(0.0671) 		0.203
(0.315) 		0.155
(0.262) 		0.44
(0.54)
21q loss 24 (5%) 468 0.0032
(0.0152) 		0.0573
(0.132) 		0.0971
(0.187) 		0.159
(0.265) 		0.0188
(0.0592) 		0.328
(0.439) 		0.0991
(0.189) 		0.102
(0.193) 		0.259
(0.371) 		0.453
(0.55)
13q gain 8 (2%) 484 0.0588
(0.135) 		0.0439
(0.111) 		0.135
(0.232) 		0.851
(0.897) 		0.546
(0.634) 		0.66
(0.734) 		0.568
(0.649) 		0.561
(0.643) 		0.539
(0.628) 		0.908
(0.939)
17q gain 11 (2%) 481 0.0473
(0.117) 		0.535
(0.625) 		0.0728
(0.157) 		0.957
(0.975) 		0.125
(0.219) 		0.217
(0.329) 		0.465
(0.562) 		0.111
(0.205) 		0.746
(0.807) 		0.376
(0.482)
18p gain 19 (4%) 473 0.00077
(0.00522) 		0.234
(0.347) 		0.0905
(0.18) 		1
(1.00) 		0.442
(0.54) 		0.792
(0.848) 		0.925
(0.95) 		0.675
(0.747) 		1
(1.00) 		0.972
(0.987)
1q loss 6 (1%) 486 0.0501
(0.121) 		0.111
(0.205) 		0.158
(0.264) 		0.474
(0.569) 		0.0631
(0.141) 		0.0963
(0.186) 		0.0743
(0.159) 		0.102
(0.193) 		0.0284
(0.0833) 		0.207
(0.32)
11p loss 8 (2%) 484 0.0519
(0.124) 		0.284
(0.397) 		0.541
(0.629) 		0.702
(0.767) 		0.0594
(0.136) 		0.117
(0.21) 		0.114
(0.206) 		0.262
(0.374) 		0.611
(0.687) 		0.0463
(0.115)
11q loss 5 (1%) 487 0.295
(0.407) 		0.206
(0.318) 		0.0395
(0.103) 		0.888
(0.921) 		0.078
(0.164) 		0.301
(0.413) 		0.237
(0.351) 		0.188
(0.298) 		0.187
(0.296) 		0.172
(0.282)
16p loss 31 (6%) 461 1e-05
(0.000163) 		0.267
(0.378) 		0.968
(0.984) 		0.137
(0.234) 		0.242
(0.355) 		0.442
(0.54) 		0.387
(0.492) 		0.325
(0.435) 		0.156
(0.262) 		0.955
(0.975)
20p loss 19 (4%) 473 0.0528
(0.125) 		0.0032
(0.0152) 		0.984
(0.997) 		0.954
(0.975) 		0.876
(0.916) 		0.184
(0.294) 		0.379
(0.485) 		0.185
(0.295) 		0.536
(0.626) 		0.793
(0.848)
4p gain 9 (2%) 483 0.165
(0.272) 		0.698
(0.765) 		0.806
(0.859) 		0.42
(0.518) 		0.881
(0.92) 		0.769
(0.828) 		0.657
(0.733) 		0.413
(0.513) 		0.554
(0.64) 		0.581
(0.659)
4q gain 10 (2%) 482 0.0864
(0.174) 		0.678
(0.749) 		0.608
(0.685) 		0.404
(0.508) 		0.279
(0.393) 		0.558
(0.642) 		0.831
(0.884) 		0.174
(0.284) 		0.401
(0.508) 		0.215
(0.329)
5q gain 12 (2%) 480 0.0867
(0.174) 		0.113
(0.205) 		0.0707
(0.153) 		0.578
(0.659) 		0.097
(0.187) 		0.229
(0.344) 		0.386
(0.492) 		0.159
(0.265) 		0.166
(0.272) 		0.255
(0.369)
15q gain 6 (1%) 486 0.175
(0.284) 		0.896
(0.927) 		0.213
(0.326) 		0.89
(0.922) 		0.705
(0.769) 		0.666
(0.738) 		0.746
(0.807) 		0.182
(0.293) 		0.844
(0.891) 		0.803
(0.857)
18q gain 10 (2%) 482 0.0863
(0.174) 		0.744
(0.807) 		0.411
(0.512) 		0.966
(0.983) 		0.683
(0.752) 		0.776
(0.835) 		1
(1.00) 		0.336
(0.447) 		0.955
(0.975) 		0.223
(0.337)
22q gain 4 (1%) 488 0.692
(0.76) 		0.311
(0.422) 		0.287
(0.399) 		0.888
(0.921) 		0.562
(0.643) 		0.222
(0.337) 		0.392
(0.498) 		0.407
(0.509) 		0.56
(0.643) 		0.651
(0.728)
'1p gain' versus 'CN_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0069

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
1P GAIN MUTATED 0 0 2 13
1P GAIN WILD-TYPE 108 91 96 182

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.0089

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
1P GAIN MUTATED 0 12 3
1P GAIN WILD-TYPE 171 193 112

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
1Q GAIN MUTATED 3 0 2 21
1Q GAIN WILD-TYPE 105 91 96 174

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0048

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
1Q GAIN MUTATED 1 15 10
1Q GAIN WILD-TYPE 170 190 105

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.094

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
1Q GAIN MUTATED 4 4 3 14 1
1Q GAIN WILD-TYPE 143 94 56 114 55

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 0.00596 (Fisher's exact test), Q value = 0.024

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
2P GAIN MUTATED 0 1 0 10
2P GAIN WILD-TYPE 108 90 98 185

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.095

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
2P GAIN MUTATED 1 5 1 4
2P GAIN WILD-TYPE 160 132 123 66

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00348 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
2P GAIN MUTATED 1 1 9 0
2P GAIN WILD-TYPE 94 140 138 108

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

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.063

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
2P GAIN MUTATED 0 4 0 6 1
2P GAIN WILD-TYPE 147 94 59 122 55

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.059

Table S10.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
2Q GAIN MUTATED 0 0 0 7
2Q GAIN WILD-TYPE 108 91 98 188

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.059

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
2Q GAIN MUTATED 0 1 6 0
2Q GAIN WILD-TYPE 95 140 141 108

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S12.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
3P GAIN MUTATED 0 1 1 38
3P GAIN WILD-TYPE 108 90 97 157

Figure S12.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.045

Table S13.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
3P GAIN MUTATED 7 13 8 12
3P GAIN WILD-TYPE 154 124 116 58

Figure S13.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.081

Table S14.  Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
3P GAIN MUTATED 2 13 4 9
3P GAIN WILD-TYPE 72 100 88 59

Figure S14.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00039

Table S15.  Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
3P GAIN MUTATED 3 7 26 4
3P GAIN WILD-TYPE 92 134 121 104

Figure S15.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0027

Table S16.  Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
3P GAIN MUTATED 4 27 9
3P GAIN WILD-TYPE 167 178 106

Figure S16.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00496 (Fisher's exact test), Q value = 0.021

Table S17.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
3P GAIN MUTATED 7 6 2 21 3
3P GAIN WILD-TYPE 140 92 57 107 53

Figure S17.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00458 (Fisher's exact test), Q value = 0.02

Table S18.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
3P GAIN MUTATED 0 13 6 5
3P GAIN WILD-TYPE 65 78 72 79

Figure S18.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0055

Table S19.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
3P GAIN MUTATED 2 16 4 0 2
3P GAIN WILD-TYPE 73 70 65 23 63

Figure S19.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S20.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
3Q GAIN MUTATED 3 1 2 48
3Q GAIN WILD-TYPE 105 90 96 147

Figure S20.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.014

Table S21.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
3Q GAIN MUTATED 8 17 14 15
3Q GAIN WILD-TYPE 153 120 110 55

Figure S21.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.063

Table S22.  Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
3Q GAIN MUTATED 3 17 7 12
3Q GAIN WILD-TYPE 71 96 85 56

Figure S22.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 7e-04

Table S23.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
3Q GAIN MUTATED 3 14 31 6
3Q GAIN WILD-TYPE 92 127 116 102

Figure S23.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00192 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
3Q GAIN MUTATED 8 32 14
3Q GAIN WILD-TYPE 163 173 101

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

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.04

Table S25.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
3Q GAIN MUTATED 11 10 4 25 3
3Q GAIN WILD-TYPE 136 88 55 103 53

Figure S25.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00286 (Fisher's exact test), Q value = 0.015

Table S26.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
3Q GAIN MUTATED 1 17 8 6
3Q GAIN WILD-TYPE 64 74 70 78

Figure S26.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0046

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
3Q GAIN MUTATED 3 19 7 1 2
3Q GAIN WILD-TYPE 72 67 62 22 63

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 7e-04

Table S28.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
5P GAIN MUTATED 2 0 1 20
5P GAIN WILD-TYPE 106 91 97 175

Figure S28.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0038

Table S29.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
5P GAIN MUTATED 3 5 4 11
5P GAIN WILD-TYPE 158 132 120 59

Figure S29.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.1

Table S30.  Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
5P GAIN MUTATED 1 4 2 1 5 4
5P GAIN WILD-TYPE 104 47 42 50 53 34

Figure S30.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.015

Table S31.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
5P GAIN MUTATED 1 7 14 1
5P GAIN WILD-TYPE 94 134 133 107

Figure S31.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.01

Table S32.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
5P GAIN MUTATED 4 3 0 15 1
5P GAIN WILD-TYPE 143 95 59 113 55

Figure S32.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0075 (Fisher's exact test), Q value = 0.03

Table S33.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
5P GAIN MUTATED 0 10 2 3
5P GAIN WILD-TYPE 65 81 76 81

Figure S33.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.01

Table S34.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
5P GAIN MUTATED 3 11 1 0 0
5P GAIN WILD-TYPE 72 75 68 23 65

Figure S34.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.05

Table S35.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
6P GAIN MUTATED 0 0 1 9
6P GAIN WILD-TYPE 108 91 97 186

Figure S35.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.099

Table S36.  Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
6P GAIN MUTATED 0 4 4 0
6P GAIN WILD-TYPE 65 87 74 84

Figure S36.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'CN_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 0.12

Table S37.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
6Q GAIN MUTATED 0 0 0 6
6Q GAIN WILD-TYPE 108 91 98 189

Figure S37.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0382 (Fisher's exact test), Q value = 0.1

Table S38.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
6Q GAIN MUTATED 0 1 0 5 0
6Q GAIN WILD-TYPE 147 97 59 123 56

Figure S38.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S39.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
7P GAIN MUTATED 7 6 12 76
7P GAIN WILD-TYPE 101 85 86 119

Figure S39.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S40.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
7P GAIN MUTATED 13 47 19 22
7P GAIN WILD-TYPE 148 90 105 48

Figure S40.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00293 (Fisher's exact test), Q value = 0.015

Table S41.  Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
7P GAIN MUTATED 18 12 9 4 23 8
7P GAIN WILD-TYPE 87 39 35 47 35 30

Figure S41.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S42.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
7P GAIN MUTATED 14 20 59 8
7P GAIN WILD-TYPE 81 121 88 100

Figure S42.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00039

Table S43.  Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
7P GAIN MUTATED 21 63 17
7P GAIN WILD-TYPE 150 142 98

Figure S43.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0028

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
7P GAIN MUTATED 57 17 11 15
7P GAIN WILD-TYPE 151 54 112 71

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

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 7e-04

Table S45.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
7P GAIN MUTATED 16 27 15 38 4
7P GAIN WILD-TYPE 131 71 44 90 52

Figure S45.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0069

Table S46.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
7P GAIN MUTATED 4 28 20 17
7P GAIN WILD-TYPE 61 63 58 67

Figure S46.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0022

Table S47.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
7P GAIN MUTATED 9 31 19 1 9
7P GAIN WILD-TYPE 66 55 50 22 56

Figure S47.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S48.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
7Q GAIN MUTATED 7 6 11 70
7Q GAIN WILD-TYPE 101 85 87 125

Figure S48.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S49.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
7Q GAIN MUTATED 11 44 17 22
7Q GAIN WILD-TYPE 150 93 107 48

Figure S49.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.00954 (Fisher's exact test), Q value = 0.036

Table S50.  Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
7Q GAIN MUTATED 17 12 8 4 21 7
7Q GAIN WILD-TYPE 88 39 36 47 37 31

Figure S50.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S51.  Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
7Q GAIN MUTATED 13 19 55 7
7Q GAIN WILD-TYPE 82 122 92 101

Figure S51.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00088

Table S52.  Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
7Q GAIN MUTATED 20 58 16
7Q GAIN WILD-TYPE 151 147 99

Figure S52.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0026

Table S53.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
7Q GAIN MUTATED 53 17 10 13
7Q GAIN WILD-TYPE 155 54 113 73

Figure S53.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 7e-04

Table S54.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
7Q GAIN MUTATED 14 26 14 35 4
7Q GAIN WILD-TYPE 133 72 45 93 52

Figure S54.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0041

Table S55.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
7Q GAIN MUTATED 4 28 20 14
7Q GAIN WILD-TYPE 61 63 58 70

Figure S55.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0025

Table S56.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
7Q GAIN MUTATED 9 29 19 1 8
7Q GAIN WILD-TYPE 66 57 50 22 57

Figure S56.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S57.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
8P GAIN MUTATED 3 4 3 58
8P GAIN WILD-TYPE 105 87 95 137

Figure S57.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S58.  Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
8P GAIN MUTATED 7 32 10 19
8P GAIN WILD-TYPE 154 105 114 51

Figure S58.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S59.  Gene #15: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
8P GAIN MUTATED 4 9 2 7 18 10
8P GAIN WILD-TYPE 101 42 42 44 40 28

Figure S59.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0026

Table S60.  Gene #15: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
8P GAIN MUTATED 7 13 8 22
8P GAIN WILD-TYPE 67 100 84 46

Figure S60.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S61.  Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
8P GAIN MUTATED 6 12 40 10
8P GAIN WILD-TYPE 89 129 107 98

Figure S61.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0026

Table S62.  Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
8P GAIN MUTATED 13 44 11
8P GAIN WILD-TYPE 158 161 104

Figure S62.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.003

Table S63.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
8P GAIN MUTATED 44 7 7 9
8P GAIN WILD-TYPE 164 64 116 77

Figure S63.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00518 (Fisher's exact test), Q value = 0.022

Table S64.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
8P GAIN MUTATED 11 14 10 28 4
8P GAIN WILD-TYPE 136 84 49 100 52

Figure S64.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 7e-04

Table S65.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
8P GAIN MUTATED 1 24 7 13
8P GAIN WILD-TYPE 64 67 71 71

Figure S65.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00619 (Fisher's exact test), Q value = 0.025

Table S66.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
8P GAIN MUTATED 4 22 9 2 8
8P GAIN WILD-TYPE 71 64 60 21 57

Figure S66.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S67.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
8Q GAIN MUTATED 12 8 7 99
8Q GAIN WILD-TYPE 96 83 91 96

Figure S67.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S68.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
8Q GAIN MUTATED 18 49 27 32
8Q GAIN WILD-TYPE 143 88 97 38

Figure S68.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0022

Table S69.  Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
8Q GAIN MUTATED 16 14 5 13 24 16
8Q GAIN WILD-TYPE 89 37 39 38 34 22

Figure S69.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0016

Table S70.  Gene #16: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
8Q GAIN MUTATED 12 24 20 32
8Q GAIN WILD-TYPE 62 89 72 36

Figure S70.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S71.  Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
8Q GAIN MUTATED 14 26 67 19
8Q GAIN WILD-TYPE 81 115 80 89

Figure S71.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00039

Table S72.  Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
8Q GAIN MUTATED 27 74 25
8Q GAIN WILD-TYPE 144 131 90

Figure S72.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00088

Table S73.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
8Q GAIN MUTATED 74 17 15 19
8Q GAIN WILD-TYPE 134 54 108 67

Figure S73.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S74.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
8Q GAIN MUTATED 18 26 18 54 9
8Q GAIN WILD-TYPE 129 72 41 74 47

Figure S74.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S75.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
8Q GAIN MUTATED 6 41 16 20
8Q GAIN WILD-TYPE 59 50 62 64

Figure S75.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0017

Table S76.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
8Q GAIN MUTATED 13 39 15 2 14
8Q GAIN WILD-TYPE 62 47 54 21 51

Figure S76.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S77.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
9P GAIN MUTATED 3 0 0 31
9P GAIN WILD-TYPE 105 91 98 164

Figure S77.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0014

Table S78.  Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
9P GAIN MUTATED 6 8 5 15
9P GAIN WILD-TYPE 155 129 119 55

Figure S78.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.12

Table S79.  Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
9P GAIN MUTATED 3 5 3 1 7 5
9P GAIN WILD-TYPE 102 46 41 50 51 33

Figure S79.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00612 (Fisher's exact test), Q value = 0.025

Table S80.  Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
9P GAIN MUTATED 1 9 18 6
9P GAIN WILD-TYPE 94 132 129 102

Figure S80.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S81.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
9Q GAIN MUTATED 5 1 1 41
9Q GAIN WILD-TYPE 103 90 97 154

Figure S81.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0015

Table S82.  Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
9Q GAIN MUTATED 11 7 12 18
9Q GAIN WILD-TYPE 150 130 112 52

Figure S82.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CNMF'

P value = 0.00782 (Fisher's exact test), Q value = 0.031

Table S83.  Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
9Q GAIN MUTATED 3 7 4 3 8 8
9Q GAIN WILD-TYPE 102 44 40 48 50 30

Figure S83.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0026

Table S84.  Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
9Q GAIN MUTATED 1 15 24 8
9Q GAIN WILD-TYPE 94 126 123 100

Figure S84.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.048

Table S85.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
9Q GAIN MUTATED 10 6 5 23 3
9Q GAIN WILD-TYPE 137 92 54 105 53

Figure S85.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.013

Table S86.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
10P GAIN MUTATED 1 1 0 13
10P GAIN WILD-TYPE 107 90 98 182

Figure S86.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.006

Table S87.  Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
10P GAIN MUTATED 0 9 2 4
10P GAIN WILD-TYPE 161 128 122 66

Figure S87.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.095

Table S88.  Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
10P GAIN MUTATED 1 10 4
10P GAIN WILD-TYPE 170 195 111

Figure S88.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.019

Table S89.  Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
10P GAIN MUTATED 5 3 0 7
10P GAIN WILD-TYPE 203 68 123 79

Figure S89.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.045

Table S90.  Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
10P GAIN MUTATED 1 1 1 8 4
10P GAIN WILD-TYPE 146 97 58 120 52

Figure S90.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.023

Table S91.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
10Q GAIN MUTATED 1 1 0 12
10Q GAIN WILD-TYPE 107 90 98 183

Figure S91.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.024

Table S92.  Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
10Q GAIN MUTATED 0 8 3 3
10Q GAIN WILD-TYPE 161 129 121 67

Figure S92.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.093

Table S93.  Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
10Q GAIN MUTATED 1 10 3
10Q GAIN WILD-TYPE 170 195 112

Figure S93.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.042

Table S94.  Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
10Q GAIN MUTATED 5 3 0 6
10Q GAIN WILD-TYPE 203 68 123 80

Figure S94.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S95.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
11P GAIN MUTATED 2 0 1 24
11P GAIN WILD-TYPE 106 91 97 171

Figure S95.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.053

Table S96.  Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
11P GAIN MUTATED 4 9 5 9
11P GAIN WILD-TYPE 157 128 119 61

Figure S96.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.064

Table S97.  Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
11P GAIN MUTATED 4 18 5
11P GAIN WILD-TYPE 167 187 110

Figure S97.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.095

Table S98.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
11P GAIN MUTATED 4 6 4 12 0
11P GAIN WILD-TYPE 143 92 55 116 56

Figure S98.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.07

Table S99.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
11P GAIN MUTATED 1 9 6 1
11P GAIN WILD-TYPE 64 82 72 83

Figure S99.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S100.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
11Q GAIN MUTATED 2 0 1 27
11Q GAIN WILD-TYPE 106 91 97 168

Figure S100.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.099

Table S101.  Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
11Q GAIN MUTATED 5 10 6 9
11Q GAIN WILD-TYPE 156 127 118 61

Figure S101.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0325 (Fisher's exact test), Q value = 0.092

Table S102.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
11Q GAIN MUTATED 5 7 4 13 0
11Q GAIN WILD-TYPE 142 91 55 115 56

Figure S102.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.11

Table S103.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
11Q GAIN MUTATED 1 9 7 2
11Q GAIN WILD-TYPE 64 82 71 82

Figure S103.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.013

Table S104.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
12P GAIN MUTATED 1 1 0 13
12P GAIN WILD-TYPE 107 90 98 182

Figure S104.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00298 (Fisher's exact test), Q value = 0.015

Table S105.  Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
12P GAIN MUTATED 2 5 1 7
12P GAIN WILD-TYPE 159 132 123 63

Figure S105.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.04

Table S106.  Gene #23: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
12P GAIN MUTATED 0 3 1 0 4 0
12P GAIN WILD-TYPE 105 48 43 51 54 38

Figure S106.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00376 (Fisher's exact test), Q value = 0.017

Table S107.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
12P GAIN MUTATED 2 1 1 11 0
12P GAIN WILD-TYPE 145 97 58 117 56

Figure S107.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0087

Table S108.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
12Q GAIN MUTATED 2 1 0 15
12Q GAIN WILD-TYPE 106 90 98 180

Figure S108.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.015

Table S109.  Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
12Q GAIN MUTATED 6 5 0 7
12Q GAIN WILD-TYPE 155 132 124 63

Figure S109.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.00898 (Fisher's exact test), Q value = 0.034

Table S110.  Gene #24: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
12Q GAIN MUTATED 0 3 1 1 6 1
12Q GAIN WILD-TYPE 105 48 43 50 52 37

Figure S110.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.092

Table S111.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
12Q GAIN MUTATED 4 1 3 10 0
12Q GAIN WILD-TYPE 143 97 56 118 56

Figure S111.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00437 (Fisher's exact test), Q value = 0.019

Table S112.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
12Q GAIN MUTATED 2 10 0 1 1
12Q GAIN WILD-TYPE 73 76 69 22 64

Figure S112.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.11

Table S113.  Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
13Q GAIN MUTATED 0 2 3 3
13Q GAIN WILD-TYPE 161 135 121 67

Figure S113.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0085

Table S114.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
14Q GAIN MUTATED 0 0 0 10
14Q GAIN WILD-TYPE 108 91 98 185

Figure S114.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.038

Table S115.  Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
14Q GAIN MUTATED 0 1 8 1
14Q GAIN WILD-TYPE 95 140 139 107

Figure S115.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S116.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
16P GAIN MUTATED 3 1 1 27
16P GAIN WILD-TYPE 105 90 97 168

Figure S116.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00531 (Fisher's exact test), Q value = 0.023

Table S117.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
16P GAIN MUTATED 2 5 6 14 4
16P GAIN WILD-TYPE 145 93 53 114 52

Figure S117.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.11

Table S118.  Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
16P GAIN MUTATED 0 6 7 8
16P GAIN WILD-TYPE 65 85 71 76

Figure S118.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.075

Table S119.  Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
16Q GAIN MUTATED 1 1 1 4
16Q GAIN WILD-TYPE 160 136 123 66

Figure S119.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.087

Table S120.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
16Q GAIN MUTATED 0 0 1 5 1
16Q GAIN WILD-TYPE 147 98 58 123 55

Figure S120.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.052

Table S121.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
17P GAIN MUTATED 1 0 4 3 0
17P GAIN WILD-TYPE 146 98 55 125 56

Figure S121.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.039

Table S122.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
17P GAIN MUTATED 0 5 0 1 0
17P GAIN WILD-TYPE 75 81 69 22 65

Figure S122.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.12

Table S123.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
17Q GAIN MUTATED 1 0 1 9
17Q GAIN WILD-TYPE 107 91 97 186

Figure S123.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'CN_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0052

Table S124.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
18P GAIN MUTATED 2 0 1 16
18P GAIN WILD-TYPE 106 91 97 179

Figure S124.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0026

Table S125.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
19P GAIN MUTATED 0 0 0 12
19P GAIN WILD-TYPE 108 91 98 183

Figure S125.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.00362 (Fisher's exact test), Q value = 0.017

Table S126.  Gene #34: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
19P GAIN MUTATED 0 3 1 0 1 4
19P GAIN WILD-TYPE 105 48 43 51 57 34

Figure S126.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0028

Table S127.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
19Q GAIN MUTATED 0 0 0 12
19Q GAIN WILD-TYPE 108 91 98 183

Figure S127.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.11

Table S128.  Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
19Q GAIN MUTATED 1 2 1 0 1 4
19Q GAIN WILD-TYPE 104 49 43 51 57 34

Figure S128.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S129.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
20P GAIN MUTATED 1 0 2 23
20P GAIN WILD-TYPE 107 91 96 172

Figure S129.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.1

Table S130.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
20P GAIN MUTATED 3 12 6 5
20P GAIN WILD-TYPE 158 125 118 65

Figure S130.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.0088

Table S131.  Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
20P GAIN MUTATED 1 5 17 3
20P GAIN WILD-TYPE 94 136 130 105

Figure S131.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.097

Table S132.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
20P GAIN MUTATED 4 17 5
20P GAIN WILD-TYPE 167 188 110

Figure S132.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.05

Table S133.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
20P GAIN MUTATED 18 1 2 4
20P GAIN WILD-TYPE 190 70 121 82

Figure S133.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00434 (Fisher's exact test), Q value = 0.019

Table S134.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
20P GAIN MUTATED 3 5 1 15 1
20P GAIN WILD-TYPE 144 93 58 113 55

Figure S134.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S135.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
20Q GAIN MUTATED 1 0 2 26
20Q GAIN WILD-TYPE 107 91 96 169

Figure S135.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00776 (Fisher's exact test), Q value = 0.03

Table S136.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
20Q GAIN MUTATED 4 14 4 7
20Q GAIN WILD-TYPE 157 123 120 63

Figure S136.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.00917 (Fisher's exact test), Q value = 0.035

Table S137.  Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
20Q GAIN MUTATED 5 2 4 0 10 3
20Q GAIN WILD-TYPE 100 49 40 51 48 35

Figure S137.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.1

Table S138.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
20Q GAIN MUTATED 3 6 16 4
20Q GAIN WILD-TYPE 92 135 131 104

Figure S138.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00664 (Fisher's exact test), Q value = 0.026

Table S139.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
20Q GAIN MUTATED 4 8 1 15 1
20Q GAIN WILD-TYPE 143 90 58 113 55

Figure S139.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S140.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
21Q GAIN MUTATED 0 0 1 20
21Q GAIN WILD-TYPE 108 91 97 175

Figure S140.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00862 (Fisher's exact test), Q value = 0.033

Table S141.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
21Q GAIN MUTATED 2 6 5 8
21Q GAIN WILD-TYPE 159 131 119 62

Figure S141.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.08

Table S142.  Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
21Q GAIN MUTATED 2 13 6
21Q GAIN WILD-TYPE 169 192 109

Figure S142.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00318 (Fisher's exact test), Q value = 0.015

Table S143.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
21Q GAIN MUTATED 1 3 2 13 2
21Q GAIN WILD-TYPE 146 95 57 115 54

Figure S143.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.058

Table S144.  Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
21Q GAIN MUTATED 0 10 3 4
21Q GAIN WILD-TYPE 65 81 75 80

Figure S144.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.063

Table S145.  Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
21Q GAIN MUTATED 2 11 3 0 1
21Q GAIN WILD-TYPE 73 75 66 23 64

Figure S145.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.058

Table S146.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
XP GAIN MUTATED 0 0 0 7
XP GAIN WILD-TYPE 108 91 98 188

Figure S146.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00848 (Fisher's exact test), Q value = 0.033

Table S147.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
XP GAIN MUTATED 0 2 1 4
XP GAIN WILD-TYPE 161 135 123 66

Figure S147.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 0.11

Table S148.  Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
XP GAIN MUTATED 0 2 0 5 0
XP GAIN WILD-TYPE 147 96 59 123 56

Figure S148.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.062

Table S149.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
XQ GAIN MUTATED 0 0 0 7
XQ GAIN WILD-TYPE 108 91 98 188

Figure S149.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00849 (Fisher's exact test), Q value = 0.033

Table S150.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
XQ GAIN MUTATED 0 2 1 4
XQ GAIN WILD-TYPE 161 135 123 66

Figure S150.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.11

Table S151.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
XQ GAIN MUTATED 0 2 0 5 0
XQ GAIN WILD-TYPE 147 96 59 123 56

Figure S151.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S152.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
1P LOSS MUTATED 0 0 0 22
1P LOSS WILD-TYPE 108 91 98 173

Figure S152.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0062

Table S153.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
1P LOSS MUTATED 0 9 9 4
1P LOSS WILD-TYPE 161 128 115 66

Figure S153.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.043

Table S154.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
1P LOSS MUTATED 1 9 11 1
1P LOSS WILD-TYPE 94 132 136 107

Figure S154.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0018

Table S155.  Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
1P LOSS MUTATED 0 13 9
1P LOSS WILD-TYPE 171 192 106

Figure S155.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00973 (Fisher's exact test), Q value = 0.036

Table S156.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
1P LOSS MUTATED 14 3 0 4
1P LOSS WILD-TYPE 194 68 123 82

Figure S156.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00355 (Fisher's exact test), Q value = 0.016

Table S157.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
1P LOSS MUTATED 1 3 4 12 1
1P LOSS WILD-TYPE 146 95 55 116 55

Figure S157.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.082

Table S158.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
1P LOSS MUTATED 0 8 7 3
1P LOSS WILD-TYPE 65 83 71 81

Figure S158.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00304 (Fisher's exact test), Q value = 0.015

Table S159.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
1P LOSS MUTATED 0 11 5 0 2
1P LOSS WILD-TYPE 75 75 64 23 63

Figure S159.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.083

Table S160.  Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
1Q LOSS MUTATED 0 1 4 0
1Q LOSS WILD-TYPE 65 90 74 84

Figure S160.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.005

Table S161.  Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
2P LOSS MUTATED 1 0 0 13
2P LOSS WILD-TYPE 107 91 98 182

Figure S161.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00839 (Fisher's exact test), Q value = 0.033

Table S162.  Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
2P LOSS MUTATED 0 4 6 4
2P LOSS WILD-TYPE 161 133 118 66

Figure S162.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.05

Table S163.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
2P LOSS MUTATED 0 8 3 1
2P LOSS WILD-TYPE 65 83 75 83

Figure S163.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0014

Table S164.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
2Q LOSS MUTATED 2 0 0 16
2Q LOSS WILD-TYPE 106 91 98 179

Figure S164.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.067

Table S165.  Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
2Q LOSS MUTATED 1 5 7 5
2Q LOSS WILD-TYPE 160 132 117 65

Figure S165.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.096

Table S166.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
2Q LOSS MUTATED 3 2 0 10 3
2Q LOSS WILD-TYPE 144 96 59 118 53

Figure S166.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00708 (Fisher's exact test), Q value = 0.028

Table S167.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
2Q LOSS MUTATED 0 10 3 2
2Q LOSS WILD-TYPE 65 81 75 82

Figure S167.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 0.1

Table S168.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
3P LOSS MUTATED 0 5 4
3P LOSS WILD-TYPE 171 200 111

Figure S168.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.058

Table S169.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
3P LOSS MUTATED 4 4 0 0
3P LOSS WILD-TYPE 204 67 123 86

Figure S169.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.067

Table S170.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
3Q LOSS MUTATED 1 3 0 0
3Q LOSS WILD-TYPE 207 68 123 86

Figure S170.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.092

Table S171.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
3Q LOSS MUTATED 0 3 1 0 0
3Q LOSS WILD-TYPE 147 95 58 128 56

Figure S171.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S172.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
4P LOSS MUTATED 1 0 0 22
4P LOSS WILD-TYPE 107 91 98 173

Figure S172.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.11

Table S173.  Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
4P LOSS MUTATED 2 9 7 5
4P LOSS WILD-TYPE 159 128 117 65

Figure S173.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0069

Table S174.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
4P LOSS MUTATED 0 11 11 1
4P LOSS WILD-TYPE 95 130 136 107

Figure S174.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0404 (Fisher's exact test), Q value = 0.1

Table S175.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
4P LOSS MUTATED 3 11 9
4P LOSS WILD-TYPE 168 194 106

Figure S175.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S176.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
4P LOSS MUTATED 21 1 1 0
4P LOSS WILD-TYPE 187 70 122 86

Figure S176.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00287 (Fisher's exact test), Q value = 0.015

Table S177.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
4P LOSS MUTATED 6 1 2 14 0
4P LOSS WILD-TYPE 141 97 57 114 56

Figure S177.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00377 (Fisher's exact test), Q value = 0.017

Table S178.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
4P LOSS MUTATED 0 11 4 2
4P LOSS WILD-TYPE 65 80 74 82

Figure S178.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0015

Table S179.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
4P LOSS MUTATED 1 13 3 0 0
4P LOSS WILD-TYPE 74 73 66 23 65

Figure S179.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0014

Table S180.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
4Q LOSS MUTATED 1 0 0 15
4Q LOSS WILD-TYPE 107 91 98 180

Figure S180.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0093

Table S181.  Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
4Q LOSS MUTATED 0 6 10 0
4Q LOSS WILD-TYPE 95 135 137 108

Figure S181.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0468 (Fisher's exact test), Q value = 0.12

Table S182.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
4Q LOSS MUTATED 3 1 1 10 1
4Q LOSS WILD-TYPE 144 97 58 118 55

Figure S182.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.11

Table S183.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
4Q LOSS MUTATED 2 8 2 0 0
4Q LOSS WILD-TYPE 73 78 67 23 65

Figure S183.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.017

Table S184.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
5P LOSS MUTATED 1 0 0 11
5P LOSS WILD-TYPE 107 91 98 184

Figure S184.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00575 (Fisher's exact test), Q value = 0.024

Table S185.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
5P LOSS MUTATED 0 6 6
5P LOSS WILD-TYPE 171 199 109

Figure S185.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00329 (Fisher's exact test), Q value = 0.016

Table S186.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
5P LOSS MUTATED 0 1 4 6 0
5P LOSS WILD-TYPE 147 97 55 122 56

Figure S186.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.12

Table S187.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
5P LOSS MUTATED 0 5 3 1 0
5P LOSS WILD-TYPE 75 81 66 22 65

Figure S187.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S188.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
5Q LOSS MUTATED 1 0 0 22
5Q LOSS WILD-TYPE 107 91 98 173

Figure S188.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.058

Table S189.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
5Q LOSS MUTATED 2 7 7 7
5Q LOSS WILD-TYPE 159 130 117 63

Figure S189.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.089

Table S190.  Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
5Q LOSS MUTATED 1 6 13 3
5Q LOSS WILD-TYPE 94 135 134 105

Figure S190.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00191 (Fisher's exact test), Q value = 0.011

Table S191.  Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
5Q LOSS MUTATED 1 15 7
5Q LOSS WILD-TYPE 170 190 108

Figure S191.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.04

Table S192.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
5Q LOSS MUTATED 17 2 2 1
5Q LOSS WILD-TYPE 191 69 121 85

Figure S192.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0039

Table S193.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
5Q LOSS MUTATED 1 2 6 12 1
5Q LOSS WILD-TYPE 146 96 53 116 55

Figure S193.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S194.  Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
6P LOSS MUTATED 2 0 1 23
6P LOSS WILD-TYPE 106 91 97 172

Figure S194.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.043

Table S195.  Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
6P LOSS MUTATED 2 9 8 7
6P LOSS WILD-TYPE 159 128 116 63

Figure S195.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0028 (Fisher's exact test), Q value = 0.014

Table S196.  Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
6P LOSS MUTATED 2 13 11
6P LOSS WILD-TYPE 169 192 104

Figure S196.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 0.11

Table S197.  Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
6P LOSS MUTATED 0 9 4 4
6P LOSS WILD-TYPE 65 82 74 80

Figure S197.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.053

Table S198.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
6P LOSS MUTATED 1 11 2 0 3
6P LOSS WILD-TYPE 74 75 67 23 62

Figure S198.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S199.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
6Q LOSS MUTATED 2 0 5 34
6Q LOSS WILD-TYPE 106 91 93 161

Figure S199.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.049

Table S200.  Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
6Q LOSS MUTATED 5 15 12 9
6Q LOSS WILD-TYPE 156 122 112 61

Figure S200.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.082

Table S201.  Gene #53: '6q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
6Q LOSS MUTATED 4 9 3 11
6Q LOSS WILD-TYPE 70 104 89 57

Figure S201.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00952 (Fisher's exact test), Q value = 0.036

Table S202.  Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
6Q LOSS MUTATED 4 12 21 4
6Q LOSS WILD-TYPE 91 129 126 104

Figure S202.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.005

Table S203.  Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
6Q LOSS MUTATED 4 25 12
6Q LOSS WILD-TYPE 167 180 103

Figure S203.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.05

Table S204.  Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
6Q LOSS MUTATED 1 14 5 9
6Q LOSS WILD-TYPE 64 77 73 75

Figure S204.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00612 (Fisher's exact test), Q value = 0.025

Table S205.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
6Q LOSS MUTATED 5 16 2 0 6
6Q LOSS WILD-TYPE 70 70 67 23 59

Figure S205.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S206.  Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
8P LOSS MUTATED 53 7 27 84
8P LOSS WILD-TYPE 55 84 71 111

Figure S206.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S207.  Gene #54: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
8P LOSS MUTATED 29 48 62 32
8P LOSS WILD-TYPE 132 89 62 38

Figure S207.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S208.  Gene #54: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
8P LOSS MUTATED 22 72 49 28
8P LOSS WILD-TYPE 73 69 98 80

Figure S208.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S209.  Gene #54: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
8P LOSS MUTATED 41 69 61
8P LOSS WILD-TYPE 130 136 54

Figure S209.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.045

Table S210.  Gene #54: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
8P LOSS MUTATED 83 17 34 36
8P LOSS WILD-TYPE 125 54 89 50

Figure S210.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.002

Table S211.  Gene #55: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
8Q LOSS MUTATED 0 6 12 3
8Q LOSS WILD-TYPE 161 131 112 67

Figure S211.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0028

Table S212.  Gene #55: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
8Q LOSS MUTATED 1 15 4 1
8Q LOSS WILD-TYPE 94 126 143 107

Figure S212.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0051

Table S213.  Gene #55: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
8Q LOSS MUTATED 2 7 12
8Q LOSS WILD-TYPE 169 198 103

Figure S213.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0022

Table S214.  Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
9P LOSS MUTATED 1 1 1 18
9P LOSS WILD-TYPE 107 90 97 177

Figure S214.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00541 (Fisher's exact test), Q value = 0.023

Table S215.  Gene #56: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
9P LOSS MUTATED 2 1 3 8
9P LOSS WILD-TYPE 72 112 89 60

Figure S215.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.067

Table S216.  Gene #56: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
9P LOSS MUTATED 3 8 10
9P LOSS WILD-TYPE 168 197 105

Figure S216.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.12

Table S217.  Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
9Q LOSS MUTATED 1 0 1 9
9Q LOSS WILD-TYPE 107 91 97 186

Figure S217.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.05

Table S218.  Gene #57: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
9Q LOSS MUTATED 2 4 0 0 0 3
9Q LOSS WILD-TYPE 103 47 44 51 58 35

Figure S218.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S219.  Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
10P LOSS MUTATED 7 0 1 33
10P LOSS WILD-TYPE 101 91 97 162

Figure S219.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S220.  Gene #58: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
10P LOSS MUTATED 2 10 20 9
10P LOSS WILD-TYPE 159 127 104 61

Figure S220.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00079

Table S221.  Gene #58: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
10P LOSS MUTATED 2 20 17 2
10P LOSS WILD-TYPE 93 121 130 106

Figure S221.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0014

Table S222.  Gene #58: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
10P LOSS MUTATED 3 22 16
10P LOSS WILD-TYPE 168 183 99

Figure S222.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S223.  Gene #58: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
10P LOSS MUTATED 26 4 0 9
10P LOSS WILD-TYPE 182 67 123 77

Figure S223.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00062

Table S224.  Gene #58: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
10P LOSS MUTATED 3 5 7 22 2
10P LOSS WILD-TYPE 144 93 52 106 54

Figure S224.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.041

Table S225.  Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
10P LOSS MUTATED 0 8 6 11
10P LOSS WILD-TYPE 65 83 72 73

Figure S225.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0077

Table S226.  Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
10P LOSS MUTATED 0 13 6 0 6
10P LOSS WILD-TYPE 75 73 63 23 59

Figure S226.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S227.  Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
10Q LOSS MUTATED 6 0 3 34
10Q LOSS WILD-TYPE 102 91 95 161

Figure S227.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00039

Table S228.  Gene #59: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
10Q LOSS MUTATED 3 11 18 11
10Q LOSS WILD-TYPE 158 126 106 59

Figure S228.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.005

Table S229.  Gene #59: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
10Q LOSS MUTATED 2 21 16 4
10Q LOSS WILD-TYPE 93 120 131 104

Figure S229.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0035

Table S230.  Gene #59: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
10Q LOSS MUTATED 5 20 18
10Q LOSS WILD-TYPE 166 185 97

Figure S230.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00039

Table S231.  Gene #59: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
10Q LOSS MUTATED 26 2 1 12
10Q LOSS WILD-TYPE 182 69 122 74

Figure S231.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0077

Table S232.  Gene #59: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
10Q LOSS MUTATED 5 4 6 21 5
10Q LOSS WILD-TYPE 142 94 53 107 51

Figure S232.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.013

Table S233.  Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
10Q LOSS MUTATED 0 11 6 13
10Q LOSS WILD-TYPE 65 80 72 71

Figure S233.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00395 (Fisher's exact test), Q value = 0.018

Table S234.  Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
10Q LOSS MUTATED 1 14 7 0 8
10Q LOSS WILD-TYPE 74 72 62 23 57

Figure S234.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.12

Table S235.  Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
11P LOSS MUTATED 0 5 0 0 1
11P LOSS WILD-TYPE 75 81 69 23 64

Figure S235.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'RPPA_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.1

Table S236.  Gene #61: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
11Q LOSS MUTATED 0 0 0 0 1 2
11Q LOSS WILD-TYPE 105 51 44 51 57 36

Figure S236.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0011

Table S237.  Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
12P LOSS MUTATED 8 1 6 32
12P LOSS WILD-TYPE 100 90 92 163

Figure S237.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.094

Table S238.  Gene #62: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
12P LOSS MUTATED 3 20 15 9
12P LOSS WILD-TYPE 92 121 132 99

Figure S238.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.11

Table S239.  Gene #62: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
12P LOSS MUTATED 27 2 8 7
12P LOSS WILD-TYPE 181 69 115 79

Figure S239.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.049

Table S240.  Gene #62: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
12P LOSS MUTATED 12 4 11 15 2
12P LOSS WILD-TYPE 135 94 48 113 54

Figure S240.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.049

Table S241.  Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
12P LOSS MUTATED 3 17 6 5
12P LOSS WILD-TYPE 62 74 72 79

Figure S241.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0084

Table S242.  Gene #63: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
12Q LOSS MUTATED 3 0 1 16
12Q LOSS WILD-TYPE 105 91 97 179

Figure S242.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.12

Table S243.  Gene #63: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
12Q LOSS MUTATED 3 4 6 5 0
12Q LOSS WILD-TYPE 144 94 53 123 56

Figure S243.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S244.  Gene #64: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
13Q LOSS MUTATED 5 2 7 64
13Q LOSS WILD-TYPE 103 89 91 131

Figure S244.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.053

Table S245.  Gene #64: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
13Q LOSS MUTATED 18 18 23 19
13Q LOSS WILD-TYPE 143 119 101 51

Figure S245.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.013

Table S246.  Gene #64: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
13Q LOSS MUTATED 11 8 6 3 12 14
13Q LOSS WILD-TYPE 94 43 38 48 46 24

Figure S246.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.038

Table S247.  Gene #64: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
13Q LOSS MUTATED 10 22 6 16
13Q LOSS WILD-TYPE 64 91 86 52

Figure S247.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.046

Table S248.  Gene #64: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
13Q LOSS MUTATED 43 13 13 7
13Q LOSS WILD-TYPE 165 58 110 79

Figure S248.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0263 (Fisher's exact test), Q value = 0.078

Table S249.  Gene #64: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
13Q LOSS MUTATED 16 15 9 31 5
13Q LOSS WILD-TYPE 131 83 50 97 51

Figure S249.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.086

Table S250.  Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
13Q LOSS MUTATED 4 21 12 16
13Q LOSS WILD-TYPE 61 70 66 68

Figure S250.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00342 (Fisher's exact test), Q value = 0.016

Table S251.  Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
13Q LOSS MUTATED 6 25 13 2 7
13Q LOSS WILD-TYPE 69 61 56 21 58

Figure S251.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0024

Table S252.  Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
14Q LOSS MUTATED 5 1 0 19
14Q LOSS WILD-TYPE 103 90 98 176

Figure S252.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.072

Table S253.  Gene #65: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
14Q LOSS MUTATED 3 7 7 8
14Q LOSS WILD-TYPE 158 130 117 62

Figure S253.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S254.  Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
15Q LOSS MUTATED 3 0 1 31
15Q LOSS WILD-TYPE 105 91 97 164

Figure S254.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.016

Table S255.  Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
15Q LOSS MUTATED 3 12 11 9
15Q LOSS WILD-TYPE 158 125 113 61

Figure S255.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.01

Table S256.  Gene #66: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
15Q LOSS MUTATED 3 7 3 0 5 7
15Q LOSS WILD-TYPE 102 44 41 51 53 31

Figure S256.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.01

Table S257.  Gene #66: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
15Q LOSS MUTATED 4 9 20 2
15Q LOSS WILD-TYPE 91 132 127 106

Figure S257.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.039

Table S258.  Gene #66: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
15Q LOSS MUTATED 5 22 8
15Q LOSS WILD-TYPE 166 183 107

Figure S258.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00486 (Fisher's exact test), Q value = 0.021

Table S259.  Gene #66: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
15Q LOSS MUTATED 20 6 1 7
15Q LOSS WILD-TYPE 188 65 122 79

Figure S259.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.043

Table S260.  Gene #66: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
15Q LOSS MUTATED 3 7 3 15 6
15Q LOSS WILD-TYPE 144 91 56 113 50

Figure S260.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.015

Table S261.  Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
15Q LOSS MUTATED 0 14 6 7
15Q LOSS WILD-TYPE 65 77 72 77

Figure S261.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.095

Table S262.  Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
15Q LOSS MUTATED 2 13 6 0 6
15Q LOSS WILD-TYPE 73 73 63 23 59

Figure S262.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S263.  Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
16P LOSS MUTATED 8 0 0 23
16P LOSS WILD-TYPE 100 91 98 172

Figure S263.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S264.  Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
16Q LOSS MUTATED 27 1 6 73
16Q LOSS WILD-TYPE 81 90 92 122

Figure S264.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S265.  Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
16Q LOSS MUTATED 15 34 32 26
16Q LOSS WILD-TYPE 146 103 92 44

Figure S265.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.0036 (Fisher's exact test), Q value = 0.017

Table S266.  Gene #68: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
16Q LOSS MUTATED 12 38 41 16
16Q LOSS WILD-TYPE 83 103 106 92

Figure S266.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.085

Table S267.  Gene #68: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
16Q LOSS MUTATED 26 51 30
16Q LOSS WILD-TYPE 145 154 85

Figure S267.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.023

Table S268.  Gene #68: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
16Q LOSS MUTATED 59 11 16 19
16Q LOSS WILD-TYPE 149 60 107 67

Figure S268.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0031

Table S269.  Gene #68: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
16Q LOSS MUTATED 20 15 18 42 10
16Q LOSS WILD-TYPE 127 83 41 86 46

Figure S269.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.013

Table S270.  Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
16Q LOSS MUTATED 6 31 17 17
16Q LOSS WILD-TYPE 59 60 61 67

Figure S270.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S271.  Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
17P LOSS MUTATED 11 1 3 61
17P LOSS WILD-TYPE 97 90 95 134

Figure S271.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S272.  Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
17P LOSS MUTATED 10 19 27 20
17P LOSS WILD-TYPE 151 118 97 50

Figure S272.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0016

Table S273.  Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
17P LOSS MUTATED 8 34 27 7
17P LOSS WILD-TYPE 87 107 120 101

Figure S273.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.0087

Table S274.  Gene #69: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
17P LOSS MUTATED 16 31 29
17P LOSS WILD-TYPE 155 174 86

Figure S274.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.093

Table S275.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
17P LOSS MUTATED 15 11 10 30 9
17P LOSS WILD-TYPE 132 87 49 98 47

Figure S275.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.05

Table S276.  Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
17P LOSS MUTATED 3 20 13 16
17P LOSS WILD-TYPE 62 71 65 68

Figure S276.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0029

Table S277.  Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
17Q LOSS MUTATED 1 0 2 17
17Q LOSS WILD-TYPE 107 91 96 178

Figure S277.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0094

Table S278.  Gene #70: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
17Q LOSS MUTATED 0 9 7 4
17Q LOSS WILD-TYPE 161 128 117 66

Figure S278.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.011

Table S279.  Gene #70: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
17Q LOSS MUTATED 1 7 12 0
17Q LOSS WILD-TYPE 94 134 135 108

Figure S279.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.097

Table S280.  Gene #70: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
17Q LOSS MUTATED 2 11 7
17Q LOSS WILD-TYPE 169 194 108

Figure S280.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.00985 (Fisher's exact test), Q value = 0.036

Table S281.  Gene #70: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
17Q LOSS MUTATED 12 5 0 3
17Q LOSS WILD-TYPE 196 66 123 83

Figure S281.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0457 (Fisher's exact test), Q value = 0.11

Table S282.  Gene #70: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
17Q LOSS MUTATED 1 7 2 7 3
17Q LOSS WILD-TYPE 146 91 57 121 53

Figure S282.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S283.  Gene #71: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
18P LOSS MUTATED 15 1 2 49
18P LOSS WILD-TYPE 93 90 96 146

Figure S283.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.00914 (Fisher's exact test), Q value = 0.035

Table S284.  Gene #71: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
18P LOSS MUTATED 11 20 22 14
18P LOSS WILD-TYPE 150 117 102 56

Figure S284.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00212 (Fisher's exact test), Q value = 0.011

Table S285.  Gene #71: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
18P LOSS MUTATED 8 11 7 19
18P LOSS WILD-TYPE 66 102 85 49

Figure S285.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0069

Table S286.  Gene #71: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
18P LOSS MUTATED 6 21 32 8
18P LOSS WILD-TYPE 89 120 115 100

Figure S286.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0349 (Fisher's exact test), Q value = 0.096

Table S287.  Gene #71: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
18P LOSS MUTATED 15 7 12 24 8
18P LOSS WILD-TYPE 132 91 47 104 48

Figure S287.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0052

Table S288.  Gene #71: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
18P LOSS MUTATED 1 21 11 12
18P LOSS WILD-TYPE 64 70 67 72

Figure S288.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 0.1

Table S289.  Gene #71: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
18P LOSS MUTATED 7 19 10 0 9
18P LOSS WILD-TYPE 68 67 59 23 56

Figure S289.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S290.  Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
18Q LOSS MUTATED 22 1 3 74
18Q LOSS WILD-TYPE 86 90 95 121

Figure S290.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.0092

Table S291.  Gene #72: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
18Q LOSS MUTATED 18 31 36 15
18Q LOSS WILD-TYPE 143 106 88 55

Figure S291.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.099

Table S292.  Gene #72: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 105 51 44 51 58 38
18Q LOSS MUTATED 12 15 6 10 14 11
18Q LOSS WILD-TYPE 93 36 38 41 44 27

Figure S292.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0064

Table S293.  Gene #72: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 74 113 92 68
18Q LOSS MUTATED 10 22 11 25
18Q LOSS WILD-TYPE 64 91 81 43

Figure S293.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.015

Table S294.  Gene #72: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
18Q LOSS MUTATED 12 32 42 14
18Q LOSS WILD-TYPE 83 109 105 94

Figure S294.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.087

Table S295.  Gene #72: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
18Q LOSS MUTATED 24 47 29
18Q LOSS WILD-TYPE 147 158 86

Figure S295.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0084

Table S296.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
18Q LOSS MUTATED 55 11 12 20
18Q LOSS WILD-TYPE 153 60 111 66

Figure S296.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00304 (Fisher's exact test), Q value = 0.015

Table S297.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
18Q LOSS MUTATED 21 12 17 37 11
18Q LOSS WILD-TYPE 126 86 42 91 45

Figure S297.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0052

Table S298.  Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
18Q LOSS MUTATED 4 29 17 17
18Q LOSS WILD-TYPE 61 62 61 67

Figure S298.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.0078

Table S299.  Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
18Q LOSS MUTATED 8 31 13 2 13
18Q LOSS WILD-TYPE 67 55 56 21 52

Figure S299.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S300.  Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
19P LOSS MUTATED 0 0 1 18
19P LOSS WILD-TYPE 108 91 97 177

Figure S300.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.049

Table S301.  Gene #73: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
19P LOSS MUTATED 13 2 0 3
19P LOSS WILD-TYPE 195 69 123 83

Figure S301.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S302.  Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
19Q LOSS MUTATED 0 0 1 17
19Q LOSS WILD-TYPE 108 91 97 178

Figure S302.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.067

Table S303.  Gene #74: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
19Q LOSS MUTATED 12 2 0 3
19Q LOSS WILD-TYPE 196 69 123 83

Figure S303.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.015

Table S304.  Gene #75: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
20P LOSS MUTATED 3 4 3 9
20P LOSS WILD-TYPE 158 133 121 61

Figure S304.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q loss' versus 'CN_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.12

Table S305.  Gene #76: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
20Q LOSS MUTATED 0 1 0 7
20Q LOSS WILD-TYPE 108 90 98 188

Figure S305.  Get High-res Image Gene #76: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0092

Table S306.  Gene #76: '20q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
20Q LOSS MUTATED 0 1 2 5
20Q LOSS WILD-TYPE 161 136 122 65

Figure S306.  Get High-res Image Gene #76: '20q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.11

Table S307.  Gene #76: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
20Q LOSS MUTATED 0 4 4
20Q LOSS WILD-TYPE 171 201 111

Figure S307.  Get High-res Image Gene #76: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.015

Table S308.  Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
21Q LOSS MUTATED 5 0 2 17
21Q LOSS WILD-TYPE 103 91 96 178

Figure S308.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.059

Table S309.  Gene #77: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
21Q LOSS MUTATED 2 12 9 1
21Q LOSS WILD-TYPE 93 129 138 107

Figure S309.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S310.  Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
22Q LOSS MUTATED 6 2 2 37
22Q LOSS WILD-TYPE 102 89 96 158

Figure S310.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.05

Table S311.  Gene #78: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
22Q LOSS MUTATED 5 11 24 7
22Q LOSS WILD-TYPE 90 130 123 101

Figure S311.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0479 (Fisher's exact test), Q value = 0.12

Table S312.  Gene #78: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
22Q LOSS MUTATED 9 25 13
22Q LOSS WILD-TYPE 162 180 102

Figure S312.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.083

Table S313.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
22Q LOSS MUTATED 6 11 7 18 3
22Q LOSS WILD-TYPE 141 87 52 110 53

Figure S313.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.1

Table S314.  Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
22Q LOSS MUTATED 2 12 10 1 4
22Q LOSS WILD-TYPE 73 74 59 22 61

Figure S314.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S315.  Gene #79: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
XP LOSS MUTATED 5 0 0 33
XP LOSS WILD-TYPE 103 91 98 162

Figure S315.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0016

Table S316.  Gene #79: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
XP LOSS MUTATED 2 13 13 10
XP LOSS WILD-TYPE 159 124 111 60

Figure S316.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S317.  Gene #79: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
XP LOSS MUTATED 0 13 23 2
XP LOSS WILD-TYPE 95 128 124 106

Figure S317.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00051

Table S318.  Gene #79: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
XP LOSS MUTATED 2 23 13
XP LOSS WILD-TYPE 169 182 102

Figure S318.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S319.  Gene #79: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
XP LOSS MUTATED 30 1 1 6
XP LOSS WILD-TYPE 178 70 122 80

Figure S319.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.096

Table S320.  Gene #79: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
XP LOSS MUTATED 6 5 5 18 4
XP LOSS WILD-TYPE 141 93 54 110 52

Figure S320.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00575 (Fisher's exact test), Q value = 0.024

Table S321.  Gene #79: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
XP LOSS MUTATED 0 9 2 9
XP LOSS WILD-TYPE 65 82 76 75

Figure S321.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.021

Table S322.  Gene #79: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
XP LOSS MUTATED 1 13 3 0 3
XP LOSS WILD-TYPE 74 73 66 23 62

Figure S322.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S323.  Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 108 91 98 195
XQ LOSS MUTATED 5 0 0 33
XQ LOSS WILD-TYPE 103 91 98 162

Figure S323.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0016

Table S324.  Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 161 137 124 70
XQ LOSS MUTATED 2 13 13 10
XQ LOSS WILD-TYPE 159 124 111 60

Figure S324.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S325.  Gene #80: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 95 141 147 108
XQ LOSS MUTATED 0 13 23 2
XQ LOSS WILD-TYPE 95 128 124 106

Figure S325.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00079

Table S326.  Gene #80: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 205 115
XQ LOSS MUTATED 2 23 13
XQ LOSS WILD-TYPE 169 182 102

Figure S326.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S327.  Gene #80: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 208 71 123 86
XQ LOSS MUTATED 30 1 1 6
XQ LOSS WILD-TYPE 178 70 122 80

Figure S327.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.096

Table S328.  Gene #80: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 147 98 59 128 56
XQ LOSS MUTATED 6 5 5 18 4
XQ LOSS WILD-TYPE 141 93 54 110 52

Figure S328.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00575 (Fisher's exact test), Q value = 0.024

Table S329.  Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 91 78 84
XQ LOSS MUTATED 0 9 2 9
XQ LOSS WILD-TYPE 65 82 76 75

Figure S329.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00533 (Fisher's exact test), Q value = 0.023

Table S330.  Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 75 86 69 23 65
XQ LOSS MUTATED 1 13 3 0 3
XQ LOSS WILD-TYPE 74 73 66 23 62

Figure S330.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/22533740/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/22553796/PRAD-TP.transferedmergedcluster.txt

  • Number of patients = 492

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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