Correlation between copy number variations of arm-level result and molecular subtypes
Colorectal Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1HT2NHB
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1HT2NHB
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 82 arm-level events and 12 molecular subtypes across 615 patients, 324 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'.

  • 2p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 3q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 4q gain cnv correlated to 'CN_CNMF'.

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

  • 5q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 7q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

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

  • 9p gain cnv correlated to 'CN_CNMF'.

  • 9q gain cnv correlated to 'RPPA_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

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

  • 11q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 12q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • 14q gain cnv correlated to 'CN_CNMF'.

  • 15q gain cnv correlated to 'RPPA_CNMF'.

  • 16p gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 18q gain cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF'.

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

  • xq gain cnv correlated to 'CN_CNMF'.

  • 1p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 2q loss cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 5q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 6p loss cnv correlated to 'MRNA_CHIERARCHICAL' and 'MRNASEQ_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

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

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

  • 11p loss cnv correlated to 'CN_CNMF'.

  • 11q loss cnv correlated to 'CN_CNMF'.

  • 12p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 13q loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 16q loss cnv correlated to 'MRNA_CNMF' and 'CN_CNMF'.

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

  • 17q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 21q loss cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • xp loss cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq loss cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 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, 324 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
20q gain 465 (76%) 150 1e-05
(0.000141) 		1e-05
(0.000141) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.0246
(0.0876) 		0.515
(0.748) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.0155
(0.0613) 		0.00044
(0.00349) 		0.00047
(0.00359) 		0.019
(0.0729)
18p loss 379 (62%) 236 1e-05
(0.000141) 		1e-05
(0.000141) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.322
(0.574) 		0.394
(0.648) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.00682
(0.0327) 		0.00914
(0.0416) 		0.00014
(0.00134) 		0.00114
(0.00743)
18q loss 409 (67%) 206 1e-05
(0.000141) 		1e-05
(0.000141) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.3
(0.554) 		0.227
(0.464) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.00097
(0.00682) 		0.00623
(0.0305) 		0.00012
(0.00119) 		0.00033
(0.00278)
7p gain 349 (57%) 266 0.00042
(0.00339) 		1e-05
(0.000141) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.231
(0.468) 		0.00558
(0.0283) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.00598
(0.0297) 		0.177
(0.391) 		0.0273
(0.0948) 		0.0895
(0.241)
17q gain 110 (18%) 505 0.0193
(0.0733) 		0.00665
(0.0321) 		1e-05
(0.000141) 		0.0001
(0.00101) 		0.87
(0.972) 		0.0212
(0.0792) 		2e-05
(0.000249) 		3e-05
(0.00036) 		0.00453
(0.0241) 		0.0412
(0.131) 		0.864
(0.968) 		0.28
(0.534)
14q loss 207 (34%) 408 0.00024
(0.00215) 		0.0001
(0.00101) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.837
(0.947) 		0.0241
(0.0862) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.135
(0.323) 		0.119
(0.295) 		0.0363
(0.119) 		0.0457
(0.142)
17p loss 341 (55%) 274 4e-05
(0.000463) 		5e-05
(0.000553) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.384
(0.637) 		0.918
(0.995) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.0363
(0.119) 		0.0239
(0.0857) 		0.0281
(0.097) 		0.383
(0.637)
2p gain 123 (20%) 492 0.0215
(0.0792) 		0.00576
(0.0291) 		0.00169
(0.0107) 		0.00455
(0.0241) 		0.484
(0.724) 		0.763
(0.914) 		2e-05
(0.000249) 		2e-05
(0.000249) 		0.0332
(0.111) 		0.00109
(0.00735) 		0.988
(1.00) 		0.969
(1.00)
7q gain 311 (51%) 304 0.00025
(0.00222) 		1e-05
(0.000141) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.231
(0.468) 		0.00276
(0.0163) 		0.00011
(0.0011) 		1e-05
(0.000141) 		0.011
(0.0479) 		0.195
(0.417) 		0.0771
(0.214) 		0.436
(0.683)
13q gain 368 (60%) 247 1e-05
(0.000141) 		1e-05
(0.000141) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.765
(0.914) 		0.19
(0.41) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.00049
(0.00371) 		0.439
(0.684) 		0.014
(0.057) 		0.0696
(0.199)
2q gain 121 (20%) 494 0.0131
(0.0548) 		0.00149
(0.00952) 		0.00016
(0.0015) 		0.00698
(0.0332) 		0.898
(0.988) 		0.373
(0.63) 		0.00045
(0.00351) 		2e-05
(0.000249) 		0.0923
(0.244) 		0.0095
(0.0429) 		0.937
(1.00) 		0.816
(0.939)
3q gain 98 (16%) 517 0.033
(0.111) 		0.00184
(0.0115) 		1e-05
(0.000141) 		0.0445
(0.139) 		0.381
(0.636) 		0.538
(0.763) 		0.0924
(0.244) 		0.0037
(0.0209) 		0.0442
(0.139) 		0.549
(0.772) 		0.0216
(0.0792) 		0.0504
(0.152)
8q gain 315 (51%) 300 0.33
(0.583) 		0.11
(0.276) 		1e-05
(0.000141) 		0.0047
(0.0246) 		0.294
(0.55) 		0.0421
(0.134) 		0.00229
(0.014) 		0.0201
(0.0754) 		0.289
(0.544) 		0.00901
(0.0412) 		0.106
(0.273) 		0.0451
(0.141)
8p loss 218 (35%) 397 0.00863
(0.0399) 		0.00588
(0.0295) 		1e-05
(0.000141) 		0.00045
(0.00351) 		0.124
(0.302) 		0.958
(1.00) 		0.00644
(0.0312) 		3e-05
(0.00036) 		0.663
(0.857) 		0.24
(0.479) 		0.00253
(0.0152) 		0.471
(0.71)
9q loss 78 (13%) 537 0.0482
(0.148) 		0.0137
(0.0564) 		0.00059
(0.00437) 		0.00051
(0.0038) 		0.515
(0.748) 		0.175
(0.389) 		0.00018
(0.00166) 		0.00114
(0.00743) 		0.437
(0.683) 		0.0116
(0.05) 		0.801
(0.933) 		0.327
(0.582)
6p gain 124 (20%) 491 0.0147
(0.0594) 		0.00044
(0.00349) 		1e-05
(0.000141) 		0.0835
(0.228) 		0.657
(0.855) 		0.607
(0.811) 		0.381
(0.636) 		0.0336
(0.112) 		0.458
(0.699) 		0.711
(0.886) 		0.0253
(0.0892) 		0.0335
(0.112)
11p gain 85 (14%) 530 0.0124
(0.0527) 		0.00521
(0.0267) 		1e-05
(0.000141) 		2e-05
(0.000249) 		0.802
(0.933) 		0.406
(0.656) 		0.00481
(0.025) 		0.0003
(0.00259) 		0.328
(0.583) 		0.404
(0.654) 		0.783
(0.922) 		0.972
(1.00)
11q gain 77 (13%) 538 0.0162
(0.0636) 		0.00112
(0.0074) 		1e-05
(0.000141) 		1e-05
(0.000141) 		0.736
(0.897) 		0.295
(0.55) 		5e-05
(0.000553) 		2e-05
(0.000249) 		0.301
(0.555) 		0.0601
(0.176) 		0.301
(0.555) 		0.18
(0.395)
16p gain 147 (24%) 468 0.0062
(0.0305) 		0.00358
(0.0205) 		1e-05
(0.000141) 		0.00422
(0.0229) 		0.638
(0.84) 		0.341
(0.594) 		0.00046
(0.00356) 		2e-05
(0.000249) 		0.491
(0.73) 		0.434
(0.683) 		0.226
(0.464) 		0.183
(0.399)
16q gain 145 (24%) 470 0.00878
(0.0404) 		0.00379
(0.0209) 		1e-05
(0.000141) 		0.00319
(0.0186) 		0.57
(0.786) 		0.694
(0.875) 		0.00107
(0.00731) 		4e-05
(0.000463) 		0.785
(0.922) 		0.476
(0.715) 		0.108
(0.276) 		0.123
(0.301)
18q gain 19 (3%) 596 0.0364
(0.119) 		0.701
(0.878) 		0.0124
(0.0527) 		0.0119
(0.051) 		0.45
(0.692) 		0.288
(0.544) 		0.00268
(0.016) 		6e-05
(0.000649) 		0.0922
(0.244) 		0.0148
(0.0594) 		0.673
(0.863) 		0.829
(0.946)
20p gain 352 (57%) 263 0.00024
(0.00215) 		2e-05
(0.000249) 		1e-05
(0.000141) 		0.00098
(0.00684) 		0.0559
(0.166) 		0.285
(0.54) 		0.00597
(0.0297) 		1e-05
(0.000141) 		0.369
(0.629) 		0.108
(0.276) 		0.668
(0.86) 		0.102
(0.264)
4p loss 198 (32%) 417 0.0224
(0.0811) 		0.00758
(0.0355) 		1e-05
(0.000141) 		0.00217
(0.0134) 		0.899
(0.988) 		0.432
(0.682) 		0.00076
(0.00538) 		5e-05
(0.000553) 		0.0796
(0.219) 		0.437
(0.683) 		0.2
(0.426) 		0.918
(0.995)
4q loss 191 (31%) 424 0.0411
(0.131) 		0.0739
(0.208) 		1e-05
(0.000141) 		0.00284
(0.0166) 		0.536
(0.761) 		0.508
(0.745) 		0.0036
(0.0205) 		9e-05
(0.000942) 		0.105
(0.272) 		0.137
(0.323) 		0.0388
(0.125) 		0.502
(0.742)
5q loss 121 (20%) 494 0.00936
(0.0424) 		0.03
(0.102) 		1e-05
(0.000141) 		0.0451
(0.141) 		0.824
(0.943) 		0.845
(0.951) 		0.03
(0.102) 		0.00101
(0.007) 		0.535
(0.761) 		0.666
(0.858) 		0.686
(0.868) 		0.676
(0.863)
10q loss 112 (18%) 503 0.0218
(0.0793) 		0.248
(0.493) 		1e-05
(0.000141) 		0.00424
(0.0229) 		0.454
(0.695) 		0.514
(0.748) 		0.00223
(0.0137) 		1e-05
(0.000141) 		0.557
(0.777) 		0.442
(0.684) 		0.0468
(0.145) 		0.267
(0.519)
15q loss 229 (37%) 386 0.00013
(0.00125) 		0.00137
(0.00887) 		1e-05
(0.000141) 		0.00033
(0.00278) 		0.135
(0.323) 		0.593
(0.8) 		4e-05
(0.000463) 		1e-05
(0.000141) 		0.819
(0.94) 		0.685
(0.867) 		0.081
(0.221) 		0.206
(0.433)
21q loss 194 (32%) 421 0.0172
(0.0666) 		0.0216
(0.0792) 		1e-05
(0.000141) 		0.0213
(0.0792) 		0.227
(0.464) 		0.178
(0.392) 		9e-05
(0.000942) 		0.00331
(0.0192) 		0.139
(0.327) 		0.147
(0.342) 		0.804
(0.933) 		0.186
(0.402)
1p loss 138 (22%) 477 0.0755
(0.211) 		0.0255
(0.0894) 		1e-05
(0.000141) 		0.00373
(0.0209) 		0.531
(0.758) 		0.979
(1.00) 		0.00105
(0.00723) 		0.00013
(0.00125) 		0.345
(0.599) 		0.0684
(0.196) 		0.766
(0.914) 		0.314
(0.563)
1q loss 79 (13%) 536 0.311
(0.56) 		0.297
(0.552) 		9e-05
(0.000942) 		0.157
(0.359) 		0.0135
(0.056) 		0.605
(0.81) 		0.0001
(0.00101) 		0.00062
(0.00452) 		0.716
(0.888) 		0.00684
(0.0327) 		0.167
(0.376) 		0.154
(0.353)
10p loss 102 (17%) 513 0.011
(0.0479) 		0.186
(0.402) 		1e-05
(0.000141) 		0.00455
(0.0241) 		0.76
(0.914) 		0.709
(0.884) 		0.0107
(0.0472) 		0.00015
(0.00142) 		0.211
(0.44) 		0.361
(0.62) 		0.0559
(0.166) 		0.251
(0.496)
19p loss 64 (10%) 551 0.377
(0.632) 		0.476
(0.715) 		0.0004
(0.00325) 		0.771
(0.917) 		0.979
(1.00) 		0.871
(0.972) 		0.0491
(0.149) 		0.0431
(0.136) 		0.157
(0.358) 		0.00609
(0.0301) 		0.291
(0.545) 		0.00962
(0.043)
20p loss 68 (11%) 547 0.112
(0.279) 		0.0191
(0.073) 		3e-05
(0.00036) 		0.0005
(0.00376) 		0.0603
(0.176) 		0.817
(0.939) 		0.146
(0.341) 		0.00017
(0.00158) 		0.836
(0.947) 		0.389
(0.641) 		0.0742
(0.209) 		0.00244
(0.0147)
22q loss 203 (33%) 412 0.00521
(0.0267) 		0.00027
(0.00237) 		1e-05
(0.000141) 		0.368
(0.629) 		0.19
(0.41) 		0.514
(0.748) 		0.0175
(0.0673) 		2e-05
(0.000249) 		0.977
(1.00) 		0.0699
(0.199) 		0.459
(0.699) 		0.417
(0.665)
6q gain 111 (18%) 504 0.158
(0.36) 		0.00111
(0.0074) 		1e-05
(0.000141) 		0.0904
(0.242) 		0.808
(0.933) 		0.986
(1.00) 		0.437
(0.683) 		0.137
(0.323) 		0.358
(0.619) 		0.895
(0.986) 		0.00954
(0.0429) 		0.048
(0.148)
18p gain 33 (5%) 582 0.306
(0.557) 		0.37
(0.629) 		0.00179
(0.0112) 		0.00112
(0.0074) 		0.593
(0.8) 		0.492
(0.73) 		0.0254
(0.0892) 		0.00068
(0.00488) 		0.393
(0.647) 		0.0786
(0.217) 		0.76
(0.914) 		0.976
(1.00)
19p gain 104 (17%) 511 0.33
(0.583) 		0.02
(0.0754) 		1e-05
(0.000141) 		0.091
(0.243) 		0.337
(0.591) 		0.117
(0.29) 		0.255
(0.502) 		6e-05
(0.000649) 		0.0422
(0.134) 		0.731
(0.897) 		0.517
(0.748) 		0.0894
(0.241)
2p loss 17 (3%) 598 1
(1.00) 		0.619
(0.824) 		0.00061
(0.00448) 		0.033
(0.111) 		0.402
(0.653) 		0.0129
(0.0543) 		0.0603
(0.176) 		0.00746
(0.0351) 		0.0933
(0.246) 		0.228
(0.466)
2q loss 14 (2%) 601 0.675
(0.863) 		0.246
(0.491) 		0.0148
(0.0594) 		0.12
(0.296) 		0.782
(0.922) 		0.0117
(0.0502) 		0.112
(0.279) 		0.00553
(0.0282) 		0.0896
(0.241) 		0.0222
(0.0806)
9p loss 77 (13%) 538 0.492
(0.73) 		0.201
(0.428) 		0.00074
(0.00528) 		0.00996
(0.0441) 		0.797
(0.931) 		0.385
(0.637) 		0.00039
(0.00322) 		0.0168
(0.0655) 		0.208
(0.436) 		0.112
(0.279) 		0.675
(0.863) 		0.715
(0.888)
3p gain 72 (12%) 543 0.0135
(0.056) 		0.0758
(0.211) 		1e-05
(0.000141) 		0.0886
(0.24) 		0.151
(0.347) 		0.756
(0.913) 		0.905
(0.993) 		0.0297
(0.102) 		0.107
(0.275) 		0.438
(0.683) 		0.103
(0.269) 		0.271
(0.526)
5p gain 105 (17%) 510 0.503
(0.742) 		0.129
(0.31) 		0.00031
(0.00265) 		0.549
(0.772) 		0.699
(0.878) 		0.44
(0.684) 		0.013
(0.0546) 		0.032
(0.108) 		0.755
(0.913) 		0.396
(0.648) 		0.458
(0.699) 		0.558
(0.777)
5q gain 66 (11%) 549 0.784
(0.922) 		0.595
(0.8) 		0.00067
(0.00485) 		0.774
(0.918) 		0.947
(1.00) 		0.941
(1.00) 		0.127
(0.306) 		0.0128
(0.0541) 		0.648
(0.847) 		0.00341
(0.0196) 		0.997
(1.00) 		1
(1.00)
8p gain 170 (28%) 445 0.923
(0.995) 		0.532
(0.758) 		1e-05
(0.000141) 		0.836
(0.947) 		0.431
(0.681) 		0.548
(0.772) 		0.00383
(0.0209) 		0.047
(0.145) 		0.203
(0.43) 		0.266
(0.519) 		0.397
(0.648) 		0.122
(0.3)
12p gain 127 (21%) 488 0.356
(0.616) 		0.363
(0.623) 		0.00466
(0.0245) 		0.0247
(0.0876) 		0.56
(0.777) 		0.575
(0.788) 		0.64
(0.841) 		0.0171
(0.0661) 		0.411
(0.659) 		0.784
(0.922) 		0.566
(0.782) 		0.483
(0.724)
12q gain 111 (18%) 504 0.249
(0.493) 		0.35
(0.607) 		0.00277
(0.0163) 		0.005
(0.0259) 		0.89
(0.983) 		0.296
(0.55) 		0.422
(0.67) 		0.00643
(0.0312) 		0.238
(0.478) 		0.444
(0.684) 		0.652
(0.851) 		0.64
(0.841)
19q gain 114 (19%) 501 0.0501
(0.152) 		0.00375
(0.0209) 		0.0002
(0.00182) 		0.233
(0.47) 		0.285
(0.54) 		0.311
(0.56) 		0.402
(0.653) 		0.00109
(0.00735) 		0.216
(0.448) 		1
(1.00) 		0.164
(0.369) 		0.0845
(0.23)
xp gain 99 (16%) 516 0.037
(0.121) 		0.109
(0.276) 		5e-05
(0.000553) 		0.0489
(0.149) 		0.554
(0.776) 		0.309
(0.56) 		0.305
(0.557) 		0.279
(0.534) 		0.23
(0.468) 		0.932
(1.00) 		0.861
(0.966) 		0.561
(0.778)
5p loss 86 (14%) 529 0.377
(0.632) 		0.697
(0.877) 		0.00047
(0.00359) 		0.0364
(0.119) 		0.485
(0.724) 		0.381
(0.636) 		0.737
(0.897) 		0.00381
(0.0209) 		0.957
(1.00) 		0.26
(0.509) 		0.453
(0.694) 		0.944
(1.00)
12p loss 71 (12%) 544 0.0662
(0.191) 		0.0149
(0.0594) 		1e-05
(0.000141) 		0.141
(0.331) 		0.54
(0.764) 		0.404
(0.654) 		0.0956
(0.251) 		0.0004
(0.00325) 		0.821
(0.941) 		0.822
(0.941) 		0.278
(0.534) 		0.259
(0.507)
12q loss 71 (12%) 544 0.125
(0.302) 		0.027
(0.0941) 		1e-05
(0.000141) 		0.239
(0.479) 		0.682
(0.867) 		0.109
(0.276) 		0.0655
(0.19) 		0.00013
(0.00125) 		0.224
(0.463) 		0.872
(0.973) 		0.419
(0.667) 		0.414
(0.662)
13q loss 20 (3%) 595 0.295
(0.55) 		0.0166
(0.0647) 		0.014
(0.057) 		0.679
(0.865) 		0.162
(0.367) 		1
(1.00) 		0.702
(0.878) 		0.141
(0.331) 		0.733
(0.897) 		0.787
(0.922) 		0.014
(0.057) 		0.41
(0.659)
xp loss 91 (15%) 524 0.923
(0.995) 		0.367
(0.628) 		0.0764
(0.212) 		0.84
(0.947) 		0.02
(0.0754) 		0.0144
(0.0584) 		0.888
(0.983) 		0.952
(1.00) 		0.0997
(0.26) 		0.557
(0.777) 		0.498
(0.737) 		0.0336
(0.112)
4p gain 20 (3%) 595 0.817
(0.939) 		0.573
(0.788) 		0.00737
(0.0349) 		0.175
(0.388) 		0.925
(0.995) 		0.289
(0.544) 		0.0114
(0.0492) 		0.161
(0.365) 		0.581
(0.794) 		0.505
(0.744) 		0.672
(0.863) 		0.136
(0.323)
10p gain 49 (8%) 566 0.108
(0.276) 		0.115
(0.285) 		0.0038
(0.0209) 		0.736
(0.897) 		0.24
(0.479) 		0.038
(0.123) 		0.52
(0.75) 		0.813
(0.938) 		0.506
(0.744) 		0.302
(0.556) 		0.543
(0.766) 		0.465
(0.702)
6p loss 46 (7%) 569 0.56
(0.777) 		0.0216
(0.0792) 		0.515
(0.748) 		1
(1.00) 		0.492
(0.73) 		0.793
(0.927) 		0.595
(0.8) 		0.0337
(0.112) 		0.459
(0.699) 		0.938
(1.00) 		0.528
(0.757) 		0.772
(0.917)
8q loss 37 (6%) 578 0.911
(0.994) 		0.784
(0.922) 		0.00445
(0.0239) 		1
(1.00) 		0.304
(0.557) 		0.312
(0.56) 		0.574
(0.788) 		0.646
(0.847) 		0.275
(0.531) 		0.584
(0.795) 		0.0525
(0.158) 		0.0382
(0.124)
16q loss 44 (7%) 571 0.0253
(0.0892) 		0.588
(0.798) 		0.00844
(0.0392) 		0.836
(0.947) 		0.66
(0.856) 		0.732
(0.897) 		0.785
(0.922) 		0.562
(0.778) 		0.575
(0.788) 		0.554
(0.776) 		0.276
(0.532) 		0.868
(0.971)
17q loss 96 (16%) 519 0.889
(0.983) 		0.6
(0.804) 		0.00149
(0.00952) 		0.76
(0.914) 		0.332
(0.584) 		0.755
(0.913) 		0.831
(0.947) 		0.0284
(0.0976) 		0.733
(0.897) 		0.519
(0.75) 		0.716
(0.888) 		0.961
(1.00)
xq loss 80 (13%) 535 0.955
(1.00) 		0.77
(0.917) 		0.131
(0.315) 		0.621
(0.825) 		0.106
(0.272) 		0.078
(0.216) 		0.444
(0.684) 		0.377
(0.632) 		0.0487
(0.149) 		0.827
(0.945) 		0.462
(0.7) 		0.00766
(0.0357)
1p gain 50 (8%) 565 0.204
(0.432) 		0.453
(0.694) 		0.0411
(0.131) 		0.429
(0.678) 		0.303
(0.557) 		0.45
(0.692) 		0.979
(1.00) 		0.631
(0.833) 		0.387
(0.639) 		0.312
(0.56) 		0.193
(0.414) 		0.587
(0.798)
1q gain 117 (19%) 498 0.737
(0.897) 		0.807
(0.933) 		0.0104
(0.0458) 		0.0963
(0.253) 		0.0629
(0.183) 		0.282
(0.536) 		0.911
(0.994) 		0.336
(0.59) 		0.171
(0.381) 		0.14
(0.328) 		0.555
(0.776) 		0.411
(0.659)
4q gain 21 (3%) 594 0.227
(0.464) 		0.216
(0.448) 		0.0233
(0.084) 		0.681
(0.867) 		0.726
(0.895) 		0.2
(0.426) 		0.0569
(0.169) 		0.222
(0.46) 		0.331
(0.584) 		0.366
(0.627) 		0.877
(0.976) 		1
(1.00)
9p gain 123 (20%) 492 0.541
(0.764) 		0.588
(0.798) 		0.00233
(0.0142) 		0.889
(0.983) 		0.124
(0.302) 		0.322
(0.574) 		0.92
(0.995) 		0.382
(0.636) 		0.977
(1.00) 		0.921
(0.995) 		0.631
(0.833) 		0.791
(0.925)
9q gain 101 (16%) 514 0.659
(0.856) 		0.833
(0.947) 		0.0535
(0.16) 		0.984
(1.00) 		0.0165
(0.0646) 		0.0693
(0.198) 		0.948
(1.00) 		0.764
(0.914) 		0.624
(0.827) 		0.306
(0.557) 		0.934
(1.00) 		0.837
(0.947)
14q gain 43 (7%) 572 0.734
(0.897) 		0.399
(0.651) 		0.0152
(0.0605) 		0.583
(0.795) 		0.664
(0.857) 		0.906
(0.993) 		0.594
(0.8) 		0.607
(0.811) 		0.882
(0.98) 		0.891
(0.983) 		0.783
(0.922) 		0.34
(0.594)
15q gain 15 (2%) 600 0.299
(0.553) 		0.151
(0.347) 		0.0619
(0.18) 		0.59
(0.799) 		0.0408
(0.131) 		1
(1.00) 		0.926
(0.995) 		0.93
(0.999) 		1
(1.00) 		0.728
(0.896)
21q gain 34 (6%) 581 0.311
(0.56) 		0.263
(0.514) 		0.00038
(0.00317) 		0.205
(0.433) 		0.373
(0.63) 		0.181
(0.396) 		0.676
(0.863) 		0.108
(0.276) 		0.409
(0.658) 		0.969
(1.00) 		0.461
(0.7) 		0.744
(0.903)
22q gain 23 (4%) 592 0.117
(0.29) 		0.135
(0.323) 		0.00989
(0.044) 		0.274
(0.529) 		0.463
(0.7) 		0.507
(0.744) 		0.112
(0.279) 		0.28
(0.534) 		0.688
(0.869) 		0.917
(0.995) 		0.84
(0.947) 		1
(1.00)
xq gain 107 (17%) 508 0.139
(0.327) 		0.269
(0.521) 		0.00028
(0.00244) 		0.147
(0.341) 		0.526
(0.755) 		0.17
(0.379) 		0.685
(0.867) 		0.376
(0.632) 		0.339
(0.593) 		0.925
(0.995) 		0.696
(0.877) 		0.878
(0.976)
11p loss 75 (12%) 540 0.955
(1.00) 		1
(1.00) 		0.0209
(0.0782) 		0.426
(0.674) 		0.805
(0.933) 		0.947
(1.00) 		0.529
(0.757) 		0.123
(0.3) 		0.911
(0.994) 		0.235
(0.474) 		0.658
(0.856) 		0.854
(0.96)
11q loss 93 (15%) 522 0.845
(0.951) 		0.685
(0.867) 		0.028
(0.0969) 		0.17
(0.379) 		0.805
(0.933) 		0.97
(1.00) 		0.808
(0.933) 		0.17
(0.379) 		0.805
(0.933) 		0.416
(0.664) 		0.281
(0.536) 		0.284
(0.539)
19q loss 55 (9%) 560 0.664
(0.857) 		0.149
(0.344) 		0.00167
(0.0106) 		0.752
(0.913) 		0.721
(0.891) 		0.608
(0.811) 		0.112
(0.28) 		0.0923
(0.244) 		0.224
(0.462) 		0.0728
(0.207) 		0.721
(0.891) 		0.0529
(0.159)
10q gain 29 (5%) 586 0.912
(0.994) 		0.258
(0.506) 		0.0592
(0.175) 		0.0671
(0.193) 		0.647
(0.847) 		0.477
(0.716) 		0.422
(0.67) 		0.599
(0.804) 		0.517
(0.748) 		0.662
(0.857) 		0.179
(0.393) 		0.954
(1.00)
17p gain 38 (6%) 577 0.442
(0.684) 		0.161
(0.365) 		0.754
(0.913) 		0.761
(0.914) 		0.591
(0.8) 		0.186
(0.402) 		0.192
(0.414) 		0.0801
(0.219) 		0.168
(0.378) 		0.719
(0.891) 		0.0748
(0.21) 		0.938
(1.00)
3p loss 70 (11%) 545 0.36
(0.62) 		0.838
(0.947) 		0.491
(0.73) 		0.701
(0.878) 		0.373
(0.63) 		0.399
(0.651) 		0.435
(0.683) 		0.764
(0.914) 		0.774
(0.918) 		0.396
(0.648) 		0.384
(0.637) 		0.352
(0.61)
3q loss 45 (7%) 570 0.248
(0.492) 		0.251
(0.496) 		0.904
(0.993) 		0.918
(0.995) 		0.521
(0.75) 		0.77
(0.917) 		0.704
(0.879) 		0.229
(0.467) 		0.575
(0.788) 		0.34
(0.593) 		0.653
(0.851) 		0.787
(0.922)
6q loss 69 (11%) 546 0.443
(0.684) 		0.31
(0.56) 		0.317
(0.567) 		0.924
(0.995) 		0.908
(0.994) 		0.371
(0.63) 		0.0995
(0.26) 		0.0594
(0.175) 		0.514
(0.748) 		0.516
(0.748) 		0.136
(0.323) 		0.533
(0.759)
7p loss 3 (0%) 612 0.618
(0.822) 		0.631
(0.833) 		0.153
(0.353)
7q loss 5 (1%) 610 0.626
(0.829) 		0.463
(0.7) 		0.888
(0.983) 		0.522
(0.751) 		0.873
(0.973) 		0.699
(0.878) 		1
(1.00) 		0.222
(0.46)
16p loss 41 (7%) 574 0.0737
(0.208) 		0.372
(0.63) 		0.33
(0.583) 		0.94
(1.00) 		0.194
(0.417) 		0.559
(0.777) 		0.732
(0.897) 		0.29
(0.544) 		0.835
(0.947) 		0.236
(0.474) 		0.306
(0.557) 		0.953
(1.00)
20q loss 6 (1%) 609 0.581
(0.795) 		0.178
(0.392) 		0.206
(0.433) 		0.721
(0.891) 		0.207
(0.433) 		0.649
(0.849) 		0.407
(0.656) 		0.53
(0.757)
'1p gain' versus 'CN_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
1P GAIN MUTATED 13 24 13
1P GAIN WILD-TYPE 240 185 140

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

'1q gain' versus 'CN_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.046

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
1Q GAIN MUTATED 35 52 30
1Q GAIN WILD-TYPE 218 157 123

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

'2p gain' versus 'MRNA_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.079

Table S3.  Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
2P GAIN MUTATED 3 11 16 2
2P GAIN WILD-TYPE 40 51 53 39

Figure S3.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00576 (Fisher's exact test), Q value = 0.029

Table S4.  Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
2P GAIN MUTATED 2 10 8 12
2P GAIN WILD-TYPE 47 31 68 37

Figure S4.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
2P GAIN MUTATED 34 55 34
2P GAIN WILD-TYPE 219 154 119

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00455 (Fisher's exact test), Q value = 0.024

Table S6.  Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
2P GAIN MUTATED 20 49 20
2P GAIN WILD-TYPE 82 108 110

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
2P GAIN MUTATED 52 15 25 30
2P GAIN WILD-TYPE 96 126 105 163

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
2P GAIN MUTATED 25 14 8 12 28 31 4
2P GAIN WILD-TYPE 55 72 56 45 62 107 93

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.11

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
2P GAIN MUTATED 52 16 35
2P GAIN WILD-TYPE 159 79 197

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0073

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
2P GAIN MUTATED 42 40 21
2P GAIN WILD-TYPE 186 99 150

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.055

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
2Q GAIN MUTATED 3 13 16 2
2Q GAIN WILD-TYPE 40 49 53 39

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0095

Table S12.  Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
2Q GAIN MUTATED 2 12 8 12
2Q GAIN WILD-TYPE 47 29 68 37

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0015

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
2Q GAIN MUTATED 30 56 35
2Q GAIN WILD-TYPE 223 153 118

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00698 (Fisher's exact test), Q value = 0.033

Table S14.  Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
2Q GAIN MUTATED 18 47 20
2Q GAIN WILD-TYPE 84 110 110

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0035

Table S15.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
2Q GAIN MUTATED 46 16 25 33
2Q GAIN WILD-TYPE 102 125 105 160

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S16.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
2Q GAIN MUTATED 22 15 5 12 29 32 5
2Q GAIN WILD-TYPE 58 71 59 45 61 106 92

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0095 (Fisher's exact test), Q value = 0.043

Table S17.  Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
2Q GAIN MUTATED 41 37 22
2Q GAIN WILD-TYPE 187 102 149

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MRNA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.056

Table S18.  Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
3P GAIN MUTATED 1 10 11 1
3P GAIN WILD-TYPE 42 52 58 40

Figure S18.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
3P GAIN MUTATED 13 44 15
3P GAIN WILD-TYPE 240 165 138

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

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.1

Table S20.  Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
3P GAIN MUTATED 7 13 3 6 18 19 6
3P GAIN WILD-TYPE 73 73 61 51 72 119 91

Figure S20.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.11

Table S21.  Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
3Q GAIN MUTATED 3 11 15 2
3Q GAIN WILD-TYPE 40 51 54 39

Figure S21.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.011

Table S22.  Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
3Q GAIN MUTATED 2 6 8 15
3Q GAIN WILD-TYPE 47 35 68 34

Figure S22.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
3Q GAIN MUTATED 14 58 26
3Q GAIN WILD-TYPE 239 151 127

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.14

Table S24.  Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
3Q GAIN MUTATED 12 36 19
3Q GAIN WILD-TYPE 90 121 111

Figure S24.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0037 (Fisher's exact test), Q value = 0.021

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
3Q GAIN MUTATED 10 17 4 9 24 26 8
3Q GAIN WILD-TYPE 70 69 60 48 66 112 89

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

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
3Q GAIN MUTATED 45 11 32
3Q GAIN WILD-TYPE 166 84 200

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

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.079

Table S27.  Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
3Q GAIN MUTATED 6 3 8 4 8 0
3Q GAIN WILD-TYPE 18 17 20 24 10 17

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.00737 (Fisher's exact test), Q value = 0.035

Table S28.  Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
4P GAIN MUTATED 2 11 7
4P GAIN WILD-TYPE 251 198 146

Figure S28.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.049

Table S29.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
4P GAIN MUTATED 11 2 1 6
4P GAIN WILD-TYPE 137 139 129 187

Figure S29.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.084

Table S30.  Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
4Q GAIN MUTATED 3 11 7
4Q GAIN WILD-TYPE 250 198 146

Figure S30.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0027

Table S31.  Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
5P GAIN MUTATED 26 50 29
5P GAIN WILD-TYPE 227 159 124

Figure S31.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.055

Table S32.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
5P GAIN MUTATED 30 12 25 38
5P GAIN WILD-TYPE 118 129 105 155

Figure S32.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.11

Table S33.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
5P GAIN MUTATED 15 9 8 6 24 30 13
5P GAIN WILD-TYPE 65 77 56 51 66 108 84

Figure S33.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

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

Table S34.  Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
5Q GAIN MUTATED 16 36 14
5Q GAIN WILD-TYPE 237 173 139

Figure S34.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.054

Table S35.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
5Q GAIN MUTATED 8 11 1 2 14 21 9
5Q GAIN WILD-TYPE 72 75 63 55 76 117 88

Figure S35.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00341 (Fisher's exact test), Q value = 0.02

Table S36.  Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
5Q GAIN MUTATED 24 5 25
5Q GAIN WILD-TYPE 204 134 146

Figure S36.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MRNA_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.059

Table S37.  Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
6P GAIN MUTATED 9 11 20 2
6P GAIN WILD-TYPE 34 51 49 39

Figure S37.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0035

Table S38.  Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
6P GAIN MUTATED 5 10 8 19
6P GAIN WILD-TYPE 44 31 68 30

Figure S38.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S39.  Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
6P GAIN MUTATED 22 66 36
6P GAIN WILD-TYPE 231 143 117

Figure S39.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.11

Table S40.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
6P GAIN MUTATED 15 15 6 16 23 35 14
6P GAIN WILD-TYPE 65 71 58 41 67 103 83

Figure S40.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.089

Table S41.  Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
6P GAIN MUTATED 6 2 13 4 6 2
6P GAIN WILD-TYPE 18 18 15 24 12 15

Figure S41.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.11

Table S42.  Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
6P GAIN MUTATED 8 6 7 12
6P GAIN WILD-TYPE 47 9 27 19

Figure S42.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0074

Table S43.  Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
6Q GAIN MUTATED 5 8 5 16
6Q GAIN WILD-TYPE 44 33 71 33

Figure S43.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S44.  Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
6Q GAIN MUTATED 18 60 33
6Q GAIN WILD-TYPE 235 149 120

Figure S44.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00954 (Fisher's exact test), Q value = 0.043

Table S45.  Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
6Q GAIN MUTATED 7 1 12 3 6 2
6Q GAIN WILD-TYPE 17 19 16 25 12 15

Figure S45.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.048 (Fisher's exact test), Q value = 0.15

Table S46.  Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
6Q GAIN MUTATED 8 5 6 12
6Q GAIN WILD-TYPE 47 10 28 19

Figure S46.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'MRNA_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0034

Table S47.  Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
7P GAIN MUTATED 14 41 38 13
7P GAIN WILD-TYPE 29 21 31 28

Figure S47.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S48.  Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
7P GAIN MUTATED 12 27 30 37
7P GAIN WILD-TYPE 37 14 46 12

Figure S48.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S49.  Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
7P GAIN MUTATED 86 159 104
7P GAIN WILD-TYPE 167 50 49

Figure S49.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S50.  Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
7P GAIN MUTATED 53 123 62
7P GAIN WILD-TYPE 49 34 68

Figure S50.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00558 (Fisher's exact test), Q value = 0.028

Table S51.  Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
7P GAIN MUTATED 135 78 56
7P GAIN WILD-TYPE 93 90 29

Figure S51.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S52.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
7P GAIN MUTATED 108 63 76 100
7P GAIN WILD-TYPE 40 78 54 93

Figure S52.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S53.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
7P GAIN MUTATED 50 50 14 41 72 90 30
7P GAIN WILD-TYPE 30 36 50 16 18 48 67

Figure S53.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00598 (Fisher's exact test), Q value = 0.03

Table S54.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
7P GAIN MUTATED 138 53 117
7P GAIN WILD-TYPE 73 42 115

Figure S54.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.095

Table S55.  Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
7P GAIN MUTATED 16 11 22 20 15 6
7P GAIN WILD-TYPE 8 9 6 8 3 11

Figure S55.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MRNA_CNMF'

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

Table S56.  Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
7Q GAIN MUTATED 9 36 35 12
7Q GAIN WILD-TYPE 34 26 34 29

Figure S56.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S57.  Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
7Q GAIN MUTATED 9 22 26 35
7Q GAIN WILD-TYPE 40 19 50 14

Figure S57.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S58.  Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
7Q GAIN MUTATED 82 140 89
7Q GAIN WILD-TYPE 171 69 64

Figure S58.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S59.  Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
7Q GAIN MUTATED 47 109 56
7Q GAIN WILD-TYPE 55 48 74

Figure S59.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00276 (Fisher's exact test), Q value = 0.016

Table S60.  Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
7Q GAIN MUTATED 126 65 46
7Q GAIN WILD-TYPE 102 103 39

Figure S60.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0011

Table S61.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
7Q GAIN MUTATED 97 56 66 90
7Q GAIN WILD-TYPE 51 85 64 103

Figure S61.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S62.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
7Q GAIN MUTATED 46 46 13 36 63 79 26
7Q GAIN WILD-TYPE 34 40 51 21 27 59 71

Figure S62.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.048

Table S63.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
7Q GAIN MUTATED 124 48 103
7Q GAIN WILD-TYPE 87 47 129

Figure S63.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S64.  Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
8P GAIN MUTATED 54 48 68
8P GAIN WILD-TYPE 199 161 85

Figure S64.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00383 (Fisher's exact test), Q value = 0.021

Table S65.  Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
8P GAIN MUTATED 53 33 43 39
8P GAIN WILD-TYPE 95 108 87 154

Figure S65.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.15

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
8P GAIN MUTATED 25 23 22 16 33 25 24
8P GAIN WILD-TYPE 55 63 42 41 57 113 73

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

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S67.  Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
8Q GAIN MUTATED 81 95 139
8Q GAIN WILD-TYPE 172 114 14

Figure S67.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.025

Table S68.  Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
8Q GAIN MUTATED 53 101 59
8Q GAIN WILD-TYPE 49 56 71

Figure S68.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.13

Table S69.  Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
8Q GAIN MUTATED 127 72 43
8Q GAIN WILD-TYPE 101 96 42

Figure S69.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.014

Table S70.  Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
8Q GAIN MUTATED 88 55 74 95
8Q GAIN WILD-TYPE 60 86 56 98

Figure S70.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.075

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
8Q GAIN MUTATED 46 38 29 30 58 72 39
8Q GAIN WILD-TYPE 34 48 35 27 32 66 58

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

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00901 (Fisher's exact test), Q value = 0.041

Table S72.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
8Q GAIN MUTATED 112 87 79
8Q GAIN WILD-TYPE 116 52 92

Figure S72.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0451 (Fisher's exact test), Q value = 0.14

Table S73.  Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
8Q GAIN MUTATED 28 10 19 25
8Q GAIN WILD-TYPE 27 5 15 6

Figure S73.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.014

Table S74.  Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
9P GAIN MUTATED 36 57 30
9P GAIN WILD-TYPE 217 152 123

Figure S74.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'RPPA_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.065

Table S75.  Gene #18: '9q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 75 86 47 66 108 87 12
9Q GAIN MUTATED 15 19 12 6 9 12 3
9Q GAIN WILD-TYPE 60 67 35 60 99 75 9

Figure S75.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 0.0038 (Fisher's exact test), Q value = 0.021

Table S76.  Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
10P GAIN MUTATED 10 25 14
10P GAIN WILD-TYPE 243 184 139

Figure S76.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 0.12

Table S77.  Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
10P GAIN MUTATED 25 14 2
10P GAIN WILD-TYPE 203 154 83

Figure S77.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p gain' versus 'MRNA_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.053

Table S78.  Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
11P GAIN MUTATED 2 11 13 1
11P GAIN WILD-TYPE 41 51 56 40

Figure S78.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00521 (Fisher's exact test), Q value = 0.027

Table S79.  Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
11P GAIN MUTATED 1 8 7 11
11P GAIN WILD-TYPE 48 33 69 38

Figure S79.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S80.  Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
11P GAIN MUTATED 13 42 30
11P GAIN WILD-TYPE 240 167 123

Figure S80.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S81.  Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
11P GAIN MUTATED 12 39 7
11P GAIN WILD-TYPE 90 118 123

Figure S81.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00481 (Fisher's exact test), Q value = 0.025

Table S82.  Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
11P GAIN MUTATED 32 10 17 26
11P GAIN WILD-TYPE 116 131 113 167

Figure S82.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S83.  Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
11P GAIN MUTATED 17 9 1 9 17 26 6
11P GAIN WILD-TYPE 63 77 63 48 73 112 91

Figure S83.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.064

Table S84.  Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
11Q GAIN MUTATED 3 8 15 1
11Q GAIN WILD-TYPE 40 54 54 40

Figure S84.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.0074

Table S85.  Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
11Q GAIN MUTATED 1 7 6 13
11Q GAIN WILD-TYPE 48 34 70 36

Figure S85.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S86.  Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
11Q GAIN MUTATED 7 39 31
11Q GAIN WILD-TYPE 246 170 122

Figure S86.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S87.  Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
11Q GAIN MUTATED 8 37 5
11Q GAIN WILD-TYPE 94 120 125

Figure S87.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00055

Table S88.  Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
11Q GAIN MUTATED 32 5 15 25
11Q GAIN WILD-TYPE 116 136 115 168

Figure S88.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S89.  Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
11Q GAIN MUTATED 17 6 0 7 18 24 5
11Q GAIN WILD-TYPE 63 80 64 50 72 114 92

Figure S89.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.025

Table S90.  Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
12P GAIN MUTATED 63 28 36
12P GAIN WILD-TYPE 190 181 117

Figure S90.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.088

Table S91.  Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
12P GAIN MUTATED 19 21 34
12P GAIN WILD-TYPE 83 136 96

Figure S91.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.066

Table S92.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
12P GAIN MUTATED 13 24 16 7 14 23 30
12P GAIN WILD-TYPE 67 62 48 50 76 115 67

Figure S92.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.016

Table S93.  Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
12Q GAIN MUTATED 58 23 30
12Q GAIN WILD-TYPE 195 186 123

Figure S93.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.005 (Fisher's exact test), Q value = 0.026

Table S94.  Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
12Q GAIN MUTATED 16 16 32
12Q GAIN WILD-TYPE 86 141 98

Figure S94.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00643 (Fisher's exact test), Q value = 0.031

Table S95.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
12Q GAIN MUTATED 13 23 13 5 10 20 27
12Q GAIN WILD-TYPE 67 63 51 52 80 118 70

Figure S95.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S96.  Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
13Q GAIN MUTATED 16 46 51 14
13Q GAIN WILD-TYPE 27 16 18 27

Figure S96.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S97.  Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
13Q GAIN MUTATED 12 29 48 38
13Q GAIN WILD-TYPE 37 12 28 11

Figure S97.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S98.  Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
13Q GAIN MUTATED 87 184 97
13Q GAIN WILD-TYPE 166 25 56

Figure S98.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S99.  Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
13Q GAIN MUTATED 55 124 60
13Q GAIN WILD-TYPE 47 33 70

Figure S99.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S100.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
13Q GAIN MUTATED 110 61 72 122
13Q GAIN WILD-TYPE 38 80 58 71

Figure S100.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S101.  Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
13Q GAIN MUTATED 57 48 14 43 66 103 34
13Q GAIN WILD-TYPE 23 38 50 14 24 35 63

Figure S101.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0037

Table S102.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
13Q GAIN MUTATED 149 48 130
13Q GAIN WILD-TYPE 62 47 102

Figure S102.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.057

Table S103.  Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
13Q GAIN MUTATED 21 9 23 19 14 9
13Q GAIN WILD-TYPE 3 11 5 9 4 8

Figure S103.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.061

Table S104.  Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
14Q GAIN MUTATED 14 10 19
14Q GAIN WILD-TYPE 239 199 134

Figure S104.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'RPPA_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.13

Table S105.  Gene #27: '15q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 75 86 47 66 108 87 12
15Q GAIN MUTATED 5 0 3 2 1 1 0
15Q GAIN WILD-TYPE 70 86 44 64 107 86 12

Figure S105.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'MRNA_CNMF'

P value = 0.0062 (Fisher's exact test), Q value = 0.03

Table S106.  Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
16P GAIN MUTATED 6 21 24 5
16P GAIN WILD-TYPE 37 41 45 36

Figure S106.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.02

Table S107.  Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
16P GAIN MUTATED 5 13 18 20
16P GAIN WILD-TYPE 44 28 58 29

Figure S107.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S108.  Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
16P GAIN MUTATED 17 88 42
16P GAIN WILD-TYPE 236 121 111

Figure S108.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00422 (Fisher's exact test), Q value = 0.023

Table S109.  Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
16P GAIN MUTATED 18 50 22
16P GAIN WILD-TYPE 84 107 108

Figure S109.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0036

Table S110.  Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
16P GAIN MUTATED 47 19 25 55
16P GAIN WILD-TYPE 101 122 105 138

Figure S110.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S111.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
16P GAIN MUTATED 15 19 4 14 30 49 15
16P GAIN WILD-TYPE 65 67 60 43 60 89 82

Figure S111.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MRNA_CNMF'

P value = 0.00878 (Fisher's exact test), Q value = 0.04

Table S112.  Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
16Q GAIN MUTATED 5 19 23 5
16Q GAIN WILD-TYPE 38 43 46 36

Figure S112.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00379 (Fisher's exact test), Q value = 0.021

Table S113.  Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
16Q GAIN MUTATED 4 13 17 18
16Q GAIN WILD-TYPE 45 28 59 31

Figure S113.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S114.  Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
16Q GAIN MUTATED 16 90 39
16Q GAIN WILD-TYPE 237 119 114

Figure S114.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00319 (Fisher's exact test), Q value = 0.019

Table S115.  Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
16Q GAIN MUTATED 19 51 22
16Q GAIN WILD-TYPE 83 106 108

Figure S115.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0073

Table S116.  Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
16Q GAIN MUTATED 47 19 26 52
16Q GAIN WILD-TYPE 101 122 104 141

Figure S116.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00046

Table S117.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
16Q GAIN MUTATED 16 19 4 13 32 46 14
16Q GAIN WILD-TYPE 64 67 60 44 58 92 83

Figure S117.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MRNA_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.073

Table S118.  Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
17Q GAIN MUTATED 3 16 14 3
17Q GAIN WILD-TYPE 40 46 55 38

Figure S118.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00665 (Fisher's exact test), Q value = 0.032

Table S119.  Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
17Q GAIN MUTATED 3 12 9 12
17Q GAIN WILD-TYPE 46 29 67 37

Figure S119.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S120.  Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
17Q GAIN MUTATED 22 47 41
17Q GAIN WILD-TYPE 231 162 112

Figure S120.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S121.  Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
17Q GAIN MUTATED 12 47 16
17Q GAIN WILD-TYPE 90 110 114

Figure S121.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.079

Table S122.  Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
17Q GAIN MUTATED 39 20 22
17Q GAIN WILD-TYPE 189 148 63

Figure S122.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S123.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
17Q GAIN MUTATED 47 14 15 34
17Q GAIN WILD-TYPE 101 127 115 159

Figure S123.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S124.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
17Q GAIN MUTATED 25 16 3 7 19 33 7
17Q GAIN WILD-TYPE 55 70 61 50 71 105 90

Figure S124.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.024

Table S125.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
17Q GAIN MUTATED 49 8 38
17Q GAIN WILD-TYPE 162 87 194

Figure S125.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.13

Table S126.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
17Q GAIN MUTATED 38 34 23
17Q GAIN WILD-TYPE 190 105 148

Figure S126.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.011

Table S127.  Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
18P GAIN MUTATED 16 3 14
18P GAIN WILD-TYPE 237 206 139

Figure S127.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0074

Table S128.  Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
18P GAIN MUTATED 8 2 14
18P GAIN WILD-TYPE 94 155 116

Figure S128.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.089

Table S129.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
18P GAIN MUTATED 4 12 11 6
18P GAIN WILD-TYPE 144 129 119 187

Figure S129.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0049

Table S130.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
18P GAIN MUTATED 1 3 11 3 6 2 7
18P GAIN WILD-TYPE 79 83 53 54 84 136 90

Figure S130.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.12

Table S131.  Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18Q GAIN MUTATED 1 0 0 2
18Q GAIN WILD-TYPE 42 62 69 39

Figure S131.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.053

Table S132.  Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
18Q GAIN MUTATED 12 1 6
18Q GAIN WILD-TYPE 241 208 147

Figure S132.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.051

Table S133.  Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
18Q GAIN MUTATED 6 1 8
18Q GAIN WILD-TYPE 96 156 122

Figure S133.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.016

Table S134.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
18Q GAIN MUTATED 1 7 9 2
18Q GAIN WILD-TYPE 147 134 121 191

Figure S134.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00065

Table S135.  Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
18Q GAIN MUTATED 0 1 8 1 5 0 4
18Q GAIN WILD-TYPE 80 85 56 56 85 138 93

Figure S135.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.059

Table S136.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
18Q GAIN MUTATED 14 1 4
18Q GAIN WILD-TYPE 214 138 167

Figure S136.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.075

Table S137.  Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
19P GAIN MUTATED 2 10 9 10
19P GAIN WILD-TYPE 47 31 67 39

Figure S137.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S138.  Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
19P GAIN MUTATED 19 54 31
19P GAIN WILD-TYPE 234 155 122

Figure S138.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00065

Table S139.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
19P GAIN MUTATED 11 19 3 13 23 29 5
19P GAIN WILD-TYPE 69 67 61 44 67 109 92

Figure S139.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.13

Table S140.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
19P GAIN MUTATED 41 19 27
19P GAIN WILD-TYPE 170 76 205

Figure S140.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00375 (Fisher's exact test), Q value = 0.021

Table S141.  Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
19Q GAIN MUTATED 1 11 14 7
19Q GAIN WILD-TYPE 48 30 62 42

Figure S141.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

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

Table S142.  Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
19Q GAIN MUTATED 29 55 30
19Q GAIN WILD-TYPE 224 154 123

Figure S142.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0073

Table S143.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
19Q GAIN MUTATED 14 21 4 12 24 30 8
19Q GAIN WILD-TYPE 66 65 60 45 66 108 89

Figure S143.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0021

Table S144.  Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20P GAIN MUTATED 16 40 51 18
20P GAIN WILD-TYPE 27 22 18 23

Figure S144.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S145.  Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
20P GAIN MUTATED 13 27 50 35
20P GAIN WILD-TYPE 36 14 26 14

Figure S145.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S146.  Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
20P GAIN MUTATED 110 154 88
20P GAIN WILD-TYPE 143 55 65

Figure S146.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0068

Table S147.  Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
20P GAIN MUTATED 57 106 60
20P GAIN WILD-TYPE 45 51 70

Figure S147.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00597 (Fisher's exact test), Q value = 0.03

Table S148.  Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
20P GAIN MUTATED 96 65 70 118
20P GAIN WILD-TYPE 52 76 60 75

Figure S148.  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 = 0.00014

Table S149.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
20P GAIN MUTATED 53 47 16 44 55 97 37
20P GAIN WILD-TYPE 27 39 48 13 35 41 60

Figure S149.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S150.  Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
20Q GAIN MUTATED 18 60 63 22
20Q GAIN WILD-TYPE 25 2 6 19

Figure S150.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S151.  Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
20Q GAIN MUTATED 15 39 61 48
20Q GAIN WILD-TYPE 34 2 15 1

Figure S151.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S152.  Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
20Q GAIN MUTATED 128 206 131
20Q GAIN WILD-TYPE 125 3 22

Figure S152.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S153.  Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
20Q GAIN MUTATED 67 154 75
20Q GAIN WILD-TYPE 35 3 55

Figure S153.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.088

Table S154.  Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 75 86 47 66 108 87 12
20Q GAIN MUTATED 64 70 38 47 70 62 10
20Q GAIN WILD-TYPE 11 16 9 19 38 25 2

Figure S154.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S155.  Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
20Q GAIN MUTATED 143 78 91 150
20Q GAIN WILD-TYPE 5 63 39 43

Figure S155.  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 = 0.00014

Table S156.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
20Q GAIN MUTATED 73 62 18 50 82 132 45
20Q GAIN WILD-TYPE 7 24 46 7 8 6 52

Figure S156.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.061

Table S157.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
20Q GAIN MUTATED 173 67 166
20Q GAIN WILD-TYPE 38 28 66

Figure S157.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0035

Table S158.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
20Q GAIN MUTATED 166 121 119
20Q GAIN WILD-TYPE 62 18 52

Figure S158.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0036

Table S159.  Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
20Q GAIN MUTATED 23 16 27 23 16 8
20Q GAIN WILD-TYPE 1 4 1 5 2 9

Figure S159.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.073

Table S160.  Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
20Q GAIN MUTATED 40 15 29 29
20Q GAIN WILD-TYPE 15 0 5 2

Figure S160.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0032

Table S161.  Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
21Q GAIN MUTATED 4 15 15
21Q GAIN WILD-TYPE 249 194 138

Figure S161.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00989 (Fisher's exact test), Q value = 0.044

Table S162.  Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
22Q GAIN MUTATED 3 13 7
22Q GAIN WILD-TYPE 250 196 146

Figure S162.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'MRNA_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.12

Table S163.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
XP GAIN MUTATED 2 15 9 8
XP GAIN WILD-TYPE 41 47 60 33

Figure S163.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00055

Table S164.  Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
XP GAIN MUTATED 22 46 31
XP GAIN WILD-TYPE 231 163 122

Figure S164.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.15

Table S165.  Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
XP GAIN MUTATED 10 33 19
XP GAIN WILD-TYPE 92 124 111

Figure S165.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0024

Table S166.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
XQ GAIN MUTATED 26 44 37
XQ GAIN WILD-TYPE 227 165 116

Figure S166.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0255 (Fisher's exact test), Q value = 0.089

Table S167.  Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
1P LOSS MUTATED 6 14 12 14
1P LOSS WILD-TYPE 43 27 64 35

Figure S167.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S168.  Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
1P LOSS MUTATED 32 75 31
1P LOSS WILD-TYPE 221 134 122

Figure S168.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00373 (Fisher's exact test), Q value = 0.021

Table S169.  Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
1P LOSS MUTATED 19 50 21
1P LOSS WILD-TYPE 83 107 109

Figure S169.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0072

Table S170.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
1P LOSS MUTATED 43 16 33 45
1P LOSS WILD-TYPE 105 125 97 148

Figure S170.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0013

Table S171.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
1P LOSS MUTATED 24 14 5 13 29 40 12
1P LOSS WILD-TYPE 56 72 59 44 61 98 85

Figure S171.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00094

Table S172.  Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
1Q LOSS MUTATED 17 41 21
1Q LOSS WILD-TYPE 236 168 132

Figure S172.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.056

Table S173.  Gene #43: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 75 86 47 66 108 87 12
1Q LOSS MUTATED 10 4 9 4 17 10 4
1Q LOSS WILD-TYPE 65 82 38 62 91 77 8

Figure S173.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S174.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
1Q LOSS MUTATED 30 5 18 25
1Q LOSS WILD-TYPE 118 136 112 168

Figure S174.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0045

Table S175.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
1Q LOSS MUTATED 16 5 3 6 19 23 6
1Q LOSS WILD-TYPE 64 81 61 51 71 115 91

Figure S175.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00684 (Fisher's exact test), Q value = 0.033

Table S176.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
1Q LOSS MUTATED 22 28 16
1Q LOSS WILD-TYPE 206 111 155

Figure S176.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0045

Table S177.  Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
2P LOSS MUTATED 1 13 3
2P LOSS WILD-TYPE 252 196 150

Figure S177.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.11

Table S178.  Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
2P LOSS MUTATED 0 5 0
2P LOSS WILD-TYPE 102 152 130

Figure S178.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.054

Table S179.  Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
2P LOSS MUTATED 5 1 6
2P LOSS WILD-TYPE 223 167 79

Figure S179.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00746 (Fisher's exact test), Q value = 0.035

Table S180.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
2P LOSS MUTATED 0 0 0 2 3 4 8
2P LOSS WILD-TYPE 80 86 64 55 87 134 89

Figure S180.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.059

Table S181.  Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
2Q LOSS MUTATED 2 10 2
2Q LOSS WILD-TYPE 251 199 151

Figure S181.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.05

Table S182.  Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
2Q LOSS MUTATED 5 0 4
2Q LOSS WILD-TYPE 223 168 81

Figure S182.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00553 (Fisher's exact test), Q value = 0.028

Table S183.  Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
2Q LOSS MUTATED 0 0 0 1 2 3 8
2Q LOSS WILD-TYPE 80 86 64 56 88 135 89

Figure S183.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.081

Table S184.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
2Q LOSS MUTATED 2 2 9
2Q LOSS WILD-TYPE 226 137 162

Figure S184.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.081

Table S185.  Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
4P LOSS MUTATED 13 24 28 6
4P LOSS WILD-TYPE 30 38 41 35

Figure S185.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00758 (Fisher's exact test), Q value = 0.036

Table S186.  Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
4P LOSS MUTATED 11 13 21 26
4P LOSS WILD-TYPE 38 28 55 23

Figure S186.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S187.  Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
4P LOSS MUTATED 44 107 47
4P LOSS WILD-TYPE 209 102 106

Figure S187.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.013

Table S188.  Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
4P LOSS MUTATED 25 66 33
4P LOSS WILD-TYPE 77 91 97

Figure S188.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0054

Table S189.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
4P LOSS MUTATED 62 28 42 65
4P LOSS WILD-TYPE 86 113 88 128

Figure S189.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00055

Table S190.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
4P LOSS MUTATED 33 22 7 20 37 54 24
4P LOSS WILD-TYPE 47 64 57 37 53 84 73

Figure S190.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.13

Table S191.  Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
4Q LOSS MUTATED 12 23 26 6
4Q LOSS WILD-TYPE 31 39 43 35

Figure S191.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S192.  Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
4Q LOSS MUTATED 38 103 50
4Q LOSS WILD-TYPE 215 106 103

Figure S192.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.017

Table S193.  Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
4Q LOSS MUTATED 30 63 28
4Q LOSS WILD-TYPE 72 94 102

Figure S193.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0036 (Fisher's exact test), Q value = 0.02

Table S194.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
4Q LOSS MUTATED 58 28 40 64
4Q LOSS WILD-TYPE 90 113 90 129

Figure S194.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00094

Table S195.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
4Q LOSS MUTATED 32 21 6 21 35 51 24
4Q LOSS WILD-TYPE 48 65 58 36 55 87 73

Figure S195.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.13

Table S196.  Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
4Q LOSS MUTATED 12 5 15 9 8 2
4Q LOSS WILD-TYPE 12 15 13 19 10 15

Figure S196.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0036

Table S197.  Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
5P LOSS MUTATED 20 33 33
5P LOSS WILD-TYPE 233 176 120

Figure S197.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.12

Table S198.  Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
5P LOSS MUTATED 11 33 15
5P LOSS WILD-TYPE 91 124 115

Figure S198.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.021

Table S199.  Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
5P LOSS MUTATED 14 13 1 15 10 21 12
5P LOSS WILD-TYPE 66 73 63 42 80 117 85

Figure S199.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 0.00936 (Fisher's exact test), Q value = 0.042

Table S200.  Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
5Q LOSS MUTATED 7 14 17 1
5Q LOSS WILD-TYPE 36 48 52 40

Figure S200.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.03 (Fisher's exact test), Q value = 0.1

Table S201.  Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
5Q LOSS MUTATED 7 13 8 11
5Q LOSS WILD-TYPE 42 28 68 38

Figure S201.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S202.  Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
5Q LOSS MUTATED 23 49 49
5Q LOSS WILD-TYPE 230 160 104

Figure S202.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.14

Table S203.  Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
5Q LOSS MUTATED 20 43 20
5Q LOSS WILD-TYPE 82 114 110

Figure S203.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.1

Table S204.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
5Q LOSS MUTATED 39 18 28 36
5Q LOSS WILD-TYPE 109 123 102 157

Figure S204.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.007

Table S205.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
5Q LOSS MUTATED 20 12 4 19 21 32 13
5Q LOSS WILD-TYPE 60 74 60 38 69 106 84

Figure S205.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.079

Table S206.  Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
6P LOSS MUTATED 5 0 11 2
6P LOSS WILD-TYPE 44 41 65 47

Figure S206.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.11

Table S207.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
6P LOSS MUTATED 7 3 4 1 12 7 12
6P LOSS WILD-TYPE 73 83 60 56 78 131 85

Figure S207.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 0.00863 (Fisher's exact test), Q value = 0.04

Table S208.  Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
8P LOSS MUTATED 12 31 31 9
8P LOSS WILD-TYPE 31 31 38 32

Figure S208.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00588 (Fisher's exact test), Q value = 0.03

Table S209.  Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
8P LOSS MUTATED 9 20 31 23
8P LOSS WILD-TYPE 40 21 45 26

Figure S209.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S210.  Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
8P LOSS MUTATED 36 103 79
8P LOSS WILD-TYPE 217 106 74

Figure S210.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0035

Table S211.  Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
8P LOSS MUTATED 30 72 32
8P LOSS WILD-TYPE 72 85 98

Figure S211.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.00644 (Fisher's exact test), Q value = 0.031

Table S212.  Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
8P LOSS MUTATED 58 34 45 80
8P LOSS WILD-TYPE 90 107 85 113

Figure S212.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S213.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
8P LOSS MUTATED 28 26 8 23 40 66 26
8P LOSS WILD-TYPE 52 60 56 34 50 72 71

Figure S213.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00253 (Fisher's exact test), Q value = 0.015

Table S214.  Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
8P LOSS MUTATED 14 5 9 10 11 1
8P LOSS WILD-TYPE 10 15 19 18 7 16

Figure S214.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 0.00445 (Fisher's exact test), Q value = 0.024

Table S215.  Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
8Q LOSS MUTATED 7 21 9
8Q LOSS WILD-TYPE 246 188 144

Figure S215.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0382 (Fisher's exact test), Q value = 0.12

Table S216.  Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
8Q LOSS MUTATED 9 0 4 0
8Q LOSS WILD-TYPE 46 15 30 31

Figure S216.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0053

Table S217.  Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
9P LOSS MUTATED 17 34 26
9P LOSS WILD-TYPE 236 175 127

Figure S217.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00996 (Fisher's exact test), Q value = 0.044

Table S218.  Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
9P LOSS MUTATED 12 31 10
9P LOSS WILD-TYPE 90 126 120

Figure S218.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0032

Table S219.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
9P LOSS MUTATED 31 7 19 20
9P LOSS WILD-TYPE 117 134 111 173

Figure S219.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.065

Table S220.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
9P LOSS MUTATED 13 9 2 12 15 19 7
9P LOSS WILD-TYPE 67 77 62 45 75 119 90

Figure S220.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.15

Table S221.  Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
9Q LOSS MUTATED 3 11 11 1
9Q LOSS WILD-TYPE 40 51 58 40

Figure S221.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.056

Table S222.  Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
9Q LOSS MUTATED 2 10 6 8
9Q LOSS WILD-TYPE 47 31 70 41

Figure S222.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0044

Table S223.  Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
9Q LOSS MUTATED 17 38 23
9Q LOSS WILD-TYPE 236 171 130

Figure S223.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

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

Table S224.  Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
9Q LOSS MUTATED 13 33 7
9Q LOSS WILD-TYPE 89 124 123

Figure S224.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

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

Table S225.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
9Q LOSS MUTATED 30 6 21 21
9Q LOSS WILD-TYPE 118 135 109 172

Figure S225.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.0074

Table S226.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
9Q LOSS MUTATED 10 7 2 12 19 22 6
9Q LOSS WILD-TYPE 70 79 62 45 71 116 91

Figure S226.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.05

Table S227.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
9Q LOSS MUTATED 26 28 15
9Q LOSS WILD-TYPE 202 111 156

Figure S227.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.048

Table S228.  Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
10P LOSS MUTATED 3 4 17 4
10P LOSS WILD-TYPE 40 58 52 37

Figure S228.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S229.  Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
10P LOSS MUTATED 20 47 35
10P LOSS WILD-TYPE 233 162 118

Figure S229.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00455 (Fisher's exact test), Q value = 0.024

Table S230.  Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
10P LOSS MUTATED 14 42 17
10P LOSS WILD-TYPE 88 115 113

Figure S230.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.047

Table S231.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
10P LOSS MUTATED 36 14 22 29
10P LOSS WILD-TYPE 112 127 108 164

Figure S231.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0014

Table S232.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
10P LOSS MUTATED 16 10 3 11 28 23 10
10P LOSS WILD-TYPE 64 76 61 46 62 115 87

Figure S232.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MRNA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.079

Table S233.  Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
10Q LOSS MUTATED 5 6 19 4
10Q LOSS WILD-TYPE 38 56 50 37

Figure S233.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S234.  Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
10Q LOSS MUTATED 16 53 43
10Q LOSS WILD-TYPE 237 156 110

Figure S234.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00424 (Fisher's exact test), Q value = 0.023

Table S235.  Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
10Q LOSS MUTATED 15 44 18
10Q LOSS WILD-TYPE 87 113 112

Figure S235.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.014

Table S236.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
10Q LOSS MUTATED 40 14 22 35
10Q LOSS WILD-TYPE 108 127 108 158

Figure S236.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S237.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
10Q LOSS MUTATED 18 10 1 10 32 26 14
10Q LOSS WILD-TYPE 62 76 63 47 58 112 83

Figure S237.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0468 (Fisher's exact test), Q value = 0.14

Table S238.  Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
10Q LOSS MUTATED 4 3 10 6 6 0
10Q LOSS WILD-TYPE 20 17 18 22 12 17

Figure S238.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.078

Table S239.  Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
11P LOSS MUTATED 22 36 17
11P LOSS WILD-TYPE 231 173 136

Figure S239.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.097

Table S240.  Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
11Q LOSS MUTATED 28 42 23
11Q LOSS WILD-TYPE 225 167 130

Figure S240.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.059

Table S241.  Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
12P LOSS MUTATED 0 5 9 8
12P LOSS WILD-TYPE 49 36 67 41

Figure S241.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S242.  Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
12P LOSS MUTATED 6 44 21
12P LOSS WILD-TYPE 247 165 132

Figure S242.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0033

Table S243.  Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
12P LOSS MUTATED 16 3 2 8 15 21 6
12P LOSS WILD-TYPE 64 83 62 49 75 117 91

Figure S243.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.094

Table S244.  Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
12Q LOSS MUTATED 0 4 9 7
12Q LOSS WILD-TYPE 49 37 67 42

Figure S244.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S245.  Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
12Q LOSS MUTATED 8 42 21
12Q LOSS WILD-TYPE 245 167 132

Figure S245.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0013

Table S246.  Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
12Q LOSS MUTATED 18 2 3 8 15 20 5
12Q LOSS WILD-TYPE 62 84 61 49 75 118 92

Figure S246.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.065

Table S247.  Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
13Q LOSS MUTATED 5 0 2 0
13Q LOSS WILD-TYPE 44 41 74 49

Figure S247.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.057

Table S248.  Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
13Q LOSS MUTATED 8 2 10
13Q LOSS WILD-TYPE 245 207 143

Figure S248.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.057

Table S249.  Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
13Q LOSS MUTATED 0 4 1 0 1 0
13Q LOSS WILD-TYPE 24 16 27 28 17 17

Figure S249.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0021

Table S250.  Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
14Q LOSS MUTATED 10 29 33 6
14Q LOSS WILD-TYPE 33 33 36 35

Figure S250.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.001

Table S251.  Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
14Q LOSS MUTATED 6 20 27 25
14Q LOSS WILD-TYPE 43 21 49 24

Figure S251.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S252.  Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
14Q LOSS MUTATED 33 141 33
14Q LOSS WILD-TYPE 220 68 120

Figure S252.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S253.  Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
14Q LOSS MUTATED 29 74 25
14Q LOSS WILD-TYPE 73 83 105

Figure S253.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 0.086

Table S254.  Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
14Q LOSS MUTATED 70 55 40
14Q LOSS WILD-TYPE 158 113 45

Figure S254.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S255.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
14Q LOSS MUTATED 77 25 28 76
14Q LOSS WILD-TYPE 71 116 102 117

Figure S255.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S256.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
14Q LOSS MUTATED 35 26 3 21 37 65 19
14Q LOSS WILD-TYPE 45 60 61 36 53 73 78

Figure S256.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.12

Table S257.  Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
14Q LOSS MUTATED 13 5 12 14 9 2
14Q LOSS WILD-TYPE 11 15 16 14 9 15

Figure S257.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0457 (Fisher's exact test), Q value = 0.14

Table S258.  Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
14Q LOSS MUTATED 15 6 17 17
14Q LOSS WILD-TYPE 40 9 17 14

Figure S258.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0013

Table S259.  Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
15Q LOSS MUTATED 11 32 36 7
15Q LOSS WILD-TYPE 32 30 33 34

Figure S259.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0089

Table S260.  Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
15Q LOSS MUTATED 11 22 26 27
15Q LOSS WILD-TYPE 38 19 50 22

Figure S260.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S261.  Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
15Q LOSS MUTATED 38 124 67
15Q LOSS WILD-TYPE 215 85 86

Figure S261.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0028

Table S262.  Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
15Q LOSS MUTATED 33 76 34
15Q LOSS WILD-TYPE 69 81 96

Figure S262.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00046

Table S263.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
15Q LOSS MUTATED 71 31 46 80
15Q LOSS WILD-TYPE 77 110 84 113

Figure S263.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S264.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
15Q LOSS MUTATED 35 27 2 23 46 64 31
15Q LOSS WILD-TYPE 45 59 62 34 44 74 66

Figure S264.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.089

Table S265.  Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
16Q LOSS MUTATED 5 7 2 0
16Q LOSS WILD-TYPE 38 55 67 41

Figure S265.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00844 (Fisher's exact test), Q value = 0.039

Table S266.  Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
16Q LOSS MUTATED 14 10 20
16Q LOSS WILD-TYPE 239 199 133

Figure S266.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00046

Table S267.  Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
17P LOSS MUTATED 15 44 47 15
17P LOSS WILD-TYPE 28 18 22 26

Figure S267.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00055

Table S268.  Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
17P LOSS MUTATED 13 27 47 34
17P LOSS WILD-TYPE 36 14 29 15

Figure S268.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S269.  Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
17P LOSS MUTATED 68 156 117
17P LOSS WILD-TYPE 185 53 36

Figure S269.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S270.  Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
17P LOSS MUTATED 41 118 58
17P LOSS WILD-TYPE 61 39 72

Figure S270.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S271.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
17P LOSS MUTATED 104 54 70 111
17P LOSS WILD-TYPE 44 87 60 82

Figure S271.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S272.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
17P LOSS MUTATED 50 44 8 38 66 94 39
17P LOSS WILD-TYPE 30 42 56 19 24 44 58

Figure S272.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.12

Table S273.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
17P LOSS MUTATED 130 44 125
17P LOSS WILD-TYPE 81 51 107

Figure S273.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.086

Table S274.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
17P LOSS MUTATED 119 91 89
17P LOSS WILD-TYPE 109 48 82

Figure S274.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.097

Table S275.  Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
17P LOSS MUTATED 18 14 21 15 11 5
17P LOSS WILD-TYPE 6 6 7 13 7 12

Figure S275.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.0095

Table S276.  Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
17Q LOSS MUTATED 24 44 28
17Q LOSS WILD-TYPE 229 165 125

Figure S276.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.098

Table S277.  Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
17Q LOSS MUTATED 15 14 2 12 19 19 15
17Q LOSS WILD-TYPE 65 72 62 45 71 119 82

Figure S277.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S278.  Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18P LOSS MUTATED 13 52 54 12
18P LOSS WILD-TYPE 30 10 15 29

Figure S278.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S279.  Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
18P LOSS MUTATED 10 35 44 42
18P LOSS WILD-TYPE 39 6 32 7

Figure S279.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S280.  Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
18P LOSS MUTATED 75 190 114
18P LOSS WILD-TYPE 178 19 39

Figure S280.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S281.  Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
18P LOSS MUTATED 47 147 52
18P LOSS WILD-TYPE 55 10 78

Figure S281.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S282.  Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
18P LOSS MUTATED 133 51 72 121
18P LOSS WILD-TYPE 15 90 58 72

Figure S282.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S283.  Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
18P LOSS MUTATED 67 50 6 39 71 108 36
18P LOSS WILD-TYPE 13 36 58 18 19 30 61

Figure S283.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.00682 (Fisher's exact test), Q value = 0.033

Table S284.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
18P LOSS MUTATED 146 51 132
18P LOSS WILD-TYPE 65 44 100

Figure S284.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00914 (Fisher's exact test), Q value = 0.042

Table S285.  Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
18P LOSS MUTATED 131 100 98
18P LOSS WILD-TYPE 97 39 73

Figure S285.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0013

Table S286.  Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
18P LOSS MUTATED 21 10 25 20 12 5
18P LOSS WILD-TYPE 3 10 3 8 6 12

Figure S286.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.0074

Table S287.  Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
18P LOSS MUTATED 28 14 25 26
18P LOSS WILD-TYPE 27 1 9 5

Figure S287.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S288.  Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
18Q LOSS MUTATED 17 54 56 14
18Q LOSS WILD-TYPE 26 8 13 27

Figure S288.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S289.  Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
18Q LOSS MUTATED 14 36 49 42
18Q LOSS WILD-TYPE 35 5 27 7

Figure S289.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S290.  Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
18Q LOSS MUTATED 84 193 132
18Q LOSS WILD-TYPE 169 16 21

Figure S290.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S291.  Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
18Q LOSS MUTATED 54 148 63
18Q LOSS WILD-TYPE 48 9 67

Figure S291.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S292.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
18Q LOSS MUTATED 133 60 82 132
18Q LOSS WILD-TYPE 15 81 48 61

Figure S292.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S293.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
18Q LOSS MUTATED 67 57 9 44 75 112 43
18Q LOSS WILD-TYPE 13 29 55 13 15 26 54

Figure S293.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0068

Table S294.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
18Q LOSS MUTATED 158 52 146
18Q LOSS WILD-TYPE 53 43 86

Figure S294.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00623 (Fisher's exact test), Q value = 0.03

Table S295.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
18Q LOSS MUTATED 144 107 105
18Q LOSS WILD-TYPE 84 32 66

Figure S295.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0012

Table S296.  Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 20 28 28 18 17
18Q LOSS MUTATED 21 12 26 21 14 5
18Q LOSS WILD-TYPE 3 8 2 7 4 12

Figure S296.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.0028

Table S297.  Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
18Q LOSS MUTATED 31 14 25 29
18Q LOSS WILD-TYPE 24 1 9 2

Figure S297.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0033

Table S298.  Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
19P LOSS MUTATED 13 25 26
19P LOSS WILD-TYPE 240 184 127

Figure S298.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.15

Table S299.  Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
19P LOSS MUTATED 24 9 11 20
19P LOSS WILD-TYPE 124 132 119 173

Figure S299.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0431 (Fisher's exact test), Q value = 0.14

Table S300.  Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
19P LOSS MUTATED 16 4 3 5 11 15 10
19P LOSS WILD-TYPE 64 82 61 52 79 123 87

Figure S300.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00609 (Fisher's exact test), Q value = 0.03

Table S301.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 139 171
19P LOSS MUTATED 15 24 17
19P LOSS WILD-TYPE 213 115 154

Figure S301.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00962 (Fisher's exact test), Q value = 0.043

Table S302.  Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
19P LOSS MUTATED 2 2 9 6
19P LOSS WILD-TYPE 53 13 25 25

Figure S302.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.011

Table S303.  Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
19Q LOSS MUTATED 12 20 23
19Q LOSS WILD-TYPE 241 189 130

Figure S303.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.073

Table S304.  Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
20P LOSS MUTATED 2 9 6 9
20P LOSS WILD-TYPE 47 32 70 40

Figure S304.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S305.  Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
20P LOSS MUTATED 12 28 28
20P LOSS WILD-TYPE 241 181 125

Figure S305.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0038

Table S306.  Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
20P LOSS MUTATED 7 28 6
20P LOSS WILD-TYPE 95 129 124

Figure S306.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S307.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
20P LOSS MUTATED 8 9 0 4 18 23 6
20P LOSS WILD-TYPE 72 77 64 53 72 115 91

Figure S307.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00244 (Fisher's exact test), Q value = 0.015

Table S308.  Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
20P LOSS MUTATED 3 6 3 1
20P LOSS WILD-TYPE 52 9 31 30

Figure S308.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.067

Table S309.  Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
21Q LOSS MUTATED 10 26 23 6
21Q LOSS WILD-TYPE 33 36 46 35

Figure S309.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.079

Table S310.  Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
21Q LOSS MUTATED 10 19 18 18
21Q LOSS WILD-TYPE 39 22 58 31

Figure S310.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S311.  Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
21Q LOSS MUTATED 54 97 43
21Q LOSS WILD-TYPE 199 112 110

Figure S311.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.079

Table S312.  Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 157 130
21Q LOSS MUTATED 28 64 35
21Q LOSS WILD-TYPE 74 93 95

Figure S312.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00094

Table S313.  Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
21Q LOSS MUTATED 68 29 36 59
21Q LOSS WILD-TYPE 80 112 94 134

Figure S313.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00331 (Fisher's exact test), Q value = 0.019

Table S314.  Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
21Q LOSS MUTATED 30 24 10 21 35 51 21
21Q LOSS WILD-TYPE 50 62 54 36 55 87 76

Figure S314.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00521 (Fisher's exact test), Q value = 0.027

Table S315.  Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 62 69 41
22Q LOSS MUTATED 12 28 28 6
22Q LOSS WILD-TYPE 31 34 41 35

Figure S315.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0024

Table S316.  Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 41 76 49
22Q LOSS MUTATED 5 16 31 22
22Q LOSS WILD-TYPE 44 25 45 27

Figure S316.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00014

Table S317.  Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 253 209 153
22Q LOSS MUTATED 49 104 50
22Q LOSS WILD-TYPE 204 105 103

Figure S317.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.067

Table S318.  Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 141 130 193
22Q LOSS MUTATED 58 33 40 71
22Q LOSS WILD-TYPE 90 108 90 122

Figure S318.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00025

Table S319.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 80 86 64 57 90 138 97
22Q LOSS MUTATED 30 27 5 23 35 59 23
22Q LOSS WILD-TYPE 50 59 59 34 55 79 74

Figure S319.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'RPPA_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.075

Table S320.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 75 86 47 66 108 87 12
XP LOSS MUTATED 10 11 10 15 9 12 5
XP LOSS WILD-TYPE 65 75 37 51 99 75 7

Figure S320.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.058

Table S321.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 228 168 85
XP LOSS MUTATED 23 33 16
XP LOSS WILD-TYPE 205 135 69

Figure S321.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.11

Table S322.  Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
XP LOSS MUTATED 3 4 8 4
XP LOSS WILD-TYPE 52 11 26 27

Figure S322.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.15

Table S323.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 211 95 232
XQ LOSS MUTATED 31 5 30
XQ LOSS WILD-TYPE 180 90 202

Figure S323.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00766 (Fisher's exact test), Q value = 0.036

Table S324.  Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 15 34 31
XQ LOSS MUTATED 3 4 9 2
XQ LOSS WILD-TYPE 52 11 25 29

Figure S324.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/19781252/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/COADREAD-TP/20147373/COADREAD-TP.transferedmergedcluster.txt

  • Number of patients = 615

  • Number of significantly arm-level cnvs = 82

  • 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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