Correlation between copy number variations of arm-level result and molecular subtypes
Liver Hepatocellular Carcinoma (Primary solid tumor)
14 July 2016  |  awg_lihc__2016_07_14
Maintainer Information
Citation Information
doi:10.7908/C1M044ZC
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1M044ZC
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 370 patients, 297 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'RPPA_CNMF'.

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

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

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

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

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

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

  • 4q gain cnv correlated to 'RPPA_CNMF'.

  • 5p gain cnv correlated to 'CN_CNMF'.

  • 5q gain cnv correlated to 'CN_CNMF'.

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

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

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

  • 7q gain cnv correlated to 'METHLYATION_CNMF'.

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

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

  • 9p gain cnv correlated to 'RPPA_CNMF'.

  • 9q gain cnv correlated to 'RPPA_CNMF'.

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

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

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

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

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

  • 13q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 16q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

  • 21q gain cnv correlated to 'RPPA_CNMF'.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • 8p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

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

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

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

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

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

  • 12q loss cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

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

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

  • 19q loss cnv correlated to 'CN_CNMF'.

  • 20q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

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

  • xp loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 297 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
16p loss 108 (29%) 262 1e-05
(0.000205) 		6e-05
(0.000946) 		0.00287
(0.0176) 		0.00281
(0.0175) 		1e-05
(0.000205) 		1e-05
(0.000205) 		1e-05
(0.000205) 		1e-05
(0.000205) 		1e-05
(0.000205) 		1e-05
(0.000205)
16q loss 145 (39%) 225 1e-05
(0.000205) 		1e-05
(0.000205) 		0.00048
(0.00474) 		0.00017
(0.00211) 		1e-05
(0.000205) 		1e-05
(0.000205) 		1e-05
(0.000205) 		1e-05
(0.000205) 		1e-05
(0.000205) 		1e-05
(0.000205)
1p loss 78 (21%) 292 1e-05
(0.000205) 		1e-05
(0.000205) 		0.0286
(0.09) 		0.0783
(0.191) 		1e-05
(0.000205) 		1e-05
(0.000205) 		0.00013
(0.00172) 		0.02
(0.0702) 		0.00087
(0.00721) 		0.0167
(0.062)
4q loss 146 (39%) 224 1e-05
(0.000205) 		0.00624
(0.0299) 		0.00371
(0.0208) 		0.204
(0.358) 		1e-05
(0.000205) 		0.00076
(0.00649) 		0.00241
(0.0156) 		0.005
(0.0258) 		6e-05
(0.000946) 		0.00243
(0.0156)
10q loss 78 (21%) 292 1e-05
(0.000205) 		0.0445
(0.125) 		0.00475
(0.0251) 		0.042
(0.119) 		1e-05
(0.000205) 		6e-05
(0.000946) 		0.00313
(0.0188) 		0.00016
(0.00205) 		0.0798
(0.192) 		1e-05
(0.000205)
13q loss 122 (33%) 248 1e-05
(0.000205) 		0.0386
(0.114) 		0.359
(0.507) 		0.0222
(0.0749) 		0.00201
(0.0137) 		0.00053
(0.00505) 		0.00321
(0.0188) 		0.00411
(0.0226) 		0.00061
(0.00538) 		0.00066
(0.00576)
xq gain 60 (16%) 310 0.0123
(0.0497) 		0.0108
(0.0456) 		0.285
(0.442) 		0.217
(0.373) 		0.00097
(0.00788) 		0.00413
(0.0226) 		0.00083
(0.00694) 		0.00011
(0.00153) 		0.00542
(0.0274) 		6e-05
(0.000946)
15q loss 67 (18%) 303 0.00059
(0.00532) 		0.158
(0.307) 		0.00621
(0.0299) 		0.00165
(0.0119) 		0.00014
(0.00182) 		8e-05
(0.00119) 		0.0316
(0.098) 		0.25
(0.407) 		0.00145
(0.0109) 		0.0208
(0.0716)
6p gain 116 (31%) 254 2e-05
(0.000381) 		0.00578
(0.0284) 		0.00025
(0.00293) 		0.147
(0.295) 		0.00123
(0.0097) 		0.0224
(0.0754) 		0.00967
(0.0426) 		0.00424
(0.023) 		0.61
(0.728) 		0.226
(0.385)
19q gain 71 (19%) 299 0.154
(0.303) 		0.00233
(0.0153) 		0.464
(0.611) 		0.0502
(0.138) 		0.00067
(0.00578) 		5e-05
(0.000872) 		0.0221
(0.0748) 		0.00125
(0.00976) 		6e-05
(0.000946) 		0.00036
(0.00383)
4p loss 105 (28%) 265 1e-05
(0.000205) 		0.071
(0.177) 		0.00099
(0.00796) 		0.0604
(0.156) 		0.00058
(0.00532) 		0.0196
(0.0694) 		0.132
(0.274) 		0.0162
(0.0608) 		0.0177
(0.0644) 		0.00045
(0.00456)
9p loss 119 (32%) 251 1e-05
(0.000205) 		0.041
(0.118) 		0.171
(0.325) 		0.638
(0.752) 		0.00017
(0.00211) 		0.00637
(0.0304) 		0.0094
(0.0417) 		0.00834
(0.0376) 		0.0987
(0.223) 		0.00812
(0.0368)
9q loss 110 (30%) 260 1e-05
(0.000205) 		0.00987
(0.043) 		0.362
(0.51) 		0.793
(0.862) 		0.00205
(0.0138) 		0.00145
(0.0109) 		0.0278
(0.088) 		0.00855
(0.0383) 		0.26
(0.418) 		0.0004
(0.00421)
17p loss 185 (50%) 185 1e-05
(0.000205) 		0.0825
(0.195) 		0.131
(0.272) 		0.034
(0.104) 		0.00187
(0.013) 		0.0229
(0.0762) 		0.00202
(0.0137) 		0.00029
(0.00321) 		0.28
(0.441) 		0.0005
(0.00482)
18p gain 36 (10%) 334 0.00156
(0.0114) 		0.55
(0.688) 		0.119
(0.255) 		0.0409
(0.118) 		0.0215
(0.0735) 		0.018
(0.0649) 		0.0341
(0.104) 		0.196
(0.352) 		0.012
(0.0491) 		0.476
(0.621)
19p gain 56 (15%) 314 0.244
(0.404) 		0.00981
(0.043) 		0.648
(0.76) 		0.113
(0.248) 		0.00353
(0.0202) 		0.0102
(0.044) 		0.0391
(0.115) 		0.00676
(0.0315) 		0.00267
(0.0167) 		0.0607
(0.156)
20p gain 107 (29%) 263 1e-05
(0.000205) 		0.29
(0.449) 		0.0879
(0.207) 		0.00373
(0.0208) 		0.0142
(0.0555) 		0.00138
(0.0106) 		0.163
(0.313) 		0.0445
(0.125) 		0.00027
(0.00303) 		0.0518
(0.14)
22q gain 48 (13%) 322 0.00026
(0.003) 		0.144
(0.291) 		0.00386
(0.0214) 		0.00562
(0.0279) 		0.0386
(0.114) 		0.00201
(0.0137) 		0.122
(0.259) 		0.736
(0.82) 		0.0118
(0.0485) 		0.0688
(0.174)
5q loss 37 (10%) 333 0.0125
(0.0501) 		0.0145
(0.0563) 		0.185
(0.34) 		0.0742
(0.183) 		0.0571
(0.15) 		0.00047
(0.0047) 		0.00436
(0.0234) 		0.06
(0.155) 		7e-05
(0.00106) 		0.00061
(0.00538)
10p loss 47 (13%) 323 0.00012
(0.00164) 		0.413
(0.562) 		0.436
(0.587) 		0.386
(0.539) 		0.00327
(0.019) 		0.00432
(0.0233) 		0.0103
(0.0441) 		0.0137
(0.0539) 		0.121
(0.257) 		0.0148
(0.0574)
14q loss 109 (29%) 261 1e-05
(0.000205) 		0.163
(0.313) 		0.00579
(0.0284) 		0.074
(0.183) 		0.0001
(0.00141) 		1e-05
(0.000205) 		0.0557
(0.148) 		0.157
(0.307) 		0.00019
(0.00233) 		0.00489
(0.0255)
1q gain 226 (61%) 144 1e-05
(0.000205) 		9e-05
(0.00132) 		0.348
(0.498) 		0.271
(0.431) 		3e-05
(0.000559) 		0.00157
(0.0114) 		0.555
(0.693) 		0.021
(0.0721) 		0.714
(0.805) 		0.108
(0.239)
8q gain 184 (50%) 186 2e-05
(0.000381) 		0.272
(0.431) 		0.119
(0.255) 		0.242
(0.403) 		1e-05
(0.000205) 		1e-05
(0.000205) 		0.446
(0.597) 		0.00692
(0.0321) 		0.463
(0.61) 		0.00187
(0.013)
12p gain 40 (11%) 330 0.609
(0.728) 		0.283
(0.442) 		0.0794
(0.192) 		0.00491
(0.0255) 		0.00517
(0.0265) 		0.00056
(0.00522) 		0.0562
(0.149) 		0.342
(0.493) 		0.0001
(0.00141) 		0.0266
(0.0852)
20q gain 112 (30%) 258 1e-05
(0.000205) 		0.276
(0.435) 		0.221
(0.379) 		0.0116
(0.0482) 		0.118
(0.255) 		0.0106
(0.0451) 		0.298
(0.453) 		0.0392
(0.115) 		0.00042
(0.0043) 		0.137
(0.282)
3p loss 52 (14%) 318 0.102
(0.23) 		0.0677
(0.172) 		0.565
(0.699) 		0.206
(0.359) 		0.00365
(0.0206) 		0.0102
(0.044) 		0.00356
(0.0203) 		0.318
(0.467) 		0.00461
(0.0245) 		0.042
(0.119)
5p loss 29 (8%) 341 0.0159
(0.0604) 		0.148
(0.296) 		0.763
(0.839) 		0.294
(0.45) 		0.139
(0.284) 		0.0242
(0.079) 		0.0125
(0.0501) 		0.113
(0.248) 		0.0102
(0.044) 		0.0154
(0.0591)
3p gain 35 (9%) 335 0.0182
(0.0654) 		0.0266
(0.0852) 		0.234
(0.395) 		0.318
(0.467) 		0.0018
(0.0127) 		0.0889
(0.208) 		0.0347
(0.105) 		0.518
(0.656) 		0.0688
(0.174) 		0.309
(0.46)
4p gain 27 (7%) 343 0.434
(0.586) 		0.00647
(0.0304) 		0.00237
(0.0154) 		0.131
(0.272) 		0.0136
(0.0538) 		0.0018
(0.0127) 		0.253
(0.41) 		0.441
(0.592) 		0.0887
(0.208) 		0.163
(0.313)
10p gain 58 (16%) 312 0.00316
(0.0188) 		0.605
(0.724) 		0.195
(0.352) 		0.145
(0.291) 		0.00759
(0.0348) 		0.0207
(0.0716) 		0.142
(0.288) 		0.474
(0.62) 		0.0527
(0.141) 		0.0109
(0.0459)
12q gain 47 (13%) 323 0.198
(0.355) 		0.72
(0.808) 		0.198
(0.355) 		0.0339
(0.104) 		0.00925
(0.0412) 		0.0025
(0.0159) 		0.0994
(0.224) 		0.623
(0.738) 		0.00025
(0.00293) 		0.0577
(0.151)
18q gain 28 (8%) 342 0.0459
(0.128) 		0.85
(0.905) 		0.284
(0.442) 		0.065
(0.166) 		0.0517
(0.14) 		0.00316
(0.0188) 		0.0177
(0.0644) 		0.0533
(0.142) 		0.00329
(0.019) 		0.303
(0.457)
7q loss 21 (6%) 349 0.157
(0.307) 		0.285
(0.442) 		0.0589
(0.153) 		0.257
(0.416) 		0.019
(0.068) 		0.0853
(0.201) 		0.674
(0.774) 		0.0341
(0.104) 		0.00013
(0.00172) 		0.0073
(0.0336)
11p loss 63 (17%) 307 0.0111
(0.0463) 		0.864
(0.913) 		0.635
(0.749) 		0.454
(0.604) 		0.0567
(0.149) 		0.0111
(0.0463) 		0.0965
(0.22) 		0.158
(0.307) 		0.0151
(0.0582) 		0.0161
(0.0608)
2q gain 40 (11%) 330 0.0471
(0.131) 		0.482
(0.625) 		0.942
(0.956) 		0.124
(0.259) 		0.0142
(0.0555) 		0.00049
(0.00478) 		0.0684
(0.174) 		0.899
(0.934) 		0.0811
(0.194) 		0.345
(0.495)
3q gain 38 (10%) 332 0.0126
(0.0503) 		0.256
(0.414) 		0.515
(0.656) 		0.588
(0.716) 		0.00302
(0.0183) 		0.0924
(0.214) 		0.0312
(0.0973) 		0.512
(0.655) 		0.0601
(0.155) 		0.715
(0.805)
6q gain 67 (18%) 303 0.00027
(0.00303) 		0.158
(0.307) 		0.00233
(0.0153) 		0.722
(0.808) 		0.0348
(0.105) 		0.293
(0.449) 		0.241
(0.401) 		0.24
(0.401) 		0.65
(0.76) 		0.578
(0.708)
7p gain 109 (29%) 261 0.00122
(0.0097) 		0.0236
(0.0782) 		0.569
(0.7) 		0.92
(0.942) 		0.793
(0.862) 		0.891
(0.933) 		0.0366
(0.11) 		0.104
(0.232) 		0.64
(0.753) 		0.453
(0.604)
8p gain 73 (20%) 297 0.402
(0.553) 		0.405
(0.555) 		0.0643
(0.165) 		0.153
(0.302) 		0.00259
(0.0163) 		0.0171
(0.063) 		0.274
(0.434) 		0.373
(0.523) 		0.886
(0.93) 		0.0272
(0.0867)
10q gain 36 (10%) 334 0.00031
(0.00334) 		0.0298
(0.0933) 		0.176
(0.331) 		0.151
(0.299) 		5e-05
(0.000872) 		0.119
(0.255) 		0.191
(0.349) 		0.0788
(0.191) 		0.216
(0.372) 		0.0816
(0.194)
17q gain 93 (25%) 277 0.00649
(0.0304) 		0.341
(0.493) 		0.14
(0.284) 		0.2
(0.355) 		0.304
(0.457) 		0.0949
(0.219) 		0.0775
(0.19) 		0.00077
(0.00651) 		0.808
(0.873) 		0.0164
(0.0613)
xp gain 41 (11%) 329 0.0253
(0.0824) 		0.123
(0.259) 		0.202
(0.356) 		0.65
(0.76) 		0.024
(0.0787) 		0.376
(0.528) 		0.151
(0.299) 		0.0513
(0.14) 		0.845
(0.902) 		0.0392
(0.115)
2p loss 33 (9%) 337 0.00587
(0.0287) 		0.394
(0.544) 		0.667
(0.773) 		0.149
(0.297) 		0.00544
(0.0274) 		0.0403
(0.117) 		0.255
(0.414) 		0.707
(0.801) 		0.39
(0.543) 		0.265
(0.422)
2q loss 38 (10%) 332 0.00127
(0.00982) 		0.388
(0.54) 		0.799
(0.867) 		0.357
(0.506) 		0.00097
(0.00788) 		0.0201
(0.0702) 		0.581
(0.71) 		0.592
(0.719) 		0.902
(0.934) 		0.407
(0.555)
3q loss 41 (11%) 329 0.0899
(0.209) 		0.344
(0.494) 		0.518
(0.656) 		0.689
(0.784) 		0.00548
(0.0274) 		0.0528
(0.141) 		0.042
(0.119) 		0.47
(0.618) 		0.00785
(0.0358) 		0.235
(0.395)
7p loss 16 (4%) 354 0.401
(0.552) 		0.309
(0.459) 		0.00151
(0.0113) 		0.822
(0.884) 		0.119
(0.255) 		0.352
(0.501) 		0.863
(0.913) 		0.226
(0.385) 		0.0199
(0.07) 		0.0417
(0.119)
11q loss 72 (19%) 298 0.0398
(0.116) 		0.804
(0.87) 		0.934
(0.95) 		0.549
(0.688) 		0.194
(0.351) 		0.177
(0.331) 		0.433
(0.586) 		0.212
(0.368) 		0.0122
(0.0495) 		0.0499
(0.138)
18p loss 74 (20%) 296 0.0263
(0.085) 		0.00233
(0.0153) 		0.895
(0.933) 		0.907
(0.934) 		0.565
(0.699) 		0.00318
(0.0188) 		0.901
(0.934) 		0.71
(0.802) 		0.213
(0.369) 		0.292
(0.449)
18q loss 79 (21%) 291 0.0156
(0.0595) 		0.00154
(0.0114) 		0.929
(0.949) 		0.576
(0.706) 		0.517
(0.656) 		0.00042
(0.0043) 		0.758
(0.835) 		0.405
(0.555) 		0.286
(0.442) 		0.284
(0.442)
21q loss 110 (30%) 260 0.0165
(0.0614) 		0.595
(0.72) 		0.448
(0.599) 		0.352
(0.501) 		0.00031
(0.00334) 		0.123
(0.259) 		0.454
(0.604) 		0.931
(0.949) 		0.0118
(0.0485) 		0.114
(0.249)
22q loss 70 (19%) 300 0.0048
(0.0252) 		0.174
(0.329) 		0.00644
(0.0304) 		0.996
(1.00) 		0.00286
(0.0176) 		0.159
(0.308) 		0.83
(0.891) 		0.461
(0.608) 		0.568
(0.7) 		0.989
(0.997)
xp loss 95 (26%) 275 0.286
(0.442) 		0.0208
(0.0716) 		0.671
(0.774) 		0.235
(0.395) 		0.125
(0.262) 		0.024
(0.0787) 		0.0708
(0.177) 		0.318
(0.467) 		0.0229
(0.0762) 		0.199
(0.355)
2p gain 43 (12%) 327 0.136
(0.281) 		0.249
(0.407) 		0.951
(0.964) 		0.0281
(0.0887) 		0.146
(0.293) 		0.00024
(0.00289) 		0.0957
(0.22) 		0.968
(0.978) 		0.119
(0.255) 		0.302
(0.457)
11p gain 18 (5%) 352 0.439
(0.59) 		0.306
(0.457) 		0.0216
(0.0735) 		0.492
(0.633) 		0.2
(0.356) 		0.0229
(0.0762) 		0.613
(0.728) 		0.485
(0.628) 		0.058
(0.151) 		0.227
(0.385)
1q loss 20 (5%) 350 0.0325
(0.101) 		0.673
(0.774) 		0.227
(0.385) 		0.276
(0.435) 		0.292
(0.449) 		0.482
(0.625) 		0.25
(0.407) 		0.112
(0.248) 		0.519
(0.656) 		0.0195
(0.0694)
8p loss 196 (53%) 174 1e-05
(0.000205) 		0.182
(0.339) 		0.905
(0.934) 		0.782
(0.853) 		0.0338
(0.104) 		0.772
(0.847) 		0.774
(0.847) 		0.258
(0.416) 		0.305
(0.457) 		0.741
(0.823)
12p loss 66 (18%) 304 4e-05
(0.000729) 		0.359
(0.507) 		0.815
(0.878) 		0.816
(0.878) 		0.0178
(0.0647) 		0.306
(0.457) 		0.352
(0.501) 		0.121
(0.257) 		0.178
(0.331) 		0.213
(0.368)
19p loss 52 (14%) 318 1e-05
(0.000205) 		0.858
(0.91) 		0.887
(0.93) 		0.248
(0.407) 		0.0692
(0.174) 		0.247
(0.407) 		0.0805
(0.193) 		0.148
(0.296) 		0.319
(0.467) 		0.0173
(0.0637)
xq loss 74 (20%) 296 0.0476
(0.132) 		0.0443
(0.125) 		0.721
(0.808) 		0.515
(0.656) 		0.205
(0.358) 		0.185
(0.34) 		0.357
(0.506) 		0.569
(0.7) 		0.614
(0.728) 		0.53
(0.67)
1p gain 62 (17%) 308 0.0561
(0.149) 		0.238
(0.4) 		0.0197
(0.0697) 		0.203
(0.356) 		0.167
(0.319) 		0.657
(0.767) 		0.35
(0.499) 		0.106
(0.236) 		0.194
(0.351) 		0.0823
(0.195)
4q gain 7 (2%) 363 0.305
(0.457) 		0.708
(0.801) 		7e-05
(0.00106) 		0.312
(0.46) 		0.727
(0.812) 		0.407
(0.555) 		0.194
(0.351) 		0.848
(0.905) 		0.295
(0.451) 		0.597
(0.72)
5p gain 134 (36%) 236 1e-05
(0.000205) 		0.248
(0.407) 		0.17
(0.323) 		0.0777
(0.19) 		0.907
(0.934) 		0.75
(0.829) 		0.63
(0.745) 		0.144
(0.291) 		0.0971
(0.221) 		0.556
(0.693)
5q gain 110 (30%) 260 1e-05
(0.000205) 		0.0805
(0.193) 		0.7
(0.795) 		0.181
(0.336) 		0.743
(0.824) 		0.907
(0.934) 		0.561
(0.698) 		0.901
(0.934) 		0.787
(0.857) 		0.892
(0.933)
7q gain 110 (30%) 260 0.204
(0.358) 		0.00059
(0.00532) 		0.333
(0.484) 		0.959
(0.97) 		0.535
(0.675) 		0.842
(0.901) 		0.247
(0.407) 		0.236
(0.396) 		0.677
(0.774) 		0.441
(0.592)
9p gain 19 (5%) 351 0.31
(0.46) 		0.69
(0.784) 		0.00054
(0.00509) 		0.0747
(0.184) 		0.75
(0.829) 		0.667
(0.773) 		0.6
(0.721) 		0.4
(0.552) 		0.124
(0.259) 		0.322
(0.471)
9q gain 19 (5%) 351 0.604
(0.724) 		0.689
(0.784) 		0.00533
(0.0271) 		0.0759
(0.186) 		0.6
(0.721) 		0.658
(0.767) 		0.737
(0.82) 		0.399
(0.55) 		0.59
(0.717) 		0.435
(0.587)
13q gain 23 (6%) 347 0.0363
(0.109) 		0.474
(0.62) 		0.543
(0.682) 		0.488
(0.63) 		0.17
(0.323) 		0.41
(0.558) 		0.051
(0.14) 		0.294
(0.45) 		0.167
(0.319) 		0.244
(0.404)
16p gain 32 (9%) 338 0.175
(0.329) 		0.918
(0.94) 		0.596
(0.72) 		0.569
(0.7) 		0.0452
(0.126) 		0.996
(1.00) 		0.209
(0.364) 		0.185
(0.34) 		0.115
(0.25) 		0.217
(0.374)
16q gain 17 (5%) 353 0.121
(0.257) 		0.0699
(0.175) 		1
(1.00) 		0.595
(0.72) 		0.00594
(0.0288) 		0.312
(0.46) 		0.935
(0.951) 		0.913
(0.938) 		0.192
(0.349) 		0.716
(0.806)
17p gain 30 (8%) 340 0.0369
(0.11) 		0.384
(0.538) 		0.498
(0.638) 		0.874
(0.921) 		0.457
(0.604) 		0.0987
(0.223) 		0.272
(0.432) 		0.756
(0.835) 		0.177
(0.331) 		0.327
(0.476)
21q gain 26 (7%) 344 0.187
(0.342) 		0.934
(0.95) 		0.0273
(0.0867) 		0.595
(0.72) 		0.0911
(0.212) 		0.387
(0.54) 		0.925
(0.946) 		0.224
(0.383) 		0.306
(0.457) 		0.489
(0.63)
12q loss 36 (10%) 334 0.026
(0.0842) 		0.901
(0.934) 		0.456
(0.604) 		0.816
(0.878) 		0.302
(0.457) 		0.66
(0.769) 		0.598
(0.72) 		0.914
(0.939) 		0.802
(0.868) 		0.881
(0.927)
19q loss 39 (11%) 331 2e-05
(0.000381) 		0.325
(0.475) 		0.536
(0.676) 		0.153
(0.302) 		0.156
(0.306) 		0.906
(0.934) 		0.114
(0.25) 		0.0965
(0.22) 		0.239
(0.4) 		0.135
(0.279)
20q loss 13 (4%) 357 1
(1.00) 		0.259
(0.417) 		1
(1.00) 		1
(1.00) 		0.202
(0.356) 		0.113
(0.248) 		0.553
(0.691) 		0.641
(0.753) 		0.0406
(0.118) 		0.296
(0.451)
11q gain 20 (5%) 350 0.342
(0.494) 		0.669
(0.773) 		0.107
(0.239) 		0.863
(0.913) 		0.476
(0.621) 		0.0928
(0.214) 		0.781
(0.853) 		0.612
(0.728) 		0.0521
(0.141) 		0.25
(0.407)
14q gain 22 (6%) 348 0.186
(0.341) 		0.498
(0.638) 		0.0976
(0.222) 		0.773
(0.847) 		0.363
(0.51) 		0.136
(0.279) 		0.563
(0.699) 		0.176
(0.331) 		0.138
(0.283) 		0.734
(0.818)
15q gain 33 (9%) 337 0.183
(0.339) 		0.584
(0.713) 		0.302
(0.457) 		0.194
(0.351) 		0.901
(0.934) 		0.718
(0.807) 		0.953
(0.965) 		0.286
(0.442) 		0.542
(0.681) 		0.843
(0.901)
6p loss 31 (8%) 339 0.748
(0.828) 		0.489
(0.63) 		0.574
(0.704) 		0.759
(0.835) 		0.391
(0.543) 		0.484
(0.627) 		0.0729
(0.181) 		0.851
(0.905) 		0.343
(0.494) 		0.392
(0.543)
6q loss 94 (25%) 276 0.202
(0.356) 		0.163
(0.313) 		0.895
(0.933) 		0.866
(0.914) 		0.429
(0.581) 		0.837
(0.897) 		0.125
(0.262) 		0.262
(0.418) 		0.664
(0.772) 		0.996
(1.00)
8q loss 45 (12%) 325 0.2
(0.355) 		0.224
(0.383) 		0.564
(0.699) 		0.675
(0.774) 		0.0855
(0.201) 		0.63
(0.745) 		0.707
(0.801) 		0.883
(0.928) 		0.775
(0.848) 		0.672
(0.774)
17q loss 40 (11%) 330 0.0515
(0.14) 		0.457
(0.604) 		0.306
(0.457) 		0.48
(0.625) 		0.515
(0.656) 		0.25
(0.407) 		0.678
(0.775) 		0.612
(0.728) 		0.473
(0.62) 		0.341
(0.493)
20p loss 26 (7%) 344 0.421
(0.572) 		0.337
(0.489) 		0.677
(0.774) 		0.667
(0.773) 		0.275
(0.434) 		0.105
(0.236) 		0.262
(0.418) 		0.855
(0.908) 		0.677
(0.774) 		0.312
(0.46)
'1p gain' versus 'RPPA_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.07

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
1P GAIN MUTATED 11 6 2 6 7 0
1P GAIN WILD-TYPE 30 67 17 16 15 1

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

'1q gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
1Q GAIN MUTATED 37 87 102
1Q GAIN WILD-TYPE 56 64 24

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

'1q gain' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
1Q GAIN MUTATED 41 99 86
1Q GAIN WILD-TYPE 52 62 30

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

'1q gain' versus 'MRNASEQ_CNMF'

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

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
1Q GAIN MUTATED 39 37 58 41 46
1Q GAIN WILD-TYPE 28 49 13 30 23

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.011

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
1Q GAIN MUTATED 28 35 56 63 39
1Q GAIN WILD-TYPE 26 21 58 21 17

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.072

Table S6.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
1Q GAIN MUTATED 27 46 40 74 35
1Q GAIN WILD-TYPE 17 49 16 48 13

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.089

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

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

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0029

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
2P GAIN MUTATED 13 2 6 16 4
2P GAIN WILD-TYPE 41 54 108 68 52

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 0.13

Table S9.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
2Q GAIN MUTATED 5 15 20
2Q GAIN WILD-TYPE 88 136 106

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.056

Table S10.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
2Q GAIN MUTATED 7 2 13 8 8
2Q GAIN WILD-TYPE 60 84 58 63 61

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0048

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
2Q GAIN MUTATED 10 2 4 16 6
2Q GAIN WILD-TYPE 44 54 110 68 50

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.065

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
3P GAIN MUTATED 4 22 9
3P GAIN WILD-TYPE 89 129 117

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.085

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
3P GAIN MUTATED 5 23 7
3P GAIN WILD-TYPE 88 138 109

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

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
3P GAIN MUTATED 11 7 7 0 10
3P GAIN WILD-TYPE 56 79 64 71 59

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

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.11

Table S15.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
3P GAIN MUTATED 5 5 2 13 5 4
3P GAIN WILD-TYPE 35 58 90 71 41 36

Figure S15.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.05

Table S16.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
3Q GAIN MUTATED 5 24 9
3Q GAIN WILD-TYPE 88 127 117

Figure S16.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.018

Table S17.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
3Q GAIN MUTATED 14 8 6 1 9
3Q GAIN WILD-TYPE 53 78 65 70 60

Figure S17.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.097

Table S18.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
3Q GAIN MUTATED 7 5 3 11 8 3
3Q GAIN WILD-TYPE 33 58 89 73 38 37

Figure S18.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00647 (Fisher's exact test), Q value = 0.03

Table S19.  Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
4P GAIN MUTATED 5 6 16
4P GAIN WILD-TYPE 88 155 100

Figure S19.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'RPPA_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.015

Table S20.  Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

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

Figure S20.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.054

Table S21.  Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
4P GAIN MUTATED 4 5 12 4 1
4P GAIN WILD-TYPE 63 81 59 67 68

Figure S21.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.013

Table S22.  Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
4P GAIN MUTATED 5 3 3 14 1
4P GAIN WILD-TYPE 49 53 111 70 55

Figure S22.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'RPPA_CNMF'

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

Table S23.  Gene #8: '4q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

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

Figure S23.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'5p gain' versus 'CN_CNMF'

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

Table S24.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
5P GAIN MUTATED 13 63 58
5P GAIN WILD-TYPE 80 88 68

Figure S24.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

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

Table S25.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
5Q GAIN MUTATED 10 46 54
5Q GAIN WILD-TYPE 83 105 72

Figure S25.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S26.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
6P GAIN MUTATED 10 57 49
6P GAIN WILD-TYPE 83 94 77

Figure S26.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 0.00578 (Fisher's exact test), Q value = 0.028

Table S27.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
6P GAIN MUTATED 17 57 42
6P GAIN WILD-TYPE 76 104 74

Figure S27.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0029

Table S28.  Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
6P GAIN MUTATED 8 17 3 11 14 1
6P GAIN WILD-TYPE 33 56 16 11 8 0

Figure S28.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0097

Table S29.  Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
6P GAIN MUTATED 25 18 28 14 31
6P GAIN WILD-TYPE 42 68 43 57 38

Figure S29.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.075

Table S30.  Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
6P GAIN MUTATED 16 11 31 33 25
6P GAIN WILD-TYPE 38 45 83 51 31

Figure S30.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.00967 (Fisher's exact test), Q value = 0.043

Table S31.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
6P GAIN MUTATED 18 15 19 35 17 11
6P GAIN WILD-TYPE 22 48 73 49 29 29

Figure S31.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.023

Table S32.  Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
6P GAIN MUTATED 18 18 19 37 23
6P GAIN WILD-TYPE 26 77 37 85 25

Figure S32.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.003

Table S33.  Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
6Q GAIN MUTATED 5 36 26
6Q GAIN WILD-TYPE 88 115 100

Figure S33.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.015

Table S34.  Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

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

Figure S34.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.11

Table S35.  Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
6Q GAIN MUTATED 19 10 15 8 15
6Q GAIN WILD-TYPE 48 76 56 63 54

Figure S35.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0097

Table S36.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
7P GAIN MUTATED 14 51 44
7P GAIN WILD-TYPE 79 100 82

Figure S36.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.078

Table S37.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
7P GAIN MUTATED 20 59 30
7P GAIN WILD-TYPE 73 102 86

Figure S37.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.11

Table S38.  Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
7P GAIN MUTATED 8 18 22 31 9 18
7P GAIN WILD-TYPE 32 45 70 53 37 22

Figure S38.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0053

Table S39.  Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
7Q GAIN MUTATED 21 65 24
7Q GAIN WILD-TYPE 72 96 92

Figure S39.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.016

Table S40.  Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
8P GAIN MUTATED 15 6 12 18 20
8P GAIN WILD-TYPE 52 80 59 53 49

Figure S40.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.063

Table S41.  Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
8P GAIN MUTATED 12 12 11 22 14
8P GAIN WILD-TYPE 42 44 103 62 42

Figure S41.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 0.087

Table S42.  Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
8P GAIN MUTATED 19 8 22 5 15
8P GAIN WILD-TYPE 51 74 78 29 39

Figure S42.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S43.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
8Q GAIN MUTATED 38 61 85
8Q GAIN WILD-TYPE 55 90 41

Figure S43.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

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

Table S44.  Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
8Q GAIN MUTATED 39 21 38 37 44
8Q GAIN WILD-TYPE 28 65 33 34 25

Figure S44.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S45.  Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
8Q GAIN MUTATED 31 31 30 51 36
8Q GAIN WILD-TYPE 23 25 84 33 20

Figure S45.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00692 (Fisher's exact test), Q value = 0.032

Table S46.  Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
8Q GAIN MUTATED 19 34 28 70 30
8Q GAIN WILD-TYPE 25 61 28 52 18

Figure S46.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.013

Table S47.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
8Q GAIN MUTATED 42 29 54 13 35
8Q GAIN WILD-TYPE 28 53 46 21 19

Figure S47.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'RPPA_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0051

Table S48.  Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

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

Figure S48.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9q gain' versus 'RPPA_CNMF'

P value = 0.00533 (Fisher's exact test), Q value = 0.027

Table S49.  Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

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

Figure S49.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 0.00316 (Fisher's exact test), Q value = 0.019

Table S50.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
10P GAIN MUTATED 5 29 24
10P GAIN WILD-TYPE 88 122 102

Figure S50.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00759 (Fisher's exact test), Q value = 0.035

Table S51.  Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
10P GAIN MUTATED 10 8 20 6 13
10P GAIN WILD-TYPE 57 78 51 65 56

Figure S51.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.072

Table S52.  Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
10P GAIN MUTATED 11 6 10 21 9
10P GAIN WILD-TYPE 43 50 104 63 47

Figure S52.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.046

Table S53.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
10P GAIN MUTATED 17 5 17 8 6
10P GAIN WILD-TYPE 53 77 83 26 48

Figure S53.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0033

Table S54.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
10Q GAIN MUTATED 2 12 22
10Q GAIN WILD-TYPE 91 139 104

Figure S54.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.093

Table S55.  Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
10Q GAIN MUTATED 3 18 15
10Q GAIN WILD-TYPE 90 143 101

Figure S55.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00087

Table S56.  Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
10Q GAIN MUTATED 2 4 17 3 10
10Q GAIN WILD-TYPE 65 82 54 68 59

Figure S56.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p gain' versus 'RPPA_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.073

Table S57.  Gene #21: '11p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

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

Figure S57.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.076

Table S58.  Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
11P GAIN MUTATED 6 2 3 7 0
11P GAIN WILD-TYPE 48 54 111 77 56

Figure S58.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00491 (Fisher's exact test), Q value = 0.025

Table S59.  Gene #23: '12p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

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

Figure S59.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00517 (Fisher's exact test), Q value = 0.026

Table S60.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
12P GAIN MUTATED 12 3 13 8 4
12P GAIN WILD-TYPE 55 83 58 63 65

Figure S60.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0052

Table S61.  Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
12P GAIN MUTATED 14 2 9 13 2
12P GAIN WILD-TYPE 40 54 105 71 54

Figure S61.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0014

Table S62.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
12P GAIN MUTATED 19 9 1 7
12P GAIN WILD-TYPE 88 72 101 43

Figure S62.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.085

Table S63.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
12P GAIN MUTATED 13 6 12 4 1
12P GAIN WILD-TYPE 57 76 88 30 53

Figure S63.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.1

Table S64.  Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

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

Figure S64.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00925 (Fisher's exact test), Q value = 0.041

Table S65.  Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
12Q GAIN MUTATED 13 5 14 11 4
12Q GAIN WILD-TYPE 54 81 57 60 65

Figure S65.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0025 (Fisher's exact test), Q value = 0.016

Table S66.  Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
12Q GAIN MUTATED 14 4 12 15 2
12Q GAIN WILD-TYPE 40 52 102 69 54

Figure S66.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0029

Table S67.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
12Q GAIN MUTATED 23 9 3 8
12Q GAIN WILD-TYPE 84 72 99 42

Figure S67.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.11

Table S68.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
13Q GAIN MUTATED 1 12 10
13Q GAIN WILD-TYPE 92 139 116

Figure S68.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.13

Table S69.  Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
16P GAIN MUTATED 7 7 2 12 4
16P GAIN WILD-TYPE 60 79 69 59 65

Figure S69.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00594 (Fisher's exact test), Q value = 0.029

Table S70.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
16Q GAIN MUTATED 3 2 0 9 3
16Q GAIN WILD-TYPE 64 84 71 62 66

Figure S70.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.11

Table S71.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
17P GAIN MUTATED 5 8 17
17P GAIN WILD-TYPE 88 143 109

Figure S71.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.03

Table S72.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
17Q GAIN MUTATED 13 48 32
17Q GAIN WILD-TYPE 80 103 94

Figure S72.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0065

Table S73.  Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
17Q GAIN MUTATED 21 20 17 20 15
17Q GAIN WILD-TYPE 23 75 39 102 33

Figure S73.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.061

Table S74.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
17Q GAIN MUTATED 24 18 16 13 17
17Q GAIN WILD-TYPE 46 64 84 21 37

Figure S74.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.011

Table S75.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
18P GAIN MUTATED 2 14 20
18P GAIN WILD-TYPE 91 137 106

Figure S75.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0409 (Fisher's exact test), Q value = 0.12

Table S76.  Gene #32: '18p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

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

Figure S76.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.073

Table S77.  Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
18P GAIN MUTATED 9 4 13 7 3
18P GAIN WILD-TYPE 58 82 58 64 66

Figure S77.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.065

Table S78.  Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
18P GAIN MUTATED 10 4 7 13 2
18P GAIN WILD-TYPE 44 52 107 71 54

Figure S78.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.1

Table S79.  Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
18P GAIN MUTATED 7 3 6 7 4 9
18P GAIN WILD-TYPE 33 60 86 77 42 31

Figure S79.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.049

Table S80.  Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
18P GAIN MUTATED 16 9 3 7
18P GAIN WILD-TYPE 91 72 99 43

Figure S80.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.13

Table S81.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
18Q GAIN MUTATED 2 13 13
18Q GAIN WILD-TYPE 91 138 113

Figure S81.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00316 (Fisher's exact test), Q value = 0.019

Table S82.  Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
18Q GAIN MUTATED 9 4 5 10 0
18Q GAIN WILD-TYPE 45 52 109 74 56

Figure S82.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.064

Table S83.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
18Q GAIN MUTATED 6 4 5 3 2 8
18Q GAIN WILD-TYPE 34 59 87 81 44 32

Figure S83.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.019

Table S84.  Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
18Q GAIN MUTATED 14 8 1 4
18Q GAIN WILD-TYPE 93 73 101 46

Figure S84.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00981 (Fisher's exact test), Q value = 0.043

Table S85.  Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
19P GAIN MUTATED 15 15 26
19P GAIN WILD-TYPE 78 146 90

Figure S85.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.02

Table S86.  Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
19P GAIN MUTATED 9 10 18 15 3
19P GAIN WILD-TYPE 58 76 53 56 66

Figure S86.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.044

Table S87.  Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
19P GAIN MUTATED 11 11 11 19 3
19P GAIN WILD-TYPE 43 45 103 65 53

Figure S87.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

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

Table S88.  Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
19P GAIN MUTATED 4 8 18 6 8 11
19P GAIN WILD-TYPE 36 55 74 78 38 29

Figure S88.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00676 (Fisher's exact test), Q value = 0.031

Table S89.  Gene #34: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
19P GAIN MUTATED 4 13 10 27 1
19P GAIN WILD-TYPE 40 82 46 95 47

Figure S89.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00267 (Fisher's exact test), Q value = 0.017

Table S90.  Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
19P GAIN MUTATED 19 16 5 11
19P GAIN WILD-TYPE 88 65 97 39

Figure S90.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.015

Table S91.  Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
19Q GAIN MUTATED 19 19 33
19Q GAIN WILD-TYPE 74 142 83

Figure S91.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0058

Table S92.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
19Q GAIN MUTATED 12 11 23 19 5
19Q GAIN WILD-TYPE 55 75 48 52 64

Figure S92.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00087

Table S93.  Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
19Q GAIN MUTATED 12 15 11 28 4
19Q GAIN WILD-TYPE 42 41 103 56 52

Figure S93.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.075

Table S94.  Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
19Q GAIN MUTATED 6 7 23 10 11 13
19Q GAIN WILD-TYPE 34 56 69 74 35 27

Figure S94.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.0098

Table S95.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
19Q GAIN MUTATED 6 14 17 31 2
19Q GAIN WILD-TYPE 38 81 39 91 46

Figure S95.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S96.  Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
19Q GAIN MUTATED 25 21 5 14
19Q GAIN WILD-TYPE 82 60 97 36

Figure S96.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0038

Table S97.  Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
19Q GAIN MUTATED 20 11 27 5 2
19Q GAIN WILD-TYPE 50 71 73 29 52

Figure S97.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

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

Table S98.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
20P GAIN MUTATED 8 60 39
20P GAIN WILD-TYPE 85 91 87

Figure S98.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

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

Table S99.  Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
20P GAIN MUTATED 20 11 10 10 7
20P GAIN WILD-TYPE 19 34 28 8 31

Figure S99.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.056

Table S100.  Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
20P GAIN MUTATED 24 19 31 17 16
20P GAIN WILD-TYPE 43 67 40 54 53

Figure S100.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.011

Table S101.  Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
20P GAIN MUTATED 19 15 25 38 10
20P GAIN WILD-TYPE 35 41 89 46 46

Figure S101.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0445 (Fisher's exact test), Q value = 0.13

Table S102.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
20P GAIN MUTATED 18 21 21 37 9
20P GAIN WILD-TYPE 26 74 35 85 39

Figure S102.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.003

Table S103.  Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
20P GAIN MUTATED 36 22 16 24
20P GAIN WILD-TYPE 71 59 86 26

Figure S103.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

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

Table S104.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
20Q GAIN MUTATED 8 63 41
20Q GAIN WILD-TYPE 85 88 85

Figure S104.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.048

Table S105.  Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

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

Figure S105.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.045

Table S106.  Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
20Q GAIN MUTATED 17 15 32 38 10
20Q GAIN WILD-TYPE 37 41 82 46 46

Figure S106.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 0.11

Table S107.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
20Q GAIN MUTATED 19 23 23 36 10
20Q GAIN WILD-TYPE 25 72 33 86 38

Figure S107.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.0043

Table S108.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
20Q GAIN MUTATED 39 21 18 24
20Q GAIN WILD-TYPE 68 60 84 26

Figure S108.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.087

Table S109.  Gene #38: '21q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

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

Figure S109.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.003

Table S110.  Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
22Q GAIN MUTATED 2 27 19
22Q GAIN WILD-TYPE 91 124 107

Figure S110.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 0.00386 (Fisher's exact test), Q value = 0.021

Table S111.  Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

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

Figure S111.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00562 (Fisher's exact test), Q value = 0.028

Table S112.  Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

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

Figure S112.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.11

Table S113.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
22Q GAIN MUTATED 8 8 18 7 7
22Q GAIN WILD-TYPE 59 78 53 64 62

Figure S113.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00201 (Fisher's exact test), Q value = 0.014

Table S114.  Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
22Q GAIN MUTATED 14 5 8 17 4
22Q GAIN WILD-TYPE 40 51 106 67 52

Figure S114.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.048

Table S115.  Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
22Q GAIN MUTATED 16 11 5 11
22Q GAIN WILD-TYPE 91 70 97 39

Figure S115.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.082

Table S116.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
XP GAIN MUTATED 7 12 22
XP GAIN WILD-TYPE 86 139 104

Figure S116.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.079

Table S117.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
XP GAIN MUTATED 5 6 6 8 16
XP GAIN WILD-TYPE 62 80 65 63 53

Figure S117.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 0.11

Table S118.  Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
XP GAIN MUTATED 9 4 10 3 12
XP GAIN WILD-TYPE 61 78 90 31 42

Figure S118.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.05

Table S119.  Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
XQ GAIN MUTATED 14 16 30
XQ GAIN WILD-TYPE 79 135 96

Figure S119.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.046

Table S120.  Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
XQ GAIN MUTATED 7 35 18
XQ GAIN WILD-TYPE 86 126 98

Figure S120.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0079

Table S121.  Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
XQ GAIN MUTATED 7 13 8 8 24
XQ GAIN WILD-TYPE 60 73 63 63 45

Figure S121.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00413 (Fisher's exact test), Q value = 0.023

Table S122.  Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
XQ GAIN MUTATED 5 6 20 10 19
XQ GAIN WILD-TYPE 49 50 94 74 37

Figure S122.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0069

Table S123.  Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
XQ GAIN MUTATED 3 11 10 27 5 3
XQ GAIN WILD-TYPE 37 52 82 57 41 37

Figure S123.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S124.  Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
XQ GAIN MUTATED 5 13 9 12 20
XQ GAIN WILD-TYPE 39 82 47 110 28

Figure S124.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00542 (Fisher's exact test), Q value = 0.027

Table S125.  Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
XQ GAIN MUTATED 15 7 27 5
XQ GAIN WILD-TYPE 92 74 75 45

Figure S125.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S126.  Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
XQ GAIN MUTATED 12 9 9 3 21
XQ GAIN WILD-TYPE 58 73 91 31 33

Figure S126.  Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

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

Table S127.  Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
1P LOSS MUTATED 4 32 42
1P LOSS WILD-TYPE 89 119 84

Figure S127.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

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

Table S128.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
1P LOSS MUTATED 8 26 44
1P LOSS WILD-TYPE 85 135 72

Figure S128.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.09

Table S129.  Gene #42: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
1P LOSS MUTATED 7 11 7 8 9 0
1P LOSS WILD-TYPE 34 62 12 14 13 1

Figure S129.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

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

Table S130.  Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
1P LOSS MUTATED 8 11 37 14 7
1P LOSS WILD-TYPE 59 75 34 57 62

Figure S130.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S131.  Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
1P LOSS MUTATED 11 8 15 37 6
1P LOSS WILD-TYPE 43 48 99 47 50

Figure S131.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0017

Table S132.  Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
1P LOSS MUTATED 5 8 15 14 17 18
1P LOSS WILD-TYPE 35 55 77 70 29 22

Figure S132.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.07

Table S133.  Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
1P LOSS MUTATED 5 17 15 35 5
1P LOSS WILD-TYPE 39 78 41 87 43

Figure S133.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0072

Table S134.  Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
1P LOSS MUTATED 27 18 10 18
1P LOSS WILD-TYPE 80 63 92 32

Figure S134.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.062

Table S135.  Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
1P LOSS MUTATED 16 15 32 4 6
1P LOSS WILD-TYPE 54 67 68 30 48

Figure S135.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.1

Table S136.  Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
1Q LOSS MUTATED 1 13 6
1Q LOSS WILD-TYPE 92 138 120

Figure S136.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.069

Table S137.  Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
1Q LOSS MUTATED 1 7 10 1 0
1Q LOSS WILD-TYPE 69 75 90 33 54

Figure S137.  Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00587 (Fisher's exact test), Q value = 0.029

Table S138.  Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
2P LOSS MUTATED 3 22 8
2P LOSS WILD-TYPE 90 129 118

Figure S138.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.00544 (Fisher's exact test), Q value = 0.027

Table S139.  Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
2P LOSS MUTATED 11 9 7 6 0
2P LOSS WILD-TYPE 56 77 64 65 69

Figure S139.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.12

Table S140.  Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
2P LOSS MUTATED 6 7 10 10 0
2P LOSS WILD-TYPE 48 49 104 74 56

Figure S140.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.0098

Table S141.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
2Q LOSS MUTATED 4 26 8
2Q LOSS WILD-TYPE 89 125 118

Figure S141.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0079

Table S142.  Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
2Q LOSS MUTATED 10 14 9 5 0
2Q LOSS WILD-TYPE 57 72 62 66 69

Figure S142.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.07

Table S143.  Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
2Q LOSS MUTATED 5 7 16 10 0
2Q LOSS WILD-TYPE 49 49 98 74 56

Figure S143.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.021

Table S144.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
3P LOSS MUTATED 8 6 18 14 5
3P LOSS WILD-TYPE 59 80 53 57 64

Figure S144.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.044

Table S145.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
3P LOSS MUTATED 14 5 10 17 5
3P LOSS WILD-TYPE 40 51 104 67 51

Figure S145.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00356 (Fisher's exact test), Q value = 0.02

Table S146.  Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
3P LOSS MUTATED 4 4 15 8 6 14
3P LOSS WILD-TYPE 36 59 77 76 40 26

Figure S146.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00461 (Fisher's exact test), Q value = 0.025

Table S147.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
3P LOSS MUTATED 20 17 6 4
3P LOSS WILD-TYPE 87 64 96 46

Figure S147.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 0.12

Table S148.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
3P LOSS MUTATED 13 9 20 2 3
3P LOSS WILD-TYPE 57 73 80 32 51

Figure S148.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.00548 (Fisher's exact test), Q value = 0.027

Table S149.  Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
3Q LOSS MUTATED 7 5 17 7 4
3Q LOSS WILD-TYPE 60 81 54 64 65

Figure S149.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.12

Table S150.  Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
3Q LOSS MUTATED 3 4 11 7 4 11
3Q LOSS WILD-TYPE 37 59 81 77 42 29

Figure S150.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00785 (Fisher's exact test), Q value = 0.036

Table S151.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
3Q LOSS MUTATED 19 10 5 2
3Q LOSS WILD-TYPE 88 71 97 48

Figure S151.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'CN_CNMF'

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

Table S152.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
4P LOSS MUTATED 3 65 37
4P LOSS WILD-TYPE 90 86 89

Figure S152.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.008

Table S153.  Gene #48: '4p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

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

Figure S153.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0053

Table S154.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
4P LOSS MUTATED 26 26 29 12 11
4P LOSS WILD-TYPE 41 60 42 59 58

Figure S154.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.069

Table S155.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
4P LOSS MUTATED 15 11 36 33 9
4P LOSS WILD-TYPE 39 45 78 51 47

Figure S155.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.061

Table S156.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
4P LOSS MUTATED 14 25 25 33 7
4P LOSS WILD-TYPE 30 70 31 89 41

Figure S156.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.064

Table S157.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
4P LOSS MUTATED 40 18 21 18
4P LOSS WILD-TYPE 67 63 81 32

Figure S157.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0046

Table S158.  Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
4P LOSS MUTATED 33 25 22 10 7
4P LOSS WILD-TYPE 37 57 78 24 47

Figure S158.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

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

Table S159.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
4Q LOSS MUTATED 4 91 51
4Q LOSS WILD-TYPE 89 60 75

Figure S159.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00624 (Fisher's exact test), Q value = 0.03

Table S160.  Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
4Q LOSS MUTATED 28 59 59
4Q LOSS WILD-TYPE 65 102 57

Figure S160.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.00371 (Fisher's exact test), Q value = 0.021

Table S161.  Gene #49: '4q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

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

Figure S161.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

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

Table S162.  Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
4Q LOSS MUTATED 33 33 46 17 15
4Q LOSS WILD-TYPE 34 53 25 54 54

Figure S162.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.0065

Table S163.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
4Q LOSS MUTATED 24 19 42 47 12
4Q LOSS WILD-TYPE 30 37 72 37 44

Figure S163.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00241 (Fisher's exact test), Q value = 0.016

Table S164.  Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
4Q LOSS MUTATED 18 22 30 25 26 24
4Q LOSS WILD-TYPE 22 41 62 59 20 16

Figure S164.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S165.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
4Q LOSS MUTATED 18 35 30 53 9
4Q LOSS WILD-TYPE 26 60 26 69 39

Figure S165.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S166.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
4Q LOSS MUTATED 53 28 26 31
4Q LOSS WILD-TYPE 54 53 76 19

Figure S166.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.016

Table S167.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
4Q LOSS MUTATED 39 33 42 13 11
4Q LOSS WILD-TYPE 31 49 58 21 43

Figure S167.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.06

Table S168.  Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
5P LOSS MUTATED 2 18 9
5P LOSS WILD-TYPE 91 133 117

Figure S168.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.079

Table S169.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
5P LOSS MUTATED 7 1 7 12 2
5P LOSS WILD-TYPE 47 55 107 72 54

Figure S169.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.05

Table S170.  Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
5P LOSS MUTATED 5 3 3 4 7 7
5P LOSS WILD-TYPE 35 60 89 80 39 33

Figure S170.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.044

Table S171.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
5P LOSS MUTATED 14 2 4 6
5P LOSS WILD-TYPE 93 79 98 44

Figure S171.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.059

Table S172.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
5P LOSS MUTATED 11 5 7 3 0
5P LOSS WILD-TYPE 59 77 93 31 54

Figure S172.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.05

Table S173.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
5Q LOSS MUTATED 3 22 12
5Q LOSS WILD-TYPE 90 129 114

Figure S173.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.056

Table S174.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
5Q LOSS MUTATED 9 9 19
5Q LOSS WILD-TYPE 84 152 97

Figure S174.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0047

Table S175.  Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
5Q LOSS MUTATED 12 1 8 14 2
5Q LOSS WILD-TYPE 42 55 106 70 54

Figure S175.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.023

Table S176.  Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
5Q LOSS MUTATED 5 4 4 6 8 10
5Q LOSS WILD-TYPE 35 59 88 78 38 30

Figure S176.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S177.  Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
5Q LOSS MUTATED 21 3 3 7
5Q LOSS WILD-TYPE 86 78 99 43

Figure S177.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0054

Table S178.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
5Q LOSS MUTATED 16 7 9 2 0
5Q LOSS WILD-TYPE 54 75 91 32 54

Figure S178.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'RPPA_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.011

Table S179.  Gene #54: '7p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
7P LOSS MUTATED 0 2 4 0 4 0
7P LOSS WILD-TYPE 41 71 15 22 18 1

Figure S179.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.07

Table S180.  Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
7P LOSS MUTATED 10 2 1 3
7P LOSS WILD-TYPE 97 79 101 47

Figure S180.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.12

Table S181.  Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
7P LOSS MUTATED 7 5 2 2 0
7P LOSS WILD-TYPE 63 77 98 32 54

Figure S181.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.068

Table S182.  Gene #55: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
7Q LOSS MUTATED 8 1 7 3 2
7Q LOSS WILD-TYPE 59 85 64 68 67

Figure S182.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.1

Table S183.  Gene #55: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
7Q LOSS MUTATED 5 6 6 4 0
7Q LOSS WILD-TYPE 39 89 50 118 48

Figure S183.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0017

Table S184.  Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
7Q LOSS MUTATED 15 3 0 3
7Q LOSS WILD-TYPE 92 78 102 47

Figure S184.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0073 (Fisher's exact test), Q value = 0.034

Table S185.  Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
7Q LOSS MUTATED 8 5 3 5 0
7Q LOSS WILD-TYPE 62 77 97 29 54

Figure S185.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

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

Table S186.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
8P LOSS MUTATED 30 82 84
8P LOSS WILD-TYPE 63 69 42

Figure S186.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.1

Table S187.  Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
8P LOSS MUTATED 37 44 48 30 33
8P LOSS WILD-TYPE 30 42 23 41 36

Figure S187.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'CN_CNMF'

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

Table S188.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
9P LOSS MUTATED 7 67 45
9P LOSS WILD-TYPE 86 84 81

Figure S188.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.12

Table S189.  Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
9P LOSS MUTATED 26 45 48
9P LOSS WILD-TYPE 67 116 68

Figure S189.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0021

Table S190.  Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
9P LOSS MUTATED 25 24 36 22 10
9P LOSS WILD-TYPE 42 62 35 49 59

Figure S190.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.03

Table S191.  Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
9P LOSS MUTATED 21 17 31 38 10
9P LOSS WILD-TYPE 33 39 83 46 46

Figure S191.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.0094 (Fisher's exact test), Q value = 0.042

Table S192.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
9P LOSS MUTATED 15 15 31 18 21 19
9P LOSS WILD-TYPE 25 48 61 66 25 21

Figure S192.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00834 (Fisher's exact test), Q value = 0.038

Table S193.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
9P LOSS MUTATED 16 28 22 47 6
9P LOSS WILD-TYPE 28 67 34 75 42

Figure S193.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00812 (Fisher's exact test), Q value = 0.037

Table S194.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
9P LOSS MUTATED 30 25 38 13 8
9P LOSS WILD-TYPE 40 57 62 21 46

Figure S194.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

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

Table S195.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
9Q LOSS MUTATED 7 61 42
9Q LOSS WILD-TYPE 86 90 84

Figure S195.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 0.00987 (Fisher's exact test), Q value = 0.043

Table S196.  Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
9Q LOSS MUTATED 22 41 47
9Q LOSS WILD-TYPE 71 120 69

Figure S196.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.014

Table S197.  Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
9Q LOSS MUTATED 24 25 30 21 9
9Q LOSS WILD-TYPE 43 61 41 50 60

Figure S197.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.011

Table S198.  Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
9Q LOSS MUTATED 20 15 31 36 7
9Q LOSS WILD-TYPE 34 41 83 48 49

Figure S198.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.088

Table S199.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
9Q LOSS MUTATED 15 15 27 16 17 18
9Q LOSS WILD-TYPE 25 48 65 68 29 22

Figure S199.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00855 (Fisher's exact test), Q value = 0.038

Table S200.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
9Q LOSS MUTATED 15 25 21 42 5
9Q LOSS WILD-TYPE 29 70 35 80 43

Figure S200.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0042

Table S201.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
9Q LOSS MUTATED 29 21 35 13 5
9Q LOSS WILD-TYPE 41 61 65 21 49

Figure S201.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

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

Table S202.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
10P LOSS MUTATED 5 33 9
10P LOSS WILD-TYPE 88 118 117

Figure S202.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00327 (Fisher's exact test), Q value = 0.019

Table S203.  Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
10P LOSS MUTATED 15 13 5 11 2
10P LOSS WILD-TYPE 52 73 66 60 67

Figure S203.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00432 (Fisher's exact test), Q value = 0.023

Table S204.  Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
10P LOSS MUTATED 12 4 21 7 2
10P LOSS WILD-TYPE 42 52 93 77 54

Figure S204.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.044

Table S205.  Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
10P LOSS MUTATED 4 15 9 4 9 6
10P LOSS WILD-TYPE 36 48 83 80 37 34

Figure S205.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.054

Table S206.  Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
10P LOSS MUTATED 4 20 3 18 2
10P LOSS WILD-TYPE 40 75 53 104 46

Figure S206.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.057

Table S207.  Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
10P LOSS MUTATED 7 19 14 3 2
10P LOSS WILD-TYPE 63 63 86 31 52

Figure S207.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

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

Table S208.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
10Q LOSS MUTATED 10 56 12
10Q LOSS WILD-TYPE 83 95 114

Figure S208.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.13

Table S209.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
10Q LOSS MUTATED 28 31 19
10Q LOSS WILD-TYPE 65 130 97

Figure S209.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 0.00475 (Fisher's exact test), Q value = 0.025

Table S210.  Gene #61: '10q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
10Q LOSS MUTATED 13 14 1 6 12 0
10Q LOSS WILD-TYPE 28 59 18 16 10 1

Figure S210.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 0.12

Table S211.  Gene #61: '10q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
10Q LOSS MUTATED 10 6 16 6 8
10Q LOSS WILD-TYPE 29 39 22 12 30

Figure S211.  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 = 2e-04

Table S212.  Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
10Q LOSS MUTATED 30 21 6 15 4
10Q LOSS WILD-TYPE 37 65 65 56 65

Figure S212.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S213.  Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
10Q LOSS MUTATED 23 8 30 10 5
10Q LOSS WILD-TYPE 31 48 84 74 51

Figure S213.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.019

Table S214.  Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
10Q LOSS MUTATED 10 23 15 9 9 12
10Q LOSS WILD-TYPE 30 40 77 75 37 28

Figure S214.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.002

Table S215.  Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
10Q LOSS MUTATED 10 34 8 24 2
10Q LOSS WILD-TYPE 34 61 48 98 46

Figure S215.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S216.  Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
10Q LOSS MUTATED 16 31 19 9 1
10Q LOSS WILD-TYPE 54 51 81 25 53

Figure S216.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.046

Table S217.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
11P LOSS MUTATED 7 32 24
11P LOSS WILD-TYPE 86 119 102

Figure S217.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.046

Table S218.  Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
11P LOSS MUTATED 14 5 15 22 6
11P LOSS WILD-TYPE 40 51 99 62 50

Figure S218.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.058

Table S219.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
11P LOSS MUTATED 27 12 9 9
11P LOSS WILD-TYPE 80 69 93 41

Figure S219.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.061

Table S220.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
11P LOSS MUTATED 21 13 15 4 4
11P LOSS WILD-TYPE 49 69 85 30 50

Figure S220.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.12

Table S221.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
11Q LOSS MUTATED 10 35 27
11Q LOSS WILD-TYPE 83 116 99

Figure S221.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.049

Table S222.  Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
11Q LOSS MUTATED 32 12 13 9
11Q LOSS WILD-TYPE 75 69 89 41

Figure S222.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0499 (Fisher's exact test), Q value = 0.14

Table S223.  Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
11Q LOSS MUTATED 21 19 15 5 6
11Q LOSS WILD-TYPE 49 63 85 29 48

Figure S223.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00073

Table S224.  Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
12P LOSS MUTATED 4 40 22
12P LOSS WILD-TYPE 89 111 104

Figure S224.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.065

Table S225.  Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
12P LOSS MUTATED 19 21 9 10 7
12P LOSS WILD-TYPE 48 65 62 61 62

Figure S225.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.084

Table S226.  Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
12Q LOSS MUTATED 3 20 13
12Q LOSS WILD-TYPE 90 131 113

Figure S226.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

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

Table S227.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
13Q LOSS MUTATED 13 72 37
13Q LOSS WILD-TYPE 80 79 89

Figure S227.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.11

Table S228.  Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
13Q LOSS MUTATED 31 43 48
13Q LOSS WILD-TYPE 62 118 68

Figure S228.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.075

Table S229.  Gene #66: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
13Q LOSS MUTATED 21 11 16 3 14
13Q LOSS WILD-TYPE 18 34 22 15 24

Figure S229.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.014

Table S230.  Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
13Q LOSS MUTATED 30 24 28 26 11
13Q LOSS WILD-TYPE 37 62 43 45 58

Figure S230.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0051

Table S231.  Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
13Q LOSS MUTATED 24 11 38 37 9
13Q LOSS WILD-TYPE 30 45 76 47 47

Figure S231.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.019

Table S232.  Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
13Q LOSS MUTATED 18 25 34 14 13 17
13Q LOSS WILD-TYPE 22 38 58 70 33 23

Figure S232.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00411 (Fisher's exact test), Q value = 0.023

Table S233.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
13Q LOSS MUTATED 19 35 15 46 6
13Q LOSS WILD-TYPE 25 60 41 76 42

Figure S233.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0054

Table S234.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
13Q LOSS MUTATED 40 37 19 20
13Q LOSS WILD-TYPE 67 44 83 30

Figure S234.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.0058

Table S235.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
13Q LOSS MUTATED 23 30 42 15 6
13Q LOSS WILD-TYPE 47 52 58 19 48

Figure S235.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

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

Table S236.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
14Q LOSS MUTATED 5 72 32
14Q LOSS WILD-TYPE 88 79 94

Figure S236.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.00579 (Fisher's exact test), Q value = 0.028

Table S237.  Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
14Q LOSS MUTATED 20 17 6 5 13 0
14Q LOSS WILD-TYPE 21 56 13 17 9 1

Figure S237.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0014

Table S238.  Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
14Q LOSS MUTATED 32 17 27 22 10
14Q LOSS WILD-TYPE 35 69 44 49 59

Figure S238.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S239.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
14Q LOSS MUTATED 30 11 26 33 8
14Q LOSS WILD-TYPE 24 45 88 51 48

Figure S239.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0023

Table S240.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
14Q LOSS MUTATED 44 28 15 17
14Q LOSS WILD-TYPE 63 53 87 33

Figure S240.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00489 (Fisher's exact test), Q value = 0.025

Table S241.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
14Q LOSS MUTATED 29 21 35 12 7
14Q LOSS WILD-TYPE 41 61 65 22 47

Figure S241.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0053

Table S242.  Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
15Q LOSS MUTATED 7 40 20
15Q LOSS WILD-TYPE 86 111 106

Figure S242.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.00621 (Fisher's exact test), Q value = 0.03

Table S243.  Gene #68: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
15Q LOSS MUTATED 15 10 3 3 10 0
15Q LOSS WILD-TYPE 26 63 16 19 12 1

Figure S243.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00165 (Fisher's exact test), Q value = 0.012

Table S244.  Gene #68: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
15Q LOSS MUTATED 9 3 17 3 9
15Q LOSS WILD-TYPE 30 42 21 15 29

Figure S244.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

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

Table S245.  Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
15Q LOSS MUTATED 22 9 20 9 6
15Q LOSS WILD-TYPE 45 77 51 62 63

Figure S245.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S246.  Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
15Q LOSS MUTATED 20 5 12 22 7
15Q LOSS WILD-TYPE 34 51 102 62 49

Figure S246.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.098

Table S247.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
15Q LOSS MUTATED 6 11 10 13 13 13
15Q LOSS WILD-TYPE 34 52 82 71 33 27

Figure S247.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.011

Table S248.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
15Q LOSS MUTATED 27 11 10 16
15Q LOSS WILD-TYPE 80 70 92 34

Figure S248.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.072

Table S249.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
15Q LOSS MUTATED 20 12 23 5 4
15Q LOSS WILD-TYPE 50 70 77 29 50

Figure S249.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

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

Table S250.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
16P LOSS MUTATED 6 60 42
16P LOSS WILD-TYPE 87 91 84

Figure S250.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

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

Table S251.  Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
16P LOSS MUTATED 26 31 51
16P LOSS WILD-TYPE 67 130 65

Figure S251.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.018

Table S252.  Gene #69: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
16P LOSS MUTATED 13 15 8 10 14 0
16P LOSS WILD-TYPE 28 58 11 12 8 1

Figure S252.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.017

Table S253.  Gene #69: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
16P LOSS MUTATED 20 8 15 9 8
16P LOSS WILD-TYPE 19 37 23 9 30

Figure S253.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

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

Table S254.  Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
16P LOSS MUTATED 24 16 51 11 4
16P LOSS WILD-TYPE 43 70 20 60 65

Figure S254.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S255.  Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
16P LOSS MUTATED 22 13 24 44 3
16P LOSS WILD-TYPE 32 43 90 40 53

Figure S255.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

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

Table S256.  Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
16P LOSS MUTATED 9 12 16 17 30 23
16P LOSS WILD-TYPE 31 51 76 67 16 17

Figure S256.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S257.  Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
16P LOSS MUTATED 10 20 27 48 2
16P LOSS WILD-TYPE 34 75 29 74 46

Figure S257.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S258.  Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
16P LOSS MUTATED 39 20 13 31
16P LOSS WILD-TYPE 68 61 89 19

Figure S258.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S259.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
16P LOSS MUTATED 32 18 41 7 5
16P LOSS WILD-TYPE 38 64 59 27 49

Figure S259.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

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

Table S260.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
16Q LOSS MUTATED 6 75 64
16Q LOSS WILD-TYPE 87 76 62

Figure S260.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

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

Table S261.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
16Q LOSS MUTATED 26 48 71
16Q LOSS WILD-TYPE 67 113 45

Figure S261.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0047

Table S262.  Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
16Q LOSS MUTATED 16 18 10 12 16 0
16Q LOSS WILD-TYPE 25 55 9 10 6 1

Figure S262.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0021

Table S263.  Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
16Q LOSS MUTATED 20 10 20 13 9
16Q LOSS WILD-TYPE 19 35 18 5 29

Figure S263.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

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

Table S264.  Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
16Q LOSS MUTATED 33 26 60 17 7
16Q LOSS WILD-TYPE 34 60 11 54 62

Figure S264.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S265.  Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
16Q LOSS MUTATED 23 16 46 53 5
16Q LOSS WILD-TYPE 31 40 68 31 51

Figure S265.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

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

Table S266.  Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
16Q LOSS MUTATED 15 25 27 20 31 26
16Q LOSS WILD-TYPE 25 38 65 64 15 14

Figure S266.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S267.  Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
16Q LOSS MUTATED 15 33 33 60 3
16Q LOSS WILD-TYPE 29 62 23 62 45

Figure S267.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S268.  Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
16Q LOSS MUTATED 59 28 21 31
16Q LOSS WILD-TYPE 48 53 81 19

Figure S268.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S269.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
16Q LOSS MUTATED 41 32 48 10 8
16Q LOSS WILD-TYPE 29 50 52 24 46

Figure S269.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

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

Table S270.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
17P LOSS MUTATED 32 119 34
17P LOSS WILD-TYPE 61 32 92

Figure S270.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.1

Table S271.  Gene #71: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 45 38 18 38
17P LOSS MUTATED 15 18 25 12 22
17P LOSS WILD-TYPE 24 27 13 6 16

Figure S271.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.013

Table S272.  Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
17P LOSS MUTATED 45 50 31 29 27
17P LOSS WILD-TYPE 22 36 40 42 42

Figure S272.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.076

Table S273.  Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
17P LOSS MUTATED 32 23 68 36 23
17P LOSS WILD-TYPE 22 33 46 48 33

Figure S273.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.014

Table S274.  Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 63 92 84 46 40
17P LOSS MUTATED 29 40 38 34 24 19
17P LOSS WILD-TYPE 11 23 54 50 22 21

Figure S274.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0032

Table S275.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 95 56 122 48
17P LOSS MUTATED 34 54 23 52 21
17P LOSS WILD-TYPE 10 41 33 70 27

Figure S275.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0048

Table S276.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
17P LOSS MUTATED 30 51 46 27 22
17P LOSS WILD-TYPE 40 31 54 7 32

Figure S276.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.085

Table S277.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
18P LOSS MUTATED 11 39 24
18P LOSS WILD-TYPE 82 112 102

Figure S277.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.015

Table S278.  Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
18P LOSS MUTATED 13 25 36
18P LOSS WILD-TYPE 80 136 80

Figure S278.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00318 (Fisher's exact test), Q value = 0.019

Table S279.  Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
18P LOSS MUTATED 10 5 18 29 12
18P LOSS WILD-TYPE 44 51 96 55 44

Figure S279.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.059

Table S280.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
18Q LOSS MUTATED 11 41 27
18Q LOSS WILD-TYPE 82 110 99

Figure S280.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.011

Table S281.  Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
18Q LOSS MUTATED 13 28 38
18Q LOSS WILD-TYPE 80 133 78

Figure S281.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0043

Table S282.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
18Q LOSS MUTATED 8 5 21 32 13
18Q LOSS WILD-TYPE 46 51 93 52 43

Figure S282.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

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

Table S283.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
19P LOSS MUTATED 3 37 12
19P LOSS WILD-TYPE 90 114 114

Figure S283.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.064

Table S284.  Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 70 82 100 34 54
19P LOSS MUTATED 15 12 10 9 3
19P LOSS WILD-TYPE 55 70 90 25 51

Figure S284.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00038

Table S285.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
19Q LOSS MUTATED 2 30 7
19Q LOSS WILD-TYPE 91 121 119

Figure S285.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.12

Table S286.  Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
20Q LOSS MUTATED 8 3 1 0
20Q LOSS WILD-TYPE 99 78 101 50

Figure S286.  Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.061

Table S287.  Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
21Q LOSS MUTATED 17 50 43
21Q LOSS WILD-TYPE 76 101 83

Figure S287.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0033

Table S288.  Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
21Q LOSS MUTATED 34 15 22 17 19
21Q LOSS WILD-TYPE 33 71 49 54 50

Figure S288.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.049

Table S289.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
21Q LOSS MUTATED 43 23 21 19
21Q LOSS WILD-TYPE 64 58 81 31

Figure S289.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.0048 (Fisher's exact test), Q value = 0.025

Table S290.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
22Q LOSS MUTATED 16 40 14
22Q LOSS WILD-TYPE 77 111 112

Figure S290.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.00644 (Fisher's exact test), Q value = 0.03

Table S291.  Gene #80: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 41 73 19 22 22 1
22Q LOSS MUTATED 11 17 1 3 12 0
22Q LOSS WILD-TYPE 30 56 18 19 10 1

Figure S291.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00286 (Fisher's exact test), Q value = 0.018

Table S292.  Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 67 86 71 71 69
22Q LOSS MUTATED 24 17 8 13 8
22Q LOSS WILD-TYPE 43 69 63 58 61

Figure S292.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.072

Table S293.  Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
XP LOSS MUTATED 14 46 35
XP LOSS WILD-TYPE 79 115 81

Figure S293.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.079

Table S294.  Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 54 56 114 84 56
XP LOSS MUTATED 14 11 40 13 16
XP LOSS WILD-TYPE 40 45 74 71 40

Figure S294.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.076

Table S295.  Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 81 102 50
XP LOSS MUTATED 27 16 37 8
XP LOSS WILD-TYPE 80 65 65 42

Figure S295.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.13

Table S296.  Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 151 126
XQ LOSS MUTATED 11 37 26
XQ LOSS WILD-TYPE 82 114 100

Figure S296.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.13

Table S297.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 93 161 116
XQ LOSS MUTATED 12 31 31
XQ LOSS WILD-TYPE 81 130 85

Figure S297.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/26852961/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/26874095/LIHC-TP.transferedmergedcluster.txt

  • Number of patients = 370

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2016 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle