Correlation between copy number variations of arm-level result and molecular subtypes
Sarcoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1ST7NZJ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ST7NZJ
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 256 patients, 353 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 1q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • 4q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

  • 6q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 8q gain cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

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

  • 10p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 10q gain cnv correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

  • 11q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • 13q gain cnv correlated to 'CN_CNMF'.

  • 14q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • 15q gain cnv correlated to 'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 17q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 18q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 20p gain cnv correlated to 'CN_CNMF'.

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

  • 21q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

  • xq gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • 1p loss cnv correlated to 'METHLYATION_CNMF'.

  • 1q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 2p 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'.

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

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

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

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 5p loss cnv correlated to 'RPPA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 5q loss cnv correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 6q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 7p loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 8p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 9q loss cnv correlated to 'CN_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_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',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 14q loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • 16p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 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 'RPPA_CHIERARCHICAL'.

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

  • 18p loss cnv correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.

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

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

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

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

  • 21q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.

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

  • xp loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 353 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
7q gain 68 (27%) 188 1e-05
(0.000256) 		0.0003
(0.003) 		0.042
(0.104) 		0.0036
(0.0174) 		0.00054
(0.00456) 		0.0312
(0.0841) 		0.045
(0.108) 		0.0116
(0.0432) 		0.00029
(0.00294) 		0.00282
(0.0146)
2p loss 88 (34%) 168 1e-05
(0.000256) 		1e-05
(0.000256) 		0.0134
(0.0482) 		0.00079
(0.00584) 		1e-05
(0.000256) 		5e-05
(0.00082) 		0.00235
(0.013) 		0.00034
(0.00332) 		0.00065
(0.00512) 		0.00048
(0.00419)
10q loss 131 (51%) 125 1e-05
(0.000256) 		1e-05
(0.000256) 		2e-05
(0.000421) 		0.00079
(0.00584) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		2e-05
(0.000421) 		2e-05
(0.000421) 		0.00024
(0.00262)
16q loss 124 (48%) 132 0.0001
(0.00141) 		9e-05
(0.00129) 		0.00037
(0.00354) 		0.0181
(0.0596) 		0.00067
(0.00523) 		0.00017
(0.00205) 		0.00987
(0.0393) 		0.0232
(0.0699) 		0.00013
(0.00169) 		0.00063
(0.00506)
2p gain 22 (9%) 234 0.00154
(0.00957) 		0.0143
(0.05) 		0.0687
(0.145) 		0.0102
(0.0397) 		0.00074
(0.00567) 		0.00087
(0.00631) 		0.0185
(0.0604) 		0.0376
(0.0963) 		0.0184
(0.0603) 		0.00291
(0.015)
9q gain 73 (29%) 183 1e-05
(0.000256) 		0.00012
(0.00161) 		0.0059
(0.026) 		0.00105
(0.00724) 		6e-05
(0.000946) 		2e-05
(0.000421) 		0.0665
(0.141) 		0.00027
(0.00287) 		0.0283
(0.0785) 		0.00766
(0.0324)
17q gain 57 (22%) 199 1e-05
(0.000256) 		0.0307
(0.0832) 		0.0109
(0.0412) 		0.0142
(0.05) 		0.0614
(0.134) 		0.00445
(0.0203) 		0.0172
(0.0578) 		0.00335
(0.0166) 		0.00627
(0.0272) 		0.0305
(0.0832)
xq loss 101 (39%) 155 0.00057
(0.00477) 		1e-05
(0.000256) 		7e-05
(0.00106) 		0.00325
(0.0163) 		3e-05
(0.000559) 		0.00022
(0.00247) 		0.0015
(0.00946) 		0.00361
(0.0174) 		0.12
(0.212) 		0.0225
(0.069)
3q gain 36 (14%) 220 0.00209
(0.0122) 		0.00261
(0.0137) 		0.0145
(0.0504) 		0.194
(0.302) 		0.0043
(0.02) 		0.00335
(0.0166) 		0.0476
(0.111) 		0.13
(0.223) 		0.00091
(0.00649) 		0.00138
(0.00897)
4p gain 68 (27%) 188 2e-05
(0.000421) 		3e-05
(0.000559) 		0.0391
(0.099) 		0.0107
(0.0408) 		0.0247
(0.0736) 		0.00444
(0.0203) 		0.0436
(0.106) 		0.0177
(0.0591) 		0.307
(0.424) 		0.0764
(0.158)
6p gain 51 (20%) 205 1e-05
(0.000256) 		3e-05
(0.000559) 		0.0037
(0.0177) 		0.00044
(0.00396) 		0.00028
(0.00287) 		0.00015
(0.00184) 		0.0635
(0.137) 		0.0119
(0.0436) 		0.509
(0.614) 		0.0385
(0.0977)
6q gain 50 (20%) 206 0.00038
(0.00354) 		0.00044
(0.00396) 		0.0437
(0.106) 		0.0207
(0.066) 		0.00028
(0.00287) 		0.00048
(0.00419) 		0.0799
(0.162) 		0.00595
(0.0261) 		0.301
(0.42) 		0.035
(0.0905)
7p gain 82 (32%) 174 1e-05
(0.000256) 		0.00192
(0.0115) 		0.0106
(0.0406) 		0.00711
(0.0305) 		0.00247
(0.0133) 		0.021
(0.0664) 		0.197
(0.305) 		0.198
(0.306) 		0.00419
(0.0197) 		0.0022
(0.0127)
12p gain 43 (17%) 213 1e-05
(0.000256) 		0.0283
(0.0785) 		0.027
(0.0762) 		0.0213
(0.0672) 		0.00014
(0.00177) 		0.00062
(0.00506) 		0.0827
(0.164) 		0.0891
(0.172) 		0.0469
(0.11) 		0.00082
(0.006)
20q gain 83 (32%) 173 4e-05
(0.000713) 		0.00217
(0.0126) 		0.00564
(0.0251) 		0.00237
(0.013) 		0.0396
(0.0994) 		0.0335
(0.0878) 		0.227
(0.337) 		0.015
(0.0512) 		0.136
(0.23) 		0.0204
(0.0654)
3p loss 56 (22%) 200 0.0518
(0.119) 		0.00012
(0.00161) 		0.123
(0.215) 		0.00404
(0.0191) 		0.00014
(0.00177) 		0.00047
(0.00419) 		0.00038
(0.00354) 		0.00098
(0.00693) 		0.00076
(0.00577) 		0.00064
(0.0051)
1q gain 49 (19%) 207 0.00273
(0.0143) 		0.00941
(0.0382) 		0.116
(0.207) 		0.014
(0.05) 		0.00906
(0.0375) 		0.21
(0.319) 		0.0241
(0.0724) 		0.109
(0.198) 		0.00062
(0.00506) 		0.00514
(0.0231)
2q gain 22 (9%) 234 0.00022
(0.00247) 		0.0941
(0.18) 		0.08
(0.162) 		0.035
(0.0905) 		0.00432
(0.02) 		0.00145
(0.00922) 		0.034
(0.0886) 		0.00918
(0.0378) 		0.033
(0.0872) 		0.183
(0.291)
3p gain 39 (15%) 217 0.00052
(0.00444) 		7e-05
(0.00106) 		0.0641
(0.138) 		0.217
(0.326) 		0.00314
(0.016) 		4e-05
(0.000713) 		0.0422
(0.104) 		0.114
(0.205) 		0.00091
(0.00649) 		0.00117
(0.00793)
9p gain 57 (22%) 199 8e-05
(0.00119) 		0.00197
(0.0116) 		0.0258
(0.0751) 		0.0004
(0.00369) 		0.0061
(0.0266) 		0.00063
(0.00506) 		0.0891
(0.172) 		0.00343
(0.0169) 		0.708
(0.778) 		0.288
(0.404)
19q gain 65 (25%) 191 1e-05
(0.000256) 		1e-05
(0.000256) 		0.00763
(0.0324) 		1e-05
(0.000256) 		0.00052
(0.00444) 		0.00073
(0.00565) 		0.565
(0.67) 		0.0628
(0.137) 		0.799
(0.849) 		0.0221
(0.0689)
3q loss 49 (19%) 207 0.00139
(0.00897) 		0.0121
(0.0442) 		0.484
(0.595) 		0.107
(0.198) 		0.00962
(0.0387) 		0.0598
(0.132) 		0.0164
(0.0559) 		0.0168
(0.0568) 		0.0111
(0.0417) 		0.0464
(0.109)
5p gain 98 (38%) 158 1e-05
(0.000256) 		3e-05
(0.000559) 		0.158
(0.259) 		0.00232
(0.0129) 		0.0118
(0.0435) 		5e-05
(0.00082) 		0.803
(0.851) 		0.00294
(0.0151) 		0.7
(0.773) 		0.535
(0.64)
17p gain 61 (24%) 195 1e-05
(0.000256) 		0.00346
(0.017) 		0.0012
(0.008) 		0.0256
(0.0746) 		0.0284
(0.0785) 		0.0521
(0.119) 		0.0698
(0.147) 		0.00222
(0.0127) 		0.0756
(0.157) 		0.0533
(0.12)
22q gain 60 (23%) 196 0.0093
(0.0381) 		0.00232
(0.0129) 		0.0141
(0.05) 		0.0131
(0.0473) 		0.0077
(0.0324) 		0.00261
(0.0137) 		0.674
(0.754) 		0.113
(0.203) 		0.106
(0.198) 		0.134
(0.228)
18q loss 72 (28%) 184 0.00018
(0.00211) 		0.00649
(0.028) 		0.0196
(0.0633) 		0.00038
(0.00354) 		0.0629
(0.137) 		0.0248
(0.0736) 		0.494
(0.601) 		0.51
(0.614) 		0.196
(0.304) 		0.012
(0.0439)
20p loss 55 (21%) 201 0.0418
(0.104) 		0.00318
(0.0161) 		0.7
(0.773) 		0.0378
(0.0967) 		0.0399
(0.0998) 		0.0778
(0.159) 		0.797
(0.848) 		0.0116
(0.0432) 		0.0792
(0.161) 		0.0262
(0.0752)
xp loss 62 (24%) 194 0.415
(0.53) 		0.00131
(0.00859) 		0.0012
(0.008) 		0.127
(0.219) 		0.00105
(0.00724) 		0.00717
(0.0306) 		0.0221
(0.0689) 		0.044
(0.106) 		0.477
(0.589) 		0.0943
(0.18)
12q gain 34 (13%) 222 0.0011
(0.00752) 		0.0337
(0.088) 		0.0224
(0.069) 		0.127
(0.219) 		0.00428
(0.02) 		0.0519
(0.119) 		0.0809
(0.163) 		0.0721
(0.151) 		0.0636
(0.137) 		0.0173
(0.0578)
14q gain 57 (22%) 199 0.00359
(0.0174) 		0.0464
(0.109) 		0.0321
(0.0854) 		0.00123
(0.00813) 		0.264
(0.377) 		0.00101
(0.00708) 		0.756
(0.812) 		0.718
(0.784) 		0.245
(0.358) 		0.613
(0.704)
19p gain 87 (34%) 169 1e-05
(0.000256) 		0.00228
(0.0129) 		0.186
(0.294) 		0.00024
(0.00262) 		0.0259
(0.0752) 		0.00816
(0.0341) 		0.44
(0.554) 		0.247
(0.36) 		0.841
(0.879) 		0.115
(0.205)
1q loss 40 (16%) 216 0.0102
(0.0397) 		0.00144
(0.00922) 		0.354
(0.472) 		0.0395
(0.0994) 		0.0775
(0.159) 		0.192
(0.299) 		0.028
(0.0785) 		0.00248
(0.0133) 		0.057
(0.127) 		0.0554
(0.124)
7p loss 32 (12%) 224 0.0896
(0.173) 		0.0384
(0.0977) 		0.00481
(0.0218) 		0.0521
(0.119) 		0.00976
(0.039) 		0.0335
(0.0878) 		0.389
(0.503) 		0.517
(0.622) 		0.256
(0.369) 		0.0204
(0.0654)
11q loss 91 (36%) 165 1e-05
(0.000256) 		0.00026
(0.00281) 		0.199
(0.306) 		0.00156
(0.00962) 		0.396
(0.51) 		0.0179
(0.0591) 		0.504
(0.609) 		0.622
(0.713) 		0.88
(0.91) 		0.0102
(0.0397)
13q loss 132 (52%) 124 1e-05
(0.000256) 		0.00079
(0.00584) 		0.00991
(0.0393) 		0.0232
(0.0699) 		0.0982
(0.186) 		0.00172
(0.0104) 		0.407
(0.52) 		0.312
(0.429) 		0.137
(0.231) 		0.164
(0.267)
15q loss 45 (18%) 211 0.0255
(0.0746) 		0.0325
(0.0861) 		0.0803
(0.162) 		0.108
(0.198) 		0.0832
(0.165) 		0.0875
(0.17) 		0.0216
(0.0678) 		0.0305
(0.0832) 		0.0264
(0.0752) 		0.111
(0.201)
1p gain 56 (22%) 200 0.00015
(0.00184) 		1e-05
(0.000256) 		0.112
(0.203) 		0.0361
(0.0929) 		0.283
(0.398) 		0.0445
(0.107) 		0.256
(0.369) 		0.652
(0.736) 		0.07
(0.147) 		0.256
(0.37)
16q gain 21 (8%) 235 0.0142
(0.05) 		0.227
(0.337) 		0.0332
(0.0875) 		0.00571
(0.0253) 		0.0263
(0.0752) 		0.232
(0.342) 		0.608
(0.702) 		1
(1.00) 		0.777
(0.83) 		0.0735
(0.153)
5q loss 35 (14%) 221 0.0846
(0.167) 		0.109
(0.199) 		0.025
(0.0736) 		0.0266
(0.0756) 		0.155
(0.255) 		0.042
(0.104) 		0.747
(0.807) 		0.0407
(0.101) 		0.305
(0.422) 		0.318
(0.435)
8p loss 62 (24%) 194 0.00022
(0.00247) 		0.00394
(0.0188) 		0.104
(0.195) 		0.00032
(0.00316) 		0.118
(0.209) 		0.052
(0.119) 		0.102
(0.192) 		0.0149
(0.0512) 		0.281
(0.396) 		0.108
(0.198)
8q loss 46 (18%) 210 2e-05
(0.000421) 		0.00441
(0.0203) 		0.252
(0.366) 		5e-05
(0.00082) 		0.0555
(0.124) 		0.0799
(0.162) 		0.152
(0.251) 		0.00261
(0.0137) 		0.765
(0.82) 		0.131
(0.224)
12p loss 65 (25%) 191 1e-05
(0.000256) 		0.00243
(0.0133) 		0.685
(0.765) 		0.489
(0.597) 		0.0168
(0.0568) 		0.0127
(0.0459) 		0.896
(0.923) 		0.552
(0.659) 		0.796
(0.848) 		0.385
(0.5)
19p loss 21 (8%) 235 0.0308
(0.0832) 		0.00187
(0.0113) 		0.693
(0.769) 		0.358
(0.475) 		0.395
(0.509) 		0.0316
(0.0848) 		0.448
(0.561) 		0.756
(0.812) 		0.663
(0.745) 		0.0281
(0.0785)
5q gain 71 (28%) 185 0.00011
(0.00153) 		0.0141
(0.05) 		0.264
(0.377) 		0.0816
(0.163) 		0.28
(0.395) 		0.0146
(0.0504) 		0.424
(0.538) 		0.163
(0.266) 		0.752
(0.811) 		0.706
(0.777)
10p gain 23 (9%) 233 0.0249
(0.0736) 		0.044
(0.106) 		0.0529
(0.12) 		0.974
(0.986) 		0.152
(0.251) 		0.17
(0.273) 		0.346
(0.465) 		0.57
(0.674) 		0.0262
(0.0752) 		0.0577
(0.128)
11p gain 23 (9%) 233 0.0463
(0.109) 		0.0269
(0.0759) 		0.187
(0.295) 		0.208
(0.317) 		0.126
(0.219) 		0.0103
(0.0398) 		0.402
(0.515) 		0.593
(0.692) 		0.129
(0.223) 		0.18
(0.287)
15q gain 63 (25%) 193 1e-05
(0.000256) 		0.1
(0.189) 		0.896
(0.923) 		0.863
(0.896) 		0.121
(0.213) 		0.0583
(0.129) 		0.224
(0.335) 		0.498
(0.605) 		0.0178
(0.0591) 		0.0225
(0.069)
11p loss 94 (37%) 162 1e-05
(0.000256) 		0.00013
(0.00169) 		0.951
(0.966) 		0.0101
(0.0397) 		0.818
(0.863) 		0.14
(0.235) 		0.646
(0.731) 		0.594
(0.692) 		0.634
(0.721) 		0.103
(0.194)
12q loss 54 (21%) 202 5e-05
(0.00082) 		0.0295
(0.081) 		0.721
(0.785) 		0.482
(0.594) 		0.239
(0.35) 		0.0395
(0.0994) 		0.866
(0.898) 		0.415
(0.53) 		0.602
(0.696) 		0.431
(0.546)
21q loss 50 (20%) 206 0.00249
(0.0133) 		0.0227
(0.0693) 		0.219
(0.327) 		0.00516
(0.0231) 		0.136
(0.23) 		0.239
(0.35) 		0.0856
(0.167) 		0.277
(0.393) 		0.376
(0.492) 		0.145
(0.242)
22q loss 66 (26%) 190 1e-05
(0.000256) 		0.143
(0.239) 		0.594
(0.692) 		0.0428
(0.105) 		0.205
(0.314) 		0.0451
(0.108) 		0.144
(0.24) 		0.275
(0.39) 		0.0811
(0.163) 		0.255
(0.369)
4q gain 47 (18%) 209 0.0313
(0.0841) 		0.00874
(0.0364) 		0.106
(0.198) 		0.628
(0.717) 		0.189
(0.296) 		0.0704
(0.147) 		0.36
(0.478) 		0.108
(0.198) 		0.168
(0.271) 		0.368
(0.485)
10q gain 12 (5%) 244 0.72
(0.785) 		0.111
(0.202) 		0.0286
(0.0786) 		0.82
(0.863) 		0.108
(0.198) 		0.0524
(0.119) 		0.367
(0.485) 		0.323
(0.439) 		0.0452
(0.108) 		0.335
(0.453)
11q gain 22 (9%) 234 0.0111
(0.0416) 		0.121
(0.213) 		1
(1.00) 		0.371
(0.488) 		0.631
(0.719) 		0.0357
(0.0921) 		0.917
(0.939) 		0.905
(0.93) 		0.377
(0.492) 		0.752
(0.811)
16p gain 40 (16%) 216 9e-05
(0.00129) 		0.113
(0.204) 		0.0318
(0.085) 		0.164
(0.267) 		0.128
(0.221) 		0.383
(0.499) 		0.792
(0.845) 		0.264
(0.377) 		0.917
(0.939) 		0.343
(0.461)
18p gain 53 (21%) 203 2e-05
(0.000421) 		0.0231
(0.0699) 		0.0956
(0.182) 		0.167
(0.271) 		0.0876
(0.17) 		0.389
(0.503) 		0.566
(0.67) 		0.396
(0.51) 		0.691
(0.768) 		0.231
(0.342)
18q gain 36 (14%) 220 0.0222
(0.0689) 		0.0495
(0.115) 		0.701
(0.773) 		0.0897
(0.173) 		0.76
(0.816) 		0.217
(0.326) 		0.534
(0.64) 		0.435
(0.549) 		0.25
(0.364) 		0.995
(1.00)
21q gain 58 (23%) 198 1e-05
(0.000256) 		0.0284
(0.0785) 		0.052
(0.119) 		0.0603
(0.132) 		0.631
(0.719) 		0.494
(0.601) 		0.922
(0.941) 		0.825
(0.866) 		0.219
(0.327) 		0.347
(0.465)
xp gain 74 (29%) 182 6e-05
(0.000946) 		0.0484
(0.113) 		0.213
(0.321) 		0.365
(0.482) 		0.771
(0.825) 		0.287
(0.403) 		0.254
(0.368) 		0.543
(0.649) 		0.174
(0.279) 		0.356
(0.474)
xq gain 33 (13%) 223 0.0146
(0.0504) 		0.0639
(0.138) 		0.0429
(0.105) 		0.432
(0.547) 		0.21
(0.319) 		0.147
(0.245) 		0.308
(0.425) 		0.136
(0.23) 		0.209
(0.318) 		0.187
(0.295)
2q loss 71 (28%) 185 1e-05
(0.000256) 		0.00152
(0.00951) 		0.132
(0.226) 		0.218
(0.326) 		0.113
(0.204) 		0.0991
(0.187) 		0.721
(0.785) 		0.163
(0.266) 		0.696
(0.772) 		0.667
(0.749)
5p loss 22 (9%) 234 0.595
(0.693) 		0.0676
(0.143) 		0.0227
(0.0693) 		0.0798
(0.162) 		0.0587
(0.13) 		0.025
(0.0736) 		0.437
(0.551) 		0.416
(0.53) 		0.0947
(0.181) 		0.257
(0.37)
6q loss 53 (21%) 203 0.0243
(0.0728) 		0.0108
(0.041) 		0.184
(0.291) 		0.338
(0.456) 		0.484
(0.595) 		0.119
(0.21) 		0.863
(0.896) 		0.658
(0.741) 		0.71
(0.778) 		0.57
(0.674)
10p loss 120 (47%) 136 0.0187
(0.0608) 		0.0852
(0.167) 		0.0556
(0.124) 		0.2
(0.307) 		0.0824
(0.164) 		0.0094
(0.0382) 		0.065
(0.139) 		0.207
(0.316) 		0.117
(0.208) 		0.738
(0.798)
16p loss 75 (29%) 181 0.00018
(0.00211) 		0.00954
(0.0385) 		0.194
(0.301) 		0.0784
(0.16) 		0.821
(0.863) 		0.0855
(0.167) 		0.184
(0.291) 		0.733
(0.795) 		0.167
(0.27) 		0.611
(0.703)
17q loss 48 (19%) 208 0.00232
(0.0129) 		0.211
(0.319) 		0.821
(0.863) 		0.0194
(0.0629) 		0.978
(0.987) 		0.487
(0.597) 		0.812
(0.86) 		0.689
(0.768) 		0.395
(0.509) 		0.67
(0.751)
18p loss 62 (24%) 194 0.0145
(0.0504) 		0.232
(0.342) 		0.32
(0.436) 		0.0208
(0.0662) 		0.801
(0.849) 		0.58
(0.681) 		0.925
(0.941) 		0.832
(0.871) 		0.462
(0.573) 		0.4
(0.514)
19q loss 39 (15%) 217 0.0401
(0.0999) 		0.0477
(0.111) 		0.641
(0.728) 		0.69
(0.768) 		0.924
(0.941) 		0.454
(0.568) 		0.921
(0.941) 		1
(1.00) 		0.599
(0.694) 		0.176
(0.281)
8q gain 65 (25%) 191 0.108
(0.198) 		0.0824
(0.164) 		0.279
(0.395) 		0.15
(0.249) 		0.965
(0.978) 		0.0769
(0.159) 		0.335
(0.453) 		0.596
(0.693) 		0.0451
(0.108) 		0.158
(0.259)
13q gain 15 (6%) 241 0.0017
(0.0104) 		0.198
(0.306) 		0.554
(0.659) 		0.321
(0.437) 		0.0926
(0.178) 		0.126
(0.219) 		0.457
(0.57) 		0.575
(0.676) 		0.575
(0.676) 		0.236
(0.347)
20p gain 62 (24%) 194 0.00028
(0.00287) 		0.121
(0.213) 		0.16
(0.261) 		0.271
(0.385) 		0.353
(0.472) 		0.0853
(0.167) 		0.858
(0.894) 		0.294
(0.41) 		0.553
(0.659) 		0.385
(0.5)
1p loss 32 (12%) 224 0.155
(0.255) 		0.0264
(0.0752) 		0.304
(0.422) 		0.486
(0.597) 		1
(1.00) 		0.46
(0.573) 		0.855
(0.892) 		0.602
(0.696) 		0.338
(0.456) 		0.666
(0.748)
4q loss 51 (20%) 205 0.00197
(0.0116) 		0.373
(0.49) 		0.465
(0.577) 		0.375
(0.492) 		0.919
(0.939) 		0.644
(0.73) 		0.897
(0.923) 		0.779
(0.832) 		0.875
(0.906) 		0.585
(0.685)
9p loss 83 (32%) 173 1e-05
(0.000256) 		0.232
(0.342) 		0.122
(0.213) 		0.488
(0.597) 		0.343
(0.461) 		0.0526
(0.119) 		0.714
(0.781) 		0.859
(0.894) 		0.169
(0.272) 		0.347
(0.465)
9q loss 51 (20%) 205 1e-05
(0.000256) 		0.108
(0.198) 		0.19
(0.297) 		0.462
(0.573) 		0.232
(0.342) 		0.169
(0.272) 		1
(1.00) 		0.496
(0.602) 		0.71
(0.778) 		0.286
(0.402)
14q loss 62 (24%) 194 0.135
(0.229) 		0.189
(0.296) 		0.735
(0.796) 		0.831
(0.871) 		0.293
(0.409) 		3e-05
(0.000559) 		0.321
(0.437) 		0.0601
(0.132) 		0.502
(0.607) 		0.0632
(0.137)
17p loss 57 (22%) 199 0.313
(0.429) 		0.214
(0.322) 		0.976
(0.987) 		0.0105
(0.0406) 		0.98
(0.988) 		0.319
(0.436) 		0.58
(0.681) 		0.699
(0.773) 		0.306
(0.423) 		0.383
(0.499)
8p gain 52 (20%) 204 0.0652
(0.139) 		0.572
(0.675) 		0.887
(0.916) 		0.69
(0.768) 		0.731
(0.794) 		0.0746
(0.155) 		0.371
(0.488) 		0.264
(0.377) 		0.358
(0.475) 		0.0675
(0.143)
4p loss 42 (16%) 214 0.0836
(0.165) 		0.961
(0.975) 		0.592
(0.692) 		0.842
(0.879) 		0.906
(0.93) 		0.986
(0.994) 		0.623
(0.713) 		0.502
(0.607) 		0.819
(0.863) 		0.529
(0.635)
6p loss 60 (23%) 196 0.494
(0.601) 		0.0551
(0.124) 		0.098
(0.186) 		0.611
(0.703) 		0.124
(0.217) 		0.262
(0.376) 		0.296
(0.413) 		0.418
(0.531) 		0.457
(0.57) 		0.173
(0.276)
7q loss 34 (13%) 222 0.0653
(0.139) 		0.448
(0.561) 		0.644
(0.73) 		0.651
(0.735) 		0.131
(0.224) 		0.0973
(0.185) 		0.441
(0.555) 		0.613
(0.704) 		0.319
(0.436) 		0.468
(0.58)
20q loss 25 (10%) 231 0.142
(0.237) 		0.303
(0.421) 		0.626
(0.716) 		0.203
(0.311) 		0.472
(0.584) 		0.709
(0.778) 		0.56
(0.665) 		0.124
(0.217) 		0.114
(0.205) 		0.19
(0.297)
'1p gain' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
1P GAIN MUTATED 27 8 16 5
1P GAIN WILD-TYPE 43 78 58 21

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S2.  Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
1P GAIN MUTATED 9 7 13 2 22 0 3
1P GAIN WILD-TYPE 39 39 48 32 25 15 2

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.093

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
1P GAIN MUTATED 7 5 16 12 4 5
1P GAIN WILD-TYPE 17 23 23 56 33 17

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
1P GAIN MUTATED 9 6 9 4 10 6 12
1P GAIN WILD-TYPE 37 17 40 42 18 23 21

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

'1q gain' versus 'CN_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
1Q GAIN MUTATED 20 8 19 2
1Q GAIN WILD-TYPE 50 78 55 24

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 0.00941 (Fisher's exact test), Q value = 0.038

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
1Q GAIN MUTATED 5 4 18 5 14 1 2
1Q GAIN WILD-TYPE 43 42 43 29 33 14 3

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

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.05

Table S7.  Gene #2: '1q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
1Q GAIN MUTATED 4 3 11 18 1 3
1Q GAIN WILD-TYPE 20 25 28 50 36 19

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.00906 (Fisher's exact test), Q value = 0.038

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
1Q GAIN MUTATED 20 23 6
1Q GAIN WILD-TYPE 94 54 57

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.072

Table S9.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
1Q GAIN MUTATED 12 10 25
1Q GAIN WILD-TYPE 95 40 72

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0051

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
1Q GAIN MUTATED 8 23 10
1Q GAIN WILD-TYPE 75 41 36

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00514 (Fisher's exact test), Q value = 0.023

Table S11.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
1Q GAIN MUTATED 4 1 14 8 2 7 3 2
1Q GAIN WILD-TYPE 20 31 23 16 9 15 18 20

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0096

Table S12.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
2P GAIN MUTATED 2 3 12 5
2P GAIN WILD-TYPE 68 83 62 21

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
2P GAIN MUTATED 3 3 1 7 7 0 1
2P GAIN WILD-TYPE 45 43 60 27 40 15 4

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

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.04

Table S14.  Gene #3: '2p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
2P GAIN MUTATED 2 3 7 2 2 6
2P GAIN WILD-TYPE 22 25 32 66 35 16

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0057

Table S15.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
2P GAIN MUTATED 9 1 12
2P GAIN WILD-TYPE 105 76 51

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0063

Table S16.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
2P GAIN MUTATED 3 1 1 10 6 0 1
2P GAIN WILD-TYPE 43 22 48 36 22 29 32

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

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

Table S17.  Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
2P GAIN MUTATED 15 4 3
2P GAIN WILD-TYPE 92 46 94

Figure S17.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.096

Table S18.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
2P GAIN MUTATED 9 7 3 3
2P GAIN WILD-TYPE 70 45 97 20

Figure S18.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.06

Table S19.  Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
2P GAIN MUTATED 11 1 6
2P GAIN WILD-TYPE 72 63 40

Figure S19.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00291 (Fisher's exact test), Q value = 0.015

Table S20.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
2P GAIN MUTATED 1 4 0 1 0 1 5 6
2P GAIN WILD-TYPE 23 28 37 23 11 21 16 16

Figure S20.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0025

Table S21.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
2Q GAIN MUTATED 2 2 14 4
2Q GAIN WILD-TYPE 68 84 60 22

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.09

Table S22.  Gene #4: '2q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
2Q GAIN MUTATED 4 5 7 2 2 2
2Q GAIN WILD-TYPE 20 23 32 66 35 20

Figure S22.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.00432 (Fisher's exact test), Q value = 0.02

Table S23.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
2Q GAIN MUTATED 11 1 10
2Q GAIN WILD-TYPE 103 76 53

Figure S23.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.0092

Table S24.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
2Q GAIN MUTATED 4 3 1 8 6 0 0
2Q GAIN WILD-TYPE 42 20 48 38 22 29 33

Figure S24.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.089

Table S25.  Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
2Q GAIN MUTATED 13 6 3
2Q GAIN WILD-TYPE 94 44 94

Figure S25.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00918 (Fisher's exact test), Q value = 0.038

Table S26.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
2Q GAIN MUTATED 7 10 3 2
2Q GAIN WILD-TYPE 72 42 97 21

Figure S26.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.087

Table S27.  Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
2Q GAIN MUTATED 9 2 8
2Q GAIN WILD-TYPE 74 62 38

Figure S27.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0044

Table S28.  Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
3P GAIN MUTATED 16 6 17 0
3P GAIN WILD-TYPE 54 80 57 26

Figure S28.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0011

Table S29.  Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
3P GAIN MUTATED 2 10 13 0 14 0 0
3P GAIN WILD-TYPE 46 36 48 34 33 15 5

Figure S29.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00314 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
3P GAIN MUTATED 23 14 2
3P GAIN WILD-TYPE 91 63 61

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

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00071

Table S31.  Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
3P GAIN MUTATED 3 4 9 0 11 4 8
3P GAIN WILD-TYPE 43 19 40 46 17 25 25

Figure S31.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.1

Table S32.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
3P GAIN MUTATED 10 12 17
3P GAIN WILD-TYPE 97 38 80

Figure S32.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0065

Table S33.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
3P GAIN MUTATED 7 14 16
3P GAIN WILD-TYPE 76 50 30

Figure S33.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.0079

Table S34.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
3P GAIN MUTATED 3 1 9 8 2 6 8 0
3P GAIN WILD-TYPE 21 31 28 16 9 16 13 22

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

'3q gain' versus 'CN_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.012

Table S35.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
3Q GAIN MUTATED 14 6 16 0
3Q GAIN WILD-TYPE 56 80 58 26

Figure S35.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

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

Table S36.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
3Q GAIN MUTATED 2 11 10 1 12 0 0
3Q GAIN WILD-TYPE 46 35 51 33 35 15 5

Figure S36.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.05

Table S37.  Gene #6: '3q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
3Q GAIN MUTATED 3 21 6
3Q GAIN WILD-TYPE 55 79 54

Figure S37.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.0043 (Fisher's exact test), Q value = 0.02

Table S38.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
3Q GAIN MUTATED 23 11 2
3Q GAIN WILD-TYPE 91 66 61

Figure S38.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.017

Table S39.  Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
3Q GAIN MUTATED 4 4 7 1 10 3 7
3Q GAIN WILD-TYPE 42 19 42 45 18 26 26

Figure S39.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.11

Table S40.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
3Q GAIN MUTATED 9 11 16
3Q GAIN WILD-TYPE 98 39 81

Figure S40.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0065

Table S41.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
3Q GAIN MUTATED 6 13 15
3Q GAIN WILD-TYPE 77 51 31

Figure S41.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.009

Table S42.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
3Q GAIN MUTATED 3 1 8 9 1 5 7 0
3Q GAIN WILD-TYPE 21 31 29 15 10 17 14 22

Figure S42.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S43.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
4P GAIN MUTATED 27 7 27 7
4P GAIN WILD-TYPE 43 79 47 19

Figure S43.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00056

Table S44.  Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
4P GAIN MUTATED 14 9 13 4 26 0 2
4P GAIN WILD-TYPE 34 37 48 30 21 15 3

Figure S44.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'RPPA_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.099

Table S45.  Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
4P GAIN MUTATED 15 35 10
4P GAIN WILD-TYPE 43 65 50

Figure S45.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.041

Table S46.  Gene #7: '4p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
4P GAIN MUTATED 8 7 18 11 13 3
4P GAIN WILD-TYPE 16 21 21 57 24 19

Figure S46.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.074

Table S47.  Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
4P GAIN MUTATED 40 14 14
4P GAIN WILD-TYPE 74 63 49

Figure S47.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.02

Table S48.  Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
4P GAIN MUTATED 13 4 8 8 14 6 15
4P GAIN WILD-TYPE 33 19 41 38 14 23 18

Figure S48.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.0436 (Fisher's exact test), Q value = 0.11

Table S49.  Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
4P GAIN MUTATED 32 17 17
4P GAIN WILD-TYPE 75 33 80

Figure S49.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.059

Table S50.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
4P GAIN MUTATED 27 18 18 3
4P GAIN WILD-TYPE 52 34 82 20

Figure S50.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.084

Table S51.  Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
4Q GAIN MUTATED 18 8 17 4
4Q GAIN WILD-TYPE 52 78 57 22

Figure S51.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.00874 (Fisher's exact test), Q value = 0.036

Table S52.  Gene #8: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
4Q GAIN MUTATED 9 8 10 2 17 0 1
4Q GAIN WILD-TYPE 39 38 51 32 30 15 4

Figure S52.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S53.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
5P GAIN MUTATED 31 11 48 8
5P GAIN WILD-TYPE 39 75 26 18

Figure S53.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00056

Table S54.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
5P GAIN MUTATED 23 15 24 5 29 1 1
5P GAIN WILD-TYPE 25 31 37 29 18 14 4

Figure S54.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00232 (Fisher's exact test), Q value = 0.013

Table S55.  Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
5P GAIN MUTATED 11 7 25 20 17 5
5P GAIN WILD-TYPE 13 21 14 48 20 17

Figure S55.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.044

Table S56.  Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
5P GAIN MUTATED 55 26 17
5P GAIN WILD-TYPE 59 51 46

Figure S56.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00082

Table S57.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
5P GAIN MUTATED 25 5 21 10 17 4 16
5P GAIN WILD-TYPE 21 18 28 36 11 25 17

Figure S57.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.015

Table S58.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
5P GAIN MUTATED 39 18 38 2
5P GAIN WILD-TYPE 40 34 62 21

Figure S58.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0015

Table S59.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
5Q GAIN MUTATED 26 11 30 4
5Q GAIN WILD-TYPE 44 75 44 22

Figure S59.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.05

Table S60.  Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
5Q GAIN MUTATED 13 13 18 5 20 0 2
5Q GAIN WILD-TYPE 35 33 43 29 27 15 3

Figure S60.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.05

Table S61.  Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
5Q GAIN MUTATED 18 3 16 8 11 3 11
5Q GAIN WILD-TYPE 28 20 33 38 17 26 22

Figure S61.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S62.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
6P GAIN MUTATED 21 3 20 7
6P GAIN WILD-TYPE 49 83 54 19

Figure S62.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00056

Table S63.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
6P GAIN MUTATED 21 7 5 4 13 0 1
6P GAIN WILD-TYPE 27 39 56 30 34 15 4

Figure S63.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.018

Table S64.  Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
6P GAIN MUTATED 15 26 4
6P GAIN WILD-TYPE 43 74 56

Figure S64.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.004

Table S65.  Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
6P GAIN MUTATED 12 4 12 5 7 5
6P GAIN WILD-TYPE 12 24 27 63 30 17

Figure S65.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0029

Table S66.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
6P GAIN MUTATED 35 6 10
6P GAIN WILD-TYPE 79 71 53

Figure S66.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0018

Table S67.  Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
6P GAIN MUTATED 21 3 3 6 6 3 9
6P GAIN WILD-TYPE 25 20 46 40 22 26 24

Figure S67.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.044

Table S68.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
6P GAIN MUTATED 23 13 12 2
6P GAIN WILD-TYPE 56 39 88 21

Figure S68.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.098

Table S69.  Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
6P GAIN MUTATED 5 11 4 10 1 6 3 2
6P GAIN WILD-TYPE 19 21 33 14 10 16 18 20

Figure S69.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0035

Table S70.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
6Q GAIN MUTATED 19 5 18 8
6Q GAIN WILD-TYPE 51 81 56 18

Figure S70.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.004

Table S71.  Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
6Q GAIN MUTATED 21 8 6 3 10 1 1
6Q GAIN WILD-TYPE 27 38 55 31 37 14 4

Figure S71.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.11

Table S72.  Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
6Q GAIN MUTATED 16 21 6
6Q GAIN WILD-TYPE 42 79 54

Figure S72.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.066

Table S73.  Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
6Q GAIN MUTATED 10 6 11 7 6 3
6Q GAIN WILD-TYPE 14 22 28 61 31 19

Figure S73.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0029

Table S74.  Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
6Q GAIN MUTATED 35 7 8
6Q GAIN WILD-TYPE 79 70 55

Figure S74.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0042

Table S75.  Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
6Q GAIN MUTATED 21 5 4 6 5 3 6
6Q GAIN WILD-TYPE 25 18 45 40 23 26 27

Figure S75.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00595 (Fisher's exact test), Q value = 0.026

Table S76.  Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
6Q GAIN MUTATED 25 10 12 2
6Q GAIN WILD-TYPE 54 42 88 21

Figure S76.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.09

Table S77.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
6Q GAIN MUTATED 7 13 4 8 1 5 3 2
6Q GAIN WILD-TYPE 17 19 33 16 10 17 18 20

Figure S77.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S78.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
7P GAIN MUTATED 29 10 38 5
7P GAIN WILD-TYPE 41 76 36 21

Figure S78.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

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

Table S79.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
7P GAIN MUTATED 21 13 12 9 24 1 2
7P GAIN WILD-TYPE 27 33 49 25 23 14 3

Figure S79.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.041

Table S80.  Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
7P GAIN MUTATED 22 43 12
7P GAIN WILD-TYPE 36 57 48

Figure S80.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00711 (Fisher's exact test), Q value = 0.031

Table S81.  Gene #13: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
7P GAIN MUTATED 13 8 20 14 15 7
7P GAIN WILD-TYPE 11 20 19 54 22 15

Figure S81.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.013

Table S82.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
7P GAIN MUTATED 49 15 18
7P GAIN WILD-TYPE 65 62 45

Figure S82.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.066

Table S83.  Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
7P GAIN MUTATED 21 6 9 12 14 7 13
7P GAIN WILD-TYPE 25 17 40 34 14 22 20

Figure S83.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.02

Table S84.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
7P GAIN MUTATED 25 16 25
7P GAIN WILD-TYPE 58 48 21

Figure S84.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.013

Table S85.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
7P GAIN MUTATED 9 11 6 15 2 4 12 7
7P GAIN WILD-TYPE 15 21 31 9 9 18 9 15

Figure S85.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S86.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
7Q GAIN MUTATED 19 10 35 4
7Q GAIN WILD-TYPE 51 76 39 22

Figure S86.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.003

Table S87.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
7Q GAIN MUTATED 20 13 10 4 19 0 2
7Q GAIN WILD-TYPE 28 33 51 30 28 15 3

Figure S87.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.1

Table S88.  Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
7Q GAIN MUTATED 16 35 10
7Q GAIN WILD-TYPE 42 65 50

Figure S88.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0036 (Fisher's exact test), Q value = 0.017

Table S89.  Gene #14: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
7Q GAIN MUTATED 10 8 18 10 12 3
7Q GAIN WILD-TYPE 14 20 21 58 25 19

Figure S89.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0046

Table S90.  Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
7Q GAIN MUTATED 44 11 13
7Q GAIN WILD-TYPE 70 66 50

Figure S90.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.084

Table S91.  Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
7Q GAIN MUTATED 18 6 8 9 11 4 12
7Q GAIN WILD-TYPE 28 17 41 37 17 25 21

Figure S91.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.11

Table S92.  Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
7Q GAIN MUTATED 28 20 20
7Q GAIN WILD-TYPE 79 30 77

Figure S92.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.043

Table S93.  Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
7Q GAIN MUTATED 25 21 19 3
7Q GAIN WILD-TYPE 54 31 81 20

Figure S93.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0029

Table S94.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
7Q GAIN MUTATED 20 11 24
7Q GAIN WILD-TYPE 63 53 22

Figure S94.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 0.015

Table S95.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
7Q GAIN MUTATED 7 10 5 12 1 4 12 4
7Q GAIN WILD-TYPE 17 22 32 12 10 18 9 18

Figure S95.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.11

Table S96.  Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
8Q GAIN MUTATED 16 19 18
8Q GAIN WILD-TYPE 67 45 28

Figure S96.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0012

Table S97.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
9P GAIN MUTATED 28 8 14 7
9P GAIN WILD-TYPE 42 78 60 19

Figure S97.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.012

Table S98.  Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
9P GAIN MUTATED 20 9 8 5 14 0 1
9P GAIN WILD-TYPE 28 37 53 29 33 15 4

Figure S98.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.075

Table S99.  Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
9P GAIN MUTATED 16 29 7
9P GAIN WILD-TYPE 42 71 53

Figure S99.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0037

Table S100.  Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
9P GAIN MUTATED 12 3 16 8 8 5
9P GAIN WILD-TYPE 12 25 23 60 29 17

Figure S100.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.0061 (Fisher's exact test), Q value = 0.027

Table S101.  Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
9P GAIN MUTATED 36 10 11
9P GAIN WILD-TYPE 78 67 52

Figure S101.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0051

Table S102.  Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
9P GAIN MUTATED 18 8 6 3 9 4 9
9P GAIN WILD-TYPE 28 15 43 43 19 25 24

Figure S102.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00343 (Fisher's exact test), Q value = 0.017

Table S103.  Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
9P GAIN MUTATED 29 10 16 2
9P GAIN WILD-TYPE 50 42 84 21

Figure S103.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S104.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
9Q GAIN MUTATED 31 9 23 10
9Q GAIN WILD-TYPE 39 77 51 16

Figure S104.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0016

Table S105.  Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
9Q GAIN MUTATED 23 14 11 5 19 0 1
9Q GAIN WILD-TYPE 25 32 50 29 28 15 4

Figure S105.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 0.026

Table S106.  Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
9Q GAIN MUTATED 19 38 9
9Q GAIN WILD-TYPE 39 62 51

Figure S106.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9q gain' versus 'RPPA_CHIERARCHICAL'

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

Table S107.  Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
9Q GAIN MUTATED 13 7 18 10 13 5
9Q GAIN WILD-TYPE 11 21 21 58 24 17

Figure S107.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00095

Table S108.  Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
9Q GAIN MUTATED 48 12 13
9Q GAIN WILD-TYPE 66 65 50

Figure S108.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S109.  Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
9Q GAIN MUTATED 22 10 10 5 14 2 10
9Q GAIN WILD-TYPE 24 13 39 41 14 27 23

Figure S109.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0029

Table S110.  Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
9Q GAIN MUTATED 34 17 21 1
9Q GAIN WILD-TYPE 45 35 79 22

Figure S110.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.078

Table S111.  Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
9Q GAIN MUTATED 25 17 23
9Q GAIN WILD-TYPE 58 47 23

Figure S111.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00766 (Fisher's exact test), Q value = 0.032

Table S112.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
9Q GAIN MUTATED 9 15 9 13 1 7 9 2
9Q GAIN WILD-TYPE 15 17 28 11 10 15 12 20

Figure S112.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.074

Table S113.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
10P GAIN MUTATED 12 3 7 1
10P GAIN WILD-TYPE 58 83 67 25

Figure S113.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.11

Table S114.  Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
10P GAIN MUTATED 4 5 2 2 8 0 2
10P GAIN WILD-TYPE 44 41 59 32 39 15 3

Figure S114.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.075

Table S115.  Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
10P GAIN MUTATED 4 5 9
10P GAIN WILD-TYPE 79 59 37

Figure S115.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q gain' versus 'RPPA_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.079

Table S116.  Gene #20: '10q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
10Q GAIN MUTATED 3 9 0
10Q GAIN WILD-TYPE 55 91 60

Figure S116.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.11

Table S117.  Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
10Q GAIN MUTATED 4 1 6
10Q GAIN WILD-TYPE 79 63 40

Figure S117.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.11

Table S118.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
11P GAIN MUTATED 9 4 10 0
11P GAIN WILD-TYPE 61 82 64 26

Figure S118.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.076

Table S119.  Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
11P GAIN MUTATED 5 5 1 1 9 1 1
11P GAIN WILD-TYPE 43 41 60 33 38 14 4

Figure S119.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.04

Table S120.  Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
11P GAIN MUTATED 6 0 1 2 7 2 4
11P GAIN WILD-TYPE 40 23 48 44 21 27 29

Figure S120.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.042

Table S121.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
11Q GAIN MUTATED 7 3 12 0
11Q GAIN WILD-TYPE 63 83 62 26

Figure S121.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.092

Table S122.  Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
11Q GAIN MUTATED 4 0 2 2 7 3 4
11Q GAIN WILD-TYPE 42 23 47 44 21 26 29

Figure S122.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S123.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
12P GAIN MUTATED 7 7 28 1
12P GAIN WILD-TYPE 63 79 46 25

Figure S123.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.078

Table S124.  Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
12P GAIN MUTATED 9 10 4 8 12 0 0
12P GAIN WILD-TYPE 39 36 57 26 35 15 5

Figure S124.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.076

Table S125.  Gene #23: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
12P GAIN MUTATED 12 25 5
12P GAIN WILD-TYPE 46 75 55

Figure S125.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.067

Table S126.  Gene #23: '12p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
12P GAIN MUTATED 5 5 13 5 9 5
12P GAIN WILD-TYPE 19 23 26 63 28 17

Figure S126.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0018

Table S127.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
12P GAIN MUTATED 19 4 20
12P GAIN WILD-TYPE 95 73 43

Figure S127.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0051

Table S128.  Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
12P GAIN MUTATED 8 1 4 13 9 0 8
12P GAIN WILD-TYPE 38 22 45 33 19 29 25

Figure S128.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.11

Table S129.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
12P GAIN MUTATED 18 6 12
12P GAIN WILD-TYPE 65 58 34

Figure S129.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.006

Table S130.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
12P GAIN MUTATED 1 8 2 6 0 3 10 6
12P GAIN WILD-TYPE 23 24 35 18 11 19 11 16

Figure S130.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0075

Table S131.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
12Q GAIN MUTATED 7 6 20 1
12Q GAIN WILD-TYPE 63 80 54 25

Figure S131.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.088

Table S132.  Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
12Q GAIN MUTATED 9 8 2 5 9 0 1
12Q GAIN WILD-TYPE 39 38 59 29 38 15 4

Figure S132.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.069

Table S133.  Gene #24: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
12Q GAIN MUTATED 10 20 3
12Q GAIN WILD-TYPE 48 80 57

Figure S133.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00428 (Fisher's exact test), Q value = 0.02

Table S134.  Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
12Q GAIN MUTATED 18 3 13
12Q GAIN WILD-TYPE 96 74 50

Figure S134.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.058

Table S135.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
12Q GAIN MUTATED 4 7 1 5 0 1 7 4
12Q GAIN WILD-TYPE 20 25 36 19 11 21 14 18

Figure S135.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.01

Table S136.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
13Q GAIN MUTATED 11 2 2 0
13Q GAIN WILD-TYPE 59 84 72 26

Figure S136.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.017

Table S137.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
14Q GAIN MUTATED 22 10 22 3
14Q GAIN WILD-TYPE 48 76 52 23

Figure S137.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.11

Table S138.  Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
14Q GAIN MUTATED 11 7 13 5 19 1 1
14Q GAIN WILD-TYPE 37 39 48 29 28 14 4

Figure S138.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.085

Table S139.  Gene #26: '14q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
14Q GAIN MUTATED 11 32 9
14Q GAIN WILD-TYPE 47 68 51

Figure S139.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.0081

Table S140.  Gene #26: '14q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
14Q GAIN MUTATED 9 5 19 10 6 3
14Q GAIN WILD-TYPE 15 23 20 58 31 19

Figure S140.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0071

Table S141.  Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
14Q GAIN MUTATED 10 3 12 6 16 3 7
14Q GAIN WILD-TYPE 36 20 37 40 12 26 26

Figure S141.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S142.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
15Q GAIN MUTATED 23 6 29 5
15Q GAIN WILD-TYPE 47 80 45 21

Figure S142.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.059

Table S143.  Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
15Q GAIN MUTATED 13 23 12
15Q GAIN WILD-TYPE 70 41 34

Figure S143.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.069

Table S144.  Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
15Q GAIN MUTATED 1 5 15 9 2 4 7 5
15Q GAIN WILD-TYPE 23 27 22 15 9 18 14 17

Figure S144.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0013

Table S145.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
16P GAIN MUTATED 17 2 14 7
16P GAIN WILD-TYPE 53 84 60 19

Figure S145.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.085

Table S146.  Gene #28: '16p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
16P GAIN MUTATED 8 22 4
16P GAIN WILD-TYPE 50 78 56

Figure S146.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.05

Table S147.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
16Q GAIN MUTATED 10 2 5 4
16Q GAIN WILD-TYPE 60 84 69 22

Figure S147.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'RPPA_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.088

Table S148.  Gene #29: '16q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
16Q GAIN MUTATED 4 13 1
16Q GAIN WILD-TYPE 54 87 59

Figure S148.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00571 (Fisher's exact test), Q value = 0.025

Table S149.  Gene #29: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
16Q GAIN MUTATED 4 1 8 1 2 2
16Q GAIN WILD-TYPE 20 27 31 67 35 20

Figure S149.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.075

Table S150.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
16Q GAIN MUTATED 15 2 4
16Q GAIN WILD-TYPE 99 75 59

Figure S150.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S151.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
17P GAIN MUTATED 29 5 22 5
17P GAIN WILD-TYPE 41 81 52 21

Figure S151.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.00346 (Fisher's exact test), Q value = 0.017

Table S152.  Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
17P GAIN MUTATED 19 8 10 5 18 1 0
17P GAIN WILD-TYPE 29 38 51 29 29 14 5

Figure S152.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'RPPA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.008

Table S153.  Gene #30: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
17P GAIN MUTATED 9 36 8
17P GAIN WILD-TYPE 49 64 52

Figure S153.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.075

Table S154.  Gene #30: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
17P GAIN MUTATED 9 6 10 9 15 4
17P GAIN WILD-TYPE 15 22 29 59 22 18

Figure S154.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.078

Table S155.  Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
17P GAIN MUTATED 36 12 12
17P GAIN WILD-TYPE 78 65 51

Figure S155.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00222 (Fisher's exact test), Q value = 0.013

Table S156.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
17P GAIN MUTATED 24 19 17 1
17P GAIN WILD-TYPE 55 33 83 22

Figure S156.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S157.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
17Q GAIN MUTATED 29 6 19 3
17Q GAIN WILD-TYPE 41 80 55 23

Figure S157.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.083

Table S158.  Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
17Q GAIN MUTATED 15 8 9 5 18 2 0
17Q GAIN WILD-TYPE 33 38 52 29 29 13 5

Figure S158.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.041

Table S159.  Gene #31: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
17Q GAIN MUTATED 13 30 6
17Q GAIN WILD-TYPE 45 70 54

Figure S159.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.05

Table S160.  Gene #31: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
17Q GAIN MUTATED 11 5 9 8 12 4
17Q GAIN WILD-TYPE 13 23 30 60 25 18

Figure S160.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00445 (Fisher's exact test), Q value = 0.02

Table S161.  Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
17Q GAIN MUTATED 16 3 4 6 11 8 8
17Q GAIN WILD-TYPE 30 20 45 40 17 21 25

Figure S161.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.058

Table S162.  Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
17Q GAIN MUTATED 21 19 17
17Q GAIN WILD-TYPE 86 31 80

Figure S162.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.017

Table S163.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
17Q GAIN MUTATED 21 19 16 1
17Q GAIN WILD-TYPE 58 33 84 22

Figure S163.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00627 (Fisher's exact test), Q value = 0.027

Table S164.  Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
17Q GAIN MUTATED 15 14 20
17Q GAIN WILD-TYPE 68 50 26

Figure S164.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.083

Table S165.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
17Q GAIN MUTATED 11 4 7 8 2 7 8 2
17Q GAIN WILD-TYPE 13 28 30 16 9 15 13 20

Figure S165.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S166.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
18P GAIN MUTATED 25 5 20 3
18P GAIN WILD-TYPE 45 81 54 23

Figure S166.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.07

Table S167.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
18P GAIN MUTATED 14 9 9 4 15 0 2
18P GAIN WILD-TYPE 34 37 52 30 32 15 3

Figure S167.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.069

Table S168.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
18Q GAIN MUTATED 15 5 13 3
18Q GAIN WILD-TYPE 55 81 61 23

Figure S168.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.0495 (Fisher's exact test), Q value = 0.12

Table S169.  Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
18Q GAIN MUTATED 10 5 9 5 4 0 3
18Q GAIN WILD-TYPE 38 41 52 29 43 15 2

Figure S169.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S170.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
19P GAIN MUTATED 28 6 45 8
19P GAIN WILD-TYPE 42 80 29 18

Figure S170.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00228 (Fisher's exact test), Q value = 0.013

Table S171.  Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
19P GAIN MUTATED 27 16 17 7 18 1 1
19P GAIN WILD-TYPE 21 30 44 27 29 14 4

Figure S171.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0026

Table S172.  Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
19P GAIN MUTATED 15 6 22 17 15 4
19P GAIN WILD-TYPE 9 22 17 51 22 18

Figure S172.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.075

Table S173.  Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
19P GAIN MUTATED 49 19 19
19P GAIN WILD-TYPE 65 58 44

Figure S173.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00816 (Fisher's exact test), Q value = 0.034

Table S174.  Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
19P GAIN MUTATED 27 8 11 13 11 9 8
19P GAIN WILD-TYPE 19 15 38 33 17 20 25

Figure S174.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S175.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
19Q GAIN MUTATED 24 5 29 7
19Q GAIN WILD-TYPE 46 81 45 19

Figure S175.  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 = 0.00026

Table S176.  Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
19Q GAIN MUTATED 23 12 9 3 18 0 0
19Q GAIN WILD-TYPE 25 34 52 31 29 15 5

Figure S176.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.032

Table S177.  Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
19Q GAIN MUTATED 22 28 8
19Q GAIN WILD-TYPE 36 72 52

Figure S177.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S178.  Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
19Q GAIN MUTATED 15 7 15 7 12 2
19Q GAIN WILD-TYPE 9 21 24 61 25 20

Figure S178.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0044

Table S179.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
19Q GAIN MUTATED 42 10 13
19Q GAIN WILD-TYPE 72 67 50

Figure S179.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0056

Table S180.  Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
19Q GAIN MUTATED 23 5 6 8 10 4 9
19Q GAIN WILD-TYPE 23 18 43 38 18 25 24

Figure S180.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.069

Table S181.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
19Q GAIN MUTATED 7 14 6 10 3 5 6 1
19Q GAIN WILD-TYPE 17 18 31 14 8 17 15 21

Figure S181.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0029

Table S182.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
20P GAIN MUTATED 19 9 29 5
20P GAIN WILD-TYPE 51 77 45 21

Figure S182.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00071

Table S183.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
20Q GAIN MUTATED 26 12 36 9
20Q GAIN WILD-TYPE 44 74 38 17

Figure S183.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.013

Table S184.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
20Q GAIN MUTATED 20 13 13 8 26 2 1
20Q GAIN WILD-TYPE 28 33 48 26 21 13 4

Figure S184.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.00564 (Fisher's exact test), Q value = 0.025

Table S185.  Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
20Q GAIN MUTATED 18 46 13
20Q GAIN WILD-TYPE 40 54 47

Figure S185.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.013

Table S186.  Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
20Q GAIN MUTATED 9 9 24 14 13 8
20Q GAIN WILD-TYPE 15 19 15 54 24 14

Figure S186.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.0396 (Fisher's exact test), Q value = 0.099

Table S187.  Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
20Q GAIN MUTATED 45 17 21
20Q GAIN WILD-TYPE 69 60 42

Figure S187.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.088

Table S188.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
20Q GAIN MUTATED 19 6 12 14 14 4 14
20Q GAIN WILD-TYPE 27 17 37 32 14 25 19

Figure S188.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.051

Table S189.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
20Q GAIN MUTATED 32 20 29 2
20Q GAIN WILD-TYPE 47 32 71 21

Figure S189.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.065

Table S190.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
20Q GAIN MUTATED 7 13 8 12 3 10 12 3
20Q GAIN WILD-TYPE 17 19 29 12 8 12 9 19

Figure S190.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S191.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
21Q GAIN MUTATED 27 4 20 7
21Q GAIN WILD-TYPE 43 82 54 19

Figure S191.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.078

Table S192.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
21Q GAIN MUTATED 15 7 12 6 16 0 2
21Q GAIN WILD-TYPE 33 39 49 28 31 15 3

Figure S192.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.0093 (Fisher's exact test), Q value = 0.038

Table S193.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
22Q GAIN MUTATED 21 12 24 3
22Q GAIN WILD-TYPE 49 74 50 23

Figure S193.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.013

Table S194.  Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
22Q GAIN MUTATED 11 9 13 4 21 0 2
22Q GAIN WILD-TYPE 37 37 48 30 26 15 3

Figure S194.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.05

Table S195.  Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
22Q GAIN MUTATED 8 33 11
22Q GAIN WILD-TYPE 50 67 49

Figure S195.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.047

Table S196.  Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
22Q GAIN MUTATED 4 5 18 13 10 2
22Q GAIN WILD-TYPE 20 23 21 55 27 20

Figure S196.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.0077 (Fisher's exact test), Q value = 0.032

Table S197.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
22Q GAIN MUTATED 37 15 8
22Q GAIN WILD-TYPE 77 62 55

Figure S197.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S198.  Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
22Q GAIN MUTATED 13 3 11 4 13 4 12
22Q GAIN WILD-TYPE 33 20 38 42 15 25 21

Figure S198.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00095

Table S199.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
XP GAIN MUTATED 29 10 28 7
XP GAIN WILD-TYPE 41 76 46 19

Figure S199.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.11

Table S200.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
XP GAIN MUTATED 20 8 17 9 17 1 2
XP GAIN WILD-TYPE 28 38 44 25 30 14 3

Figure S200.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.05

Table S201.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
XQ GAIN MUTATED 8 5 17 3
XQ GAIN WILD-TYPE 62 81 57 23

Figure S201.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.1

Table S202.  Gene #41: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
XQ GAIN MUTATED 11 16 3
XQ GAIN WILD-TYPE 47 84 57

Figure S202.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.075

Table S203.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
1P LOSS MUTATED 7 3 4 6 5 6 1
1P LOSS WILD-TYPE 41 43 57 28 42 9 4

Figure S203.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.04

Table S204.  Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
1Q LOSS MUTATED 15 5 14 6
1Q LOSS WILD-TYPE 55 81 60 20

Figure S204.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0092

Table S205.  Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
1Q LOSS MUTATED 15 5 4 1 11 3 1
1Q LOSS WILD-TYPE 33 41 57 33 36 12 4

Figure S205.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.099

Table S206.  Gene #43: '1q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
1Q LOSS MUTATED 7 2 9 6 10 4
1Q LOSS WILD-TYPE 17 26 30 62 27 18

Figure S206.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.078

Table S207.  Gene #43: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
1Q LOSS MUTATED 21 11 8
1Q LOSS WILD-TYPE 86 39 89

Figure S207.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.013

Table S208.  Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
1Q LOSS MUTATED 21 10 8 1
1Q LOSS WILD-TYPE 58 42 92 22

Figure S208.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S209.  Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
2P LOSS MUTATED 45 8 29 6
2P LOSS WILD-TYPE 25 78 45 20

Figure S209.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S210.  Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
2P LOSS MUTATED 21 10 36 4 16 0 1
2P LOSS WILD-TYPE 27 36 25 30 31 15 4

Figure S210.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.048

Table S211.  Gene #44: '2p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
2P LOSS MUTATED 16 29 30
2P LOSS WILD-TYPE 42 71 30

Figure S211.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0058

Table S212.  Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
2P LOSS MUTATED 13 5 9 31 15 2
2P LOSS WILD-TYPE 11 23 30 37 22 20

Figure S212.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S213.  Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
2P LOSS MUTATED 40 39 8
2P LOSS WILD-TYPE 74 38 55

Figure S213.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00082

Table S214.  Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
2P LOSS MUTATED 21 6 28 5 6 10 11
2P LOSS WILD-TYPE 25 17 21 41 22 19 22

Figure S214.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.013

Table S215.  Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
2P LOSS MUTATED 25 18 45
2P LOSS WILD-TYPE 82 32 52

Figure S215.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.0033

Table S216.  Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
2P LOSS MUTATED 25 15 47 1
2P LOSS WILD-TYPE 54 37 53 22

Figure S216.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0051

Table S217.  Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
2P LOSS MUTATED 19 34 17
2P LOSS WILD-TYPE 64 30 29

Figure S217.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0042

Table S218.  Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
2P LOSS MUTATED 11 10 22 11 5 5 5 1
2P LOSS WILD-TYPE 13 22 15 13 6 17 16 21

Figure S218.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S219.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
2Q LOSS MUTATED 36 5 23 7
2Q LOSS WILD-TYPE 34 81 51 19

Figure S219.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.0095

Table S220.  Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
2Q LOSS MUTATED 14 8 22 5 21 0 1
2Q LOSS WILD-TYPE 34 38 39 29 26 15 4

Figure S220.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0016

Table S221.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
3P LOSS MUTATED 21 8 3 8 12 2 2
3P LOSS WILD-TYPE 27 38 58 26 35 13 3

Figure S221.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00404 (Fisher's exact test), Q value = 0.019

Table S222.  Gene #46: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
3P LOSS MUTATED 9 6 12 5 11 6
3P LOSS WILD-TYPE 15 22 27 63 26 16

Figure S222.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0018

Table S223.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
3P LOSS MUTATED 31 5 20
3P LOSS WILD-TYPE 83 72 43

Figure S223.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0042

Table S224.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
3P LOSS MUTATED 19 4 3 14 8 2 6
3P LOSS WILD-TYPE 27 19 46 32 20 27 27

Figure S224.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0035

Table S225.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
3P LOSS MUTATED 32 14 9
3P LOSS WILD-TYPE 75 36 88

Figure S225.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0069

Table S226.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
3P LOSS MUTATED 26 12 10 7
3P LOSS WILD-TYPE 53 40 90 16

Figure S226.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0058

Table S227.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
3P LOSS MUTATED 27 5 13
3P LOSS WILD-TYPE 56 59 33

Figure S227.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0051

Table S228.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
3P LOSS MUTATED 7 16 2 5 0 4 4 7
3P LOSS WILD-TYPE 17 16 35 19 11 18 17 15

Figure S228.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.009

Table S229.  Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
3Q LOSS MUTATED 13 7 19 10
3Q LOSS WILD-TYPE 57 79 55 16

Figure S229.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.044

Table S230.  Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
3Q LOSS MUTATED 16 7 5 6 12 1 2
3Q LOSS WILD-TYPE 32 39 56 28 35 14 3

Figure S230.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.00962 (Fisher's exact test), Q value = 0.039

Table S231.  Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
3Q LOSS MUTATED 24 7 18
3Q LOSS WILD-TYPE 90 70 45

Figure S231.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.056

Table S232.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
3Q LOSS MUTATED 27 11 10
3Q LOSS WILD-TYPE 80 39 87

Figure S232.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.057

Table S233.  Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
3Q LOSS MUTATED 22 11 10 5
3Q LOSS WILD-TYPE 57 41 90 18

Figure S233.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.042

Table S234.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
3Q LOSS MUTATED 22 5 10
3Q LOSS WILD-TYPE 61 59 36

Figure S234.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0464 (Fisher's exact test), Q value = 0.11

Table S235.  Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
3Q LOSS MUTATED 5 13 3 2 1 4 4 5
3Q LOSS WILD-TYPE 19 19 34 22 10 18 17 17

Figure S235.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.012

Table S236.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
4Q LOSS MUTATED 21 7 19 4
4Q LOSS WILD-TYPE 49 79 55 22

Figure S236.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.069

Table S237.  Gene #50: '5p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
5P LOSS MUTATED 6 14 1
5P LOSS WILD-TYPE 52 86 59

Figure S237.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.074

Table S238.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
5P LOSS MUTATED 5 3 0 2 4 2 6
5P LOSS WILD-TYPE 41 20 49 44 24 27 27

Figure S238.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'RPPA_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.074

Table S239.  Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
5Q LOSS MUTATED 7 22 4
5Q LOSS WILD-TYPE 51 78 56

Figure S239.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.076

Table S240.  Gene #51: '5q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
5Q LOSS MUTATED 5 4 7 4 11 2
5Q LOSS WILD-TYPE 19 24 32 64 26 20

Figure S240.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 0.1

Table S241.  Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
5Q LOSS MUTATED 8 4 2 3 5 4 9
5Q LOSS WILD-TYPE 38 19 47 43 23 25 24

Figure S241.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.1

Table S242.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
5Q LOSS MUTATED 18 4 12 1
5Q LOSS WILD-TYPE 61 48 88 22

Figure S242.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.073

Table S243.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
6Q LOSS MUTATED 16 11 23 3
6Q LOSS WILD-TYPE 54 75 51 23

Figure S243.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.041

Table S244.  Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
6Q LOSS MUTATED 5 4 17 7 16 2 2
6Q LOSS WILD-TYPE 43 42 44 27 31 13 3

Figure S244.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.098

Table S245.  Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
7P LOSS MUTATED 6 2 14 1 8 1 0
7P LOSS WILD-TYPE 42 44 47 33 39 14 5

Figure S245.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'RPPA_CNMF'

P value = 0.00481 (Fisher's exact test), Q value = 0.022

Table S246.  Gene #54: '7p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
7P LOSS MUTATED 3 10 15
7P LOSS WILD-TYPE 55 90 45

Figure S246.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00976 (Fisher's exact test), Q value = 0.039

Table S247.  Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
7P LOSS MUTATED 14 15 2
7P LOSS WILD-TYPE 100 62 61

Figure S247.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.088

Table S248.  Gene #54: '7p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
7P LOSS MUTATED 6 2 13 2 4 1 3
7P LOSS WILD-TYPE 40 21 36 44 24 28 30

Figure S248.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.065

Table S249.  Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
7P LOSS MUTATED 3 1 8 1 1 7 1 1
7P LOSS WILD-TYPE 21 31 29 23 10 15 20 21

Figure S249.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0025

Table S250.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
8P LOSS MUTATED 25 8 23 6
8P LOSS WILD-TYPE 45 78 51 20

Figure S250.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.019

Table S251.  Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
8P LOSS MUTATED 17 6 8 9 17 2 3
8P LOSS WILD-TYPE 31 40 53 25 30 13 2

Figure S251.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0032

Table S252.  Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
8P LOSS MUTATED 11 1 17 12 11 5
8P LOSS WILD-TYPE 13 27 22 56 26 17

Figure S252.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.051

Table S253.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
8P LOSS MUTATED 28 13 16 3
8P LOSS WILD-TYPE 51 39 84 20

Figure S253.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S254.  Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
8Q LOSS MUTATED 21 3 19 3
8Q LOSS WILD-TYPE 49 83 55 23

Figure S254.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 0.00441 (Fisher's exact test), Q value = 0.02

Table S255.  Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
8Q LOSS MUTATED 17 5 9 1 11 2 1
8Q LOSS WILD-TYPE 31 41 52 33 36 13 4

Figure S255.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00082

Table S256.  Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
8Q LOSS MUTATED 11 1 10 8 10 0
8Q LOSS WILD-TYPE 13 27 29 60 27 22

Figure S256.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S257.  Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
8Q LOSS MUTATED 23 10 13 0
8Q LOSS WILD-TYPE 56 42 87 23

Figure S257.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S258.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
9P LOSS MUTATED 19 16 42 6
9P LOSS WILD-TYPE 51 70 32 20

Figure S258.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S259.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
9Q LOSS MUTATED 13 6 29 3
9Q LOSS WILD-TYPE 57 80 45 23

Figure S259.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

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

Table S260.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
10P LOSS MUTATED 39 31 41 9
10P LOSS WILD-TYPE 31 55 33 17

Figure S260.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0094 (Fisher's exact test), Q value = 0.038

Table S261.  Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
10P LOSS MUTATED 23 6 34 18 11 11 16
10P LOSS WILD-TYPE 23 17 15 28 17 18 17

Figure S261.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S262.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
10Q LOSS MUTATED 54 28 42 7
10Q LOSS WILD-TYPE 16 58 32 19

Figure S262.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S263.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
10Q LOSS MUTATED 24 11 50 7 30 5 4
10Q LOSS WILD-TYPE 24 35 11 27 17 10 1

Figure S263.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S264.  Gene #61: '10q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
10Q LOSS MUTATED 17 48 45
10Q LOSS WILD-TYPE 41 52 15

Figure S264.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0058

Table S265.  Gene #61: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
10Q LOSS MUTATED 13 6 24 44 16 7
10Q LOSS WILD-TYPE 11 22 15 24 21 15

Figure S265.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S266.  Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
10Q LOSS MUTATED 53 59 18
10Q LOSS WILD-TYPE 61 18 45

Figure S266.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S267.  Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
10Q LOSS MUTATED 24 6 44 9 12 15 20
10Q LOSS WILD-TYPE 22 17 5 37 16 14 13

Figure S267.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S268.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
10Q LOSS MUTATED 37 26 68
10Q LOSS WILD-TYPE 70 24 29

Figure S268.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S269.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
10Q LOSS MUTATED 35 23 69 4
10Q LOSS WILD-TYPE 44 29 31 19

Figure S269.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00042

Table S270.  Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
10Q LOSS MUTATED 29 47 26
10Q LOSS WILD-TYPE 54 17 20

Figure S270.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0026

Table S271.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
10Q LOSS MUTATED 12 12 31 14 7 11 10 5
10Q LOSS WILD-TYPE 12 20 6 10 4 11 11 17

Figure S271.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S272.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
11P LOSS MUTATED 36 8 33 17
11P LOSS WILD-TYPE 34 78 41 9

Figure S272.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0017

Table S273.  Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
11P LOSS MUTATED 30 10 24 10 16 1 3
11P LOSS WILD-TYPE 18 36 37 24 31 14 2

Figure S273.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.04

Table S274.  Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
11P LOSS MUTATED 16 7 10 23 18 7
11P LOSS WILD-TYPE 8 21 29 45 19 15

Figure S274.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S275.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
11Q LOSS MUTATED 36 8 29 18
11Q LOSS WILD-TYPE 34 78 45 8

Figure S275.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0028

Table S276.  Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
11Q LOSS MUTATED 30 12 19 10 16 1 3
11Q LOSS WILD-TYPE 18 34 42 24 31 14 2

Figure S276.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00156 (Fisher's exact test), Q value = 0.0096

Table S277.  Gene #63: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
11Q LOSS MUTATED 15 9 10 15 19 10
11Q LOSS WILD-TYPE 9 19 29 53 18 12

Figure S277.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.059

Table S278.  Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
11Q LOSS MUTATED 23 11 16 19 4 6 11
11Q LOSS WILD-TYPE 23 12 33 27 24 23 22

Figure S278.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.04

Table S279.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
11Q LOSS MUTATED 12 20 12 12 2 4 5 8
11Q LOSS WILD-TYPE 12 12 25 12 9 18 16 14

Figure S279.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S280.  Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
12P LOSS MUTATED 31 7 18 9
12P LOSS WILD-TYPE 39 79 56 17

Figure S280.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.00243 (Fisher's exact test), Q value = 0.013

Table S281.  Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
12P LOSS MUTATED 20 6 20 4 14 1 0
12P LOSS WILD-TYPE 28 40 41 30 33 14 5

Figure S281.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.057

Table S282.  Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
12P LOSS MUTATED 36 20 8
12P LOSS WILD-TYPE 78 57 55

Figure S282.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.046

Table S283.  Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
12P LOSS MUTATED 21 5 14 5 5 6 8
12P LOSS WILD-TYPE 25 18 35 41 23 23 25

Figure S283.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00082

Table S284.  Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
12Q LOSS MUTATED 24 5 16 9
12Q LOSS WILD-TYPE 46 81 58 17

Figure S284.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.081

Table S285.  Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
12Q LOSS MUTATED 15 5 19 4 10 1 0
12Q LOSS WILD-TYPE 33 41 42 30 37 14 5

Figure S285.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.099

Table S286.  Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
12Q LOSS MUTATED 16 3 15 4 5 5 6
12Q LOSS WILD-TYPE 30 20 34 42 23 24 27

Figure S286.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S287.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
13Q LOSS MUTATED 39 25 57 11
13Q LOSS WILD-TYPE 31 61 17 15

Figure S287.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0058

Table S288.  Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
13Q LOSS MUTATED 26 20 36 11 34 3 2
13Q LOSS WILD-TYPE 22 26 25 23 13 12 3

Figure S288.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.00991 (Fisher's exact test), Q value = 0.039

Table S289.  Gene #66: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
13Q LOSS MUTATED 21 61 33
13Q LOSS WILD-TYPE 37 39 27

Figure S289.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

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

Table S290.  Gene #66: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
13Q LOSS MUTATED 10 12 28 33 24 8
13Q LOSS WILD-TYPE 14 16 11 35 13 14

Figure S290.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00172 (Fisher's exact test), Q value = 0.01

Table S291.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
13Q LOSS MUTATED 25 9 30 14 21 11 20
13Q LOSS WILD-TYPE 21 14 19 32 7 18 13

Figure S291.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00056

Table S292.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
14Q LOSS MUTATED 17 5 6 8 1 15 10
14Q LOSS WILD-TYPE 29 18 43 38 27 14 23

Figure S292.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.075

Table S293.  Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
15Q LOSS MUTATED 17 7 15 6
15Q LOSS WILD-TYPE 53 79 59 20

Figure S293.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.086

Table S294.  Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
15Q LOSS MUTATED 14 6 5 4 13 3 0
15Q LOSS WILD-TYPE 34 40 56 30 34 12 5

Figure S294.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.068

Table S295.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
15Q LOSS MUTATED 21 14 10
15Q LOSS WILD-TYPE 86 36 87

Figure S295.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.083

Table S296.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
15Q LOSS MUTATED 21 11 11 2
15Q LOSS WILD-TYPE 58 41 89 21

Figure S296.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.075

Table S297.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
15Q LOSS MUTATED 18 6 13
15Q LOSS WILD-TYPE 65 58 33

Figure S297.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0021

Table S298.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
16P LOSS MUTATED 26 12 31 6
16P LOSS WILD-TYPE 44 74 43 20

Figure S298.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00954 (Fisher's exact test), Q value = 0.039

Table S299.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
16P LOSS MUTATED 16 9 17 6 24 2 1
16P LOSS WILD-TYPE 32 37 44 28 23 13 4

Figure S299.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0014

Table S300.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
16Q LOSS MUTATED 44 27 44 9
16Q LOSS WILD-TYPE 26 59 30 17

Figure S300.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0013

Table S301.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
16Q LOSS MUTATED 24 13 43 10 27 5 2
16Q LOSS WILD-TYPE 24 33 18 24 20 10 3

Figure S301.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0035

Table S302.  Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
16Q LOSS MUTATED 17 49 39
16Q LOSS WILD-TYPE 41 51 21

Figure S302.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.06

Table S303.  Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
16Q LOSS MUTATED 11 6 23 39 18 8
16Q LOSS WILD-TYPE 13 22 16 29 19 14

Figure S303.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0052

Table S304.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
16Q LOSS MUTATED 52 50 21
16Q LOSS WILD-TYPE 62 27 42

Figure S304.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.002

Table S305.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
16Q LOSS MUTATED 25 6 34 11 14 16 17
16Q LOSS WILD-TYPE 21 17 15 35 14 13 16

Figure S305.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.00987 (Fisher's exact test), Q value = 0.039

Table S306.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
16Q LOSS MUTATED 41 24 58
16Q LOSS WILD-TYPE 66 26 39

Figure S306.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S307.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
16Q LOSS MUTATED 37 20 59 7
16Q LOSS WILD-TYPE 42 32 41 16

Figure S307.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0017

Table S308.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 64 46
16Q LOSS MUTATED 29 44 26
16Q LOSS WILD-TYPE 54 20 20

Figure S308.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0051

Table S309.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
16Q LOSS MUTATED 13 10 30 11 7 10 12 6
16Q LOSS WILD-TYPE 11 22 7 13 4 12 9 16

Figure S309.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.041

Table S310.  Gene #71: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
17P LOSS MUTATED 5 3 17 13 4 6
17P LOSS WILD-TYPE 19 25 22 55 33 16

Figure S310.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.013

Table S311.  Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
17Q LOSS MUTATED 15 6 21 6
17Q LOSS WILD-TYPE 55 80 53 20

Figure S311.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.063

Table S312.  Gene #72: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
17Q LOSS MUTATED 4 2 15 13 4 6
17Q LOSS WILD-TYPE 20 26 24 55 33 16

Figure S312.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.05

Table S313.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
18P LOSS MUTATED 19 11 24 8
18P LOSS WILD-TYPE 51 75 50 18

Figure S313.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.066

Table S314.  Gene #73: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
18P LOSS MUTATED 4 4 18 14 8 8
18P LOSS WILD-TYPE 20 24 21 54 29 14

Figure S314.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0021

Table S315.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
18Q LOSS MUTATED 23 10 30 9
18Q LOSS WILD-TYPE 47 76 44 17

Figure S315.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.028

Table S316.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
18Q LOSS MUTATED 13 11 13 7 25 2 1
18Q LOSS WILD-TYPE 35 35 48 27 22 13 4

Figure S316.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.063

Table S317.  Gene #74: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
18Q LOSS MUTATED 14 38 11
18Q LOSS WILD-TYPE 44 62 49

Figure S317.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0035

Table S318.  Gene #74: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
18Q LOSS MUTATED 5 7 21 9 12 9
18Q LOSS WILD-TYPE 19 21 18 59 25 13

Figure S318.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.074

Table S319.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
18Q LOSS MUTATED 12 6 11 11 15 4 13
18Q LOSS WILD-TYPE 34 17 38 35 13 25 20

Figure S319.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.044

Table S320.  Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
18Q LOSS MUTATED 3 9 9 11 1 12 10 6
18Q LOSS WILD-TYPE 21 23 28 13 10 10 11 16

Figure S320.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.083

Table S321.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
19P LOSS MUTATED 10 2 6 3
19P LOSS WILD-TYPE 60 84 68 23

Figure S321.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.011

Table S322.  Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
19P LOSS MUTATED 1 1 3 3 12 1 0
19P LOSS WILD-TYPE 47 45 58 31 35 14 5

Figure S322.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.085

Table S323.  Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
19P LOSS MUTATED 1 1 1 4 5 3 6
19P LOSS WILD-TYPE 45 22 48 42 23 26 27

Figure S323.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.078

Table S324.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
19P LOSS MUTATED 0 1 1 4 2 5 3 2
19P LOSS WILD-TYPE 24 31 36 20 9 17 18 20

Figure S324.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.1

Table S325.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
19Q LOSS MUTATED 12 6 16 5
19Q LOSS WILD-TYPE 58 80 58 21

Figure S325.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.11

Table S326.  Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
19Q LOSS MUTATED 4 3 10 5 14 3 0
19Q LOSS WILD-TYPE 44 43 51 29 33 12 5

Figure S326.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'CN_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.1

Table S327.  Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
20P LOSS MUTATED 23 12 15 5
20P LOSS WILD-TYPE 47 74 59 21

Figure S327.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.016

Table S328.  Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
20P LOSS MUTATED 12 10 17 0 14 1 1
20P LOSS WILD-TYPE 36 36 44 34 33 14 4

Figure S328.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.097

Table S329.  Gene #77: '20p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
20P LOSS MUTATED 8 5 14 12 4 2
20P LOSS WILD-TYPE 16 23 25 56 33 20

Figure S329.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.1

Table S330.  Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
20P LOSS MUTATED 31 16 7
20P LOSS WILD-TYPE 83 61 56

Figure S330.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.043

Table S331.  Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
20P LOSS MUTATED 23 10 21 0
20P LOSS WILD-TYPE 56 42 79 23

Figure S331.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 0.075

Table S332.  Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
20P LOSS MUTATED 8 5 10 6 1 6 8 0
20P LOSS WILD-TYPE 16 27 27 18 10 16 13 22

Figure S332.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.00249 (Fisher's exact test), Q value = 0.013

Table S333.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
21Q LOSS MUTATED 12 8 24 6
21Q LOSS WILD-TYPE 58 78 50 20

Figure S333.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.069

Table S334.  Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
21Q LOSS MUTATED 13 7 10 2 16 1 1
21Q LOSS WILD-TYPE 35 39 51 32 31 14 4

Figure S334.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00516 (Fisher's exact test), Q value = 0.023

Table S335.  Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
21Q LOSS MUTATED 3 5 16 8 11 2
21Q LOSS WILD-TYPE 21 23 23 60 26 20

Figure S335.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S336.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
22Q LOSS MUTATED 30 7 20 9
22Q LOSS WILD-TYPE 40 79 54 17

Figure S336.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.1

Table S337.  Gene #80: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
22Q LOSS MUTATED 13 5 9 15 9 8
22Q LOSS WILD-TYPE 11 23 30 53 28 14

Figure S337.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0451 (Fisher's exact test), Q value = 0.11

Table S338.  Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
22Q LOSS MUTATED 16 3 9 14 3 12 8
22Q LOSS WILD-TYPE 30 20 40 32 25 17 25

Figure S338.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0086

Table S339.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
XP LOSS MUTATED 13 2 24 6 11 5 1
XP LOSS WILD-TYPE 35 44 37 28 36 10 4

Figure S339.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.008

Table S340.  Gene #81: 'xp loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
XP LOSS MUTATED 9 18 25
XP LOSS WILD-TYPE 49 82 35

Figure S340.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

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

Table S341.  Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
XP LOSS MUTATED 22 30 9
XP LOSS WILD-TYPE 92 47 54

Figure S341.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00717 (Fisher's exact test), Q value = 0.031

Table S342.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
XP LOSS MUTATED 11 1 17 7 5 13 7
XP LOSS WILD-TYPE 35 22 32 39 23 16 26

Figure S342.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.069

Table S343.  Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
XP LOSS MUTATED 22 7 32
XP LOSS WILD-TYPE 85 43 65

Figure S343.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.11

Table S344.  Gene #81: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
XP LOSS MUTATED 16 7 33 5
XP LOSS WILD-TYPE 63 45 67 18

Figure S344.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0048

Table S345.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 86 74 26
XQ LOSS MUTATED 40 21 29 11
XQ LOSS WILD-TYPE 30 65 45 15

Figure S345.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

Table S346.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 48 46 61 34 47 15 5
XQ LOSS MUTATED 23 6 39 9 17 6 1
XQ LOSS WILD-TYPE 25 40 22 25 30 9 4

Figure S346.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0011

Table S347.  Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 100 60
XQ LOSS MUTATED 16 31 37
XQ LOSS WILD-TYPE 42 69 23

Figure S347.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00325 (Fisher's exact test), Q value = 0.016

Table S348.  Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 24 28 39 68 37 22
XQ LOSS MUTATED 8 4 14 37 16 5
XQ LOSS WILD-TYPE 16 24 25 31 21 17

Figure S348.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00056

Table S349.  Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 77 63
XQ LOSS MUTATED 36 47 17
XQ LOSS WILD-TYPE 78 30 46

Figure S349.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0025

Table S350.  Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 46 23 49 46 28 29 33
XQ LOSS MUTATED 20 4 30 14 4 16 12
XQ LOSS WILD-TYPE 26 19 19 32 24 13 21

Figure S350.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0095

Table S351.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 107 50 97
XQ LOSS MUTATED 33 15 52
XQ LOSS WILD-TYPE 74 35 45

Figure S351.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.017

Table S352.  Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 52 100 23
XQ LOSS MUTATED 27 14 53 6
XQ LOSS WILD-TYPE 52 38 47 17

Figure S352.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.069

Table S353.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 32 37 24 11 22 21 22
XQ LOSS MUTATED 12 15 20 7 6 4 5 5
XQ LOSS WILD-TYPE 12 17 17 17 5 18 16 17

Figure S353.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/15098587/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/15111074/SARC-TP.transferedmergedcluster.txt

  • Number of patients = 256

  • 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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