Correlation between copy number variations of arm-level result and molecular subtypes
Liver Hepatocellular Carcinoma
14 July 2016  |  awg_lihc__2016_07_14
Maintainer Information
Citation Information
doi:10.7908/C1N29WFN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1N29WFN
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 10 molecular subtypes across 370 patients, 319 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 2p gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 3p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 3q gain cnv correlated to 'CN_CNMF'.

  • 4p gain cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 5q gain cnv correlated to 'CN_CNMF'.

  • 6p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 6q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

  • 9p gain cnv correlated to 'RPPA_CNMF'.

  • 9q gain cnv correlated to 'RPPA_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 12p gain cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 12q gain cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 16p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 16q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 19p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 21q gain cnv correlated to 'RPPA_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • xp gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

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

  • 2p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

  • 3q loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

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

  • 5p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • 7p loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 7q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

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

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

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

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

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

  • 11p loss cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 12q loss cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

  • 17q loss cnv correlated to 'CN_CNMF'.

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

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

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

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

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

  • 22q loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • xp loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • xq loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 319 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
10q loss 79 (21%) 291 1e-05
(0.000195) 		0.00041
(0.00358) 		0.00453
(0.0203) 		0.042
(0.112) 		0.00026
(0.00245) 		0.0149
(0.0502) 		0.00255
(0.0132) 		0.00432
(0.0197) 		0.00407
(0.0189) 		0.00088
(0.00601)
16p loss 109 (29%) 261 1e-05
(0.000195) 		1e-05
(0.000195) 		0.00182
(0.01) 		0.00138
(0.00808) 		1e-05
(0.000195) 		1e-05
(0.000195) 		1e-05
(0.000195) 		1e-05
(0.000195) 		1e-05
(0.000195) 		1e-05
(0.000195)
16q loss 145 (39%) 225 1e-05
(0.000195) 		1e-05
(0.000195) 		0.00043
(0.00367) 		0.00014
(0.00145) 		1e-05
(0.000195) 		1e-05
(0.000195) 		2e-05
(0.000315) 		1e-05
(0.000195) 		1e-05
(0.000195) 		3e-05
(0.000439)
1p loss 81 (22%) 289 1e-05
(0.000195) 		1e-05
(0.000195) 		0.0462
(0.121) 		0.129
(0.24) 		0.00011
(0.00125) 		0.00011
(0.00125) 		0.00023
(0.00225) 		0.00139
(0.00808) 		0.00036
(0.00321) 		0.00159
(0.00881)
4q loss 146 (39%) 224 1e-05
(0.000195) 		2e-05
(0.000315) 		0.00381
(0.0181) 		0.203
(0.327) 		1e-05
(0.000195) 		8e-05
(0.000994) 		0.00055
(0.00438) 		0.00011
(0.00125) 		1e-05
(0.000195) 		5e-05
(0.000661)
13q loss 122 (33%) 248 1e-05
(0.000195) 		0.00838
(0.0323) 		0.424
(0.556) 		0.0259
(0.0774) 		0.00082
(0.00575) 		0.00014
(0.00145) 		0.0013
(0.00778) 		0.00391
(0.0184) 		0.00021
(0.00207) 		0.00013
(0.00142)
14q loss 108 (29%) 262 1e-05
(0.000195) 		0.00051
(0.00414) 		0.00612
(0.026) 		0.0741
(0.168) 		1e-05
(0.000195) 		1e-05
(0.000195) 		0.025
(0.076) 		0.00436
(0.0198) 		3e-05
(0.000439) 		0.00921
(0.035)
15q loss 67 (18%) 303 1e-05
(0.000195) 		0.00116
(0.00721) 		0.006
(0.0256) 		0.00147
(0.00837) 		2e-05
(0.000315) 		5e-05
(0.000661) 		0.0107
(0.0387) 		0.0588
(0.143) 		0.0012
(0.0074) 		0.0239
(0.0741)
19q gain 71 (19%) 299 0.0006
(0.00459) 		1e-05
(0.000195) 		0.462
(0.585) 		0.0518
(0.131) 		2e-05
(0.000315) 		0.00066
(0.00483) 		0.0449
(0.119) 		0.00035
(0.00315) 		0.00099
(0.00644) 		4e-05
(0.000547)
20p gain 108 (29%) 262 2e-05
(0.000315) 		0.00901
(0.0344) 		0.0523
(0.132) 		0.00145
(0.00831) 		0.00635
(0.0265) 		0.00452
(0.0203) 		0.0547
(0.136) 		0.0119
(0.0417) 		0.00019
(0.0019) 		0.0272
(0.0806)
4p loss 105 (28%) 265 1e-05
(0.000195) 		0.00215
(0.0114) 		0.00095
(0.00633) 		0.0602
(0.146) 		0.0038
(0.0181) 		0.0103
(0.0378) 		0.295
(0.428) 		0.00157
(0.00881) 		0.0011
(0.00694) 		0.00013
(0.00142)
9p loss 119 (32%) 251 1e-05
(0.000195) 		0.00061
(0.00459) 		0.168
(0.285) 		0.637
(0.734) 		0.00016
(0.00162) 		0.00085
(0.00586) 		0.00592
(0.0254) 		0.0071
(0.0284) 		0.00033
(0.00304) 		2e-05
(0.000315)
9q loss 110 (30%) 260 1e-05
(0.000195) 		0.00127
(0.00777) 		0.36
(0.494) 		0.792
(0.845) 		0.00068
(0.00493) 		0.0001
(0.00121) 		0.028
(0.0821) 		0.0027
(0.0138) 		0.00061
(0.00459) 		1e-05
(0.000195)
17p loss 185 (50%) 185 1e-05
(0.000195) 		0.00717
(0.0284) 		0.131
(0.241) 		0.0346
(0.0974) 		1e-05
(0.000195) 		0.128
(0.24) 		9e-05
(0.0011) 		0.00251
(0.0131) 		2e-05
(0.000315) 		1e-05
(0.000195)
6p gain 117 (32%) 253 1e-05
(0.000195) 		0.0249
(0.0759) 		0.00037
(0.00326) 		0.241
(0.37) 		0.00347
(0.0169) 		0.00331
(0.0163) 		0.0398
(0.108) 		0.00098
(0.00643) 		0.115
(0.222) 		0.204
(0.327)
8q gain 184 (50%) 186 2e-05
(0.000315) 		0.0232
(0.0721) 		0.12
(0.23) 		0.244
(0.373) 		1e-05
(0.000195) 		1e-05
(0.000195) 		0.124
(0.234) 		0.00157
(0.00881) 		0.00071
(0.00506) 		0.00194
(0.0105)
19p gain 56 (15%) 314 0.00143
(0.00826) 		2e-05
(0.000315) 		0.649
(0.745) 		0.113
(0.22) 		0.00085
(0.00586) 		0.00685
(0.0279) 		0.0526
(0.132) 		0.00733
(0.0288) 		0.00109
(0.00693) 		0.00187
(0.0102)
22q gain 48 (13%) 322 6e-05
(0.000781) 		0.155
(0.27) 		0.00423
(0.0194) 		0.00556
(0.0243) 		0.00137
(0.00808) 		0.00251
(0.0131) 		0.0414
(0.111) 		0.377
(0.511) 		0.0391
(0.107) 		0.238
(0.369)
3p loss 52 (14%) 318 0.035
(0.0981) 		0.0272
(0.0806) 		0.564
(0.674) 		0.206
(0.328) 		0.00011
(0.00125) 		0.00054
(0.00434) 		0.0013
(0.00778) 		0.0491
(0.127) 		0.00026
(0.00245) 		0.0525
(0.132)
1q gain 225 (61%) 145 1e-05
(0.000195) 		2e-05
(0.000315) 		0.347
(0.481) 		0.27
(0.403) 		0.00042
(0.00363) 		0.00014
(0.00145) 		0.142
(0.255) 		0.00267
(0.0137) 		0.166
(0.282) 		0.0311
(0.0888)
4p gain 27 (7%) 343 0.0972
(0.203) 		0.00293
(0.0146) 		0.00259
(0.0134) 		0.134
(0.246) 		0.0185
(0.0602) 		0.011
(0.0393) 		0.0252
(0.0763) 		0.224
(0.353) 		0.0321
(0.0913) 		0.249
(0.377)
20q gain 112 (30%) 258 1e-05
(0.000195) 		0.00999
(0.0375) 		0.216
(0.341) 		0.0124
(0.0425) 		0.0753
(0.17) 		0.0211
(0.067) 		0.2
(0.323) 		0.0287
(0.0829) 		0.00024
(0.00232) 		0.0625
(0.148)
xq gain 60 (16%) 310 0.0108
(0.0388) 		0.00307
(0.0152) 		0.335
(0.467) 		0.0939
(0.199) 		0.00058
(0.00453) 		0.0006
(0.00459) 		0.166
(0.282) 		0.00057
(0.00449) 		0.0783
(0.175) 		0.00062
(0.00462)
11p loss 63 (17%) 307 0.00106
(0.00684) 		0.0708
(0.163) 		0.633
(0.732) 		0.454
(0.58) 		0.0213
(0.0673) 		0.00682
(0.0279) 		0.437
(0.566) 		0.0241
(0.0742) 		0.0124
(0.0425) 		0.0029
(0.0146)
2q gain 40 (11%) 330 0.0403
(0.109) 		0.0305
(0.0874) 		0.942
(0.956) 		0.122
(0.232) 		0.0255
(0.0768) 		0.00093
(0.00625) 		0.468
(0.591) 		0.483
(0.602) 		0.0103
(0.0378) 		0.521
(0.632)
10p gain 58 (16%) 312 0.0008
(0.00566) 		0.115
(0.222) 		0.197
(0.319) 		0.147
(0.262) 		0.00353
(0.0169) 		0.00636
(0.0265) 		0.0899
(0.194) 		0.0516
(0.131) 		0.00623
(0.0263) 		0.0013
(0.00778)
3q loss 41 (11%) 329 0.047
(0.122) 		0.35
(0.483) 		0.516
(0.627) 		0.688
(0.772) 		0.00534
(0.0235) 		0.0079
(0.0308) 		0.0391
(0.107) 		0.242
(0.372) 		0.0142
(0.0482) 		0.279
(0.412)
5q loss 37 (10%) 333 0.0118
(0.0415) 		0.01
(0.0375) 		0.188
(0.309) 		0.0752
(0.17) 		0.00044
(0.00368) 		0.00111
(0.00695) 		0.0952
(0.2) 		0.125
(0.236) 		0.00836
(0.0323) 		0.0775
(0.174)
10p loss 48 (13%) 322 3e-05
(0.000439) 		0.206
(0.328) 		0.434
(0.564) 		0.385
(0.522) 		0.00859
(0.0329) 		0.0436
(0.116) 		0.0326
(0.0922) 		0.0139
(0.0472) 		0.143
(0.257) 		0.156
(0.271)
2p gain 43 (12%) 327 0.0531
(0.133) 		0.00063
(0.00465) 		0.95
(0.962) 		0.0281
(0.0821) 		0.0279
(0.0821) 		0.00107
(0.00685) 		0.568
(0.676) 		0.724
(0.794) 		0.0561
(0.139) 		0.467
(0.591)
6q gain 68 (18%) 302 7e-05
(0.000897) 		0.0123
(0.0425) 		0.00216
(0.0114) 		0.721
(0.793) 		0.157
(0.272) 		0.118
(0.228) 		0.426
(0.557) 		0.0995
(0.204) 		0.0324
(0.092) 		0.809
(0.86)
10q gain 36 (10%) 334 1e-05
(0.000195) 		0.104
(0.209) 		0.176
(0.297) 		0.15
(0.265) 		0.00096
(0.00635) 		0.0209
(0.0667) 		0.102
(0.207) 		0.0115
(0.0408) 		0.0576
(0.142) 		0.112
(0.22)
12p gain 40 (11%) 330 0.297
(0.428) 		0.159
(0.274) 		0.0799
(0.176) 		0.00494
(0.022) 		0.00029
(0.0027) 		0.00197
(0.0106) 		0.00541
(0.0237) 		0.0605
(0.146) 		0.0575
(0.142) 		0.253
(0.382)
12q gain 47 (13%) 323 0.272
(0.404) 		0.246
(0.374) 		0.196
(0.319) 		0.0347
(0.0975) 		0.00044
(0.00368) 		0.00394
(0.0184) 		0.023
(0.0719) 		0.257
(0.385) 		0.254
(0.383) 		0.396
(0.53)
17q gain 93 (25%) 277 0.00695
(0.0281) 		0.0784
(0.175) 		0.141
(0.254) 		0.199
(0.322) 		0.0421
(0.112) 		0.0927
(0.197) 		0.0713
(0.163) 		0.00804
(0.0312) 		0.0707
(0.163) 		0.0159
(0.0535)
18p gain 36 (10%) 334 0.00034
(0.0031) 		0.106
(0.212) 		0.12
(0.23) 		0.0397
(0.108) 		0.00278
(0.0141) 		0.00563
(0.0244) 		0.206
(0.328) 		0.139
(0.251) 		0.263
(0.393) 		0.513
(0.627)
8p loss 196 (53%) 174 0.00091
(0.00617) 		0.00069
(0.00496) 		0.933
(0.951) 		0.874
(0.911) 		0.588
(0.694) 		0.039
(0.107) 		0.784
(0.841) 		0.314
(0.446) 		0.0242
(0.0742) 		0.763
(0.825)
18q loss 79 (21%) 291 0.0178
(0.0583) 		0.0283
(0.0821) 		0.929
(0.951) 		0.577
(0.684) 		0.682
(0.766) 		0.0271
(0.0806) 		0.459
(0.584) 		0.147
(0.262) 		0.0164
(0.0547) 		0.107
(0.212)
5p gain 135 (36%) 235 1e-05
(0.000195) 		0.11
(0.216) 		0.24
(0.37) 		0.0873
(0.189) 		0.0448
(0.119) 		0.179
(0.299) 		0.24
(0.37) 		0.0275
(0.0811) 		0.146
(0.262) 		0.115
(0.222)
8p gain 73 (20%) 297 0.297
(0.428) 		0.613
(0.713) 		0.107
(0.212) 		0.184
(0.305) 		0.00012
(0.00135) 		0.0105
(0.0381) 		0.114
(0.222) 		0.102
(0.206) 		0.0167
(0.0551) 		0.386
(0.522)
13q gain 23 (6%) 347 0.0187
(0.0605) 		0.0662
(0.155) 		0.543
(0.654) 		0.49
(0.608) 		0.239
(0.37) 		0.307
(0.44) 		0.0384
(0.106) 		0.432
(0.563) 		0.038
(0.106) 		0.676
(0.763)
18q gain 28 (8%) 342 0.00198
(0.0106) 		0.0973
(0.203) 		0.285
(0.42) 		0.0645
(0.152) 		0.0101
(0.0377) 		0.00306
(0.0152) 		0.079
(0.176) 		0.117
(0.226) 		0.18
(0.3) 		0.165
(0.281)
2q loss 38 (10%) 332 4e-05
(0.000547) 		0.142
(0.255) 		0.799
(0.851) 		0.354
(0.489) 		0.0464
(0.121) 		0.0434
(0.116) 		0.814
(0.862) 		0.694
(0.778) 		0.669
(0.761) 		0.393
(0.527)
5p loss 29 (8%) 341 0.0164
(0.0547) 		0.374
(0.51) 		0.762
(0.825) 		0.295
(0.428) 		0.0353
(0.0984) 		0.0683
(0.158) 		0.0679
(0.158) 		0.0617
(0.147) 		0.0231
(0.0719) 		0.182
(0.302)
7p loss 16 (4%) 354 0.325
(0.458) 		0.0498
(0.128) 		0.00159
(0.00881) 		0.82
(0.866) 		0.56
(0.669) 		0.398
(0.532) 		0.945
(0.958) 		0.509
(0.626) 		0.00691
(0.0281) 		0.129
(0.24)
11q loss 72 (19%) 298 0.01
(0.0375) 		0.0621
(0.148) 		0.935
(0.952) 		0.55
(0.661) 		0.082
(0.18) 		0.191
(0.313) 		0.788
(0.843) 		0.0731
(0.166) 		0.0105
(0.0381) 		0.0244
(0.0747)
18p loss 74 (20%) 296 0.0105
(0.0381) 		0.097
(0.203) 		0.895
(0.927) 		0.908
(0.935) 		0.738
(0.807) 		0.0189
(0.0609) 		0.634
(0.732) 		0.223
(0.351) 		0.0108
(0.0388) 		0.0502
(0.129)
19p loss 52 (14%) 318 1e-05
(0.000195) 		0.241
(0.37) 		0.887
(0.922) 		0.247
(0.375) 		0.0165
(0.0549) 		0.169
(0.286) 		0.0583
(0.143) 		0.0671
(0.156) 		0.105
(0.21) 		0.0187
(0.0605)
1p gain 60 (16%) 310 0.128
(0.24) 		0.0837
(0.183) 		0.00711
(0.0284) 		0.0997
(0.204) 		0.299
(0.43) 		0.141
(0.254) 		0.164
(0.28) 		0.0951
(0.2) 		0.0915
(0.195) 		0.0408
(0.11)
3p gain 35 (9%) 335 0.0111
(0.0396) 		0.123
(0.234) 		0.231
(0.362) 		0.318
(0.448) 		0.0458
(0.12) 		0.412
(0.542) 		0.494
(0.612) 		0.556
(0.665) 		0.0614
(0.147) 		0.905
(0.935)
4q gain 7 (2%) 363 0.0881
(0.19) 		0.434
(0.564) 		8e-05
(0.000994) 		0.312
(0.444) 		0.649
(0.745) 		0.472
(0.594) 		0.0288
(0.083) 		0.439
(0.566) 		0.626
(0.725) 		0.696
(0.778)
7q gain 110 (30%) 260 0.0167
(0.0551) 		0.00133
(0.0079) 		0.332
(0.465) 		0.958
(0.968) 		0.658
(0.754) 		0.74
(0.808) 		0.446
(0.573) 		0.697
(0.778) 		0.25
(0.378) 		0.552
(0.662)
11p gain 18 (5%) 352 0.717
(0.793) 		0.0649
(0.152) 		0.0218
(0.0685) 		0.493
(0.611) 		0.0504
(0.129) 		0.0399
(0.108) 		0.401
(0.533) 		0.431
(0.563) 		0.149
(0.263) 		0.409
(0.539)
xp gain 42 (11%) 328 0.0064
(0.0265) 		0.0708
(0.163) 		0.245
(0.373) 		0.423
(0.555) 		0.00392
(0.0184) 		0.0908
(0.194) 		0.932
(0.951) 		0.134
(0.246) 		0.157
(0.272) 		0.131
(0.241)
1q loss 21 (6%) 349 0.0282
(0.0821) 		0.309
(0.44) 		0.228
(0.358) 		0.277
(0.411) 		0.287
(0.421) 		0.335
(0.467) 		0.329
(0.462) 		0.159
(0.274) 		0.905
(0.935) 		0.0175
(0.0575)
2p loss 33 (9%) 337 0.00051
(0.00414) 		0.234
(0.364) 		0.668
(0.761) 		0.148
(0.263) 		0.0479
(0.124) 		0.0857
(0.187) 		0.238
(0.369) 		0.746
(0.814) 		0.159
(0.274) 		0.188
(0.309)
7q loss 21 (6%) 349 0.0988
(0.204) 		0.128
(0.24) 		0.0584
(0.143) 		0.256
(0.385) 		0.296
(0.428) 		0.316
(0.446) 		0.165
(0.282) 		0.0458
(0.12) 		0.0124
(0.0425) 		0.0945
(0.2)
19q loss 39 (11%) 331 1e-05
(0.000195) 		0.186
(0.307) 		0.533
(0.643) 		0.156
(0.271) 		0.105
(0.211) 		0.863
(0.905) 		0.0878
(0.19) 		0.101
(0.205) 		0.00353
(0.0169) 		0.129
(0.24)
21q loss 110 (30%) 260 0.0602
(0.146) 		0.00631
(0.0265) 		0.45
(0.577) 		0.347
(0.481) 		0.0191
(0.0613) 		0.0798
(0.176) 		0.472
(0.594) 		0.669
(0.761) 		0.0665
(0.155) 		0.105
(0.211)
22q loss 70 (19%) 300 4e-05
(0.000547) 		0.159
(0.274) 		0.00666
(0.0274) 		0.996
(1.00) 		0.186
(0.307) 		0.336
(0.468) 		0.815
(0.862) 		0.287
(0.421) 		0.179
(0.299) 		0.28
(0.413)
xp loss 93 (25%) 277 0.0997
(0.204) 		0.00415
(0.0191) 		0.673
(0.763) 		0.233
(0.363) 		0.0212
(0.067) 		0.102
(0.206) 		0.0603
(0.146) 		0.44
(0.566) 		0.053
(0.133) 		0.375
(0.511)
xq loss 73 (20%) 297 0.00573
(0.0247) 		0.00729
(0.0287) 		0.723
(0.794) 		0.514
(0.627) 		0.0609
(0.146) 		0.392
(0.527) 		0.255
(0.384) 		0.925
(0.949) 		0.703
(0.781) 		0.623
(0.723)
3q gain 38 (10%) 332 0.00353
(0.0169) 		0.0837
(0.183) 		0.513
(0.627) 		0.587
(0.694) 		0.147
(0.262) 		0.73
(0.8) 		0.207
(0.329) 		0.705
(0.782) 		0.098
(0.204) 		0.672
(0.763)
5q gain 110 (30%) 260 4e-05
(0.000547) 		0.231
(0.362) 		0.699
(0.779) 		0.18
(0.3) 		0.0858
(0.187) 		0.36
(0.494) 		0.197
(0.319) 		0.315
(0.446) 		0.529
(0.639) 		0.421
(0.554)
7p gain 109 (29%) 261 3e-05
(0.000439) 		0.0555
(0.138) 		0.569
(0.676) 		0.918
(0.945) 		0.362
(0.497) 		0.836
(0.88) 		0.112
(0.22) 		0.183
(0.304) 		0.401
(0.533) 		0.327
(0.46)
9p gain 19 (5%) 351 0.206
(0.328) 		0.243
(0.372) 		0.0005
(0.00414) 		0.0731
(0.166) 		0.479
(0.599) 		0.772
(0.831) 		0.391
(0.526) 		0.48
(0.6) 		0.516
(0.627) 		0.676
(0.763)
9q gain 19 (5%) 351 0.763
(0.825) 		0.931
(0.951) 		0.00508
(0.0225) 		0.0733
(0.166) 		0.509
(0.626) 		0.62
(0.72) 		0.771
(0.831) 		0.756
(0.822) 		0.719
(0.793) 		0.697
(0.778)
16p gain 31 (8%) 339 0.312
(0.444) 		0.929
(0.951) 		0.597
(0.699) 		0.664
(0.76) 		0.00716
(0.0284) 		0.682
(0.766) 		0.349
(0.483) 		0.515
(0.627) 		0.11
(0.216) 		0.119
(0.228)
16q gain 17 (5%) 353 0.203
(0.326) 		0.129
(0.24) 		1
(1.00) 		0.598
(0.699) 		0.00014
(0.00145) 		0.439
(0.566) 		0.736
(0.806) 		0.921
(0.947) 		0.291
(0.424) 		0.0796
(0.176)
17p gain 30 (8%) 340 0.0117
(0.0413) 		0.862
(0.905) 		0.501
(0.617) 		0.873
(0.91) 		0.172
(0.29) 		0.305
(0.438) 		0.999
(1.00) 		0.332
(0.465) 		0.187
(0.308) 		0.755
(0.822)
21q gain 26 (7%) 344 0.138
(0.251) 		0.477
(0.599) 		0.0258
(0.0774) 		0.594
(0.697) 		0.12
(0.23) 		0.234
(0.364) 		0.889
(0.923) 		0.365
(0.5) 		0.0903
(0.194) 		0.15
(0.265)
12p loss 67 (18%) 303 0.00015
(0.00154) 		0.153
(0.268) 		0.815
(0.862) 		0.814
(0.862) 		0.064
(0.151) 		0.289
(0.423) 		0.459
(0.584) 		0.16
(0.275) 		0.128
(0.24) 		0.13
(0.24)
12q loss 36 (10%) 334 0.0123
(0.0425) 		0.439
(0.566) 		0.457
(0.583) 		0.819
(0.865) 		0.612
(0.713) 		0.939
(0.955) 		0.83
(0.874) 		0.976
(0.983) 		0.79
(0.844) 		0.719
(0.793)
17q loss 40 (11%) 330 0.01
(0.0375) 		0.498
(0.615) 		0.308
(0.44) 		0.479
(0.599) 		0.0591
(0.144) 		0.461
(0.585) 		0.402
(0.533) 		0.757
(0.822) 		0.571
(0.678) 		0.135
(0.247)
11q gain 20 (5%) 350 0.649
(0.745) 		0.204
(0.327) 		0.107
(0.212) 		0.863
(0.905) 		0.191
(0.313) 		0.135
(0.247) 		0.714
(0.792) 		0.7
(0.779) 		0.148
(0.263) 		0.277
(0.411)
14q gain 22 (6%) 348 0.107
(0.212) 		0.138
(0.251) 		0.0981
(0.204) 		0.773
(0.831) 		0.472
(0.594) 		0.0994
(0.204) 		0.102
(0.206) 		0.589
(0.694) 		0.4
(0.533) 		0.451
(0.577)
15q gain 33 (9%) 337 0.259
(0.387) 		0.587
(0.694) 		0.305
(0.437) 		0.196
(0.319) 		0.6
(0.701) 		0.594
(0.697) 		0.976
(0.983) 		0.556
(0.665) 		0.387
(0.522) 		0.398
(0.532)
6p loss 31 (8%) 339 0.44
(0.566) 		0.387
(0.522) 		0.607
(0.708) 		0.528
(0.638) 		0.644
(0.742) 		0.966
(0.976) 		0.401
(0.533) 		0.882
(0.917) 		0.516
(0.627) 		0.794
(0.846)
6q loss 93 (25%) 277 0.0915
(0.195) 		0.405
(0.535) 		0.895
(0.927) 		0.868
(0.907) 		0.771
(0.831) 		0.868
(0.907) 		0.294
(0.428) 		0.523
(0.634) 		0.774
(0.831) 		0.757
(0.822)
8q loss 45 (12%) 325 0.0992
(0.204) 		0.286
(0.42) 		0.567
(0.676) 		0.676
(0.763) 		0.216
(0.341) 		0.479
(0.599) 		0.494
(0.612) 		0.942
(0.956) 		0.405
(0.535) 		0.989
(0.996)
20p loss 26 (7%) 344 0.177
(0.298) 		0.721
(0.793) 		0.679
(0.766) 		0.667
(0.761) 		0.372
(0.509) 		0.355
(0.489) 		0.297
(0.428) 		0.906
(0.935) 		0.514
(0.627) 		0.591
(0.695)
20q loss 13 (4%) 357 0.68
(0.766) 		0.279
(0.412) 		1
(1.00) 		1
(1.00) 		0.376
(0.511) 		0.0787
(0.175) 		0.445
(0.573) 		0.866
(0.907) 		0.153
(0.268) 		0.485
(0.604)
'1p gain' versus 'RPPA_CNMF'

P value = 0.00711 (Fisher's exact test), Q value = 0.028

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
1P GAIN MUTATED 11 5 2 6 7 0
1P GAIN WILD-TYPE 30 68 17 16 15 1

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.11

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
1P GAIN MUTATED 23 3 12 12 5 1
1P GAIN WILD-TYPE 105 47 59 28 42 3

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
1Q GAIN MUTATED 42 71 112
1Q GAIN WILD-TYPE 59 60 26

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
1Q GAIN MUTATED 31 104 74 16
1Q GAIN WILD-TYPE 30 59 25 31

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0036

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
1Q GAIN MUTATED 84 43 35 49 9
1Q GAIN WILD-TYPE 41 46 15 23 19

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
1Q GAIN MUTATED 101 76 43 0
1Q GAIN WILD-TYPE 50 69 18 7

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.014

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
1Q GAIN MUTATED 26 41 37 77 39 1
1Q GAIN WILD-TYPE 15 45 15 44 18 7

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.089

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
1Q GAIN MUTATED 88 23 41 25 33 1
1Q GAIN WILD-TYPE 40 27 30 15 14 3

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0047

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
2P GAIN MUTATED 13 14 16 0
2P GAIN WILD-TYPE 48 149 83 47

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

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.082

Table S10.  Gene #3: '2p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
2P GAIN MUTATED 11 5 3 0 7
2P GAIN WILD-TYPE 28 40 35 18 31

Figure S10.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.082

Table S11.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
2P GAIN MUTATED 23 5 6 6 1
2P GAIN WILD-TYPE 102 84 44 66 27

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0069

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
2P GAIN MUTATED 29 7 5 0
2P GAIN WILD-TYPE 122 138 56 7

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.11

Table S13.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
2Q GAIN MUTATED 6 12 22
2Q GAIN WILD-TYPE 95 119 116

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.087

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
2Q GAIN MUTATED 10 14 15 1
2Q GAIN WILD-TYPE 51 149 84 46

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.077

Table S15.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
2Q GAIN MUTATED 20 3 6 8 1
2Q GAIN WILD-TYPE 105 86 44 64 27

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0063

Table S16.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
2Q GAIN MUTATED 26 5 7 0
2Q GAIN WILD-TYPE 125 140 54 7

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S17.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
2Q GAIN MUTATED 5 4 15 0 3 5 5
2Q GAIN WILD-TYPE 36 50 53 18 50 77 19

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
3P GAIN MUTATED 4 20 11
3P GAIN WILD-TYPE 97 111 127

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

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
3P GAIN MUTATED 16 8 0 9 2
3P GAIN WILD-TYPE 109 81 50 63 26

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

'3q gain' versus 'CN_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
3Q GAIN MUTATED 5 23 10
3Q GAIN WILD-TYPE 96 108 128

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

'4p gain' versus 'METHLYATION_CNMF'

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

Table S21.  Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
4P GAIN MUTATED 3 7 16 1
4P GAIN WILD-TYPE 58 156 83 46

Figure S21.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'RPPA_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.013

Table S22.  Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
4P GAIN MUTATED 2 4 6 3 1 1
4P GAIN WILD-TYPE 39 69 13 19 21 0

Figure S22.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.06

Table S23.  Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
4P GAIN MUTATED 16 6 3 1 0
4P GAIN WILD-TYPE 109 83 47 71 28

Figure S23.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.039

Table S24.  Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
4P GAIN MUTATED 19 6 1 0
4P GAIN WILD-TYPE 132 139 60 7

Figure S24.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.076

Table S25.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
4P GAIN MUTATED 1 7 4 1 8 6 0
4P GAIN WILD-TYPE 44 53 99 44 55 31 12

Figure S25.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.091

Table S26.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
4P GAIN MUTATED 2 3 12 1 6 2 1
4P GAIN WILD-TYPE 39 51 56 17 47 80 23

Figure S26.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00099

Table S27.  Gene #8: '4q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
4Q GAIN MUTATED 0 0 3 1 0 1
4Q GAIN WILD-TYPE 41 73 16 21 22 0

Figure S27.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.083

Table S28.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
4Q GAIN MUTATED 0 3 0 0 4 0 0
4Q GAIN WILD-TYPE 45 57 103 45 59 37 12

Figure S28.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S29.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
5P GAIN MUTATED 16 55 64
5P GAIN WILD-TYPE 85 76 74

Figure S29.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
5P GAIN MUTATED 48 34 20 28 3
5P GAIN WILD-TYPE 77 55 30 44 25

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.081

Table S31.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
5P GAIN MUTATED 14 36 28 36 18 1
5P GAIN WILD-TYPE 27 50 24 85 39 7

Figure S31.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00055

Table S32.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
5Q GAIN MUTATED 14 41 55
5Q GAIN WILD-TYPE 87 90 83

Figure S32.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S33.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
6P GAIN MUTATED 11 44 62
6P GAIN WILD-TYPE 90 87 76

Figure S33.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.076

Table S34.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
6P GAIN MUTATED 17 55 38 7
6P GAIN WILD-TYPE 44 108 61 40

Figure S34.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0033

Table S35.  Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
6P GAIN MUTATED 8 18 3 11 14 1
6P GAIN WILD-TYPE 33 55 16 11 8 0

Figure S35.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00347 (Fisher's exact test), Q value = 0.017

Table S36.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
6P GAIN MUTATED 42 22 14 35 4
6P GAIN WILD-TYPE 83 67 36 37 24

Figure S36.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00331 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
6P GAIN MUTATED 55 33 28 1
6P GAIN WILD-TYPE 96 112 33 6

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

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.11

Table S38.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
6P GAIN MUTATED 19 11 39 13 19 14 1
6P GAIN WILD-TYPE 26 49 64 32 44 23 11

Figure S38.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0064

Table S39.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
6P GAIN MUTATED 17 14 19 38 27 1
6P GAIN WILD-TYPE 24 72 33 83 30 7

Figure S39.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 9e-04

Table S40.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
6Q GAIN MUTATED 5 31 32
6Q GAIN WILD-TYPE 96 100 106

Figure S40.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.043

Table S41.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
6Q GAIN MUTATED 14 28 24 2
6Q GAIN WILD-TYPE 47 135 75 45

Figure S41.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.011

Table S42.  Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
6Q GAIN MUTATED 4 10 2 6 10 1
6Q GAIN WILD-TYPE 37 63 17 16 12 0

Figure S42.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.092

Table S43.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
6Q GAIN MUTATED 5 12 16 0 7 14 9
6Q GAIN WILD-TYPE 36 42 52 18 46 68 15

Figure S43.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S44.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
7P GAIN MUTATED 13 44 52
7P GAIN WILD-TYPE 88 87 86

Figure S44.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.055

Table S45.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
7Q GAIN MUTATED 19 44 47
7Q GAIN WILD-TYPE 82 87 91

Figure S45.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0079

Table S46.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
7Q GAIN MUTATED 19 63 22 6
7Q GAIN WILD-TYPE 42 100 77 41

Figure S46.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0013

Table S47.  Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
8P GAIN MUTATED 28 7 17 19 1
8P GAIN WILD-TYPE 97 82 33 53 27

Figure S47.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.038

Table S48.  Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
8P GAIN MUTATED 38 17 16 1
8P GAIN WILD-TYPE 113 128 45 6

Figure S48.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.055

Table S49.  Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
8P GAIN MUTATED 13 3 14 2 15 16 6
8P GAIN WILD-TYPE 28 51 54 16 38 66 18

Figure S49.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S50.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
8Q GAIN MUTATED 43 50 91
8Q GAIN WILD-TYPE 58 81 47

Figure S50.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.072

Table S51.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
8Q GAIN MUTATED 37 76 55 16
8Q GAIN WILD-TYPE 24 87 44 31

Figure S51.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S52.  Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
8Q GAIN MUTATED 71 22 34 47 5
8Q GAIN WILD-TYPE 54 67 16 25 23

Figure S52.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S53.  Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
8Q GAIN MUTATED 90 49 39 1
8Q GAIN WILD-TYPE 61 96 22 6

Figure S53.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.0088

Table S54.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
8Q GAIN MUTATED 17 29 28 69 36 2
8Q GAIN WILD-TYPE 24 57 24 52 21 6

Figure S54.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0051

Table S55.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
8Q GAIN MUTATED 23 18 42 3 28 42 17
8Q GAIN WILD-TYPE 18 36 26 15 25 40 7

Figure S55.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.011

Table S56.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
8Q GAIN MUTATED 68 16 41 17 31 0
8Q GAIN WILD-TYPE 60 34 30 23 16 4

Figure S56.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'RPPA_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0041

Table S57.  Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
9P GAIN MUTATED 1 1 0 6 3 0
9P GAIN WILD-TYPE 40 72 19 16 19 1

Figure S57.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9q gain' versus 'RPPA_CNMF'

P value = 0.00508 (Fisher's exact test), Q value = 0.023

Table S58.  Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
9Q GAIN MUTATED 2 1 0 5 3 0
9Q GAIN WILD-TYPE 39 72 19 17 19 1

Figure S58.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0057

Table S59.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
10P GAIN MUTATED 5 24 29
10P GAIN WILD-TYPE 96 107 109

Figure S59.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.017

Table S60.  Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
10P GAIN MUTATED 30 6 5 14 2
10P GAIN WILD-TYPE 95 83 45 58 26

Figure S60.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00636 (Fisher's exact test), Q value = 0.026

Table S61.  Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
10P GAIN MUTATED 35 13 9 0
10P GAIN WILD-TYPE 116 132 52 7

Figure S61.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00623 (Fisher's exact test), Q value = 0.026

Table S62.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
10P GAIN MUTATED 7 8 18 0 7 6 7
10P GAIN WILD-TYPE 34 46 50 18 46 76 17

Figure S62.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0078

Table S63.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
10P GAIN MUTATED 28 0 12 8 5 0
10P GAIN WILD-TYPE 100 50 59 32 42 4

Figure S63.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S64.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
10Q GAIN MUTATED 2 8 26
10Q GAIN WILD-TYPE 99 123 112

Figure S64.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0063

Table S65.  Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
10Q GAIN MUTATED 21 1 3 9 2
10Q GAIN WILD-TYPE 104 88 47 63 26

Figure S65.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.067

Table S66.  Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
10Q GAIN MUTATED 23 7 6 0
10Q GAIN WILD-TYPE 128 138 55 7

Figure S66.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.041

Table S67.  Gene #20: '10q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
10Q GAIN MUTATED 3 2 11 13 6 1
10Q GAIN WILD-TYPE 38 84 41 108 51 7

Figure S67.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'RPPA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.068

Table S68.  Gene #21: '11p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
11P GAIN MUTATED 3 3 0 2 4 1
11P GAIN WILD-TYPE 38 70 19 20 18 0

Figure S68.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0399 (Fisher's exact test), Q value = 0.11

Table S69.  Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
11P GAIN MUTATED 13 5 0 0
11P GAIN WILD-TYPE 138 140 61 7

Figure S69.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00494 (Fisher's exact test), Q value = 0.022

Table S70.  Gene #23: '12p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
12P GAIN MUTATED 7 0 8 3 3
12P GAIN WILD-TYPE 32 45 30 15 35

Figure S70.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0027

Table S71.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
12P GAIN MUTATED 27 5 4 4 0
12P GAIN WILD-TYPE 98 84 46 68 28

Figure S71.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00197 (Fisher's exact test), Q value = 0.011

Table S72.  Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
12P GAIN MUTATED 28 10 2 0
12P GAIN WILD-TYPE 123 135 59 7

Figure S72.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.00541 (Fisher's exact test), Q value = 0.024

Table S73.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
12P GAIN MUTATED 7 4 7 2 16 4 0
12P GAIN WILD-TYPE 38 56 96 43 47 33 12

Figure S73.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0347 (Fisher's exact test), Q value = 0.098

Table S74.  Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
12Q GAIN MUTATED 7 2 10 3 3
12Q GAIN WILD-TYPE 32 43 28 15 35

Figure S74.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0037

Table S75.  Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
12Q GAIN MUTATED 29 9 5 4 0
12Q GAIN WILD-TYPE 96 80 45 68 28

Figure S75.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00394 (Fisher's exact test), Q value = 0.018

Table S76.  Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
12Q GAIN MUTATED 30 15 2 0
12Q GAIN WILD-TYPE 121 130 59 7

Figure S76.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.072

Table S77.  Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
12Q GAIN MUTATED 7 5 9 4 17 5 0
12Q GAIN WILD-TYPE 38 55 94 41 46 32 12

Figure S77.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.061

Table S78.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
13Q GAIN MUTATED 1 11 11
13Q GAIN WILD-TYPE 100 120 127

Figure S78.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.11

Table S79.  Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
13Q GAIN MUTATED 5 2 4 1 4 7 0
13Q GAIN WILD-TYPE 40 58 99 44 59 30 12

Figure S79.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.11

Table S80.  Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
13Q GAIN MUTATED 0 3 8 0 2 3 4
13Q GAIN WILD-TYPE 41 51 60 18 51 79 20

Figure S80.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00716 (Fisher's exact test), Q value = 0.028

Table S81.  Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
16P GAIN MUTATED 7 6 11 7 0
16P GAIN WILD-TYPE 118 83 39 65 28

Figure S81.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

Table S82.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
16Q GAIN MUTATED 3 0 8 6 0
16Q GAIN WILD-TYPE 122 89 42 66 28

Figure S82.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.041

Table S83.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
17P GAIN MUTATED 5 6 19
17P GAIN WILD-TYPE 96 125 119

Figure S83.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.00695 (Fisher's exact test), Q value = 0.028

Table S84.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
17Q GAIN MUTATED 14 39 40
17Q GAIN WILD-TYPE 87 92 98

Figure S84.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.11

Table S85.  Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
17Q GAIN MUTATED 38 20 9 22 2
17Q GAIN WILD-TYPE 87 69 41 50 26

Figure S85.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00804 (Fisher's exact test), Q value = 0.031

Table S86.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
17Q GAIN MUTATED 18 17 17 21 18 2
17Q GAIN WILD-TYPE 23 69 35 100 39 6

Figure S86.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.053

Table S87.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
17Q GAIN MUTATED 35 13 10 18 12 0
17Q GAIN WILD-TYPE 93 37 61 22 35 4

Figure S87.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0031

Table S88.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
18P GAIN MUTATED 2 11 23
18P GAIN WILD-TYPE 99 120 115

Figure S88.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0397 (Fisher's exact test), Q value = 0.11

Table S89.  Gene #32: '18p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
18P GAIN MUTATED 5 1 7 1 1
18P GAIN WILD-TYPE 34 44 31 17 37

Figure S89.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00278 (Fisher's exact test), Q value = 0.014

Table S90.  Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
18P GAIN MUTATED 23 6 4 3 0
18P GAIN WILD-TYPE 102 83 46 69 28

Figure S90.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00563 (Fisher's exact test), Q value = 0.024

Table S91.  Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
18P GAIN MUTATED 25 9 2 0
18P GAIN WILD-TYPE 126 136 59 7

Figure S91.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.011

Table S92.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
18Q GAIN MUTATED 1 10 17
18Q GAIN WILD-TYPE 100 121 121

Figure S92.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.038

Table S93.  Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
18Q GAIN MUTATED 18 4 4 2 0
18Q GAIN WILD-TYPE 107 85 46 70 28

Figure S93.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00306 (Fisher's exact test), Q value = 0.015

Table S94.  Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
18Q GAIN MUTATED 20 8 0 0
18Q GAIN WILD-TYPE 131 137 61 7

Figure S94.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0083

Table S95.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
19P GAIN MUTATED 8 15 33
19P GAIN WILD-TYPE 93 116 105

Figure S95.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S96.  Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
19P GAIN MUTATED 14 17 25 0
19P GAIN WILD-TYPE 47 146 74 47

Figure S96.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0059

Table S97.  Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
19P GAIN MUTATED 30 6 11 5 3
19P GAIN WILD-TYPE 95 83 39 67 25

Figure S97.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00685 (Fisher's exact test), Q value = 0.028

Table S98.  Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
19P GAIN MUTATED 33 19 3 0
19P GAIN WILD-TYPE 118 126 58 7

Figure S98.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00733 (Fisher's exact test), Q value = 0.029

Table S99.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
19P GAIN MUTATED 4 11 10 28 2 0
19P GAIN WILD-TYPE 37 75 42 93 55 8

Figure S99.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S100.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
19P GAIN MUTATED 6 5 22 1 8 5 4
19P GAIN WILD-TYPE 35 49 46 17 45 77 20

Figure S100.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.01

Table S101.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
19P GAIN MUTATED 29 3 14 4 1 0
19P GAIN WILD-TYPE 99 47 57 36 46 4

Figure S101.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0046

Table S102.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
19Q GAIN MUTATED 10 21 40
19Q GAIN WILD-TYPE 91 110 98

Figure S102.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S103.  Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
19Q GAIN MUTATED 17 21 32 1
19Q GAIN WILD-TYPE 44 142 67 46

Figure S103.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S104.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
19Q GAIN MUTATED 38 8 15 5 4
19Q GAIN WILD-TYPE 87 81 35 67 24

Figure S104.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0048

Table S105.  Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
19Q GAIN MUTATED 43 23 4 0
19Q GAIN WILD-TYPE 108 122 57 7

Figure S105.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.12

Table S106.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
19Q GAIN MUTATED 6 8 13 11 19 10 3
19Q GAIN WILD-TYPE 39 52 90 34 44 27 9

Figure S106.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0032

Table S107.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
19Q GAIN MUTATED 6 11 16 34 3 0
19Q GAIN WILD-TYPE 35 75 36 87 54 8

Figure S107.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0064

Table S108.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
19Q GAIN MUTATED 7 7 24 2 13 6 6
19Q GAIN WILD-TYPE 34 47 44 16 40 76 18

Figure S108.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00055

Table S109.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
19Q GAIN MUTATED 38 3 16 6 1 1
19Q GAIN WILD-TYPE 90 47 55 34 46 3

Figure S109.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S110.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
20P GAIN MUTATED 11 49 48
20P GAIN WILD-TYPE 90 82 90

Figure S110.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00901 (Fisher's exact test), Q value = 0.034

Table S111.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
20P GAIN MUTATED 21 47 35 5
20P GAIN WILD-TYPE 40 116 64 42

Figure S111.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.0083

Table S112.  Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
20P GAIN MUTATED 20 11 10 11 7
20P GAIN WILD-TYPE 19 34 28 7 31

Figure S112.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00635 (Fisher's exact test), Q value = 0.026

Table S113.  Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
20P GAIN MUTATED 51 19 17 16 5
20P GAIN WILD-TYPE 74 70 33 56 23

Figure S113.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00452 (Fisher's exact test), Q value = 0.02

Table S114.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
20P GAIN MUTATED 58 39 11 0
20P GAIN WILD-TYPE 93 106 50 7

Figure S114.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.042

Table S115.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
20P GAIN MUTATED 16 16 22 40 12 1
20P GAIN WILD-TYPE 25 70 30 81 45 7

Figure S115.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0019

Table S116.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
20P GAIN MUTATED 12 18 27 2 11 14 15
20P GAIN WILD-TYPE 29 36 41 16 42 68 9

Figure S116.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 0.081

Table S117.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
20P GAIN MUTATED 40 8 26 16 9 0
20P GAIN WILD-TYPE 88 42 45 24 38 4

Figure S117.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S118.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
20Q GAIN MUTATED 11 51 50
20Q GAIN WILD-TYPE 90 80 88

Figure S118.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00999 (Fisher's exact test), Q value = 0.037

Table S119.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
20Q GAIN MUTATED 22 52 33 5
20Q GAIN WILD-TYPE 39 111 66 42

Figure S119.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.043

Table S120.  Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
20Q GAIN MUTATED 18 10 12 11 9
20Q GAIN WILD-TYPE 21 35 26 7 29

Figure S120.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.067

Table S121.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
20Q GAIN MUTATED 56 44 12 0
20Q GAIN WILD-TYPE 95 101 49 7

Figure S121.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.083

Table S122.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
20Q GAIN MUTATED 17 19 23 38 13 1
20Q GAIN WILD-TYPE 24 67 29 83 44 7

Figure S122.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0023

Table S123.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
20Q GAIN MUTATED 13 19 27 2 10 16 15
20Q GAIN WILD-TYPE 28 35 41 16 43 66 9

Figure S123.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.077

Table S124.  Gene #38: '21q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
21Q GAIN MUTATED 2 2 2 2 3 1
21Q GAIN WILD-TYPE 39 71 17 20 19 0

Figure S124.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00078

Table S125.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
22Q GAIN MUTATED 2 18 28
22Q GAIN WILD-TYPE 99 113 110

Figure S125.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 0.00423 (Fisher's exact test), Q value = 0.019

Table S126.  Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
22Q GAIN MUTATED 8 4 6 5 4 1
22Q GAIN WILD-TYPE 33 69 13 17 18 0

Figure S126.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00556 (Fisher's exact test), Q value = 0.024

Table S127.  Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
22Q GAIN MUTATED 10 2 11 2 3
22Q GAIN WILD-TYPE 29 43 27 16 35

Figure S127.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0081

Table S128.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
22Q GAIN MUTATED 29 6 3 9 1
22Q GAIN WILD-TYPE 96 83 47 63 27

Figure S128.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S129.  Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
22Q GAIN MUTATED 32 10 6 0
22Q GAIN WILD-TYPE 119 135 55 7

Figure S129.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.11

Table S130.  Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
22Q GAIN MUTATED 7 5 11 2 16 6 1
22Q GAIN WILD-TYPE 38 55 92 43 47 31 11

Figure S130.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.11

Table S131.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
22Q GAIN MUTATED 4 6 15 1 8 4 5
22Q GAIN WILD-TYPE 37 48 53 17 45 78 19

Figure S131.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.0064 (Fisher's exact test), Q value = 0.027

Table S132.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
XP GAIN MUTATED 9 8 25
XP GAIN WILD-TYPE 92 123 113

Figure S132.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.018

Table S133.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
XP GAIN MUTATED 10 5 8 17 2
XP GAIN WILD-TYPE 115 84 42 55 26

Figure S133.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.039

Table S134.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
XQ GAIN MUTATED 17 12 31
XQ GAIN WILD-TYPE 84 119 107

Figure S134.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.015

Table S135.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
XQ GAIN MUTATED 3 37 11 9
XQ GAIN WILD-TYPE 58 126 88 38

Figure S135.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0045

Table S136.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
XQ GAIN MUTATED 13 11 8 25 3
XQ GAIN WILD-TYPE 112 78 42 47 25

Figure S136.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0046

Table S137.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
XQ GAIN MUTATED 16 23 21 0
XQ GAIN WILD-TYPE 135 122 40 7

Figure S137.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0045

Table S138.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
XQ GAIN MUTATED 4 11 7 15 22 0
XQ GAIN WILD-TYPE 37 75 45 106 35 8

Figure S138.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0046

Table S139.  Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
XQ GAIN MUTATED 18 7 6 4 19 0
XQ GAIN WILD-TYPE 110 43 65 36 28 4

Figure S139.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S140.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
1P LOSS MUTATED 4 26 51
1P LOSS WILD-TYPE 97 105 87

Figure S140.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S141.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
1P LOSS MUTATED 7 26 45 3
1P LOSS WILD-TYPE 54 137 54 44

Figure S141.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.12

Table S142.  Gene #42: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
1P LOSS MUTATED 7 12 7 8 9 0
1P LOSS WILD-TYPE 34 61 12 14 13 1

Figure S142.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0013

Table S143.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
1P LOSS MUTATED 44 12 12 10 2
1P LOSS WILD-TYPE 81 77 38 62 26

Figure S143.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0013

Table S144.  Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
1P LOSS MUTATED 51 21 8 0
1P LOSS WILD-TYPE 100 124 53 7

Figure S144.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0022

Table S145.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
1P LOSS MUTATED 5 10 16 8 27 13 1
1P LOSS WILD-TYPE 40 50 87 37 36 24 11

Figure S145.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0081

Table S146.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
1P LOSS MUTATED 5 13 15 40 7 0
1P LOSS WILD-TYPE 36 73 37 81 50 8

Figure S146.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0032

Table S147.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
1P LOSS MUTATED 9 7 30 2 11 11 6
1P LOSS WILD-TYPE 32 47 38 16 42 71 18

Figure S147.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0088

Table S148.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
1P LOSS MUTATED 34 6 26 5 5 0
1P LOSS WILD-TYPE 94 44 45 35 42 4

Figure S148.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.082

Table S149.  Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
1Q LOSS MUTATED 1 11 9
1Q LOSS WILD-TYPE 100 120 129

Figure S149.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.057

Table S150.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
1Q LOSS MUTATED 4 4 10 2 0 0
1Q LOSS WILD-TYPE 124 46 61 38 47 4

Figure S150.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0041

Table S151.  Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
2P LOSS MUTATED 2 21 10
2P LOSS WILD-TYPE 99 110 128

Figure S151.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.12

Table S152.  Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
2P LOSS MUTATED 15 10 6 2 0
2P LOSS WILD-TYPE 110 79 44 70 28

Figure S152.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00055

Table S153.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
2Q LOSS MUTATED 2 25 11
2Q LOSS WILD-TYPE 99 106 127

Figure S153.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.12

Table S154.  Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
2Q LOSS MUTATED 17 13 5 2 1
2Q LOSS WILD-TYPE 108 76 45 70 27

Figure S154.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.12

Table S155.  Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
2Q LOSS MUTATED 18 19 1 0
2Q LOSS WILD-TYPE 133 126 60 7

Figure S155.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.098

Table S156.  Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
3P LOSS MUTATED 7 20 25
3P LOSS WILD-TYPE 94 111 113

Figure S156.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.081

Table S157.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
3P LOSS MUTATED 8 17 23 4
3P LOSS WILD-TYPE 53 146 76 43

Figure S157.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0013

Table S158.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
3P LOSS MUTATED 32 5 7 6 1
3P LOSS WILD-TYPE 93 84 43 66 27

Figure S158.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0043

Table S159.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
3P LOSS MUTATED 35 11 5 0
3P LOSS WILD-TYPE 116 134 56 7

Figure S159.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0078

Table S160.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
3P LOSS MUTATED 4 4 12 6 21 4 0
3P LOSS WILD-TYPE 41 56 91 39 42 33 12

Figure S160.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0491 (Fisher's exact test), Q value = 0.13

Table S161.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
3P LOSS MUTATED 4 6 10 25 6 0
3P LOSS WILD-TYPE 37 80 42 96 51 8

Figure S161.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0025

Table S162.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
3P LOSS MUTATED 9 4 15 0 14 4 1
3P LOSS WILD-TYPE 32 50 53 18 39 78 23

Figure S162.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.12

Table S163.  Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
3Q LOSS MUTATED 5 16 20
3Q LOSS WILD-TYPE 96 115 118

Figure S163.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.00534 (Fisher's exact test), Q value = 0.024

Table S164.  Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
3Q LOSS MUTATED 24 4 6 5 1
3Q LOSS WILD-TYPE 101 85 44 67 27

Figure S164.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0079 (Fisher's exact test), Q value = 0.031

Table S165.  Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
3Q LOSS MUTATED 27 9 4 0
3Q LOSS WILD-TYPE 124 136 57 7

Figure S165.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.11

Table S166.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
3Q LOSS MUTATED 3 3 11 5 15 3 0
3Q LOSS WILD-TYPE 42 57 92 40 48 34 12

Figure S166.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.048

Table S167.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
3Q LOSS MUTATED 6 3 14 0 8 4 1
3Q LOSS WILD-TYPE 35 51 54 18 45 78 23

Figure S167.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S168.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
4P LOSS MUTATED 2 56 47
4P LOSS WILD-TYPE 99 75 91

Figure S168.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.011

Table S169.  Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
4P LOSS MUTATED 18 46 37 4
4P LOSS WILD-TYPE 43 117 62 43

Figure S169.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0063

Table S170.  Gene #48: '4p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
4P LOSS MUTATED 9 14 3 12 12 0
4P LOSS WILD-TYPE 32 59 16 10 10 1

Figure S170.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0038 (Fisher's exact test), Q value = 0.018

Table S171.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
4P LOSS MUTATED 48 28 12 13 3
4P LOSS WILD-TYPE 77 61 38 59 25

Figure S171.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S172.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
4P LOSS MUTATED 54 40 10 0
4P LOSS WILD-TYPE 97 105 51 7

Figure S172.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.0088

Table S173.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
4P LOSS MUTATED 14 20 24 38 8 0
4P LOSS WILD-TYPE 27 66 28 83 49 8

Figure S173.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0069

Table S174.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
4P LOSS MUTATED 11 20 27 1 10 16 12
4P LOSS WILD-TYPE 30 34 41 17 43 66 12

Figure S174.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S175.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
4P LOSS MUTATED 54 10 14 14 5 0
4P LOSS WILD-TYPE 74 40 57 26 42 4

Figure S175.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S176.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
4Q LOSS MUTATED 3 79 64
4Q LOSS WILD-TYPE 98 52 74

Figure S176.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S177.  Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
4Q LOSS MUTATED 25 58 56 7
4Q LOSS WILD-TYPE 36 105 43 40

Figure S177.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.00381 (Fisher's exact test), Q value = 0.018

Table S178.  Gene #49: '4q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
4Q LOSS MUTATED 11 23 6 11 16 0
4Q LOSS WILD-TYPE 30 50 13 11 6 1

Figure S178.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S179.  Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
4Q LOSS MUTATED 71 36 17 17 3
4Q LOSS WILD-TYPE 54 53 33 55 25

Figure S179.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00099

Table S180.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
4Q LOSS MUTATED 76 55 13 0
4Q LOSS WILD-TYPE 75 90 48 7

Figure S180.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0044

Table S181.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
4Q LOSS MUTATED 20 19 32 16 34 23 1
4Q LOSS WILD-TYPE 25 41 71 29 29 14 11

Figure S181.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
4Q LOSS MUTATED 17 29 29 58 12 0
4Q LOSS WILD-TYPE 24 57 23 63 45 8

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

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S183.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
4Q LOSS MUTATED 17 26 42 2 15 20 16
4Q LOSS WILD-TYPE 24 28 26 16 38 62 8

Figure S183.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00066

Table S184.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
4Q LOSS MUTATED 69 13 31 17 8 0
4Q LOSS WILD-TYPE 59 37 40 23 39 4

Figure S184.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.055

Table S185.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
5P LOSS MUTATED 2 15 12
5P LOSS WILD-TYPE 99 116 126

Figure S185.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.098

Table S186.  Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
5P LOSS MUTATED 18 5 3 2 1
5P LOSS WILD-TYPE 107 84 47 70 27

Figure S186.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.072

Table S187.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
5P LOSS MUTATED 2 4 12 1 1 3 3
5P LOSS WILD-TYPE 39 50 56 17 52 79 21

Figure S187.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.041

Table S188.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
5Q LOSS MUTATED 3 17 17
5Q LOSS WILD-TYPE 98 114 121

Figure S188.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.037

Table S189.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
5Q LOSS MUTATED 7 9 18 3
5Q LOSS WILD-TYPE 54 154 81 44

Figure S189.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0037

Table S190.  Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
5Q LOSS MUTATED 25 5 4 2 1
5Q LOSS WILD-TYPE 100 84 46 70 27

Figure S190.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0069

Table S191.  Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
5Q LOSS MUTATED 27 8 2 0
5Q LOSS WILD-TYPE 124 137 59 7

Figure S191.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00836 (Fisher's exact test), Q value = 0.032

Table S192.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
5Q LOSS MUTATED 4 6 14 1 3 2 4
5Q LOSS WILD-TYPE 37 48 54 17 50 80 20

Figure S192.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.13

Table S193.  Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
7P LOSS MUTATED 4 4 8 0
7P LOSS WILD-TYPE 57 159 91 47

Figure S193.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'RPPA_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.0088

Table S194.  Gene #54: '7p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
7P LOSS MUTATED 0 2 4 0 4 0
7P LOSS WILD-TYPE 41 71 15 22 18 1

Figure S194.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00691 (Fisher's exact test), Q value = 0.028

Table S195.  Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
7P LOSS MUTATED 1 3 9 0 0 1 2
7P LOSS WILD-TYPE 40 51 59 18 53 81 22

Figure S195.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0458 (Fisher's exact test), Q value = 0.12

Table S196.  Gene #55: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
7Q LOSS MUTATED 5 3 7 5 1 0
7Q LOSS WILD-TYPE 36 83 45 116 56 8

Figure S196.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.043

Table S197.  Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
7Q LOSS MUTATED 2 5 10 0 1 1 2
7Q LOSS WILD-TYPE 39 49 58 18 52 81 22

Figure S197.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0062

Table S198.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
8P LOSS MUTATED 39 70 87
8P LOSS WILD-TYPE 62 61 51

Figure S198.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.005

Table S199.  Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
8P LOSS MUTATED 34 92 58 12
8P LOSS WILD-TYPE 27 71 41 35

Figure S199.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.11

Table S200.  Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
8P LOSS MUTATED 80 79 32 0
8P LOSS WILD-TYPE 71 66 29 7

Figure S200.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.074

Table S201.  Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
8P LOSS MUTATED 15 33 43 7 21 47 13
8P LOSS WILD-TYPE 26 21 25 11 32 35 11

Figure S201.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S202.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
9P LOSS MUTATED 9 59 51
9P LOSS WILD-TYPE 92 72 87

Figure S202.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0046

Table S203.  Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
9P LOSS MUTATED 22 43 46 8
9P LOSS WILD-TYPE 39 120 53 39

Figure S203.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0016

Table S204.  Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
9P LOSS MUTATED 55 29 17 14 2
9P LOSS WILD-TYPE 70 60 33 58 26

Figure S204.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0059

Table S205.  Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
9P LOSS MUTATED 64 41 12 0
9P LOSS WILD-TYPE 87 104 49 7

Figure S205.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00592 (Fisher's exact test), Q value = 0.025

Table S206.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
9P LOSS MUTATED 18 14 27 19 24 17 0
9P LOSS WILD-TYPE 27 46 76 26 39 20 12

Figure S206.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0071 (Fisher's exact test), Q value = 0.028

Table S207.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
9P LOSS MUTATED 16 24 23 46 9 1
9P LOSS WILD-TYPE 25 62 29 75 48 7

Figure S207.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.003

Table S208.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
9P LOSS MUTATED 10 21 34 4 17 15 13
9P LOSS WILD-TYPE 31 33 34 14 36 67 11

Figure S208.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S209.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
9P LOSS MUTATED 60 9 27 15 3 0
9P LOSS WILD-TYPE 68 41 44 25 44 4

Figure S209.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S210.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
9Q LOSS MUTATED 8 53 49
9Q LOSS WILD-TYPE 93 78 89

Figure S210.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.0078

Table S211.  Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
9Q LOSS MUTATED 20 40 43 7
9Q LOSS WILD-TYPE 41 123 56 40

Figure S211.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

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

Table S212.  Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
9Q LOSS MUTATED 47 31 17 12 2
9Q LOSS WILD-TYPE 78 58 33 60 26

Figure S212.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0012

Table S213.  Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
9Q LOSS MUTATED 63 37 9 0
9Q LOSS WILD-TYPE 88 108 52 7

Figure S213.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

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

Table S214.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
9Q LOSS MUTATED 16 13 25 17 24 13 0
9Q LOSS WILD-TYPE 29 47 78 28 39 24 12

Figure S214.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.014

Table S215.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
9Q LOSS MUTATED 15 21 22 42 7 1
9Q LOSS WILD-TYPE 26 65 30 79 50 7

Figure S215.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0046

Table S216.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
9Q LOSS MUTATED 11 20 30 2 17 12 11
9Q LOSS WILD-TYPE 30 34 38 16 36 70 13

Figure S216.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S217.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
9Q LOSS MUTATED 55 9 23 14 2 0
9Q LOSS WILD-TYPE 73 41 48 26 45 4

Figure S217.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S218.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
10P LOSS MUTATED 5 31 12
10P LOSS WILD-TYPE 96 100 126

Figure S218.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00859 (Fisher's exact test), Q value = 0.033

Table S219.  Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
10P LOSS MUTATED 19 18 6 2 2
10P LOSS WILD-TYPE 106 71 44 70 26

Figure S219.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.12

Table S220.  Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
10P LOSS MUTATED 22 23 2 0
10P LOSS WILD-TYPE 129 122 59 7

Figure S220.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.092

Table S221.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
10P LOSS MUTATED 6 12 9 1 13 6 1
10P LOSS WILD-TYPE 39 48 94 44 50 31 11

Figure S221.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.047

Table S222.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
10P LOSS MUTATED 5 18 3 20 2 0
10P LOSS WILD-TYPE 36 68 49 101 55 8

Figure S222.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S223.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
10Q LOSS MUTATED 11 52 16
10Q LOSS WILD-TYPE 90 79 122

Figure S223.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0036

Table S224.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
10Q LOSS MUTATED 24 33 19 3
10Q LOSS WILD-TYPE 37 130 80 44

Figure S224.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.02

Table S225.  Gene #61: '10q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
10Q LOSS MUTATED 13 14 1 6 12 0
10Q LOSS WILD-TYPE 28 59 18 16 10 1

Figure S225.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 0.11

Table S226.  Gene #61: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
10Q LOSS MUTATED 10 6 16 6 8
10Q LOSS WILD-TYPE 29 39 22 12 30

Figure S226.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0025

Table S227.  Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
10Q LOSS MUTATED 33 28 9 5 2
10Q LOSS WILD-TYPE 92 61 41 67 26

Figure S227.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.05

Table S228.  Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
10Q LOSS MUTATED 37 35 5 0
10Q LOSS WILD-TYPE 114 110 56 7

Figure S228.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.013

Table S229.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
10Q LOSS MUTATED 13 19 14 4 21 7 1
10Q LOSS WILD-TYPE 32 41 89 41 42 30 11

Figure S229.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00432 (Fisher's exact test), Q value = 0.02

Table S230.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
10Q LOSS MUTATED 11 28 10 26 4 0
10Q LOSS WILD-TYPE 30 58 42 95 53 8

Figure S230.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.019

Table S231.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
10Q LOSS MUTATED 12 21 15 2 13 8 6
10Q LOSS WILD-TYPE 29 33 53 16 40 74 18

Figure S231.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.006

Table S232.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
10Q LOSS MUTATED 32 17 16 11 1 0
10Q LOSS WILD-TYPE 96 33 55 29 46 4

Figure S232.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0068

Table S233.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
11P LOSS MUTATED 6 28 29
11P LOSS WILD-TYPE 95 103 109

Figure S233.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.067

Table S234.  Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
11P LOSS MUTATED 32 9 9 10 2
11P LOSS WILD-TYPE 93 80 41 62 26

Figure S234.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00682 (Fisher's exact test), Q value = 0.028

Table S235.  Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
11P LOSS MUTATED 38 16 8 0
11P LOSS WILD-TYPE 113 129 53 7

Figure S235.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 0.074

Table S236.  Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
11P LOSS MUTATED 7 10 17 22 6 0
11P LOSS WILD-TYPE 34 76 35 99 51 8

Figure S236.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.043

Table S237.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
11P LOSS MUTATED 6 11 21 2 7 6 4
11P LOSS WILD-TYPE 35 43 47 16 46 76 20

Figure S237.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0029 (Fisher's exact test), Q value = 0.015

Table S238.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
11P LOSS MUTATED 34 4 10 7 2 0
11P LOSS WILD-TYPE 94 46 61 33 45 4

Figure S238.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.037

Table S239.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
11Q LOSS MUTATED 10 32 30
11Q LOSS WILD-TYPE 91 99 108

Figure S239.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.038

Table S240.  Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
11Q LOSS MUTATED 7 14 23 2 6 9 5
11Q LOSS WILD-TYPE 34 40 45 16 47 73 19

Figure S240.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.075

Table S241.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
11Q LOSS MUTATED 37 8 10 7 4 0
11Q LOSS WILD-TYPE 91 42 61 33 43 4

Figure S241.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

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

Table S242.  Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
12P LOSS MUTATED 7 36 24
12P LOSS WILD-TYPE 94 95 114

Figure S242.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.043

Table S243.  Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
12Q LOSS MUTATED 3 18 15
12Q LOSS WILD-TYPE 98 113 123

Figure S243.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S244.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
13Q LOSS MUTATED 15 61 46
13Q LOSS WILD-TYPE 86 70 92

Figure S244.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00838 (Fisher's exact test), Q value = 0.032

Table S245.  Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
13Q LOSS MUTATED 24 46 43 9
13Q LOSS WILD-TYPE 37 117 56 38

Figure S245.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 0.077

Table S246.  Gene #66: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
13Q LOSS MUTATED 21 11 15 3 14
13Q LOSS WILD-TYPE 18 34 23 15 24

Figure S246.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0057

Table S247.  Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
13Q LOSS MUTATED 52 33 18 12 4
13Q LOSS WILD-TYPE 73 56 32 60 24

Figure S247.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

Table S248.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
13Q LOSS MUTATED 66 43 10 0
13Q LOSS WILD-TYPE 85 102 51 7

Figure S248.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0078

Table S249.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
13Q LOSS MUTATED 20 23 21 18 29 9 1
13Q LOSS WILD-TYPE 25 37 82 27 34 28 11

Figure S249.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00391 (Fisher's exact test), Q value = 0.018

Table S250.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
13Q LOSS MUTATED 19 30 16 47 8 1
13Q LOSS WILD-TYPE 22 56 36 74 49 7

Figure S250.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0021

Table S251.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
13Q LOSS MUTATED 16 23 29 3 22 12 11
13Q LOSS WILD-TYPE 25 31 39 15 31 70 13

Figure S251.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S252.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
13Q LOSS MUTATED 50 13 30 19 4 0
13Q LOSS WILD-TYPE 78 37 41 21 43 4

Figure S252.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S253.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
14Q LOSS MUTATED 7 62 39
14Q LOSS WILD-TYPE 94 69 99

Figure S253.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0041

Table S254.  Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
14Q LOSS MUTATED 25 38 39 6
14Q LOSS WILD-TYPE 36 125 60 41

Figure S254.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.00612 (Fisher's exact test), Q value = 0.026

Table S255.  Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
14Q LOSS MUTATED 20 17 6 5 13 0
14Q LOSS WILD-TYPE 21 56 13 17 9 1

Figure S255.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S256.  Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
14Q LOSS MUTATED 58 24 13 10 2
14Q LOSS WILD-TYPE 67 65 37 62 26

Figure S256.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S257.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
14Q LOSS MUTATED 65 33 9 0
14Q LOSS WILD-TYPE 86 112 52 7

Figure S257.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.076

Table S258.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
14Q LOSS MUTATED 16 17 23 13 27 11 0
14Q LOSS WILD-TYPE 29 43 80 32 36 26 12

Figure S258.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00436 (Fisher's exact test), Q value = 0.02

Table S259.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
14Q LOSS MUTATED 15 21 20 43 8 0
14Q LOSS WILD-TYPE 26 65 32 78 49 8

Figure S259.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S260.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
14Q LOSS MUTATED 16 20 31 1 17 10 8
14Q LOSS WILD-TYPE 25 34 37 17 36 72 16

Figure S260.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00921 (Fisher's exact test), Q value = 0.035

Table S261.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
14Q LOSS MUTATED 46 13 24 15 5 0
14Q LOSS WILD-TYPE 82 37 47 25 42 4

Figure S261.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S262.  Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
15Q LOSS MUTATED 5 40 22
15Q LOSS WILD-TYPE 96 91 116

Figure S262.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0072

Table S263.  Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
15Q LOSS MUTATED 16 21 27 3
15Q LOSS WILD-TYPE 45 142 72 44

Figure S263.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.006 (Fisher's exact test), Q value = 0.026

Table S264.  Gene #68: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
15Q LOSS MUTATED 15 10 3 3 10 0
15Q LOSS WILD-TYPE 26 63 16 19 12 1

Figure S264.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00147 (Fisher's exact test), Q value = 0.0084

Table S265.  Gene #68: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
15Q LOSS MUTATED 9 3 17 3 9
15Q LOSS WILD-TYPE 30 42 21 15 29

Figure S265.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S266.  Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
15Q LOSS MUTATED 40 10 8 8 0
15Q LOSS WILD-TYPE 85 79 42 64 28

Figure S266.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00066

Table S267.  Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
15Q LOSS MUTATED 45 14 7 0
15Q LOSS WILD-TYPE 106 131 54 7

Figure S267.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

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

Table S268.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
15Q LOSS MUTATED 7 7 16 5 20 11 0
15Q LOSS WILD-TYPE 38 53 87 40 43 26 12

Figure S268.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0074

Table S269.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
15Q LOSS MUTATED 11 9 21 1 8 6 8
15Q LOSS WILD-TYPE 30 45 47 17 45 76 16

Figure S269.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.074

Table S270.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
15Q LOSS MUTATED 30 4 19 7 4 0
15Q LOSS WILD-TYPE 98 46 52 33 43 4

Figure S270.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S271.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
16P LOSS MUTATED 7 50 52
16P LOSS WILD-TYPE 94 81 86

Figure S271.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S272.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
16P LOSS MUTATED 23 31 51 4
16P LOSS WILD-TYPE 38 132 48 43

Figure S272.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.01

Table S273.  Gene #69: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
16P LOSS MUTATED 13 15 8 11 14 0
16P LOSS WILD-TYPE 28 58 11 11 8 1

Figure S273.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0081

Table S274.  Gene #69: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
16P LOSS MUTATED 20 8 15 10 8
16P LOSS WILD-TYPE 19 37 23 8 30

Figure S274.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S275.  Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
16P LOSS MUTATED 74 19 7 4 3
16P LOSS WILD-TYPE 51 70 43 68 25

Figure S275.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S276.  Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
16P LOSS MUTATED 69 35 3 0
16P LOSS WILD-TYPE 82 110 58 7

Figure S276.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S277.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
16P LOSS MUTATED 12 8 22 9 31 25 1
16P LOSS WILD-TYPE 33 52 81 36 32 12 11

Figure S277.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S278.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
16P LOSS MUTATED 10 15 27 53 3 0
16P LOSS WILD-TYPE 31 71 25 68 54 8

Figure S278.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S279.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
16P LOSS MUTATED 14 14 41 1 10 9 14
16P LOSS WILD-TYPE 27 40 27 17 43 73 10

Figure S279.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S280.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
16P LOSS MUTATED 46 7 36 10 4 0
16P LOSS WILD-TYPE 82 43 35 30 43 4

Figure S280.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S281.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
16Q LOSS MUTATED 8 62 75
16Q LOSS WILD-TYPE 93 69 63

Figure S281.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S282.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
16Q LOSS MUTATED 22 48 68 7
16Q LOSS WILD-TYPE 39 115 31 40

Figure S282.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0037

Table S283.  Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
16Q LOSS MUTATED 16 18 10 12 16 0
16Q LOSS WILD-TYPE 25 55 9 10 6 1

Figure S283.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.0015

Table S284.  Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
16Q LOSS MUTATED 20 10 20 13 9
16Q LOSS WILD-TYPE 19 35 18 5 29

Figure S284.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S285.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
16Q LOSS MUTATED 83 36 13 7 4
16Q LOSS WILD-TYPE 42 53 37 65 24

Figure S285.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S286.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
16Q LOSS MUTATED 85 53 5 0
16Q LOSS WILD-TYPE 66 92 56 7

Figure S286.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S287.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
16Q LOSS MUTATED 18 21 27 16 36 25 1
16Q LOSS WILD-TYPE 27 39 76 29 27 12 11

Figure S287.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S288.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
16Q LOSS MUTATED 15 24 34 64 6 1
16Q LOSS WILD-TYPE 26 62 18 57 51 7

Figure S288.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S289.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
16Q LOSS MUTATED 17 23 49 2 17 18 13
16Q LOSS WILD-TYPE 24 31 19 16 36 64 11

Figure S289.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00044

Table S290.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
16Q LOSS MUTATED 59 18 41 14 7 0
16Q LOSS WILD-TYPE 69 32 30 26 40 4

Figure S290.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S291.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
17P LOSS MUTATED 33 107 45
17P LOSS WILD-TYPE 68 24 93

Figure S291.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00717 (Fisher's exact test), Q value = 0.028

Table S292.  Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
17P LOSS MUTATED 37 88 46 14
17P LOSS WILD-TYPE 24 75 53 33

Figure S292.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.097

Table S293.  Gene #71: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
17P LOSS MUTATED 15 18 25 12 22
17P LOSS WILD-TYPE 24 27 13 6 16

Figure S293.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S294.  Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
17P LOSS MUTATED 65 60 23 30 4
17P LOSS WILD-TYPE 60 29 27 42 24

Figure S294.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

Table S295.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 60 103 45 63 37 12
17P LOSS MUTATED 34 39 44 17 29 19 2
17P LOSS WILD-TYPE 11 21 59 28 34 18 10

Figure S295.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S296.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 86 52 121 57 8
17P LOSS MUTATED 32 46 24 56 24 2
17P LOSS WILD-TYPE 9 40 28 65 33 6

Figure S296.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S297.  Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
17P LOSS MUTATED 18 46 29 7 23 40 13
17P LOSS WILD-TYPE 23 8 39 11 30 42 11

Figure S297.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S298.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
17P LOSS MUTATED 59 34 34 32 17 0
17P LOSS WILD-TYPE 69 16 37 8 30 4

Figure S298.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.037

Table S299.  Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
17Q LOSS MUTATED 4 21 15
17Q LOSS WILD-TYPE 97 110 123

Figure S299.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.038

Table S300.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
18P LOSS MUTATED 13 37 24
18P LOSS WILD-TYPE 88 94 114

Figure S300.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.061

Table S301.  Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
18P LOSS MUTATED 41 20 13 0
18P LOSS WILD-TYPE 110 125 48 7

Figure S301.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.039

Table S302.  Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
18P LOSS MUTATED 8 6 23 0 11 13 5
18P LOSS WILD-TYPE 33 48 45 18 42 69 19

Figure S302.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.058

Table S303.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
18Q LOSS MUTATED 14 38 27
18Q LOSS WILD-TYPE 87 93 111

Figure S303.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.082

Table S304.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
18Q LOSS MUTATED 10 29 32 8
18Q LOSS WILD-TYPE 51 134 67 39

Figure S304.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.081

Table S305.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 151 145 61 7
18Q LOSS MUTATED 42 22 15 0
18Q LOSS WILD-TYPE 109 123 46 7

Figure S305.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.055

Table S306.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
18Q LOSS MUTATED 9 7 23 0 10 16 7
18Q LOSS WILD-TYPE 32 47 45 18 43 66 17

Figure S306.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S307.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
19P LOSS MUTATED 4 35 13
19P LOSS WILD-TYPE 97 96 125

Figure S307.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.055

Table S308.  Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
19P LOSS MUTATED 23 16 7 5 0
19P LOSS WILD-TYPE 102 73 43 67 28

Figure S308.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.061

Table S309.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 128 50 71 40 47 4
19P LOSS MUTATED 24 5 7 11 2 0
19P LOSS WILD-TYPE 104 45 64 29 45 4

Figure S309.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S310.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
19Q LOSS MUTATED 3 29 7
19Q LOSS WILD-TYPE 98 102 131

Figure S310.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.017

Table S311.  Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 41 54 68 18 53 82 24
19Q LOSS MUTATED 1 10 11 0 1 8 5
19Q LOSS WILD-TYPE 40 44 57 18 52 74 19

Figure S311.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.026

Table S312.  Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
21Q LOSS MUTATED 24 49 32 5
21Q LOSS WILD-TYPE 37 114 67 42

Figure S312.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.061

Table S313.  Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
21Q LOSS MUTATED 44 19 19 22 3
21Q LOSS WILD-TYPE 81 70 31 50 25

Figure S313.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00055

Table S314.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
22Q LOSS MUTATED 15 41 14
22Q LOSS WILD-TYPE 86 90 124

Figure S314.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.00666 (Fisher's exact test), Q value = 0.027

Table S315.  Gene #80: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
22Q LOSS MUTATED 11 17 1 3 12 0
22Q LOSS WILD-TYPE 30 56 18 19 10 1

Figure S315.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00415 (Fisher's exact test), Q value = 0.019

Table S316.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
XP LOSS MUTATED 9 47 32 5
XP LOSS WILD-TYPE 52 116 67 42

Figure S316.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.067

Table S317.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 125 89 50 72 28
XP LOSS MUTATED 31 33 7 17 4
XP LOSS WILD-TYPE 94 56 43 55 24

Figure S317.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.025

Table S318.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 131 138
XQ LOSS MUTATED 10 34 29
XQ LOSS WILD-TYPE 91 97 109

Figure S318.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.00729 (Fisher's exact test), Q value = 0.029

Table S319.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 163 99 47
XQ LOSS MUTATED 8 31 30 4
XQ LOSS WILD-TYPE 53 132 69 43

Figure S319.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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/LIHC/26852992/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC/26874120/LIHC.transferedmergedcluster.txt

  • Number of patients = 370

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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