Correlation between copy number variations of arm-level result and molecular subtypes
Pancreatic Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1SQ8ZTT
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/C1SQ8ZTT
Overview
Introduction

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

Summary

Testing the association between copy number variation 80 arm-level events and 10 molecular subtypes across 184 patients, 268 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 2q gain cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • 4q gain cnv correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 6p gain cnv correlated to 'MIRSEQ_CNMF'.

  • 6q gain cnv correlated to 'MIRSEQ_CNMF'.

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

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

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 9q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'RPPA_CNMF'.

  • 10q gain cnv correlated to 'RPPA_CNMF'.

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

  • 11q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

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

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

  • 13q gain cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 14q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 15q gain cnv correlated to 'CN_CNMF'.

  • 16p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 17p gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 18q gain cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 19q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

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

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

  • 22q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • xp gain cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq gain cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 2q loss cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 3q loss cnv correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 4q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 6q 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'.

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

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

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

  • 9q loss cnv correlated to 'CN_CNMF'.

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

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

  • 11p loss cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11q loss cnv correlated to 'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 12q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • 14q loss cnv correlated to 'METHLYATION_CNMF'.

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

  • 16p loss cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 16q loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 18p loss cnv correlated to 'CN_CNMF'.

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

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

  • 19q loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 20p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 20q loss cnv correlated to 'CN_CNMF'.

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

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • xp loss cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 268 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
6q loss 82 (45%) 102 1e-05
(0.000571) 		1e-05
(0.000571) 		0.0225
(0.0922) 		0.521
(0.679) 		2e-05
(0.000941) 		0.00089
(0.0132) 		0.00127
(0.0164) 		1e-05
(0.000571) 		0.00036
(0.0064) 		0.00027
(0.00502)
4q gain 9 (5%) 175 0.007
(0.0479) 		0.571
(0.726) 		0.359
(0.535) 		0.0451
(0.142) 		0.00798
(0.0519) 		0.0089
(0.0535) 		0.0399
(0.132) 		0.0135
(0.0663) 		0.029
(0.108) 		0.00095
(0.0135)
7p gain 53 (29%) 131 0.00117
(0.0155) 		0.0467
(0.144) 		0.00733
(0.0489) 		0.0474
(0.145) 		0.0122
(0.0624) 		0.205
(0.367) 		0.144
(0.295) 		0.0379
(0.128) 		0.033
(0.117) 		0.00133
(0.0169)
9p loss 74 (40%) 110 1e-05
(0.000571) 		0.00027
(0.00502) 		0.0261
(0.1) 		0.0623
(0.171) 		0.00172
(0.0183) 		0.0429
(0.138) 		0.0484
(0.147) 		0.0226
(0.0922) 		0.0995
(0.236) 		0.0327
(0.116)
12p loss 19 (10%) 165 0.0234
(0.0936) 		0.0349
(0.12) 		7e-05
(0.00224) 		0.00142
(0.0174) 		0.00914
(0.0539) 		0.0143
(0.0683) 		0.595
(0.75) 		0.00021
(0.00442) 		0.103
(0.237) 		0.00078
(0.012)
17p loss 79 (43%) 105 1e-05
(0.000571) 		1e-05
(0.000571) 		0.0519
(0.153) 		0.129
(0.276) 		1e-05
(0.000571) 		1e-05
(0.000571) 		0.0001
(0.00276) 		6e-05
(0.00209) 		1e-05
(0.000571) 		8e-05
(0.00237)
18q loss 104 (57%) 80 2e-05
(0.000941) 		0.00013
(0.00315) 		0.781
(0.881) 		0.533
(0.69) 		0.00436
(0.0354) 		0.00244
(0.0238) 		0.00016
(0.00366) 		0.00236
(0.0235) 		0.0342
(0.12) 		0.00011
(0.00284)
4p gain 11 (6%) 173 0.0198
(0.0833) 		0.629
(0.77) 		0.358
(0.535) 		0.0456
(0.142) 		0.0141
(0.068) 		0.0109
(0.0591) 		0.175
(0.335) 		0.0214
(0.0883) 		0.0177
(0.0769) 		0.00153
(0.0174)
12p gain 32 (17%) 152 0.0001
(0.00276) 		0.00096
(0.0135) 		0.486
(0.654) 		0.0493
(0.148) 		0.00333
(0.0306) 		0.501
(0.664) 		0.0388
(0.129) 		0.0593
(0.166) 		0.0428
(0.138) 		0.00236
(0.0235)
1q gain 52 (28%) 132 0.00709
(0.0479) 		1e-05
(0.000571) 		0.426
(0.601) 		0.294
(0.469) 		0.036
(0.122) 		0.0302
(0.11) 		0.0345
(0.12) 		0.0209
(0.0866) 		0.0561
(0.16) 		0.269
(0.44)
12q gain 24 (13%) 160 0.00428
(0.0353) 		0.0156
(0.072) 		0.233
(0.402) 		0.0522
(0.154) 		0.00675
(0.0474) 		0.169
(0.326) 		0.0833
(0.209) 		0.0461
(0.144) 		0.0167
(0.0744) 		0.00081
(0.0122)
17p gain 10 (5%) 174 0.83
(0.914) 		0.155
(0.311) 		0.746
(0.859) 		0.229
(0.398) 		0.00261
(0.0249) 		0.00157
(0.0174) 		0.0456
(0.142) 		0.00672
(0.0474) 		0.00693
(0.0478) 		1e-05
(0.000571)
20q gain 46 (25%) 138 0.00022
(0.00451) 		0.0483
(0.147) 		0.184
(0.342) 		0.0109
(0.0591) 		0.12
(0.266) 		0.156
(0.312) 		0.129
(0.276) 		0.0197
(0.0833) 		0.0486
(0.147) 		0.0164
(0.0731)
6p loss 64 (35%) 120 1e-05
(0.000571) 		6e-05
(0.00209) 		0.084
(0.21) 		0.188
(0.348) 		0.00228
(0.0234) 		0.0148
(0.0693) 		0.26
(0.432) 		0.00099
(0.0136) 		0.316
(0.489) 		0.00043
(0.00748)
13q loss 20 (11%) 164 0.00574
(0.0425) 		0.0144
(0.0683) 		0.973
(1.00) 		0.639
(0.776) 		0.00508
(0.0391) 		0.154
(0.31) 		0.0254
(0.0983) 		0.0126
(0.0635) 		0.407
(0.587) 		0.0107
(0.0589)
15q loss 30 (16%) 154 0.00872
(0.0535) 		0.0101
(0.0572) 		0.563
(0.721) 		0.619
(0.765) 		0.00156
(0.0174) 		0.00224
(0.0233) 		0.753
(0.861) 		0.00691
(0.0478) 		0.722
(0.841) 		0.00873
(0.0535)
5q gain 22 (12%) 162 0.0137
(0.0666) 		0.586
(0.74) 		0.773
(0.878) 		0.417
(0.597) 		0.137
(0.283) 		0.0229
(0.0924) 		0.0112
(0.0597) 		0.0414
(0.136) 		0.0609
(0.169) 		0.001
(0.0136)
16p gain 23 (12%) 161 0.00238
(0.0235) 		0.00419
(0.0353) 		0.00509
(0.0391) 		0.512
(0.671) 		0.0243
(0.0956) 		0.0547
(0.157) 		0.312
(0.485) 		0.00919
(0.0539) 		0.471
(0.639) 		0.248
(0.417)
18p gain 29 (16%) 155 0.00341
(0.031) 		0.0254
(0.0983) 		0.512
(0.671) 		0.574
(0.729) 		0.00888
(0.0535) 		0.123
(0.269) 		0.213
(0.376) 		0.0157
(0.072) 		0.555
(0.714) 		0.00633
(0.0452)
20p gain 36 (20%) 148 0.0153
(0.0712) 		0.0286
(0.108) 		0.15
(0.304) 		0.0697
(0.183) 		0.0449
(0.142) 		0.0797
(0.203) 		0.111
(0.253) 		0.0088
(0.0535) 		0.159
(0.313) 		0.0027
(0.0254)
xp gain 8 (4%) 176 0.88
(0.945) 		0.31
(0.485) 		0.729
(0.847) 		0.101
(0.237) 		0.0339
(0.12) 		0.0348
(0.12) 		0.184
(0.342) 		0.0399
(0.132) 		0.0103
(0.0577) 		3e-05
(0.00126)
xq gain 15 (8%) 169 0.179
(0.339) 		0.566
(0.721) 		0.202
(0.365) 		0.0284
(0.107) 		0.313
(0.485) 		0.0233
(0.0936) 		0.0296
(0.109) 		0.111
(0.252) 		0.00985
(0.0563) 		0.012
(0.0624)
1p loss 34 (18%) 150 0.00224
(0.0233) 		0.00011
(0.00284) 		0.00364
(0.0324) 		0.0723
(0.189) 		0.0449
(0.142) 		0.078
(0.199) 		0.114
(0.257) 		0.0605
(0.168) 		0.244
(0.416) 		0.0388
(0.129)
8p loss 42 (23%) 142 1e-05
(0.000571) 		0.00368
(0.0324) 		0.182
(0.341) 		0.238
(0.408) 		0.016
(0.0722) 		0.00833
(0.0525) 		0.423
(0.601) 		0.00798
(0.0519) 		0.0873
(0.216) 		0.0584
(0.165)
10q loss 30 (16%) 154 0.00015
(0.00353) 		0.903
(0.957) 		0.896
(0.953) 		0.2
(0.362) 		0.0432
(0.139) 		0.0175
(0.0769) 		0.0643
(0.174) 		0.334
(0.509) 		0.0159
(0.0722) 		0.0189
(0.0812)
12q loss 28 (15%) 156 0.0119
(0.0624) 		0.069
(0.182) 		0.0121
(0.0624) 		0.0921
(0.226) 		0.0177
(0.0769) 		0.00256
(0.0247) 		0.752
(0.861) 		0.0264
(0.1) 		0.0517
(0.153) 		0.102
(0.237)
19p loss 17 (9%) 167 0.00923
(0.0539) 		0.0456
(0.142) 		0.37
(0.547) 		0.0645
(0.174) 		0.00159
(0.0174) 		0.0294
(0.108) 		0.507
(0.669) 		0.00359
(0.0323) 		0.0809
(0.204) 		0.148
(0.301)
3q gain 20 (11%) 164 0.00833
(0.0525) 		3e-05
(0.00126) 		0.208
(0.369) 		0.0439
(0.14) 		0.00159
(0.0174) 		0.281
(0.454) 		0.768
(0.875) 		0.0592
(0.166) 		0.642
(0.776) 		0.166
(0.321)
5p gain 28 (15%) 156 0.0162
(0.073) 		0.502
(0.665) 		0.804
(0.898) 		0.461
(0.631) 		0.21
(0.372) 		0.157
(0.312) 		0.0183
(0.0791) 		0.126
(0.273) 		0.0199
(0.0833) 		0.00078
(0.012)
7q gain 49 (27%) 135 0.00513
(0.0391) 		0.26
(0.432) 		0.0368
(0.125) 		0.114
(0.257) 		0.0763
(0.196) 		0.193
(0.352) 		0.294
(0.469) 		0.266
(0.438) 		0.0353
(0.121) 		0.00428
(0.0353)
11q gain 17 (9%) 167 0.0228
(0.0924) 		0.0103
(0.0577) 		0.0974
(0.233) 		0.00826
(0.0525) 		0.049
(0.148) 		0.89
(0.95) 		0.907
(0.958) 		0.561
(0.721) 		0.0533
(0.155) 		0.192
(0.352)
16q gain 23 (12%) 161 0.00075
(0.012) 		0.00386
(0.0329) 		0.114
(0.257) 		0.835
(0.917) 		0.0109
(0.0591) 		0.0542
(0.157) 		0.405
(0.587) 		0.00074
(0.012) 		0.168
(0.324) 		0.081
(0.204)
10p loss 36 (20%) 148 2e-05
(0.000941) 		0.433
(0.604) 		0.897
(0.953) 		0.677
(0.802) 		0.00386
(0.0329) 		0.193
(0.352) 		0.659
(0.79) 		0.147
(0.3) 		0.0197
(0.0833) 		0.0425
(0.138)
19q loss 11 (6%) 173 0.0997
(0.236) 		0.0421
(0.138) 		0.297
(0.47) 		0.223
(0.39) 		0.00375
(0.0326) 		0.00596
(0.0433) 		0.73
(0.848) 		0.0136
(0.0663) 		0.311
(0.485) 		0.162
(0.318)
2p gain 16 (9%) 168 0.252
(0.423) 		0.00018
(0.00389) 		0.432
(0.604) 		0.438
(0.607) 		0.0133
(0.0656) 		0.183
(0.342) 		0.749
(0.859) 		0.0051
(0.0391) 		0.0802
(0.203) 		0.168
(0.324)
2q gain 18 (10%) 166 0.177
(0.338) 		5e-05
(0.0019) 		0.433
(0.604) 		0.438
(0.607) 		0.0244
(0.0956) 		0.121
(0.266) 		0.666
(0.793) 		0.00149
(0.0174) 		0.0614
(0.169) 		0.0728
(0.19)
19p gain 19 (10%) 165 0.00469
(0.0375) 		0.272
(0.443) 		0.642
(0.776) 		0.361
(0.537) 		0.00149
(0.0174) 		0.72
(0.841) 		0.0748
(0.193) 		0.501
(0.664) 		0.42
(0.6) 		0.0305
(0.11)
4p loss 25 (14%) 159 0.429
(0.602) 		0.00937
(0.0543) 		0.294
(0.469) 		0.85
(0.924) 		0.012
(0.0624) 		0.103
(0.237) 		0.138
(0.286) 		0.0126
(0.0635) 		0.532
(0.69) 		0.176
(0.336)
4q loss 24 (13%) 160 0.344
(0.521) 		0.0129
(0.0647) 		0.498
(0.664) 		0.359
(0.535) 		0.0384
(0.129) 		0.234
(0.403) 		0.23
(0.398) 		0.00438
(0.0354) 		0.406
(0.587) 		0.0925
(0.226)
11p loss 17 (9%) 167 0.0543
(0.157) 		0.0467
(0.144) 		0.089
(0.22) 		0.116
(0.259) 		0.275
(0.448) 		0.886
(0.947) 		0.00769
(0.0508) 		0.482
(0.65) 		0.205
(0.367) 		0.0133
(0.0656)
11q loss 15 (8%) 169 0.181
(0.341) 		0.122
(0.267) 		0.253
(0.423) 		8e-05
(0.00237) 		0.627
(0.77) 		0.565
(0.721) 		0.00024
(0.00468) 		0.402
(0.585) 		0.136
(0.283) 		5e-05
(0.0019)
21q loss 58 (32%) 126 7e-05
(0.00224) 		0.00555
(0.0415) 		0.613
(0.761) 		0.131
(0.279) 		0.344
(0.521) 		0.0961
(0.233) 		0.271
(0.442) 		0.0326
(0.116) 		0.258
(0.43) 		0.426
(0.601)
22q loss 47 (26%) 137 1e-05
(0.000571) 		0.0015
(0.0174) 		0.799
(0.894) 		0.948
(0.985) 		0.101
(0.237) 		0.303
(0.476) 		0.225
(0.393) 		0.029
(0.108) 		0.0992
(0.236) 		0.164
(0.32)
3p gain 10 (5%) 174 0.0658
(0.177) 		0.00855
(0.0534) 		0.556
(0.715) 		0.206
(0.367) 		0.0291
(0.108) 		0.618
(0.765) 		1
(1.00) 		0.444
(0.613) 		0.423
(0.601) 		0.75
(0.86)
8q gain 48 (26%) 136 0.00017
(0.00378) 		0.0143
(0.0683) 		0.844
(0.922) 		0.789
(0.887) 		0.0734
(0.19) 		0.548
(0.707) 		0.132
(0.279) 		0.08
(0.203) 		0.223
(0.39) 		0.186
(0.346)
9q gain 12 (7%) 172 0.0247
(0.0965) 		0.794
(0.891) 		0.821
(0.909) 		0.504
(0.667) 		0.133
(0.279) 		0.612
(0.761) 		0.815
(0.904) 		0.264
(0.436) 		0.179
(0.339) 		0.031
(0.112)
11p gain 14 (8%) 170 0.0237
(0.0945) 		0.0263
(0.1) 		0.205
(0.367) 		0.378
(0.553) 		0.294
(0.469) 		1
(1.00) 		0.926
(0.97) 		0.74
(0.856) 		0.77
(0.876) 		0.909
(0.958)
13q gain 28 (15%) 156 0.1
(0.236) 		0.72
(0.841) 		0.974
(1.00) 		0.972
(1.00) 		0.00168
(0.0182) 		0.319
(0.493) 		0.415
(0.595) 		0.126
(0.273) 		0.647
(0.778) 		0.05
(0.149)
14q gain 26 (14%) 158 0.00023
(0.0046) 		0.139
(0.286) 		0.589
(0.743) 		0.663
(0.791) 		0.00827
(0.0525) 		0.577
(0.731) 		0.289
(0.465) 		0.263
(0.435) 		0.922
(0.968) 		0.0999
(0.236)
17q gain 19 (10%) 165 0.121
(0.266) 		0.347
(0.523) 		0.781
(0.881) 		0.864
(0.935) 		0.0059
(0.0433) 		0.0601
(0.168) 		0.0966
(0.233) 		0.0641
(0.174) 		0.156
(0.312) 		0.00044
(0.00749)
18q gain 13 (7%) 171 0.0708
(0.186) 		0.708
(0.831) 		0.681
(0.805) 		0.181
(0.341) 		0.509
(0.67) 		0.404
(0.587) 		0.0239
(0.0949) 		0.0946
(0.231) 		0.164
(0.319) 		0.00012
(0.003)
19q gain 29 (16%) 155 0.00028
(0.00509) 		0.135
(0.281) 		0.883
(0.946) 		0.637
(0.776) 		0.00118
(0.0155) 		0.857
(0.929) 		0.166
(0.321) 		0.888
(0.949) 		0.156
(0.312) 		0.206
(0.367)
22q gain 7 (4%) 177 0.00091
(0.0132) 		0.016
(0.0722) 		0.942
(0.981) 		0.527
(0.685) 		0.279
(0.452) 		0.172
(0.33) 		0.435
(0.606) 		0.159
(0.313) 		0.409
(0.588) 		0.319
(0.493)
2q loss 4 (2%) 180 0.564
(0.721) 		0.409
(0.588) 		0.292
(0.468) 		0.0667
(0.178) 		0.00142
(0.0174) 		0.202
(0.365) 		0.348
(0.524) 		0.00529
(0.0399)
3q loss 19 (10%) 165 0.125
(0.273) 		0.466
(0.636) 		0.00289
(0.0269) 		0.0579
(0.164) 		0.352
(0.528) 		0.669
(0.796) 		0.0674
(0.179) 		1
(1.00) 		0.131
(0.279) 		0.0318
(0.114)
8q loss 16 (9%) 168 0.00068
(0.0113) 		0.229
(0.398) 		0.0633
(0.172) 		0.304
(0.476) 		0.426
(0.601) 		0.436
(0.606) 		0.324
(0.499) 		0.45
(0.618) 		0.26
(0.432) 		0.0348
(0.12)
16p loss 10 (5%) 174 0.599
(0.752) 		0.5
(0.664) 		0.0524
(0.154) 		0.0122
(0.0624) 		0.409
(0.588) 		0.245
(0.416) 		0.375
(0.553) 		0.541
(0.699) 		0.281
(0.454) 		0.0112
(0.0597)
17q loss 19 (10%) 165 0.00512
(0.0391) 		0.219
(0.384) 		0.02
(0.0833) 		0.102
(0.237) 		0.191
(0.352) 		0.584
(0.739) 		0.522
(0.679) 		0.638
(0.776) 		0.853
(0.926) 		0.704
(0.827)
20p loss 19 (10%) 165 0.00712
(0.0479) 		0.119
(0.265) 		0.645
(0.777) 		0.739
(0.855) 		0.11
(0.252) 		0.114
(0.257) 		0.0733
(0.19) 		0.0464
(0.144) 		0.153
(0.308) 		0.0913
(0.225)
xp loss 27 (15%) 157 0.00979
(0.0563) 		0.244
(0.416) 		0.0343
(0.12) 		0.644
(0.777) 		0.365
(0.541) 		0.289
(0.466) 		0.187
(0.347) 		0.957
(0.99) 		0.303
(0.476) 		0.178
(0.338)
6p gain 7 (4%) 177 0.296
(0.47) 		0.61
(0.761) 		0.747
(0.859) 		0.432
(0.604) 		0.661
(0.791) 		1
(1.00) 		0.0147
(0.069) 		0.874
(0.942) 		0.881
(0.945) 		0.471
(0.639)
6q gain 5 (3%) 179 0.606
(0.759) 		0.68
(0.804) 		1
(1.00) 		0.907
(0.958) 		0.62
(0.765) 		1
(1.00) 		0.00917
(0.0539) 		1
(1.00) 		0.248
(0.417) 		0.198
(0.359)
8p gain 25 (14%) 159 0.0106
(0.0588) 		0.192
(0.352) 		0.297
(0.47) 		0.829
(0.914) 		0.327
(0.501) 		1
(1.00) 		0.133
(0.279) 		0.629
(0.77) 		0.393
(0.574) 		0.83
(0.914)
10p gain 10 (5%) 174 1
(1.00) 		0.251
(0.422) 		0.019
(0.0813) 		0.0954
(0.232) 		0.347
(0.523) 		0.816
(0.904) 		0.0772
(0.198) 		0.902
(0.957) 		1
(1.00) 		0.234
(0.403)
10q gain 13 (7%) 171 0.955
(0.99) 		0.16
(0.314) 		0.0427
(0.138) 		0.135
(0.281) 		0.484
(0.652) 		0.377
(0.553) 		0.0675
(0.179) 		0.914
(0.963) 		0.506
(0.668) 		0.84
(0.92)
15q gain 15 (8%) 169 0.0175
(0.0769) 		0.0546
(0.157) 		0.777
(0.88) 		1
(1.00) 		0.364
(0.541) 		0.0861
(0.214) 		0.193
(0.352) 		1
(1.00) 		0.331
(0.508) 		0.462
(0.631)
9q loss 43 (23%) 141 0.00609
(0.0439) 		0.105
(0.241) 		0.515
(0.673) 		0.116
(0.259) 		0.324
(0.499) 		0.442
(0.611) 		0.147
(0.3) 		0.266
(0.438) 		0.299
(0.471) 		0.267
(0.438)
14q loss 15 (8%) 169 0.496
(0.664) 		0.0473
(0.145) 		0.426
(0.601) 		0.566
(0.721) 		0.127
(0.274) 		0.098
(0.234) 		0.182
(0.341) 		0.206
(0.367) 		0.158
(0.312) 		0.477
(0.645)
16q loss 13 (7%) 171 0.199
(0.361) 		0.666
(0.793) 		0.715
(0.837) 		0.378
(0.553) 		0.333
(0.508) 		0.121
(0.266) 		0.139
(0.286) 		0.245
(0.416) 		0.375
(0.553) 		0.026
(0.1)
18p loss 54 (29%) 130 0.0113
(0.0597) 		0.452
(0.62) 		0.722
(0.841) 		0.841
(0.921) 		0.936
(0.977) 		0.65
(0.781) 		0.0851
(0.212) 		0.975
(1.00) 		0.129
(0.276) 		0.133
(0.279)
20q loss 5 (3%) 179 0.0304
(0.11) 		0.611
(0.761) 		0.743
(0.858) 		0.847
(0.924) 		0.609
(0.761) 		0.826
(0.913) 		0.848
(0.924) 		0.672
(0.798)
1p gain 22 (12%) 162 0.637
(0.776) 		0.107
(0.246) 		0.245
(0.416) 		0.0584
(0.165) 		0.848
(0.924) 		0.421
(0.6) 		0.872
(0.942) 		0.768
(0.875) 		0.477
(0.645) 		0.943
(0.981)
9p gain 8 (4%) 176 0.158
(0.312) 		1
(1.00) 		0.798
(0.894) 		0.267
(0.438) 		0.662
(0.791) 		0.634
(0.774) 		0.875
(0.942) 		0.789
(0.887) 		0.404
(0.587) 		0.102
(0.237)
1q loss 8 (4%) 176 0.115
(0.259) 		0.519
(0.678) 		0.745
(0.859) 		0.926
(0.97) 		0.599
(0.752) 		0.512
(0.671) 		0.466
(0.636) 		0.697
(0.821) 		0.868
(0.938) 		0.0625
(0.171)
2p loss 10 (5%) 174 0.333
(0.508) 		0.218
(0.383) 		0.734
(0.851) 		0.424
(0.601) 		0.809
(0.902) 		0.248
(0.417) 		0.0576
(0.164) 		0.602
(0.755) 		0.31
(0.485) 		0.063
(0.172)
3p loss 36 (20%) 148 0.0507
(0.151) 		0.0664
(0.178) 		0.133
(0.279) 		0.447
(0.616) 		0.127
(0.274) 		0.907
(0.958) 		0.132
(0.279) 		0.297
(0.47) 		0.922
(0.968) 		0.47
(0.639)
5p loss 9 (5%) 175 0.782
(0.881) 		0.879
(0.945) 		0.933
(0.974) 		0.815
(0.904) 		0.625
(0.77) 		0.238
(0.408) 		0.815
(0.904) 		1
(1.00) 		0.836
(0.917) 		0.896
(0.953)
5q loss 11 (6%) 173 0.447
(0.616) 		0.5
(0.664) 		0.698
(0.821) 		0.158
(0.312) 		0.628
(0.77) 		0.345
(0.522) 		0.495
(0.664) 		0.694
(0.819) 		0.952
(0.987) 		0.779
(0.881)
7q loss 3 (2%) 181 0.35
(0.526) 		0.624
(0.769) 		0.929
(0.971) 		0.774
(0.878) 		0.615
(0.763) 		1
(1.00) 		1
(1.00) 		1
(1.00)
xq loss 16 (9%) 168 0.0963
(0.233) 		0.0969
(0.233) 		0.0532
(0.155) 		0.145
(0.297) 		0.34
(0.517) 		0.387
(0.567) 		0.64
(0.776) 		0.81
(0.902) 		0.214
(0.377) 		0.493
(0.661)
'1q gain' versus 'CN_CNMF'

P value = 0.00709 (Fisher's exact test), Q value = 0.048

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
1Q GAIN MUTATED 7 29 5 11
1Q GAIN WILD-TYPE 19 45 41 27

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
1Q GAIN MUTATED 25 7 16 4
1Q GAIN WILD-TYPE 20 42 36 33

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.12

Table S3.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
1Q GAIN MUTATED 18 5 12 10 4
1Q GAIN WILD-TYPE 21 21 31 29 26

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.11

Table S4.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
1Q GAIN MUTATED 19 27 3
1Q GAIN WILD-TYPE 55 48 25

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.12

Table S5.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
1Q GAIN MUTATED 22 7 7 9 4
1Q GAIN WILD-TYPE 30 40 18 22 18

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.087

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
1Q GAIN MUTATED 36 9 4
1Q GAIN WILD-TYPE 66 33 29

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0039

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
2P GAIN MUTATED 6 0 10 0
2P GAIN WILD-TYPE 39 49 42 37

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.066

Table S8.  Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
2P GAIN MUTATED 4 2 9 1 0
2P GAIN WILD-TYPE 35 24 34 38 30

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0051 (Fisher's exact test), Q value = 0.039

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
2P GAIN MUTATED 15 0 1
2P GAIN WILD-TYPE 87 42 32

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0019

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
2Q GAIN MUTATED 7 0 11 0
2Q GAIN WILD-TYPE 38 49 41 37

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

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.096

Table S11.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
2Q GAIN MUTATED 4 2 10 1 1
2Q GAIN WILD-TYPE 35 24 33 38 29

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.017

Table S12.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
2Q GAIN MUTATED 17 0 1
2Q GAIN WILD-TYPE 85 42 32

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00855 (Fisher's exact test), Q value = 0.053

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
3P GAIN MUTATED 4 0 6 0
3P GAIN WILD-TYPE 41 49 46 37

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

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
3P GAIN MUTATED 1 0 7 1 1
3P GAIN WILD-TYPE 38 26 36 38 29

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

'3q gain' versus 'CN_CNMF'

P value = 0.00833 (Fisher's exact test), Q value = 0.052

Table S15.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
3Q GAIN MUTATED 2 15 1 2
3Q GAIN WILD-TYPE 24 59 45 36

Figure S15.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0013

Table S16.  Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
3Q GAIN MUTATED 8 0 12 0
3Q GAIN WILD-TYPE 37 49 40 37

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

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0439 (Fisher's exact test), Q value = 0.14

Table S17.  Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 25 16 16 18
3Q GAIN MUTATED 5 2 1 0 6
3Q GAIN WILD-TYPE 42 23 15 16 12

Figure S17.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.017

Table S18.  Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
3Q GAIN MUTATED 2 1 13 2 2
3Q GAIN WILD-TYPE 37 25 30 37 28

Figure S18.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.083

Table S19.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
4P GAIN MUTATED 1 4 0 6
4P GAIN WILD-TYPE 25 70 46 32

Figure S19.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 25 16 16 18
4P GAIN MUTATED 1 0 0 3 1
4P GAIN WILD-TYPE 46 25 16 13 17

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

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.068

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
4P GAIN MUTATED 1 5 2 0 3
4P GAIN WILD-TYPE 38 21 41 39 27

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

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.059

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
4P GAIN MUTATED 1 5 5
4P GAIN WILD-TYPE 73 70 23

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

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.088

Table S23.  Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
4P GAIN MUTATED 6 0 5
4P GAIN WILD-TYPE 96 42 28

Figure S23.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.077

Table S24.  Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
4P GAIN MUTATED 0 1 2 2 1 1 4
4P GAIN WILD-TYPE 27 10 25 11 50 26 13

Figure S24.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00153 (Fisher's exact test), Q value = 0.017

Table S25.  Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
4P GAIN MUTATED 0 2 2 2 1 4
4P GAIN WILD-TYPE 23 42 17 51 25 4

Figure S25.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.007 (Fisher's exact test), Q value = 0.048

Table S26.  Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
4Q GAIN MUTATED 0 3 0 6
4Q GAIN WILD-TYPE 26 71 46 32

Figure S26.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 25 16 16 18
4Q GAIN MUTATED 1 0 0 3 1
4Q GAIN WILD-TYPE 46 25 16 13 17

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

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.00798 (Fisher's exact test), Q value = 0.052

Table S28.  Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
4Q GAIN MUTATED 1 5 1 0 2
4Q GAIN WILD-TYPE 38 21 42 39 28

Figure S28.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0089 (Fisher's exact test), Q value = 0.054

Table S29.  Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
4Q GAIN MUTATED 1 3 5
4Q GAIN WILD-TYPE 73 72 23

Figure S29.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.13

Table S30.  Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
4Q GAIN MUTATED 3 0 0 4 2
4Q GAIN WILD-TYPE 49 47 25 27 20

Figure S30.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.066

Table S31.  Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
4Q GAIN MUTATED 4 0 5
4Q GAIN WILD-TYPE 98 42 28

Figure S31.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.11

Table S32.  Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
4Q GAIN MUTATED 0 0 2 1 1 1 4
4Q GAIN WILD-TYPE 27 11 25 12 50 26 13

Figure S32.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.013

Table S33.  Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
4Q GAIN MUTATED 0 1 1 2 1 4
4Q GAIN WILD-TYPE 23 43 18 51 25 4

Figure S33.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.073

Table S34.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
5P GAIN MUTATED 3 12 2 11
5P GAIN WILD-TYPE 23 62 44 27

Figure S34.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.079

Table S35.  Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
5P GAIN MUTATED 8 3 4 11 2
5P GAIN WILD-TYPE 44 44 21 20 20

Figure S35.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.083

Table S36.  Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
5P GAIN MUTATED 4 1 1 2 13 1 6
5P GAIN WILD-TYPE 23 10 26 11 38 26 11

Figure S36.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.012

Table S37.  Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
5P GAIN MUTATED 1 9 4 6 2 6
5P GAIN WILD-TYPE 22 35 15 47 24 2

Figure S37.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.067

Table S38.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
5Q GAIN MUTATED 1 9 2 10
5Q GAIN WILD-TYPE 25 65 44 28

Figure S38.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.092

Table S39.  Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
5Q GAIN MUTATED 8 6 8
5Q GAIN WILD-TYPE 66 69 20

Figure S39.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.06

Table S40.  Gene #10: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
5Q GAIN MUTATED 7 1 3 9 2
5Q GAIN WILD-TYPE 45 46 22 22 20

Figure S40.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 0.14

Table S41.  Gene #10: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
5Q GAIN MUTATED 12 2 8
5Q GAIN WILD-TYPE 90 40 25

Figure S41.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.014

Table S42.  Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
5Q GAIN MUTATED 1 6 2 5 2 6
5Q GAIN WILD-TYPE 22 38 17 48 24 2

Figure S42.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.069

Table S43.  Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
6P GAIN MUTATED 1 1 0 5 0
6P GAIN WILD-TYPE 51 46 25 26 22

Figure S43.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.00917 (Fisher's exact test), Q value = 0.054

Table S44.  Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
6Q GAIN MUTATED 0 1 0 4 0
6Q GAIN WILD-TYPE 52 46 25 27 22

Figure S44.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.015

Table S45.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
7P GAIN MUTATED 6 28 4 15
7P GAIN WILD-TYPE 20 46 42 23

Figure S45.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.14

Table S46.  Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
7P GAIN MUTATED 16 10 20 6
7P GAIN WILD-TYPE 29 39 32 31

Figure S46.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.00733 (Fisher's exact test), Q value = 0.049

Table S47.  Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
7P GAIN MUTATED 16 9 1 1 7
7P GAIN WILD-TYPE 23 16 19 14 16

Figure S47.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0474 (Fisher's exact test), Q value = 0.14

Table S48.  Gene #13: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 25 16 16 18
7P GAIN MUTATED 16 9 0 4 5
7P GAIN WILD-TYPE 31 16 16 12 13

Figure S48.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.062

Table S49.  Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
7P GAIN MUTATED 16 10 15 7 3
7P GAIN WILD-TYPE 23 16 28 32 27

Figure S49.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.13

Table S50.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
7P GAIN MUTATED 37 7 7
7P GAIN WILD-TYPE 65 35 26

Figure S50.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.12

Table S51.  Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
7P GAIN MUTATED 6 5 8 1 21 3 6
7P GAIN WILD-TYPE 21 6 19 12 30 24 11

Figure S51.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.017

Table S52.  Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
7P GAIN MUTATED 6 17 8 11 2 6
7P GAIN WILD-TYPE 17 27 11 42 24 2

Figure S52.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 0.00513 (Fisher's exact test), Q value = 0.039

Table S53.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
7Q GAIN MUTATED 6 26 4 13
7Q GAIN WILD-TYPE 20 48 42 25

Figure S53.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.12

Table S54.  Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
7Q GAIN MUTATED 14 7 1 1 6
7Q GAIN WILD-TYPE 25 18 19 14 17

Figure S54.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.12

Table S55.  Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
7Q GAIN MUTATED 6 5 8 1 18 2 6
7Q GAIN WILD-TYPE 21 6 19 12 33 25 11

Figure S55.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00428 (Fisher's exact test), Q value = 0.035

Table S56.  Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
7Q GAIN MUTATED 5 13 8 12 2 6
7Q GAIN WILD-TYPE 18 31 11 41 24 2

Figure S56.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.059

Table S57.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
8P GAIN MUTATED 4 8 2 11
8P GAIN WILD-TYPE 22 66 44 27

Figure S57.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0038

Table S58.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
8Q GAIN MUTATED 6 27 2 13
8Q GAIN WILD-TYPE 20 47 44 25

Figure S58.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.068

Table S59.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
8Q GAIN MUTATED 18 8 16 5
8Q GAIN WILD-TYPE 27 41 36 32

Figure S59.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'CN_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.097

Table S60.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
9Q GAIN MUTATED 1 5 0 6
9Q GAIN WILD-TYPE 25 69 46 32

Figure S60.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.11

Table S61.  Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
9Q GAIN MUTATED 2 4 1 1 1 3
9Q GAIN WILD-TYPE 21 40 18 52 25 5

Figure S61.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'RPPA_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.081

Table S62.  Gene #19: '10p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
10P GAIN MUTATED 6 0 0 0 0
10P GAIN WILD-TYPE 33 25 20 15 23

Figure S62.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'10q gain' versus 'RPPA_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.14

Table S63.  Gene #20: '10q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
10Q GAIN MUTATED 7 0 0 1 1
10Q GAIN WILD-TYPE 32 25 20 14 22

Figure S63.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.094

Table S64.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
11P GAIN MUTATED 1 7 0 6
11P GAIN WILD-TYPE 25 67 46 32

Figure S64.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.1

Table S65.  Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
11P GAIN MUTATED 6 0 6 2
11P GAIN WILD-TYPE 39 49 46 35

Figure S65.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.092

Table S66.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
11Q GAIN MUTATED 2 9 0 6
11Q GAIN WILD-TYPE 24 65 46 32

Figure S66.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.058

Table S67.  Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
11Q GAIN MUTATED 5 0 9 3
11Q GAIN WILD-TYPE 40 49 43 34

Figure S67.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00826 (Fisher's exact test), Q value = 0.052

Table S68.  Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 25 16 16 18
11Q GAIN MUTATED 5 1 0 0 6
11Q GAIN WILD-TYPE 42 24 16 16 12

Figure S68.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.15

Table S69.  Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
11Q GAIN MUTATED 3 0 9 2 3
11Q GAIN WILD-TYPE 36 26 34 37 27

Figure S69.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0028

Table S70.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
12P GAIN MUTATED 0 20 2 10
12P GAIN WILD-TYPE 26 54 44 28

Figure S70.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.013

Table S71.  Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
12P GAIN MUTATED 12 7 13 0
12P GAIN WILD-TYPE 33 42 39 37

Figure S71.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0493 (Fisher's exact test), Q value = 0.15

Table S72.  Gene #23: '12p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 25 16 16 18
12P GAIN MUTATED 3 3 3 4 6
12P GAIN WILD-TYPE 44 22 13 12 12

Figure S72.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.031

Table S73.  Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
12P GAIN MUTATED 6 9 12 3 1
12P GAIN WILD-TYPE 33 17 31 36 29

Figure S73.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.13

Table S74.  Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
12P GAIN MUTATED 10 3 3 10 5
12P GAIN WILD-TYPE 42 44 22 21 17

Figure S74.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.14

Table S75.  Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
12P GAIN MUTATED 4 1 4 0 10 3 8
12P GAIN WILD-TYPE 23 10 23 13 41 24 9

Figure S75.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.024

Table S76.  Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
12P GAIN MUTATED 2 10 2 8 2 6
12P GAIN WILD-TYPE 21 34 17 45 24 2

Figure S76.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 0.00428 (Fisher's exact test), Q value = 0.035

Table S77.  Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
12Q GAIN MUTATED 0 16 2 6
12Q GAIN WILD-TYPE 26 58 44 32

Figure S77.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.072

Table S78.  Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
12Q GAIN MUTATED 9 6 9 0
12Q GAIN WILD-TYPE 36 43 43 37

Figure S78.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00675 (Fisher's exact test), Q value = 0.047

Table S79.  Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
12Q GAIN MUTATED 5 9 7 2 1
12Q GAIN WILD-TYPE 34 17 36 37 29

Figure S79.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0461 (Fisher's exact test), Q value = 0.14

Table S80.  Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
12Q GAIN MUTATED 14 2 8
12Q GAIN WILD-TYPE 88 40 25

Figure S80.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 0.074

Table S81.  Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
12Q GAIN MUTATED 4 0 1 0 8 3 7
12Q GAIN WILD-TYPE 23 11 26 13 43 24 10

Figure S81.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.012

Table S82.  Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
12Q GAIN MUTATED 1 7 2 5 2 6
12Q GAIN WILD-TYPE 22 37 17 48 24 2

Figure S82.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.018

Table S83.  Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
13Q GAIN MUTATED 6 10 4 1 6
13Q GAIN WILD-TYPE 33 16 39 38 24

Figure S83.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.15

Table S84.  Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
13Q GAIN MUTATED 4 4 5 7 2 4
13Q GAIN WILD-TYPE 19 40 14 46 24 4

Figure S84.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0046

Table S85.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
14Q GAIN MUTATED 0 15 1 10
14Q GAIN WILD-TYPE 26 59 45 28

Figure S85.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00827 (Fisher's exact test), Q value = 0.052

Table S86.  Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
14Q GAIN MUTATED 4 6 12 1 3
14Q GAIN WILD-TYPE 35 20 31 38 27

Figure S86.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.077

Table S87.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
15Q GAIN MUTATED 2 11 0 2
15Q GAIN WILD-TYPE 24 63 46 36

Figure S87.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.024

Table S88.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
16P GAIN MUTATED 2 15 0 6
16P GAIN WILD-TYPE 24 59 46 32

Figure S88.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.035

Table S89.  Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
16P GAIN MUTATED 9 2 11 1
16P GAIN WILD-TYPE 36 47 41 36

Figure S89.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.00509 (Fisher's exact test), Q value = 0.039

Table S90.  Gene #28: '16p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
16P GAIN MUTATED 12 3 1 1 0
16P GAIN WILD-TYPE 27 22 19 14 23

Figure S90.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.096

Table S91.  Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
16P GAIN MUTATED 8 3 9 3 0
16P GAIN WILD-TYPE 31 23 34 36 30

Figure S91.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00919 (Fisher's exact test), Q value = 0.054

Table S92.  Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
16P GAIN MUTATED 20 2 1
16P GAIN WILD-TYPE 82 40 32

Figure S92.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.012

Table S93.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
16Q GAIN MUTATED 1 15 0 7
16Q GAIN WILD-TYPE 25 59 46 31

Figure S93.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00386 (Fisher's exact test), Q value = 0.033

Table S94.  Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
16Q GAIN MUTATED 8 2 12 1
16Q GAIN WILD-TYPE 37 47 40 36

Figure S94.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.059

Table S95.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
16Q GAIN MUTATED 8 2 10 3 0
16Q GAIN WILD-TYPE 31 24 33 36 30

Figure S95.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.012

Table S96.  Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
16Q GAIN MUTATED 21 2 0
16Q GAIN WILD-TYPE 81 40 33

Figure S96.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.025

Table S97.  Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
17P GAIN MUTATED 0 6 2 1 1
17P GAIN WILD-TYPE 39 20 41 38 29

Figure S97.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.017

Table S98.  Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
17P GAIN MUTATED 1 3 6
17P GAIN WILD-TYPE 73 72 22

Figure S98.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.14

Table S99.  Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
17P GAIN MUTATED 1 2 0 5 2
17P GAIN WILD-TYPE 51 45 25 26 20

Figure S99.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00672 (Fisher's exact test), Q value = 0.047

Table S100.  Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
17P GAIN MUTATED 3 1 6
17P GAIN WILD-TYPE 99 41 27

Figure S100.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00693 (Fisher's exact test), Q value = 0.048

Table S101.  Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
17P GAIN MUTATED 1 0 0 1 3 0 5
17P GAIN WILD-TYPE 26 11 27 12 48 27 12

Figure S101.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S102.  Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
17P GAIN MUTATED 0 2 1 1 1 5
17P GAIN WILD-TYPE 23 42 18 52 25 3

Figure S102.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 0.043

Table S103.  Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
17Q GAIN MUTATED 1 6 9 2 1
17Q GAIN WILD-TYPE 38 20 34 37 29

Figure S103.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0075

Table S104.  Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
17Q GAIN MUTATED 2 8 0 3 1 5
17Q GAIN WILD-TYPE 21 36 19 50 25 3

Figure S104.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00341 (Fisher's exact test), Q value = 0.031

Table S105.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
18P GAIN MUTATED 4 19 1 5
18P GAIN WILD-TYPE 22 55 45 33

Figure S105.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.098

Table S106.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
18P GAIN MUTATED 9 4 13 2
18P GAIN WILD-TYPE 36 45 39 35

Figure S106.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00888 (Fisher's exact test), Q value = 0.054

Table S107.  Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
18P GAIN MUTATED 10 4 11 2 1
18P GAIN WILD-TYPE 29 22 32 37 29

Figure S107.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.072

Table S108.  Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
18P GAIN MUTATED 23 2 3
18P GAIN WILD-TYPE 79 40 30

Figure S108.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00633 (Fisher's exact test), Q value = 0.045

Table S109.  Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
18P GAIN MUTATED 3 11 5 5 0 3
18P GAIN WILD-TYPE 20 33 14 48 26 5

Figure S109.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.095

Table S110.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
18Q GAIN MUTATED 1 4 0 6 1
18Q GAIN WILD-TYPE 51 43 25 25 21

Figure S110.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.003

Table S111.  Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
18Q GAIN MUTATED 0 3 5 1 0 3
18Q GAIN WILD-TYPE 23 41 14 52 26 5

Figure S111.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.00469 (Fisher's exact test), Q value = 0.038

Table S112.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
19P GAIN MUTATED 1 12 0 6
19P GAIN WILD-TYPE 25 62 46 32

Figure S112.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.017

Table S113.  Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
19P GAIN MUTATED 5 8 5 1 0
19P GAIN WILD-TYPE 34 18 38 38 30

Figure S113.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.11

Table S114.  Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
19P GAIN MUTATED 3 4 3 4 1 4
19P GAIN WILD-TYPE 20 40 16 49 25 4

Figure S114.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0051

Table S115.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
19Q GAIN MUTATED 2 19 0 8
19Q GAIN WILD-TYPE 24 55 46 30

Figure S115.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.015

Table S116.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
19Q GAIN MUTATED 5 11 9 3 1
19Q GAIN WILD-TYPE 34 15 34 36 29

Figure S116.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.071

Table S117.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
20P GAIN MUTATED 2 18 4 12
20P GAIN WILD-TYPE 24 56 42 26

Figure S117.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.11

Table S118.  Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
20P GAIN MUTATED 15 7 10 3
20P GAIN WILD-TYPE 30 42 42 34

Figure S118.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.14

Table S119.  Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
20P GAIN MUTATED 9 8 11 2 5
20P GAIN WILD-TYPE 30 18 32 37 25

Figure S119.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0088 (Fisher's exact test), Q value = 0.054

Table S120.  Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
20P GAIN MUTATED 24 2 9
20P GAIN WILD-TYPE 78 40 24

Figure S120.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.025

Table S121.  Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
20P GAIN MUTATED 2 11 7 5 4 5
20P GAIN WILD-TYPE 21 33 12 48 22 3

Figure S121.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0045

Table S122.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
20Q GAIN MUTATED 2 27 4 13
20Q GAIN WILD-TYPE 24 47 42 25

Figure S122.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 0.15

Table S123.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
20Q GAIN MUTATED 16 10 15 4
20Q GAIN WILD-TYPE 29 39 37 33

Figure S123.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.059

Table S124.  Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 25 16 16 18
20Q GAIN MUTATED 11 6 0 7 8
20Q GAIN WILD-TYPE 36 19 16 9 10

Figure S124.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.083

Table S125.  Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
20Q GAIN MUTATED 31 4 9
20Q GAIN WILD-TYPE 71 38 24

Figure S125.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.15

Table S126.  Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
20Q GAIN MUTATED 2 2 5 3 20 5 6
20Q GAIN WILD-TYPE 25 9 22 10 31 22 11

Figure S126.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.073

Table S127.  Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
20Q GAIN MUTATED 4 15 7 8 4 5
20Q GAIN WILD-TYPE 19 29 12 45 22 3

Figure S127.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.013

Table S128.  Gene #38: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
22Q GAIN MUTATED 5 1 0 1
22Q GAIN WILD-TYPE 21 73 46 37

Figure S128.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.072

Table S129.  Gene #38: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
22Q GAIN MUTATED 0 0 5 1
22Q GAIN WILD-TYPE 45 49 47 36

Figure S129.  Get High-res Image Gene #38: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.12

Table S130.  Gene #39: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
XP GAIN MUTATED 2 4 2 0 0
XP GAIN WILD-TYPE 37 22 41 39 30

Figure S130.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0348 (Fisher's exact test), Q value = 0.12

Table S131.  Gene #39: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
XP GAIN MUTATED 1 3 4
XP GAIN WILD-TYPE 73 72 24

Figure S131.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0399 (Fisher's exact test), Q value = 0.13

Table S132.  Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
XP GAIN MUTATED 4 0 4
XP GAIN WILD-TYPE 98 42 29

Figure S132.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.058

Table S133.  Gene #39: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
XP GAIN MUTATED 0 1 0 0 3 0 4
XP GAIN WILD-TYPE 27 10 27 13 48 27 13

Figure S133.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0013

Table S134.  Gene #39: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
XP GAIN MUTATED 0 2 2 0 0 4
XP GAIN WILD-TYPE 23 42 17 53 26 4

Figure S134.  Get High-res Image Gene #39: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.11

Table S135.  Gene #40: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 25 16 16 18
XQ GAIN MUTATED 2 1 1 5 2
XQ GAIN WILD-TYPE 45 24 15 11 16

Figure S135.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.094

Table S136.  Gene #40: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
XQ GAIN MUTATED 3 6 6
XQ GAIN WILD-TYPE 71 69 22

Figure S136.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.11

Table S137.  Gene #40: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
XQ GAIN MUTATED 6 1 0 6 2
XQ GAIN WILD-TYPE 46 46 25 25 20

Figure S137.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00985 (Fisher's exact test), Q value = 0.056

Table S138.  Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
XQ GAIN MUTATED 0 0 2 1 7 0 5
XQ GAIN WILD-TYPE 27 11 25 12 44 27 12

Figure S138.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.062

Table S139.  Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
XQ GAIN MUTATED 1 5 1 2 2 4
XQ GAIN WILD-TYPE 22 39 18 51 24 4

Figure S139.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.023

Table S140.  Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
1P LOSS MUTATED 2 20 2 10
1P LOSS WILD-TYPE 24 54 44 28

Figure S140.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0028

Table S141.  Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
1P LOSS MUTATED 18 7 8 1
1P LOSS WILD-TYPE 27 42 44 36

Figure S141.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.00364 (Fisher's exact test), Q value = 0.032

Table S142.  Gene #41: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
1P LOSS MUTATED 15 2 2 0 5
1P LOSS WILD-TYPE 24 23 18 15 18

Figure S142.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.14

Table S143.  Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
1P LOSS MUTATED 13 3 9 5 2
1P LOSS WILD-TYPE 26 23 34 34 28

Figure S143.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.13

Table S144.  Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
1P LOSS MUTATED 6 11 4 8 0 2
1P LOSS WILD-TYPE 17 33 15 45 26 6

Figure S144.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.017

Table S145.  Gene #44: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
2Q LOSS MUTATED 0 0 0 4 0
2Q LOSS WILD-TYPE 52 47 25 27 22

Figure S145.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00529 (Fisher's exact test), Q value = 0.04

Table S146.  Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
2Q LOSS MUTATED 0 1 1 0 0 2
2Q LOSS WILD-TYPE 23 43 18 53 26 6

Figure S146.  Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'RPPA_CNMF'

P value = 0.00289 (Fisher's exact test), Q value = 0.027

Table S147.  Gene #46: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
3Q LOSS MUTATED 10 1 0 1 0
3Q LOSS WILD-TYPE 29 24 20 14 23

Figure S147.  Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
3Q LOSS MUTATED 4 3 3 5 0 3
3Q LOSS WILD-TYPE 19 41 16 48 26 5

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

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.00937 (Fisher's exact test), Q value = 0.054

Table S149.  Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
4P LOSS MUTATED 10 1 10 4
4P LOSS WILD-TYPE 35 48 42 33

Figure S149.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.062

Table S150.  Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
4P LOSS MUTATED 5 2 13 2 2
4P LOSS WILD-TYPE 34 24 30 37 28

Figure S150.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.063

Table S151.  Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
4P LOSS MUTATED 20 1 3
4P LOSS WILD-TYPE 82 41 30

Figure S151.  Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.065

Table S152.  Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
4Q LOSS MUTATED 10 1 9 4
4Q LOSS WILD-TYPE 35 48 43 33

Figure S152.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.13

Table S153.  Gene #48: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
4Q LOSS MUTATED 4 3 11 1 4
4Q LOSS WILD-TYPE 35 23 32 38 26

Figure S153.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00438 (Fisher's exact test), Q value = 0.035

Table S154.  Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
4Q LOSS MUTATED 17 0 6
4Q LOSS WILD-TYPE 85 42 27

Figure S154.  Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S155.  Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
6P LOSS MUTATED 14 30 0 20
6P LOSS WILD-TYPE 12 44 46 18

Figure S155.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0021

Table S156.  Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
6P LOSS MUTATED 22 9 26 6
6P LOSS WILD-TYPE 23 40 26 31

Figure S156.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00228 (Fisher's exact test), Q value = 0.023

Table S157.  Gene #51: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
6P LOSS MUTATED 17 7 23 8 5
6P LOSS WILD-TYPE 22 19 20 31 25

Figure S157.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.069

Table S158.  Gene #51: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
6P LOSS MUTATED 21 34 5
6P LOSS WILD-TYPE 53 41 23

Figure S158.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.014

Table S159.  Gene #51: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
6P LOSS MUTATED 46 7 7
6P LOSS WILD-TYPE 56 35 26

Figure S159.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0075

Table S160.  Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
6P LOSS MUTATED 9 26 7 12 3 3
6P LOSS WILD-TYPE 14 18 12 41 23 5

Figure S160.  Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S161.  Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
6Q LOSS MUTATED 18 43 0 21
6Q LOSS WILD-TYPE 8 31 46 17

Figure S161.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S162.  Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
6Q LOSS MUTATED 26 10 36 9
6Q LOSS WILD-TYPE 19 39 16 28

Figure S162.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.092

Table S163.  Gene #52: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
6Q LOSS MUTATED 24 7 10 3 11
6Q LOSS WILD-TYPE 15 18 10 12 12

Figure S163.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00094

Table S164.  Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
6Q LOSS MUTATED 22 7 31 10 7
6Q LOSS WILD-TYPE 17 19 12 29 23

Figure S164.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.013

Table S165.  Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
6Q LOSS MUTATED 29 43 5
6Q LOSS WILD-TYPE 45 32 23

Figure S165.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.016

Table S166.  Gene #52: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
6Q LOSS MUTATED 34 16 10 13 4
6Q LOSS WILD-TYPE 18 31 15 18 18

Figure S166.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S167.  Gene #52: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
6Q LOSS MUTATED 60 10 7
6Q LOSS WILD-TYPE 42 32 26

Figure S167.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0064

Table S168.  Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
6Q LOSS MUTATED 9 7 8 4 36 7 6
6Q LOSS WILD-TYPE 18 4 19 9 15 20 11

Figure S168.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.005

Table S169.  Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
6Q LOSS MUTATED 13 29 9 20 3 3
6Q LOSS WILD-TYPE 10 15 10 33 23 5

Figure S169.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S170.  Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
8P LOSS MUTATED 2 36 3 1
8P LOSS WILD-TYPE 24 38 43 37

Figure S170.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00368 (Fisher's exact test), Q value = 0.032

Table S171.  Gene #54: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
8P LOSS MUTATED 10 7 21 4
8P LOSS WILD-TYPE 35 42 31 33

Figure S171.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.072

Table S172.  Gene #54: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
8P LOSS MUTATED 11 5 17 5 3
8P LOSS WILD-TYPE 28 21 26 34 27

Figure S172.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00833 (Fisher's exact test), Q value = 0.052

Table S173.  Gene #54: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
8P LOSS MUTATED 12 26 3
8P LOSS WILD-TYPE 62 49 25

Figure S173.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00798 (Fisher's exact test), Q value = 0.052

Table S174.  Gene #54: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
8P LOSS MUTATED 32 4 5
8P LOSS WILD-TYPE 70 38 28

Figure S174.  Get High-res Image Gene #54: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.011

Table S175.  Gene #55: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
8Q LOSS MUTATED 0 14 2 0
8Q LOSS WILD-TYPE 26 60 44 38

Figure S175.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0348 (Fisher's exact test), Q value = 0.12

Table S176.  Gene #55: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
8Q LOSS MUTATED 3 2 5 4 0 1
8Q LOSS WILD-TYPE 20 42 14 49 26 7

Figure S176.  Get High-res Image Gene #55: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S177.  Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
9P LOSS MUTATED 11 43 3 17
9P LOSS WILD-TYPE 15 31 43 21

Figure S177.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.005

Table S178.  Gene #56: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
9P LOSS MUTATED 20 12 32 9
9P LOSS WILD-TYPE 25 37 20 28

Figure S178.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.1

Table S179.  Gene #56: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
9P LOSS MUTATED 20 13 8 1 10
9P LOSS WILD-TYPE 19 12 12 14 13

Figure S179.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.018

Table S180.  Gene #56: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
9P LOSS MUTATED 20 4 24 10 10
9P LOSS WILD-TYPE 19 22 19 29 20

Figure S180.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 0.14

Table S181.  Gene #56: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
9P LOSS MUTATED 30 33 5
9P LOSS WILD-TYPE 44 42 23

Figure S181.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.15

Table S182.  Gene #56: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
9P LOSS MUTATED 29 14 9 10 6
9P LOSS WILD-TYPE 23 33 16 21 16

Figure S182.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 0.092

Table S183.  Gene #56: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
9P LOSS MUTATED 48 12 8
9P LOSS WILD-TYPE 54 30 25

Figure S183.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.12

Table S184.  Gene #56: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
9P LOSS MUTATED 12 23 6 18 8 0
9P LOSS WILD-TYPE 11 21 13 35 18 8

Figure S184.  Get High-res Image Gene #56: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 0.00609 (Fisher's exact test), Q value = 0.044

Table S185.  Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
9Q LOSS MUTATED 6 21 3 13
9Q LOSS WILD-TYPE 20 53 43 25

Figure S185.  Get High-res Image Gene #57: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00094

Table S186.  Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
10P LOSS MUTATED 10 15 0 11
10P LOSS WILD-TYPE 16 59 46 27

Figure S186.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00386 (Fisher's exact test), Q value = 0.033

Table S187.  Gene #58: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
10P LOSS MUTATED 3 5 17 6 3
10P LOSS WILD-TYPE 36 21 26 33 27

Figure S187.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.083

Table S188.  Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
10P LOSS MUTATED 2 5 2 2 13 3 6
10P LOSS WILD-TYPE 25 6 25 11 38 24 11

Figure S188.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.14

Table S189.  Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
10P LOSS MUTATED 3 12 6 8 1 3
10P LOSS WILD-TYPE 20 32 13 45 25 5

Figure S189.  Get High-res Image Gene #58: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0035

Table S190.  Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
10Q LOSS MUTATED 9 13 0 8
10Q LOSS WILD-TYPE 17 61 46 30

Figure S190.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.14

Table S191.  Gene #59: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
10Q LOSS MUTATED 4 4 14 4 3
10Q LOSS WILD-TYPE 35 22 29 35 27

Figure S191.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.077

Table S192.  Gene #59: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
10Q LOSS MUTATED 6 19 4
10Q LOSS WILD-TYPE 68 56 24

Figure S192.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.072

Table S193.  Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
10Q LOSS MUTATED 1 4 4 2 10 1 6
10Q LOSS WILD-TYPE 26 7 23 11 41 26 11

Figure S193.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.081

Table S194.  Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
10Q LOSS MUTATED 4 8 6 7 0 3
10Q LOSS WILD-TYPE 19 36 13 46 26 5

Figure S194.  Get High-res Image Gene #59: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.14

Table S195.  Gene #60: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
11P LOSS MUTATED 5 8 4 0
11P LOSS WILD-TYPE 40 41 48 37

Figure S195.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00769 (Fisher's exact test), Q value = 0.051

Table S196.  Gene #60: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
11P LOSS MUTATED 3 1 3 8 1
11P LOSS WILD-TYPE 49 46 22 23 21

Figure S196.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.066

Table S197.  Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
11P LOSS MUTATED 0 3 3 6 0 3
11P LOSS WILD-TYPE 23 41 16 47 26 5

Figure S197.  Get High-res Image Gene #60: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.0024

Table S198.  Gene #61: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 25 16 16 18
11Q LOSS MUTATED 0 0 0 5 1
11Q LOSS WILD-TYPE 47 25 16 11 17

Figure S198.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0047

Table S199.  Gene #61: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
11Q LOSS MUTATED 1 1 2 9 1
11Q LOSS WILD-TYPE 51 46 23 22 21

Figure S199.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0019

Table S200.  Gene #61: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
11Q LOSS MUTATED 0 0 5 5 0 3
11Q LOSS WILD-TYPE 23 44 14 48 26 5

Figure S200.  Get High-res Image Gene #61: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.094

Table S201.  Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
12P LOSS MUTATED 6 10 2 1
12P LOSS WILD-TYPE 20 64 44 37

Figure S201.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.12

Table S202.  Gene #62: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
12P LOSS MUTATED 5 1 10 3
12P LOSS WILD-TYPE 40 48 42 34

Figure S202.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0022

Table S203.  Gene #62: '12p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
12P LOSS MUTATED 11 0 0 0 0
12P LOSS WILD-TYPE 28 25 20 15 23

Figure S203.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.017

Table S204.  Gene #62: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 25 16 16 18
12P LOSS MUTATED 11 0 0 0 0
12P LOSS WILD-TYPE 36 25 16 16 18

Figure S204.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.00914 (Fisher's exact test), Q value = 0.054

Table S205.  Gene #62: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
12P LOSS MUTATED 7 1 8 0 2
12P LOSS WILD-TYPE 32 25 35 39 28

Figure S205.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.068

Table S206.  Gene #62: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
12P LOSS MUTATED 5 13 0
12P LOSS WILD-TYPE 69 62 28

Figure S206.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0044

Table S207.  Gene #62: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
12P LOSS MUTATED 18 0 0
12P LOSS WILD-TYPE 84 42 33

Figure S207.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.012

Table S208.  Gene #62: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
12P LOSS MUTATED 6 5 5 1 0 0
12P LOSS WILD-TYPE 17 39 14 52 26 8

Figure S208.  Get High-res Image Gene #62: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.062

Table S209.  Gene #63: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
12Q LOSS MUTATED 8 14 2 4
12Q LOSS WILD-TYPE 18 60 44 34

Figure S209.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.062

Table S210.  Gene #63: '12q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
12Q LOSS MUTATED 11 1 1 0 2
12Q LOSS WILD-TYPE 28 24 19 15 21

Figure S210.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.077

Table S211.  Gene #63: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
12Q LOSS MUTATED 6 2 13 4 1
12Q LOSS WILD-TYPE 33 24 30 35 29

Figure S211.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00256 (Fisher's exact test), Q value = 0.025

Table S212.  Gene #63: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
12Q LOSS MUTATED 8 18 0
12Q LOSS WILD-TYPE 66 57 28

Figure S212.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.1

Table S213.  Gene #63: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
12Q LOSS MUTATED 21 4 1
12Q LOSS WILD-TYPE 81 38 32

Figure S213.  Get High-res Image Gene #63: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00574 (Fisher's exact test), Q value = 0.043

Table S214.  Gene #64: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
13Q LOSS MUTATED 4 14 1 1
13Q LOSS WILD-TYPE 22 60 45 37

Figure S214.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.068

Table S215.  Gene #64: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
13Q LOSS MUTATED 6 2 11 1
13Q LOSS WILD-TYPE 39 47 41 36

Figure S215.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.00508 (Fisher's exact test), Q value = 0.039

Table S216.  Gene #64: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
13Q LOSS MUTATED 5 1 11 1 1
13Q LOSS WILD-TYPE 34 25 32 38 29

Figure S216.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.098

Table S217.  Gene #64: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
13Q LOSS MUTATED 6 6 0 7 0
13Q LOSS WILD-TYPE 46 41 25 24 22

Figure S217.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.063

Table S218.  Gene #64: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
13Q LOSS MUTATED 17 1 1
13Q LOSS WILD-TYPE 85 41 32

Figure S218.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.059

Table S219.  Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
13Q LOSS MUTATED 1 10 4 3 0 1
13Q LOSS WILD-TYPE 22 34 15 50 26 7

Figure S219.  Get High-res Image Gene #64: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.14

Table S220.  Gene #65: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
14Q LOSS MUTATED 7 1 6 1
14Q LOSS WILD-TYPE 38 48 46 36

Figure S220.  Get High-res Image Gene #65: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.00872 (Fisher's exact test), Q value = 0.054

Table S221.  Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
15Q LOSS MUTATED 2 19 2 7
15Q LOSS WILD-TYPE 24 55 44 31

Figure S221.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.057

Table S222.  Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
15Q LOSS MUTATED 9 2 14 5
15Q LOSS WILD-TYPE 36 47 38 32

Figure S222.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.017

Table S223.  Gene #66: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
15Q LOSS MUTATED 7 2 15 1 5
15Q LOSS WILD-TYPE 32 24 28 38 25

Figure S223.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00224 (Fisher's exact test), Q value = 0.023

Table S224.  Gene #66: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
15Q LOSS MUTATED 8 21 1
15Q LOSS WILD-TYPE 66 54 27

Figure S224.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00691 (Fisher's exact test), Q value = 0.048

Table S225.  Gene #66: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
15Q LOSS MUTATED 25 2 3
15Q LOSS WILD-TYPE 77 40 30

Figure S225.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00873 (Fisher's exact test), Q value = 0.054

Table S226.  Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
15Q LOSS MUTATED 3 13 6 4 1 1
15Q LOSS WILD-TYPE 20 31 13 49 25 7

Figure S226.  Get High-res Image Gene #66: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.062

Table S227.  Gene #67: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 25 16 16 18
16P LOSS MUTATED 0 0 1 1 3
16P LOSS WILD-TYPE 47 25 15 15 15

Figure S227.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.06

Table S228.  Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
16P LOSS MUTATED 1 3 1 1 0 3
16P LOSS WILD-TYPE 22 41 18 52 26 5

Figure S228.  Get High-res Image Gene #67: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.1

Table S229.  Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
16Q LOSS MUTATED 2 3 2 1 1 3
16Q LOSS WILD-TYPE 21 41 17 52 25 5

Figure S229.  Get High-res Image Gene #68: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S230.  Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
17P LOSS MUTATED 10 51 1 17
17P LOSS WILD-TYPE 16 23 45 21

Figure S230.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S231.  Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
17P LOSS MUTATED 27 9 38 5
17P LOSS WILD-TYPE 18 40 14 32

Figure S231.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S232.  Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
17P LOSS MUTATED 26 5 29 11 5
17P LOSS WILD-TYPE 13 21 14 28 25

Figure S232.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S233.  Gene #69: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
17P LOSS MUTATED 37 38 1
17P LOSS WILD-TYPE 37 37 27

Figure S233.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0028

Table S234.  Gene #69: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
17P LOSS MUTATED 36 13 11 11 5
17P LOSS WILD-TYPE 16 34 14 20 17

Figure S234.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.0021

Table S235.  Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
17P LOSS MUTATED 57 14 5
17P LOSS WILD-TYPE 45 28 28

Figure S235.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S236.  Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
17P LOSS MUTATED 10 3 11 0 37 11 3
17P LOSS WILD-TYPE 17 8 16 13 14 16 14

Figure S236.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.0024

Table S237.  Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
17P LOSS MUTATED 12 30 6 22 5 0
17P LOSS WILD-TYPE 11 14 13 31 21 8

Figure S237.  Get High-res Image Gene #69: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.00512 (Fisher's exact test), Q value = 0.039

Table S238.  Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
17Q LOSS MUTATED 1 12 0 6
17Q LOSS WILD-TYPE 25 62 46 32

Figure S238.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.083

Table S239.  Gene #70: '17q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
17Q LOSS MUTATED 9 1 0 3 1
17Q LOSS WILD-TYPE 30 24 20 12 22

Figure S239.  Get High-res Image Gene #70: '17q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.06

Table S240.  Gene #71: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
18P LOSS MUTATED 6 21 8 19
18P LOSS WILD-TYPE 20 53 38 19

Figure S240.  Get High-res Image Gene #71: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00094

Table S241.  Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
18Q LOSS MUTATED 14 55 10 25
18Q LOSS WILD-TYPE 12 19 36 13

Figure S241.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0032

Table S242.  Gene #72: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
18Q LOSS MUTATED 30 20 40 14
18Q LOSS WILD-TYPE 15 29 12 23

Figure S242.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.035

Table S243.  Gene #72: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
18Q LOSS MUTATED 26 12 33 18 12
18Q LOSS WILD-TYPE 13 14 10 21 18

Figure S243.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00244 (Fisher's exact test), Q value = 0.024

Table S244.  Gene #72: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
18Q LOSS MUTATED 43 50 8
18Q LOSS WILD-TYPE 31 25 20

Figure S244.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0037

Table S245.  Gene #72: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 52 47 25 31 22
18Q LOSS MUTATED 41 23 16 9 12
18Q LOSS WILD-TYPE 11 24 9 22 10

Figure S245.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.024

Table S246.  Gene #72: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
18Q LOSS MUTATED 69 20 12
18Q LOSS WILD-TYPE 33 22 21

Figure S246.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.12

Table S247.  Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 11 27 13 51 27 17
18Q LOSS MUTATED 17 6 13 5 37 16 5
18Q LOSS WILD-TYPE 10 5 14 8 14 11 12

Figure S247.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0028

Table S248.  Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 44 19 53 26 8
18Q LOSS MUTATED 18 33 8 30 10 0
18Q LOSS WILD-TYPE 5 11 11 23 16 8

Figure S248.  Get High-res Image Gene #72: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.054

Table S249.  Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
19P LOSS MUTATED 4 11 0 2
19P LOSS WILD-TYPE 22 63 46 36

Figure S249.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.14

Table S250.  Gene #73: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
19P LOSS MUTATED 5 1 9 2
19P LOSS WILD-TYPE 40 48 43 35

Figure S250.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.017

Table S251.  Gene #73: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
19P LOSS MUTATED 1 0 11 2 3
19P LOSS WILD-TYPE 38 26 32 37 27

Figure S251.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.11

Table S252.  Gene #73: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
19P LOSS MUTATED 5 12 0
19P LOSS WILD-TYPE 69 63 28

Figure S252.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00359 (Fisher's exact test), Q value = 0.032

Table S253.  Gene #73: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
19P LOSS MUTATED 16 1 0
19P LOSS WILD-TYPE 86 41 33

Figure S253.  Get High-res Image Gene #73: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.14

Table S254.  Gene #74: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
19Q LOSS MUTATED 5 0 5 1
19Q LOSS WILD-TYPE 40 49 47 36

Figure S254.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.033

Table S255.  Gene #74: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 26 43 39 30
19Q LOSS MUTATED 2 0 8 0 1
19Q LOSS WILD-TYPE 37 26 35 39 29

Figure S255.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00596 (Fisher's exact test), Q value = 0.043

Table S256.  Gene #74: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 75 28
19Q LOSS MUTATED 1 10 0
19Q LOSS WILD-TYPE 73 65 28

Figure S256.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.066

Table S257.  Gene #74: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
19Q LOSS MUTATED 11 0 0
19Q LOSS WILD-TYPE 91 42 33

Figure S257.  Get High-res Image Gene #74: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.00712 (Fisher's exact test), Q value = 0.048

Table S258.  Gene #75: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
20P LOSS MUTATED 5 11 0 3
20P LOSS WILD-TYPE 21 63 46 35

Figure S258.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0464 (Fisher's exact test), Q value = 0.14

Table S259.  Gene #75: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
20P LOSS MUTATED 14 4 0
20P LOSS WILD-TYPE 88 38 33

Figure S259.  Get High-res Image Gene #75: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.11

Table S260.  Gene #76: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
20Q LOSS MUTATED 3 2 0 0
20Q LOSS WILD-TYPE 23 72 46 38

Figure S260.  Get High-res Image Gene #76: '20q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0022

Table S261.  Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
21Q LOSS MUTATED 7 32 3 16
21Q LOSS WILD-TYPE 19 42 43 22

Figure S261.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00555 (Fisher's exact test), Q value = 0.041

Table S262.  Gene #77: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
21Q LOSS MUTATED 17 9 24 7
21Q LOSS WILD-TYPE 28 40 28 30

Figure S262.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.12

Table S263.  Gene #77: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
21Q LOSS MUTATED 39 11 5
21Q LOSS WILD-TYPE 63 31 28

Figure S263.  Get High-res Image Gene #77: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S264.  Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
22Q LOSS MUTATED 1 31 2 13
22Q LOSS WILD-TYPE 25 43 44 25

Figure S264.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.017

Table S265.  Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 49 52 37
22Q LOSS MUTATED 19 7 17 4
22Q LOSS WILD-TYPE 26 42 35 33

Figure S265.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.11

Table S266.  Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 42 33
22Q LOSS MUTATED 33 6 5
22Q LOSS WILD-TYPE 69 36 28

Figure S266.  Get High-res Image Gene #78: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.00979 (Fisher's exact test), Q value = 0.056

Table S267.  Gene #79: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 74 46 38
XP LOSS MUTATED 3 17 1 6
XP LOSS WILD-TYPE 23 57 45 32

Figure S267.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.12

Table S268.  Gene #79: 'xp loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 39 25 20 15 23
XP LOSS MUTATED 9 0 1 1 4
XP LOSS WILD-TYPE 30 25 19 14 19

Figure S268.  Get High-res Image Gene #79: 'xp loss' versus Molecular Subtype #3: 'RPPA_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/PAAD-TP/22533737/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PAAD-TP/22541963/PAAD-TP.transferedmergedcluster.txt

  • Number of patients = 184

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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