Correlation between copy number variations of arm-level result and molecular subtypes
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1HT2N3Z
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1HT2N3Z
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 12 molecular subtypes across 527 patients, 222 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

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

  • 2p gain cnv correlated to 'CN_CNMF'.

  • 2q gain cnv correlated to 'CN_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • 4p gain cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

  • 4q gain cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 10p gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

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

  • 12q 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'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

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

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

  • 20p 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'.

  • 20q 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'.

  • 21q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 3p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 4p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 6p 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'.

  • 6q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 8p loss cnv correlated to 'CN_CNMF'.

  • 9p 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'.

  • 9q 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'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF'.

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

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

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

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

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

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

  • 18p 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'.

  • 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'.

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

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

  • xq loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 222 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test 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
14q loss 216 (41%) 311 2e-05
(0.0151) 		8e-05
(0.0562) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.0019
(1.00)
12q gain 122 (23%) 405 0.0134
(1.00) 		0.0329
(1.00) 		1e-05
(0.00889) 		5e-05
(0.0359) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		4e-05
(0.0289) 		1e-05
(0.00889) 		0.00027
(0.183)
20p gain 112 (21%) 415 0.117
(1.00) 		0.114
(1.00) 		1e-05
(0.00889) 		2e-05
(0.0151) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		2e-05
(0.0151) 		2e-05
(0.0151) 		0.00015
(0.103)
20q gain 115 (22%) 412 0.0416
(1.00) 		0.0742
(1.00) 		1e-05
(0.00889) 		2e-05
(0.0151) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		2e-05
(0.0151)
6p loss 100 (19%) 427 0.0109
(1.00) 		0.0145
(1.00) 		1e-05
(0.00889) 		6e-05
(0.0428) 		3e-05
(0.022) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.00034
(0.228)
9p loss 149 (28%) 378 0.00375
(1.00) 		0.0367
(1.00) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.00016
(0.11) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		8e-05
(0.0562)
18p loss 93 (18%) 434 0.0568
(1.00) 		0.457
(1.00) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		5e-05
(0.0359) 		1e-05
(0.00889)
18q loss 95 (18%) 432 0.0453
(1.00) 		0.217
(1.00) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		3e-05
(0.022) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		2e-05
(0.0151) 		1e-05
(0.00889)
12p gain 121 (23%) 406 0.0134
(1.00) 		0.0309
(1.00) 		1e-05
(0.00889) 		3e-05
(0.022) 		1e-05
(0.00889) 		6e-05
(0.0428) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.00015
(0.103) 		1e-05
(0.00889) 		0.00038
(0.253)
9q loss 150 (28%) 377 0.0103
(1.00) 		0.0581
(1.00) 		1e-05
(0.00889) 		1e-05
(0.00889) 		2e-05
(0.0151) 		0.00053
(0.349) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		8e-05
(0.0562)
13q loss 71 (13%) 456 0.00336
(1.00) 		0.0466
(1.00) 		1e-05
(0.00889) 		0.0003
(0.202) 		2e-05
(0.0151) 		0.00029
(0.196) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.0733
(1.00) 		0.0003
(0.202)
8q gain 62 (12%) 465 0.228
(1.00) 		0.104
(1.00) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.00012
(0.0832) 		0.00998
(1.00) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		8e-05
(0.0562) 		1e-05
(0.00889) 		0.00039
(0.26)
2p loss 14 (3%) 513 6e-05
(0.0428) 		0.00061
(0.397) 		0.00021
(0.143) 		0.662
(1.00) 		6e-05
(0.0428) 		4e-05
(0.0289) 		1e-05
(0.00889) 		1e-05
(0.00889) 		3e-05
(0.022) 		1e-05
(0.00889) 		0.642
(1.00) 		0.0136
(1.00)
2q loss 14 (3%) 513 0.00021
(0.143) 		0.00067
(0.431) 		0.0015
(0.936) 		1
(1.00) 		0.00012
(0.0832) 		5e-05
(0.0359) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.644
(1.00) 		0.0138
(1.00)
17p loss 46 (9%) 481 0.00014
(0.0966) 		0.00023
(0.156) 		1e-05
(0.00889) 		0.0874
(1.00) 		0.00901
(1.00) 		0.00796
(1.00) 		1e-05
(0.00889) 		1e-05
(0.00889) 		1e-05
(0.00889) 		2e-05
(0.0151) 		0.244
(1.00) 		0.0219
(1.00)
3q gain 61 (12%) 466 0.0124
(1.00) 		0.0304
(1.00) 		1e-05
(0.00889) 		0.0037
(1.00) 		0.0015
(0.936) 		1e-05
(0.00889) 		3e-05
(0.022) 		2e-05
(0.0151) 		1e-05
(0.00889) 		3e-05
(0.022) 		0.00062
(0.403) 		0.0209
(1.00)
6q loss 128 (24%) 399 0.0498
(1.00) 		0.0511
(1.00) 		1e-05
(0.00889) 		0.0059
(1.00) 		2e-05
(0.0151) 		0.00128
(0.803) 		7e-05
(0.0495) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.00096
(0.606) 		0.0002
(0.136) 		0.00695
(1.00)
8p gain 31 (6%) 496 1e-05
(0.00889) 		0.0003
(0.202) 		0.0121
(1.00) 		0.138
(1.00) 		2e-05
(0.0151) 		3e-05
(0.022) 		1e-05
(0.00889) 		0.0339
(1.00) 		0.00057
(0.373) 		0.00938
(1.00)
17q loss 28 (5%) 499 0.00072
(0.462) 		0.00043
(0.285) 		0.00034
(0.228) 		0.537
(1.00) 		0.22
(1.00) 		0.0269
(1.00) 		0.00029
(0.196) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.0002
(0.136) 		0.497
(1.00) 		0.124
(1.00)
19q gain 57 (11%) 470 0.102
(1.00) 		0.224
(1.00) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.00062
(0.403) 		0.0104
(1.00) 		0.00242
(1.00) 		1e-05
(0.00889) 		2e-05
(0.0151) 		0.288
(1.00) 		0.0461
(1.00) 		0.38
(1.00)
22q loss 39 (7%) 488 0.0102
(1.00) 		0.00142
(0.889) 		1e-05
(0.00889) 		0.00348
(1.00) 		0.00426
(1.00) 		0.0881
(1.00) 		1e-05
(0.00889) 		4e-05
(0.0289) 		2e-05
(0.0151) 		0.0223
(1.00) 		0.00882
(1.00) 		0.227
(1.00)
1q gain 51 (10%) 476 0.408
(1.00) 		0.9
(1.00) 		1e-05
(0.00889) 		0.014
(1.00) 		0.12
(1.00) 		0.0885
(1.00) 		2e-05
(0.0151) 		0.00876
(1.00) 		2e-05
(0.0151) 		0.146
(1.00) 		0.00222
(1.00) 		0.304
(1.00)
3p gain 19 (4%) 508 0.0521
(1.00) 		0.433
(1.00) 		8e-05
(0.0562) 		0.542
(1.00) 		0.0171
(1.00) 		0.00342
(1.00) 		0.0085
(1.00) 		3e-05
(0.022) 		7e-05
(0.0495) 		0.00596
(1.00) 		0.0361
(1.00) 		0.00987
(1.00)
7p gain 171 (32%) 356 0.45
(1.00) 		0.859
(1.00) 		1e-05
(0.00889) 		0.00167
(1.00) 		3e-05
(0.022) 		0.0187
(1.00) 		0.00013
(0.0898) 		0.00889
(1.00) 		0.00324
(1.00) 		0.259
(1.00) 		0.0234
(1.00) 		0.554
(1.00)
7q gain 172 (33%) 355 0.452
(1.00) 		0.86
(1.00) 		1e-05
(0.00889) 		0.00479
(1.00) 		3e-05
(0.022) 		0.00718
(1.00) 		0.00011
(0.0763) 		0.00418
(1.00) 		0.00228
(1.00) 		0.101
(1.00) 		0.0672
(1.00) 		0.213
(1.00)
19p gain 51 (10%) 476 0.227
(1.00) 		0.482
(1.00) 		1e-05
(0.00889) 		7e-05
(0.0495) 		0.00851
(1.00) 		0.0642
(1.00) 		0.00457
(1.00) 		0.00042
(0.279) 		0.0001
(0.0696) 		0.523
(1.00) 		0.116
(1.00) 		0.675
(1.00)
3p loss 380 (72%) 147 0.00319
(1.00) 		0.0101
(1.00) 		1e-05
(0.00889) 		0.00074
(0.474) 		0.0238
(1.00) 		0.017
(1.00) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.0857
(1.00) 		0.00681
(1.00) 		0.165
(1.00) 		0.0105
(1.00)
4q loss 65 (12%) 462 0.385
(1.00) 		0.783
(1.00) 		1e-05
(0.00889) 		3e-05
(0.022) 		0.0908
(1.00) 		0.215
(1.00) 		0.00062
(0.403) 		1e-05
(0.00889) 		0.438
(1.00) 		0.024
(1.00) 		0.0484
(1.00) 		0.112
(1.00)
15q loss 36 (7%) 491 0.118
(1.00) 		0.332
(1.00) 		1e-05
(0.00889) 		0.00076
(0.485) 		0.0267
(1.00) 		0.23
(1.00) 		1e-05
(0.00889) 		1e-05
(0.00889) 		0.00065
(0.421) 		0.00799
(1.00) 		0.0023
(1.00) 		0.105
(1.00)
4p gain 13 (2%) 514 0.354
(1.00) 		0.375
(1.00) 		0.311
(1.00) 		0.0179
(1.00) 		0.00034
(0.228) 		0.00101
(0.636) 		0.0001
(0.0696) 		0.116
(1.00) 		0.367
(1.00) 		0.42
(1.00)
4q gain 13 (2%) 514 0.354
(1.00) 		0.458
(1.00) 		0.312
(1.00) 		0.147
(1.00) 		0.00034
(0.228) 		0.00952
(1.00) 		0.00018
(0.123) 		0.24
(1.00) 		0.363
(1.00) 		0.423
(1.00)
1p loss 57 (11%) 470 0.00084
(0.533) 		0.00283
(1.00) 		1e-05
(0.00889) 		0.698
(1.00) 		0.00045
(0.298) 		0.117
(1.00) 		0.132
(1.00) 		0.00016
(0.11) 		0.00725
(1.00) 		0.00052
(0.343) 		0.195
(1.00) 		0.0707
(1.00)
1q loss 36 (7%) 491 0.0109
(1.00) 		0.0109
(1.00) 		4e-05
(0.0289) 		0.369
(1.00) 		0.0112
(1.00) 		0.0501
(1.00) 		0.0041
(1.00) 		1e-05
(0.00889) 		0.0104
(1.00) 		0.00074
(0.474) 		0.345
(1.00) 		0.106
(1.00)
4p loss 72 (14%) 455 0.531
(1.00) 		0.815
(1.00) 		1e-05
(0.00889) 		0.00019
(0.13) 		0.123
(1.00) 		0.675
(1.00) 		0.0015
(0.936) 		0.00087
(0.551) 		0.84
(1.00) 		0.0608
(1.00) 		0.117
(1.00) 		0.13
(1.00)
21q loss 55 (10%) 472 0.0259
(1.00) 		0.0899
(1.00) 		6e-05
(0.0428) 		0.0128
(1.00) 		0.0303
(1.00) 		0.00809
(1.00) 		0.00533
(1.00) 		7e-05
(0.0495) 		0.00351
(1.00) 		0.00381
(1.00) 		0.229
(1.00) 		0.0344
(1.00)
1p gain 24 (5%) 503 0.823
(1.00) 		0.925
(1.00) 		1e-05
(0.00889) 		0.0006
(0.391) 		0.00048
(0.317) 		0.0059
(1.00) 		0.00571
(1.00) 		0.00083
(0.527) 		0.00106
(0.667) 		0.019
(1.00) 		0.00382
(1.00) 		0.107
(1.00)
2p gain 77 (15%) 450 0.703
(1.00) 		0.46
(1.00) 		1e-05
(0.00889) 		0.0845
(1.00) 		0.00933
(1.00) 		0.329
(1.00) 		0.177
(1.00) 		0.0318
(1.00) 		0.402
(1.00) 		0.0205
(1.00) 		0.131
(1.00) 		0.369
(1.00)
2q gain 79 (15%) 448 0.56
(1.00) 		0.267
(1.00) 		1e-05
(0.00889) 		0.176
(1.00) 		0.00946
(1.00) 		0.151
(1.00) 		0.152
(1.00) 		0.0421
(1.00) 		0.541
(1.00) 		0.00586
(1.00) 		0.234
(1.00) 		0.258
(1.00)
5p gain 193 (37%) 334 0.879
(1.00) 		0.925
(1.00) 		8e-05
(0.0562) 		0.27
(1.00) 		0.0905
(1.00) 		0.838
(1.00) 		0.0131
(1.00) 		0.0708
(1.00) 		0.0875
(1.00) 		0.731
(1.00) 		0.107
(1.00) 		0.792
(1.00)
10p gain 17 (3%) 510 5e-05
(0.0359) 		0.254
(1.00) 		0.36
(1.00) 		0.055
(1.00) 		0.00078
(0.497) 		0.00057
(0.373) 		0.0595
(1.00) 		0.0263
(1.00) 		0.531
(1.00) 		0.0226
(1.00)
11p gain 31 (6%) 496 0.232
(1.00) 		0.672
(1.00) 		7e-05
(0.0495) 		0.286
(1.00) 		0.112
(1.00) 		0.355
(1.00) 		0.29
(1.00) 		0.13
(1.00) 		0.21
(1.00) 		0.349
(1.00) 		0.568
(1.00) 		0.0419
(1.00)
11q gain 29 (6%) 498 0.341
(1.00) 		0.907
(1.00) 		0.00018
(0.123) 		0.526
(1.00) 		0.364
(1.00) 		0.888
(1.00) 		0.566
(1.00) 		0.356
(1.00) 		0.539
(1.00) 		0.556
(1.00) 		0.582
(1.00) 		0.286
(1.00)
17p gain 26 (5%) 501 0.0192
(1.00) 		0.00524
(1.00) 		1e-05
(0.00889) 		0.776
(1.00) 		0.295
(1.00) 		0.0811
(1.00) 		0.229
(1.00) 		0.0501
(1.00) 		0.184
(1.00) 		0.424
(1.00) 		0.432
(1.00) 		0.0356
(1.00)
17q gain 33 (6%) 494 0.0678
(1.00) 		0.0261
(1.00) 		6e-05
(0.0428) 		0.224
(1.00) 		0.476
(1.00) 		0.0744
(1.00) 		0.139
(1.00) 		0.0224
(1.00) 		0.108
(1.00) 		0.237
(1.00) 		0.174
(1.00) 		0.0113
(1.00)
21q gain 50 (9%) 477 0.268
(1.00) 		0.208
(1.00) 		1e-05
(0.00889) 		0.00143
(0.894) 		0.00078
(0.497) 		0.31
(1.00) 		0.0007
(0.45) 		0.0081
(1.00) 		0.00986
(1.00) 		0.34
(1.00) 		0.0646
(1.00) 		0.0807
(1.00)
3q loss 99 (19%) 428 0.923
(1.00) 		0.515
(1.00) 		1e-05
(0.00889) 		0.44
(1.00) 		0.153
(1.00) 		0.28
(1.00) 		0.202
(1.00) 		0.025
(1.00) 		0.496
(1.00) 		0.751
(1.00) 		0.316
(1.00) 		0.974
(1.00)
8p loss 137 (26%) 390 0.377
(1.00) 		0.167
(1.00) 		2e-05
(0.0151) 		0.277
(1.00) 		0.197
(1.00) 		0.25
(1.00) 		0.069
(1.00) 		0.00071
(0.456) 		0.0351
(1.00) 		0.0711
(1.00) 		0.206
(1.00) 		0.0308
(1.00)
10p loss 67 (13%) 460 0.173
(1.00) 		0.405
(1.00) 		1e-05
(0.00889) 		0.0812
(1.00) 		0.774
(1.00) 		0.0325
(1.00) 		0.175
(1.00) 		0.00055
(0.361) 		0.0273
(1.00) 		0.0099
(1.00) 		0.193
(1.00) 		0.178
(1.00)
10q loss 89 (17%) 438 0.329
(1.00) 		0.396
(1.00) 		1e-05
(0.00889) 		0.00478
(1.00) 		0.991
(1.00) 		0.0113
(1.00) 		0.111
(1.00) 		0.00087
(0.551) 		0.0513
(1.00) 		0.00738
(1.00) 		0.295
(1.00) 		0.0495
(1.00)
11p loss 18 (3%) 509 3e-05
(0.022) 		0.0247
(1.00) 		0.257
(1.00) 		0.0214
(1.00) 		0.155
(1.00) 		0.0271
(1.00) 		0.137
(1.00) 		0.0108
(1.00) 		0.126
(1.00) 		0.00964
(1.00)
11q loss 23 (4%) 504 0.189
(1.00) 		0.375
(1.00) 		1e-05
(0.00889) 		0.00528
(1.00) 		0.162
(1.00) 		0.0208
(1.00) 		0.0139
(1.00) 		0.00054
(0.355) 		0.0166
(1.00) 		0.00122
(0.766) 		0.0518
(1.00) 		0.00576
(1.00)
19p loss 11 (2%) 516 5e-05
(0.0359) 		0.0312
(1.00) 		0.00317
(1.00) 		0.00209
(1.00) 		0.156
(1.00) 		0.00978
(1.00) 		0.218
(1.00) 		0.0566
(1.00) 		0.128
(1.00) 		0.0468
(1.00)
xq loss 47 (9%) 480 0.024
(1.00) 		0.0643
(1.00) 		2e-05
(0.0151) 		0.0168
(1.00) 		0.176
(1.00) 		0.00882
(1.00) 		0.0546
(1.00) 		0.00336
(1.00) 		0.01
(1.00) 		0.00396
(1.00) 		0.186
(1.00) 		0.029
(1.00)
5q gain 207 (39%) 320 0.336
(1.00) 		0.625
(1.00) 		0.00863
(1.00) 		0.462
(1.00) 		0.396
(1.00) 		0.495
(1.00) 		0.0717
(1.00) 		0.21
(1.00) 		0.54
(1.00) 		0.854
(1.00) 		0.223
(1.00) 		0.394
(1.00)
6p gain 11 (2%) 516 0.0742
(1.00) 		0.445
(1.00) 		0.0437
(1.00) 		0.244
(1.00) 		0.793
(1.00) 		0.798
(1.00) 		0.86
(1.00) 		0.0638
(1.00) 		0.739
(1.00) 		0.28
(1.00)
6q gain 9 (2%) 518 0.158
(1.00) 		0.683
(1.00) 		0.0095
(1.00) 		0.348
(1.00) 		1
(1.00) 		0.851
(1.00) 		1
(1.00) 		0.156
(1.00) 		0.554
(1.00) 		0.534
(1.00)
9p gain 13 (2%) 514 0.308
(1.00) 		0.903
(1.00) 		0.826
(1.00) 		0.71
(1.00) 		0.252
(1.00) 		0.0224
(1.00) 		0.939
(1.00) 		0.35
(1.00) 		0.378
(1.00) 		1
(1.00)
9q gain 12 (2%) 515 0.0931
(1.00) 		0.911
(1.00) 		0.626
(1.00) 		0.455
(1.00) 		0.242
(1.00) 		0.036
(1.00) 		0.816
(1.00) 		0.253
(1.00) 		0.898
(1.00) 		0.615
(1.00)
10q gain 12 (2%) 515 0.00065
(0.421) 		0.114
(1.00) 		0.0484
(1.00) 		0.131
(1.00) 		0.0119
(1.00) 		0.00706
(1.00) 		0.0656
(1.00) 		0.269
(1.00) 		0.58
(1.00) 		0.0408
(1.00)
13q gain 22 (4%) 505 0.391
(1.00) 		0.0389
(1.00) 		0.725
(1.00) 		0.686
(1.00) 		0.0733
(1.00) 		0.296
(1.00) 		0.349
(1.00) 		0.452
(1.00) 		0.648
(1.00) 		0.506
(1.00)
14q gain 16 (3%) 511 0.769
(1.00) 		0.573
(1.00) 		0.0444
(1.00) 		0.348
(1.00) 		0.0283
(1.00) 		0.0456
(1.00) 		0.0202
(1.00) 		0.00059
(0.385) 		0.00229
(1.00) 		0.00679
(1.00) 		0.767
(1.00) 		0.258
(1.00)
15q gain 26 (5%) 501 1
(1.00) 		0.117
(1.00) 		0.00499
(1.00) 		0.724
(1.00) 		0.489
(1.00) 		0.611
(1.00) 		0.645
(1.00) 		0.155
(1.00) 		0.871
(1.00) 		0.188
(1.00) 		0.918
(1.00) 		1
(1.00)
16p gain 107 (20%) 420 0.274
(1.00) 		0.379
(1.00) 		0.00066
(0.426) 		0.168
(1.00) 		0.00194
(1.00) 		0.18
(1.00) 		0.0143
(1.00) 		0.00469
(1.00) 		0.0467
(1.00) 		0.0386
(1.00) 		0.184
(1.00) 		0.0831
(1.00)
16q gain 99 (19%) 428 0.234
(1.00) 		0.349
(1.00) 		0.00053
(0.349) 		0.0823
(1.00) 		0.00233
(1.00) 		0.0419
(1.00) 		0.0124
(1.00) 		0.0205
(1.00) 		0.0122
(1.00) 		0.147
(1.00) 		0.0689
(1.00) 		0.189
(1.00)
18p gain 25 (5%) 502 0.314
(1.00) 		0.0755
(1.00) 		0.684
(1.00) 		0.477
(1.00) 		0.849
(1.00) 		0.0228
(1.00) 		0.0806
(1.00) 		0.588
(1.00) 		0.832
(1.00) 		0.628
(1.00) 		0.601
(1.00) 		0.0655
(1.00)
18q gain 25 (5%) 502 0.313
(1.00) 		0.0749
(1.00) 		0.554
(1.00) 		0.558
(1.00) 		0.703
(1.00) 		0.0877
(1.00) 		0.0796
(1.00) 		0.587
(1.00) 		0.931
(1.00) 		0.629
(1.00) 		0.603
(1.00) 		0.0654
(1.00)
22q gain 40 (8%) 487 0.326
(1.00) 		0.218
(1.00) 		0.00042
(0.279) 		0.208
(1.00) 		0.363
(1.00) 		0.949
(1.00) 		0.107
(1.00) 		0.0574
(1.00) 		0.0391
(1.00) 		0.817
(1.00) 		0.449
(1.00) 		0.25
(1.00)
xq gain 31 (6%) 496 0.39
(1.00) 		0.703
(1.00) 		0.0337
(1.00) 		0.292
(1.00) 		0.0232
(1.00) 		0.0186
(1.00) 		0.184
(1.00) 		0.141
(1.00) 		0.34
(1.00) 		0.623
(1.00) 		0.129
(1.00) 		0.0678
(1.00)
5p loss 7 (1%) 520 0.386
(1.00) 		0.29
(1.00) 		0.637
(1.00) 		0.0632
(1.00) 		0.0267
(1.00) 		0.0114
(1.00) 		0.0316
(1.00) 		0.0149
(1.00)
5q loss 6 (1%) 521 0.448
(1.00) 		0.544
(1.00) 		0.498
(1.00) 		0.151
(1.00) 		0.045
(1.00) 		0.0156
(1.00) 		0.0688
(1.00) 		0.0268
(1.00)
7p loss 3 (1%) 524 0.28
(1.00) 		0.0589
(1.00) 		0.165
(1.00) 		0.0549
(1.00) 		0.0817
(1.00) 		0.0629
(1.00) 		0.318
(1.00)
7q loss 4 (1%) 523 0.104
(1.00) 		0.342
(1.00) 		0.0753
(1.00) 		0.232
(1.00) 		0.0482
(1.00) 		0.0859
(1.00) 		0.298
(1.00) 		0.337
(1.00) 		0.0621
(1.00) 		0.313
(1.00)
8q loss 64 (12%) 463 0.645
(1.00) 		0.127
(1.00) 		0.447
(1.00) 		0.0501
(1.00) 		0.288
(1.00) 		0.883
(1.00) 		0.502
(1.00) 		0.252
(1.00) 		0.414
(1.00) 		0.704
(1.00) 		0.131
(1.00) 		0.158
(1.00)
12p loss 4 (1%) 523 0.476
(1.00) 		0.435
(1.00) 		0.79
(1.00) 		0.468
(1.00) 		0.312
(1.00)
12q loss 4 (1%) 523 1
(1.00) 		0.366
(1.00) 		0.319
(1.00) 		1
(1.00) 		1
(1.00) 		0.231
(1.00) 		0.686
(1.00)
16p loss 10 (2%) 517 0.0772
(1.00) 		0.876
(1.00) 		0.0271
(1.00) 		0.0963
(1.00) 		0.295
(1.00) 		0.0558
(1.00) 		0.072
(1.00) 		0.0167
(1.00) 		0.579
(1.00) 		0.867
(1.00)
16q loss 16 (3%) 511 0.0155
(1.00) 		0.909
(1.00) 		0.0307
(1.00) 		0.381
(1.00) 		0.218
(1.00) 		0.0299
(1.00) 		0.0429
(1.00) 		0.01
(1.00) 		0.263
(1.00) 		0.703
(1.00)
19q loss 4 (1%) 523 0.0155
(1.00) 		0.966
(1.00) 		0.078
(1.00) 		0.351
(1.00) 		0.511
(1.00) 		0.827
(1.00) 		0.547
(1.00)
20p loss 8 (2%) 519 0.228
(1.00) 		1
(1.00) 		0.0284
(1.00) 		0.788
(1.00) 		0.0913
(1.00) 		0.217
(1.00) 		0.0121
(1.00) 		0.0884
(1.00)
20q loss 3 (1%) 524 0.277
(1.00) 		0.0578
(1.00) 		0.138
(1.00) 		0.0551
(1.00) 		0.081
(1.00)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
1P GAIN MUTATED 2 1 21
1P GAIN WILD-TYPE 210 151 142

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S2.  Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
1Q GAIN MUTATED 4 2 45
1Q GAIN WILD-TYPE 208 150 118

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
1Q GAIN MUTATED 15 2 32
1Q GAIN WILD-TYPE 200 106 155

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
1Q GAIN MUTATED 3 15 31
1Q GAIN WILD-TYPE 119 191 141

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
2P GAIN MUTATED 14 15 48
2P GAIN WILD-TYPE 198 137 115

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

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
2Q GAIN MUTATED 16 16 47
2Q GAIN WILD-TYPE 196 136 116

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

'3p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
3P GAIN MUTATED 0 11 8
3P GAIN WILD-TYPE 212 141 155

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

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S8.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
3P GAIN MUTATED 0 2 9 1 2 5
3P GAIN WILD-TYPE 120 174 117 27 30 23

Figure S8.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S9.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
3P GAIN MUTATED 3 1 15
3P GAIN WILD-TYPE 119 205 157

Figure S9.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
3Q GAIN MUTATED 4 18 39
3Q GAIN WILD-TYPE 208 134 124

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

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
3Q GAIN MUTATED 7 10 38
3Q GAIN WILD-TYPE 88 188 116

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

'3q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S12.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
3Q GAIN MUTATED 11 12 38
3Q GAIN WILD-TYPE 204 96 149

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S13.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
3Q GAIN MUTATED 6 10 30 3 7 5
3Q GAIN WILD-TYPE 114 166 96 25 25 23

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S14.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
3Q GAIN MUTATED 8 10 42
3Q GAIN WILD-TYPE 114 196 130

Figure S14.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S15.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
3Q GAIN MUTATED 29 13 18
3Q GAIN WILD-TYPE 130 225 85

Figure S15.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.23

Table S16.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
4P GAIN MUTATED 0 7 5
4P GAIN WILD-TYPE 215 101 182

Figure S16.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.07

Table S17.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
4P GAIN MUTATED 2 0 11
4P GAIN WILD-TYPE 120 206 161

Figure S17.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.23

Table S18.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
4Q GAIN MUTATED 0 7 5
4Q GAIN WILD-TYPE 215 101 182

Figure S18.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.12

Table S19.  Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
4Q GAIN MUTATED 2 0 11
4Q GAIN WILD-TYPE 120 206 161

Figure S19.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S20.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
5P GAIN MUTATED 67 44 82
5P GAIN WILD-TYPE 145 108 81

Figure S20.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S21.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
7P GAIN MUTATED 28 56 87
7P GAIN WILD-TYPE 184 96 76

Figure S21.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S22.  Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
7P GAIN MUTATED 21 19 34 34 11 30
7P GAIN WILD-TYPE 79 69 50 41 32 27

Figure S22.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.09

Table S23.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
7P GAIN MUTATED 52 32 82
7P GAIN WILD-TYPE 163 76 105

Figure S23.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S24.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
7Q GAIN MUTATED 29 57 86
7Q GAIN WILD-TYPE 183 95 77

Figure S24.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S25.  Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
7Q GAIN MUTATED 21 21 34 34 10 30
7Q GAIN WILD-TYPE 79 67 50 41 33 27

Figure S25.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.076

Table S26.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
7Q GAIN MUTATED 52 33 82
7Q GAIN WILD-TYPE 163 75 105

Figure S26.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S27.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
8P GAIN MUTATED 1 5 25
8P GAIN WILD-TYPE 211 147 138

Figure S27.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.2

Table S28.  Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
8P GAIN MUTATED 2 4 16
8P GAIN WILD-TYPE 126 71 94

Figure S28.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S29.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
8P GAIN MUTATED 3 5 23
8P GAIN WILD-TYPE 212 103 164

Figure S29.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S30.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
8P GAIN MUTATED 6 1 19 2 2 1
8P GAIN WILD-TYPE 114 175 107 26 30 27

Figure S30.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S31.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
8P GAIN MUTATED 3 4 24
8P GAIN WILD-TYPE 119 202 148

Figure S31.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S32.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
8Q GAIN MUTATED 2 10 50
8Q GAIN WILD-TYPE 210 142 113

Figure S32.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S33.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
8Q GAIN MUTATED 3 11 26
8Q GAIN WILD-TYPE 125 64 84

Figure S33.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.083

Table S34.  Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
8Q GAIN MUTATED 4 10 15 9 1 16
8Q GAIN WILD-TYPE 96 78 69 66 42 41

Figure S34.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S35.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
8Q GAIN MUTATED 6 7 48
8Q GAIN WILD-TYPE 209 101 139

Figure S35.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S36.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
8Q GAIN MUTATED 8 5 42 2 3 1
8Q GAIN WILD-TYPE 112 171 84 26 29 27

Figure S36.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S37.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
8Q GAIN MUTATED 8 9 43
8Q GAIN WILD-TYPE 114 197 129

Figure S37.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S38.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
8Q GAIN MUTATED 29 13 18
8Q GAIN WILD-TYPE 130 225 85

Figure S38.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S39.  Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
8Q GAIN MUTATED 2 1 22
8Q GAIN WILD-TYPE 55 93 67

Figure S39.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.036

Table S40.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
10P GAIN MUTATED 0 5 12
10P GAIN WILD-TYPE 212 147 151

Figure S40.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S41.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
11P GAIN MUTATED 2 11 18
11P GAIN WILD-TYPE 210 141 145

Figure S41.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.12

Table S42.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
11Q GAIN MUTATED 2 12 15
11Q GAIN WILD-TYPE 210 140 148

Figure S42.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S43.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
12P GAIN MUTATED 20 31 70
12P GAIN WILD-TYPE 192 121 93

Figure S43.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S44.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
12P GAIN MUTATED 16 18 42
12P GAIN WILD-TYPE 112 57 68

Figure S44.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S45.  Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
12P GAIN MUTATED 4 17 31 15 6 31
12P GAIN WILD-TYPE 96 71 53 60 37 26

Figure S45.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S46.  Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
12P GAIN MUTATED 21 29 54
12P GAIN WILD-TYPE 74 169 100

Figure S46.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S47.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
12P GAIN MUTATED 25 18 77
12P GAIN WILD-TYPE 190 90 110

Figure S47.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S48.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
12P GAIN MUTATED 24 17 59 4 10 6
12P GAIN WILD-TYPE 96 159 67 24 22 22

Figure S48.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S49.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
12P GAIN MUTATED 21 26 72
12P GAIN WILD-TYPE 101 180 100

Figure S49.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S50.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
12P GAIN MUTATED 47 37 35
12P GAIN WILD-TYPE 112 201 68

Figure S50.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S51.  Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
12P GAIN MUTATED 8 9 36
12P GAIN WILD-TYPE 49 85 53

Figure S51.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S52.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
12Q GAIN MUTATED 20 31 71
12Q GAIN WILD-TYPE 192 121 92

Figure S52.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.036

Table S53.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
12Q GAIN MUTATED 16 18 42
12Q GAIN WILD-TYPE 112 57 68

Figure S53.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S54.  Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
12Q GAIN MUTATED 4 16 31 15 6 33
12Q GAIN WILD-TYPE 96 72 53 60 37 24

Figure S54.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S55.  Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
12Q GAIN MUTATED 21 28 56
12Q GAIN WILD-TYPE 74 170 98

Figure S55.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S56.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
12Q GAIN MUTATED 25 19 77
12Q GAIN WILD-TYPE 190 89 110

Figure S56.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S57.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
12Q GAIN MUTATED 24 17 60 4 10 6
12Q GAIN WILD-TYPE 96 159 66 24 22 22

Figure S57.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S58.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
12Q GAIN MUTATED 20 26 74
12Q GAIN WILD-TYPE 102 180 98

Figure S58.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S59.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
12Q GAIN MUTATED 47 37 36
12Q GAIN WILD-TYPE 112 201 67

Figure S59.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S60.  Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
12Q GAIN MUTATED 8 9 37
12Q GAIN WILD-TYPE 49 85 52

Figure S60.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.18

Table S61.  Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 100 47
12Q GAIN MUTATED 31 10 13
12Q GAIN WILD-TYPE 62 90 34

Figure S61.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S62.  Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
17P GAIN MUTATED 1 9 16
17P GAIN WILD-TYPE 211 143 147

Figure S62.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S63.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
17Q GAIN MUTATED 3 11 19
17Q GAIN WILD-TYPE 209 141 144

Figure S63.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S64.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
19P GAIN MUTATED 4 13 34
19P GAIN WILD-TYPE 208 139 129

Figure S64.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S65.  Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
19P GAIN MUTATED 7 3 24
19P GAIN WILD-TYPE 121 72 86

Figure S65.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.07

Table S66.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
19P GAIN MUTATED 10 9 31
19P GAIN WILD-TYPE 112 197 141

Figure S66.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S67.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
19Q GAIN MUTATED 4 13 40
19Q GAIN WILD-TYPE 208 139 123

Figure S67.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S68.  Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
19Q GAIN MUTATED 7 3 27
19Q GAIN WILD-TYPE 121 72 83

Figure S68.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S69.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
19Q GAIN MUTATED 11 8 28 1 2 6
19Q GAIN WILD-TYPE 109 168 98 27 30 22

Figure S69.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S70.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
19Q GAIN MUTATED 10 10 35
19Q GAIN WILD-TYPE 112 196 137

Figure S70.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S71.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
20P GAIN MUTATED 10 34 68
20P GAIN WILD-TYPE 202 118 95

Figure S71.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S72.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
20P GAIN MUTATED 12 16 37
20P GAIN WILD-TYPE 116 59 73

Figure S72.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S73.  Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
20P GAIN MUTATED 7 21 19 18 5 28
20P GAIN WILD-TYPE 93 67 65 57 38 29

Figure S73.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S74.  Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
20P GAIN MUTATED 12 32 54
20P GAIN WILD-TYPE 83 166 100

Figure S74.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S75.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
20P GAIN MUTATED 19 19 73
20P GAIN WILD-TYPE 196 89 114

Figure S75.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S76.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
20P GAIN MUTATED 21 12 65 3 3 7
20P GAIN WILD-TYPE 99 164 61 25 29 21

Figure S76.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S77.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
20P GAIN MUTATED 26 19 66
20P GAIN WILD-TYPE 96 187 106

Figure S77.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S78.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
20P GAIN MUTATED 54 32 25
20P GAIN WILD-TYPE 105 206 78

Figure S78.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S79.  Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
20P GAIN MUTATED 9 7 32
20P GAIN WILD-TYPE 48 87 57

Figure S79.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.1

Table S80.  Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 100 47
20P GAIN MUTATED 32 10 6
20P GAIN WILD-TYPE 61 90 41

Figure S80.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S81.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
20Q GAIN MUTATED 10 33 72
20Q GAIN WILD-TYPE 202 119 91

Figure S81.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S82.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
20Q GAIN MUTATED 12 16 37
20Q GAIN WILD-TYPE 116 59 73

Figure S82.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S83.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
20Q GAIN MUTATED 7 20 21 18 5 30
20Q GAIN WILD-TYPE 93 68 63 57 38 27

Figure S83.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S84.  Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
20Q GAIN MUTATED 13 32 56
20Q GAIN WILD-TYPE 82 166 98

Figure S84.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S85.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
20Q GAIN MUTATED 19 18 77
20Q GAIN WILD-TYPE 196 90 110

Figure S85.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S86.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
20Q GAIN MUTATED 21 12 68 3 3 7
20Q GAIN WILD-TYPE 99 164 58 25 29 21

Figure S86.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S87.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
20Q GAIN MUTATED 26 19 69
20Q GAIN WILD-TYPE 96 187 103

Figure S87.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S88.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
20Q GAIN MUTATED 56 32 26
20Q GAIN WILD-TYPE 103 206 77

Figure S88.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S89.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
20Q GAIN MUTATED 9 7 33
20Q GAIN WILD-TYPE 48 87 56

Figure S89.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S90.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 100 47
20Q GAIN MUTATED 33 10 6
20Q GAIN WILD-TYPE 60 90 41

Figure S90.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S91.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
21Q GAIN MUTATED 10 6 34
21Q GAIN WILD-TYPE 202 146 129

Figure S91.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S92.  Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
1P LOSS MUTATED 7 25 25
1P LOSS WILD-TYPE 205 127 138

Figure S92.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S93.  Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
1P LOSS MUTATED 11 14 12 3 2 13
1P LOSS WILD-TYPE 109 162 114 25 30 15

Figure S93.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S94.  Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
1Q LOSS MUTATED 3 20 13
1Q LOSS WILD-TYPE 209 132 150

Figure S94.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S95.  Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
1Q LOSS MUTATED 5 7 10 0 2 12
1Q LOSS WILD-TYPE 115 169 116 28 30 16

Figure S95.  Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S96.  Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
2P LOSS MUTATED 0 1 6
2P LOSS WILD-TYPE 33 23 7

Figure S96.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S97.  Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
2P LOSS MUTATED 1 11 2
2P LOSS WILD-TYPE 211 141 161

Figure S97.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S98.  Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
2P LOSS MUTATED 0 0 0 7 0 2
2P LOSS WILD-TYPE 100 88 84 68 43 55

Figure S98.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S99.  Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
2P LOSS MUTATED 0 0 9
2P LOSS WILD-TYPE 95 198 145

Figure S99.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S100.  Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
2P LOSS MUTATED 0 12 2
2P LOSS WILD-TYPE 215 96 185

Figure S100.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S101.  Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
2P LOSS MUTATED 0 1 2 1 0 10
2P LOSS WILD-TYPE 120 175 124 27 32 18

Figure S101.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S102.  Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
2P LOSS MUTATED 1 0 13
2P LOSS WILD-TYPE 121 206 159

Figure S102.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S103.  Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
2P LOSS MUTATED 1 1 12
2P LOSS WILD-TYPE 158 237 91

Figure S103.  Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.14

Table S104.  Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S104.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.083

Table S105.  Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
2Q LOSS MUTATED 0 0 0 6 0 3
2Q LOSS WILD-TYPE 100 88 84 69 43 54

Figure S105.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.036

Table S106.  Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
2Q LOSS MUTATED 0 0 9
2Q LOSS WILD-TYPE 95 198 145

Figure S106.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S107.  Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
2Q LOSS MUTATED 0 12 2
2Q LOSS WILD-TYPE 215 96 185

Figure S107.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S108.  Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
2Q LOSS MUTATED 0 1 3 0 0 10
2Q LOSS WILD-TYPE 120 175 123 28 32 18

Figure S108.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S109.  Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
2Q LOSS MUTATED 0 0 14
2Q LOSS WILD-TYPE 122 206 158

Figure S109.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S110.  Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
2Q LOSS MUTATED 1 0 13
2Q LOSS WILD-TYPE 158 238 90

Figure S110.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S111.  Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
3P LOSS MUTATED 192 47 141
3P LOSS WILD-TYPE 20 105 22

Figure S111.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S112.  Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
3P LOSS MUTATED 177 54 137
3P LOSS WILD-TYPE 38 54 50

Figure S112.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S113.  Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
3P LOSS MUTATED 95 142 91 14 23 3
3P LOSS WILD-TYPE 25 34 35 14 9 25

Figure S113.  Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S114.  Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
3Q LOSS MUTATED 47 9 43
3Q LOSS WILD-TYPE 165 143 120

Figure S114.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S115.  Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
4P LOSS MUTATED 9 15 48
4P LOSS WILD-TYPE 203 137 115

Figure S115.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.13

Table S116.  Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
4P LOSS MUTATED 11 8 31
4P LOSS WILD-TYPE 117 67 79

Figure S116.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S117.  Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
4Q LOSS MUTATED 7 11 47
4Q LOSS WILD-TYPE 205 141 116

Figure S117.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S118.  Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
4Q LOSS MUTATED 9 6 30
4Q LOSS WILD-TYPE 119 69 80

Figure S118.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S119.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
4Q LOSS MUTATED 15 14 33 0 3 0
4Q LOSS WILD-TYPE 105 162 93 28 29 28

Figure S119.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S120.  Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
6P LOSS MUTATED 10 23 67
6P LOSS WILD-TYPE 202 129 96

Figure S120.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S121.  Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
6P LOSS MUTATED 9 12 31
6P LOSS WILD-TYPE 119 63 79

Figure S121.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S122.  Gene #51: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
6P LOSS MUTATED 17 7 17 18 4 25
6P LOSS WILD-TYPE 83 81 67 57 39 32

Figure S122.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S123.  Gene #51: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
6P LOSS MUTATED 18 22 48
6P LOSS WILD-TYPE 77 176 106

Figure S123.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S124.  Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
6P LOSS MUTATED 20 16 60
6P LOSS WILD-TYPE 195 92 127

Figure S124.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S125.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
6P LOSS MUTATED 16 13 50 0 6 11
6P LOSS WILD-TYPE 104 163 76 28 26 17

Figure S125.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S126.  Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
6P LOSS MUTATED 13 18 64
6P LOSS WILD-TYPE 109 188 108

Figure S126.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S127.  Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
6P LOSS MUTATED 41 22 32
6P LOSS WILD-TYPE 118 216 71

Figure S127.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S128.  Gene #51: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
6P LOSS MUTATED 6 5 30
6P LOSS WILD-TYPE 51 89 59

Figure S128.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.23

Table S129.  Gene #51: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 100 47
6P LOSS MUTATED 26 7 8
6P LOSS WILD-TYPE 67 93 39

Figure S129.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S130.  Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
6Q LOSS MUTATED 23 26 79
6Q LOSS WILD-TYPE 189 126 84

Figure S130.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S131.  Gene #52: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
6Q LOSS MUTATED 28 8 24 19 6 26
6Q LOSS WILD-TYPE 72 80 60 56 37 31

Figure S131.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S132.  Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
6Q LOSS MUTATED 40 18 65
6Q LOSS WILD-TYPE 175 90 122

Figure S132.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S133.  Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
6Q LOSS MUTATED 20 29 51 4 8 11
6Q LOSS WILD-TYPE 100 147 75 24 24 17

Figure S133.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S134.  Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
6Q LOSS MUTATED 18 34 70
6Q LOSS WILD-TYPE 104 172 102

Figure S134.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.14

Table S135.  Gene #52: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
6Q LOSS MUTATED 9 14 35
6Q LOSS WILD-TYPE 48 80 54

Figure S135.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S136.  Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
8P LOSS MUTATED 38 34 65
8P LOSS WILD-TYPE 174 118 98

Figure S136.  Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S137.  Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
9P LOSS MUTATED 10 28 111
9P LOSS WILD-TYPE 202 124 52

Figure S137.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S138.  Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
9P LOSS MUTATED 6 20 67
9P LOSS WILD-TYPE 122 55 43

Figure S138.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S139.  Gene #57: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
9P LOSS MUTATED 18 24 31 18 10 33
9P LOSS WILD-TYPE 82 64 53 57 33 24

Figure S139.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S140.  Gene #57: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
9P LOSS MUTATED 28 42 64
9P LOSS WILD-TYPE 67 156 90

Figure S140.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S141.  Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
9P LOSS MUTATED 26 16 102
9P LOSS WILD-TYPE 189 92 85

Figure S141.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S142.  Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
9P LOSS MUTATED 38 13 77 2 10 4
9P LOSS WILD-TYPE 82 163 49 26 22 24

Figure S142.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S143.  Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
9P LOSS MUTATED 27 28 86
9P LOSS WILD-TYPE 95 178 86

Figure S143.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S144.  Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
9P LOSS MUTATED 69 36 36
9P LOSS WILD-TYPE 90 202 67

Figure S144.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S145.  Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
9P LOSS MUTATED 15 9 43
9P LOSS WILD-TYPE 42 85 46

Figure S145.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S146.  Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 100 47
9P LOSS MUTATED 40 15 12
9P LOSS WILD-TYPE 53 85 35

Figure S146.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S147.  Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
9Q LOSS MUTATED 10 29 111
9Q LOSS WILD-TYPE 202 123 52

Figure S147.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S148.  Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
9Q LOSS MUTATED 6 21 64
9Q LOSS WILD-TYPE 122 54 46

Figure S148.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S149.  Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
9Q LOSS MUTATED 17 24 34 18 10 33
9Q LOSS WILD-TYPE 83 64 50 57 33 24

Figure S149.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S150.  Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
9Q LOSS MUTATED 26 16 103
9Q LOSS WILD-TYPE 189 92 84

Figure S150.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S151.  Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
9Q LOSS MUTATED 38 13 77 3 10 4
9Q LOSS WILD-TYPE 82 163 49 25 22 24

Figure S151.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S152.  Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
9Q LOSS MUTATED 26 28 87
9Q LOSS WILD-TYPE 96 178 85

Figure S152.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S153.  Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
9Q LOSS MUTATED 68 36 37
9Q LOSS WILD-TYPE 91 202 66

Figure S153.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S154.  Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
9Q LOSS MUTATED 15 10 43
9Q LOSS WILD-TYPE 42 84 46

Figure S154.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S155.  Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 100 47
9Q LOSS MUTATED 39 14 15
9Q LOSS WILD-TYPE 54 86 32

Figure S155.  Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S156.  Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
10P LOSS MUTATED 10 22 35
10P LOSS WILD-TYPE 202 130 128

Figure S156.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S157.  Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
10Q LOSS MUTATED 19 24 46
10Q LOSS WILD-TYPE 193 128 117

Figure S157.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S158.  Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
11P LOSS MUTATED 0 5 13
11P LOSS WILD-TYPE 212 147 150

Figure S158.  Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S159.  Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
11Q LOSS MUTATED 0 5 18
11Q LOSS WILD-TYPE 212 147 145

Figure S159.  Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S160.  Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
13Q LOSS MUTATED 8 24 39
13Q LOSS WILD-TYPE 204 128 124

Figure S160.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.2

Table S161.  Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
13Q LOSS MUTATED 7 15 24
13Q LOSS WILD-TYPE 121 60 86

Figure S161.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S162.  Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
13Q LOSS MUTATED 3 10 14 13 3 19
13Q LOSS WILD-TYPE 97 78 70 62 40 38

Figure S162.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.2

Table S163.  Gene #65: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
13Q LOSS MUTATED 12 15 35
13Q LOSS WILD-TYPE 83 183 119

Figure S163.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S164.  Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
13Q LOSS MUTATED 13 13 43
13Q LOSS WILD-TYPE 202 95 144

Figure S164.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S165.  Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
13Q LOSS MUTATED 6 9 41 1 4 8
13Q LOSS WILD-TYPE 114 167 85 27 28 20

Figure S165.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S166.  Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
13Q LOSS MUTATED 12 12 43
13Q LOSS WILD-TYPE 110 194 129

Figure S166.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S167.  Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
13Q LOSS MUTATED 29 12 26
13Q LOSS WILD-TYPE 130 226 77

Figure S167.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.2

Table S168.  Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 100 47
13Q LOSS MUTATED 23 5 6
13Q LOSS WILD-TYPE 70 95 41

Figure S168.  Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S169.  Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
14Q LOSS MUTATED 9 19 2
14Q LOSS WILD-TYPE 24 5 11

Figure S169.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.056

Table S170.  Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
14Q LOSS MUTATED 4 7 1 11 5 0 2
14Q LOSS WILD-TYPE 7 5 3 0 8 9 8

Figure S170.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S171.  Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
14Q LOSS MUTATED 60 45 111
14Q LOSS WILD-TYPE 152 107 52

Figure S171.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S172.  Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
14Q LOSS MUTATED 25 34 64
14Q LOSS WILD-TYPE 103 41 46

Figure S172.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S173.  Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
14Q LOSS MUTATED 27 28 62 23 13 39
14Q LOSS WILD-TYPE 73 60 22 52 30 18

Figure S173.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S174.  Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
14Q LOSS MUTATED 57 62 73
14Q LOSS WILD-TYPE 38 136 81

Figure S174.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S175.  Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
14Q LOSS MUTATED 68 16 126
14Q LOSS WILD-TYPE 147 92 61

Figure S175.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S176.  Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
14Q LOSS MUTATED 47 50 75 7 29 2
14Q LOSS WILD-TYPE 73 126 51 21 3 26

Figure S176.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S177.  Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
14Q LOSS MUTATED 35 64 109
14Q LOSS WILD-TYPE 87 142 63

Figure S177.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S178.  Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
14Q LOSS MUTATED 72 75 61
14Q LOSS WILD-TYPE 87 163 42

Figure S178.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S179.  Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
14Q LOSS MUTATED 18 27 57
14Q LOSS WILD-TYPE 39 67 32

Figure S179.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S180.  Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
15Q LOSS MUTATED 2 5 29
15Q LOSS WILD-TYPE 210 147 134

Figure S180.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S181.  Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
15Q LOSS MUTATED 6 2 27
15Q LOSS WILD-TYPE 209 106 160

Figure S181.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S182.  Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
15Q LOSS MUTATED 5 4 25 0 1 0
15Q LOSS WILD-TYPE 115 172 101 28 31 28

Figure S182.  Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.097

Table S183.  Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
17P LOSS MUTATED 0 5 6
17P LOSS WILD-TYPE 33 19 7

Figure S183.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.16

Table S184.  Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
17P LOSS MUTATED 0 5 1 0 0 0 5
17P LOSS WILD-TYPE 11 7 3 11 13 9 5

Figure S184.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S185.  Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
17P LOSS MUTATED 3 17 26
17P LOSS WILD-TYPE 209 135 137

Figure S185.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S186.  Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
17P LOSS MUTATED 4 15 26
17P LOSS WILD-TYPE 211 93 161

Figure S186.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S187.  Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
17P LOSS MUTATED 5 3 23 2 1 11
17P LOSS WILD-TYPE 115 173 103 26 31 17

Figure S187.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S188.  Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
17P LOSS MUTATED 8 5 32
17P LOSS WILD-TYPE 114 201 140

Figure S188.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S189.  Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
17P LOSS MUTATED 20 7 18
17P LOSS WILD-TYPE 139 231 85

Figure S189.  Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.23

Table S190.  Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
17Q LOSS MUTATED 2 13 13
17Q LOSS WILD-TYPE 210 139 150

Figure S190.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.2

Table S191.  Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
17Q LOSS MUTATED 3 12 13
17Q LOSS WILD-TYPE 212 96 174

Figure S191.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S192.  Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
17Q LOSS MUTATED 4 2 11 0 1 10
17Q LOSS WILD-TYPE 116 174 115 28 31 18

Figure S192.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S193.  Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
17Q LOSS MUTATED 4 2 22
17Q LOSS WILD-TYPE 118 204 150

Figure S193.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.14

Table S194.  Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
17Q LOSS MUTATED 9 5 14
17Q LOSS WILD-TYPE 150 233 89

Figure S194.  Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S195.  Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
18P LOSS MUTATED 13 23 57
18P LOSS WILD-TYPE 199 129 106

Figure S195.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S196.  Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
18P LOSS MUTATED 6 19 32
18P LOSS WILD-TYPE 122 56 78

Figure S196.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S197.  Gene #72: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
18P LOSS MUTATED 5 14 23 15 2 24
18P LOSS WILD-TYPE 95 74 61 60 41 33

Figure S197.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S198.  Gene #72: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
18P LOSS MUTATED 16 20 47
18P LOSS WILD-TYPE 79 178 107

Figure S198.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S199.  Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
18P LOSS MUTATED 10 9 71
18P LOSS WILD-TYPE 205 99 116

Figure S199.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S200.  Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
18P LOSS MUTATED 14 7 53 4 8 4
18P LOSS WILD-TYPE 106 169 73 24 24 24

Figure S200.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S201.  Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
18P LOSS MUTATED 22 12 57
18P LOSS WILD-TYPE 100 194 115

Figure S201.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S202.  Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
18P LOSS MUTATED 44 16 31
18P LOSS WILD-TYPE 115 222 72

Figure S202.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.036

Table S203.  Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
18P LOSS MUTATED 10 5 27
18P LOSS WILD-TYPE 47 89 62

Figure S203.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S204.  Gene #72: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 100 47
18P LOSS MUTATED 29 6 7
18P LOSS WILD-TYPE 64 94 40

Figure S204.  Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S205.  Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
18Q LOSS MUTATED 14 24 57
18Q LOSS WILD-TYPE 198 128 106

Figure S205.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S206.  Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 75 110
18Q LOSS MUTATED 7 19 31
18Q LOSS WILD-TYPE 121 56 79

Figure S206.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S207.  Gene #73: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 100 88 84 75 43 57
18Q LOSS MUTATED 5 14 23 16 4 24
18Q LOSS WILD-TYPE 95 74 61 59 39 33

Figure S207.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S208.  Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 95 198 154
18Q LOSS MUTATED 16 23 47
18Q LOSS WILD-TYPE 79 175 107

Figure S208.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S209.  Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
18Q LOSS MUTATED 11 10 71
18Q LOSS WILD-TYPE 204 98 116

Figure S209.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S210.  Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
18Q LOSS MUTATED 14 8 53 5 8 4
18Q LOSS WILD-TYPE 106 168 73 23 24 24

Figure S210.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S211.  Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
18Q LOSS MUTATED 23 13 57
18Q LOSS WILD-TYPE 99 193 115

Figure S211.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S212.  Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 159 238 103
18Q LOSS MUTATED 45 17 31
18Q LOSS WILD-TYPE 114 221 72

Figure S212.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S213.  Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 94 89
18Q LOSS MUTATED 9 5 28
18Q LOSS WILD-TYPE 48 89 61

Figure S213.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S214.  Gene #73: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 100 47
18Q LOSS MUTATED 30 5 7
18Q LOSS WILD-TYPE 63 95 40

Figure S214.  Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.036

Table S215.  Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
19P LOSS MUTATED 0 1 10
19P LOSS WILD-TYPE 212 151 153

Figure S215.  Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.043

Table S216.  Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
21Q LOSS MUTATED 8 24 23
21Q LOSS WILD-TYPE 204 128 140

Figure S216.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.049

Table S217.  Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
21Q LOSS MUTATED 9 10 17 3 2 11
21Q LOSS WILD-TYPE 111 166 109 25 30 17

Figure S217.  Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S218.  Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
22Q LOSS MUTATED 4 10 25
22Q LOSS WILD-TYPE 208 142 138

Figure S218.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S219.  Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 108 187
22Q LOSS MUTATED 5 4 30
22Q LOSS WILD-TYPE 210 104 157

Figure S219.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S220.  Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 176 126 28 32 28
22Q LOSS MUTATED 7 3 20 5 3 1
22Q LOSS WILD-TYPE 113 173 106 23 29 27

Figure S220.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S221.  Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 206 172
22Q LOSS MUTATED 3 9 27
22Q LOSS WILD-TYPE 119 197 145

Figure S221.  Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S222.  Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 152 163
XQ LOSS MUTATED 7 11 29
XQ LOSS WILD-TYPE 205 141 134

Figure S222.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 527

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 12

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

Fisher's exact test

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

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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