Correlation between copy number variations of arm-level result and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 408 patients, 281 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 1q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 3q gain cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 5p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'CN_CNMF'.

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

  • 7p gain cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 9p gain cnv correlated to 'CN_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • 12p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • 15q gain cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF'.

  • 17p gain cnv correlated to 'CN_CNMF'.

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

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

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

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

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

  • 21q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 22q gain cnv correlated to 'MRNASEQ_CNMF'.

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

  • 1p loss cnv correlated to 'METHLYATION_CNMF'.

  • 2p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 2q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 3q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

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

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

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

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

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

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

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

  • 7q loss cnv correlated to 'CN_CNMF'.

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

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

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

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

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

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

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

  • 11q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'RPPA_CNMF'.

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

  • 12q loss cnv correlated to 'CN_CNMF'.

  • 13q loss cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

  • 16q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'CN_CNMF'.

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

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

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

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

  • 20p loss cnv correlated to 'RPPA_CHIERARCHICAL'.

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

  • 22q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xp loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • xq loss cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 281 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
9q loss 170 (42%) 238 1e-05
(0.000178) 		1e-05
(0.000178) 		0.0149
(0.0669) 		0.00499
(0.0286) 		3e-05
(0.000424) 		1e-05
(0.000178) 		0.0193
(0.0807) 		0.00059
(0.00532) 		1e-05
(0.000178) 		1e-05
(0.000178)
14q loss 122 (30%) 286 1e-05
(0.000178) 		2e-05
(0.000309) 		0.0497
(0.145) 		0.0153
(0.068) 		0.155
(0.304) 		0.00015
(0.00162) 		0.00063
(0.00562) 		0.0241
(0.0912) 		0.00237
(0.0166) 		2e-05
(0.000309)
9p loss 175 (43%) 233 1e-05
(0.000178) 		9e-05
(0.00105) 		0.201
(0.363) 		0.0518
(0.15) 		0.0009
(0.00769) 		2e-05
(0.000309) 		0.0295
(0.104) 		0.00101
(0.00828) 		3e-05
(0.000424) 		1e-05
(0.000178)
3p gain 142 (35%) 266 8e-05
(0.000965) 		0.0485
(0.142) 		0.158
(0.308) 		0.464
(0.625) 		0.00869
(0.0439) 		0.0199
(0.0807) 		0.0305
(0.106) 		0.0664
(0.175) 		0.0222
(0.0859) 		0.00037
(0.00357)
9q gain 56 (14%) 352 0.00021
(0.00224) 		0.0212
(0.0838) 		0.762
(0.84) 		0.00682
(0.0368) 		0.00229
(0.0162) 		0.0003
(0.003) 		0.866
(0.911) 		0.375
(0.549) 		0.00032
(0.00316) 		1e-05
(0.000178)
3p loss 53 (13%) 355 0.168
(0.322) 		0.0332
(0.112) 		0.0455
(0.137) 		0.145
(0.289) 		1e-05
(0.000178) 		2e-05
(0.000309) 		0.638
(0.762) 		0.00424
(0.0254) 		0.00038
(0.00362) 		0.0015
(0.0116)
22q loss 159 (39%) 249 1e-05
(0.000178) 		0.0196
(0.0807) 		0.636
(0.762) 		0.0166
(0.0727) 		0.00879
(0.0439) 		0.00103
(0.00836) 		0.234
(0.402) 		0.00397
(0.0241) 		0.0671
(0.176) 		1e-05
(0.000178)
5p gain 166 (41%) 242 1e-05
(0.000178) 		0.0398
(0.127) 		0.0354
(0.117) 		0.201
(0.363) 		0.105
(0.234) 		0.00042
(0.00396) 		0.835
(0.889) 		0.00281
(0.0186) 		0.0912
(0.217) 		0.00462
(0.0269)
21q gain 115 (28%) 293 1e-05
(0.000178) 		1e-05
(0.000178) 		0.432
(0.596) 		0.173
(0.328) 		0.00263
(0.0178) 		0.00164
(0.0125) 		0.00754
(0.0399) 		0.00783
(0.041) 		0.0589
(0.164) 		0.257
(0.431)
4p loss 143 (35%) 265 1e-05
(0.000178) 		0.114
(0.249) 		0.581
(0.718) 		0.659
(0.778) 		0.00615
(0.0338) 		9e-05
(0.00105) 		0.0337
(0.113) 		0.00945
(0.0459) 		0.014
(0.0637) 		0.0627
(0.171)
4q loss 136 (33%) 272 1e-05
(0.000178) 		0.0624
(0.171) 		0.143
(0.288) 		0.229
(0.397) 		0.038
(0.122) 		0.00099
(0.00828) 		0.389
(0.556) 		0.04
(0.127) 		0.00197
(0.0142) 		0.00287
(0.0187)
6p loss 100 (25%) 308 5e-05
(0.000651) 		0.0185
(0.0792) 		0.632
(0.76) 		0.691
(0.791) 		0.185
(0.342) 		0.0363
(0.118) 		0.0471
(0.14) 		0.00463
(0.0269) 		0.086
(0.207) 		8e-05
(0.000965)
11p loss 181 (44%) 227 1e-05
(0.000178) 		1e-05
(0.000178) 		0.17
(0.324) 		0.694
(0.793) 		4e-05
(0.000538) 		2e-05
(0.000309) 		0.101
(0.23) 		0.095
(0.223) 		0.00013
(0.00142) 		0.0005
(0.00461)
13q loss 86 (21%) 322 1e-05
(0.000178) 		0.631
(0.76) 		0.0144
(0.0649) 		0.106
(0.235) 		0.0186
(0.0792) 		0.264
(0.44) 		0.201
(0.363) 		3e-05
(0.000424) 		0.0108
(0.0507) 		0.00083
(0.00716)
15q loss 145 (36%) 263 1e-05
(0.000178) 		1e-05
(0.000178) 		0.0843
(0.204) 		0.414
(0.582) 		0.421
(0.586) 		0.305
(0.479) 		0.00899
(0.0441) 		1e-05
(0.000178) 		0.00646
(0.0353) 		0.00012
(0.00133)
2p gain 111 (27%) 297 1e-05
(0.000178) 		1e-05
(0.000178) 		0.327
(0.503) 		0.736
(0.824) 		0.354
(0.529) 		0.0201
(0.081) 		0.117
(0.252) 		0.00812
(0.0416) 		0.228
(0.397) 		0.00146
(0.0114)
3q gain 178 (44%) 230 1e-05
(0.000178) 		0.284
(0.458) 		0.68
(0.789) 		0.852
(0.904) 		0.759
(0.838) 		0.082
(0.201) 		0.0341
(0.114) 		0.0287
(0.104) 		0.0329
(0.112) 		3e-05
(0.000424)
4p gain 38 (9%) 370 0.00241
(0.0166) 		0.00873
(0.0439) 		0.341
(0.517) 		0.488
(0.637) 		0.00797
(0.0414) 		0.0101
(0.0481) 		0.0122
(0.0566) 		0.456
(0.617) 		0.246
(0.42) 		0.466
(0.626)
8q gain 203 (50%) 205 1e-05
(0.000178) 		0.00926
(0.0452) 		0.0275
(0.102) 		0.257
(0.431) 		0.452
(0.615) 		0.818
(0.877) 		0.28
(0.455) 		0.0358
(0.118) 		0.69
(0.791) 		0.042
(0.13)
2q loss 91 (22%) 317 0.00118
(0.00939) 		0.0235
(0.0898) 		0.843
(0.897) 		0.747
(0.829) 		0.0635
(0.172) 		0.0314
(0.108) 		0.745
(0.829) 		0.891
(0.929) 		0.0109
(0.0508) 		0.00519
(0.0294)
5q loss 159 (39%) 249 1e-05
(0.000178) 		0.00135
(0.0106) 		0.853
(0.904) 		0.173
(0.328) 		0.212
(0.375) 		0.0168
(0.0733) 		0.213
(0.376) 		0.0188
(0.0796) 		0.221
(0.387) 		0.00785
(0.041)
6q loss 159 (39%) 249 1e-05
(0.000178) 		0.0135
(0.0614) 		0.746
(0.829) 		0.344
(0.517) 		0.384
(0.552) 		0.0472
(0.14) 		0.0946
(0.222) 		0.00286
(0.0187) 		0.443
(0.606) 		5e-05
(0.000651)
8p loss 188 (46%) 220 1e-05
(0.000178) 		0.00596
(0.033) 		0.103
(0.232) 		0.0706
(0.179) 		0.152
(0.3) 		0.0219
(0.0855) 		0.1
(0.23) 		0.0294
(0.104) 		0.308
(0.48) 		0.00342
(0.0214)
18q loss 146 (36%) 262 0.00179
(0.0133) 		0.556
(0.696) 		0.808
(0.871) 		0.885
(0.926) 		0.592
(0.727) 		0.0465
(0.139) 		0.00028
(0.00287) 		0.00047
(0.00438) 		0.033
(0.112) 		0.163
(0.315)
7p gain 171 (42%) 237 1e-05
(0.000178) 		0.0607
(0.167) 		0.0339
(0.114) 		0.357
(0.531) 		0.663
(0.779) 		0.102
(0.231) 		0.368
(0.543) 		0.0402
(0.127) 		0.2
(0.363) 		0.00012
(0.00133)
10p gain 116 (28%) 292 1e-05
(0.000178) 		0.00503
(0.0286) 		0.902
(0.935) 		0.773
(0.847) 		0.749
(0.83) 		0.00245
(0.0167) 		0.862
(0.911) 		0.899
(0.935) 		0.807
(0.871) 		0.0101
(0.0481)
11p gain 28 (7%) 380 6e-05
(0.000757) 		0.182
(0.339) 		0.284
(0.458) 		0.0688
(0.177) 		0.0634
(0.172) 		0.00662
(0.0359) 		0.937
(0.958) 		0.571
(0.708) 		0.00224
(0.016) 		0.0175
(0.076)
14q gain 58 (14%) 350 7e-05
(0.00087) 		0.0464
(0.139) 		0.422
(0.586) 		0.0658
(0.174) 		0.0433
(0.133) 		0.0424
(0.131) 		0.596
(0.73) 		0.18
(0.338) 		0.37
(0.545) 		0.361
(0.535)
17q gain 136 (33%) 272 0.00311
(0.0199) 		0.0313
(0.108) 		0.468
(0.627) 		0.688
(0.791) 		0.0406
(0.128) 		0.305
(0.479) 		0.28
(0.455) 		0.205
(0.367) 		0.294
(0.469) 		0.00279
(0.0186)
18p gain 117 (29%) 291 1e-05
(0.000178) 		0.00384
(0.0235) 		0.953
(0.965) 		0.912
(0.941) 		0.289
(0.463) 		0.0204
(0.0816) 		0.329
(0.504) 		0.108
(0.238) 		0.0601
(0.166) 		4e-05
(0.000538)
xp gain 66 (16%) 342 0.00054
(0.00492) 		0.00101
(0.00828) 		0.122
(0.257) 		0.0641
(0.172) 		0.00804
(0.0415) 		0.0552
(0.158) 		0.0707
(0.179) 		0.131
(0.27) 		0.0215
(0.0846) 		0.111
(0.243)
5p loss 56 (14%) 352 0.0581
(0.162) 		0.00011
(0.00125) 		0.474
(0.631) 		0.537
(0.675) 		0.144
(0.289) 		0.0003
(0.003) 		0.637
(0.762) 		0.736
(0.824) 		0.0176
(0.0762) 		0.01
(0.0481)
12p loss 56 (14%) 352 0.00466
(0.0269) 		0.00317
(0.0201) 		0.988
(0.989) 		0.901
(0.935) 		0.0767
(0.19) 		0.016
(0.0706) 		0.259
(0.434) 		0.279
(0.455) 		0.0287
(0.104) 		0.192
(0.35)
21q loss 79 (19%) 329 0.209
(0.37) 		0.0897
(0.214) 		0.0685
(0.177) 		0.59
(0.727) 		0.00189
(0.0137) 		0.0106
(0.0499) 		0.383
(0.552) 		0.145
(0.289) 		0.00824
(0.042) 		0.0268
(0.0999)
xq loss 80 (20%) 328 0.133
(0.272) 		6e-05
(0.000757) 		0.978
(0.982) 		0.938
(0.958) 		0.387
(0.555) 		0.3
(0.475) 		0.036
(0.118) 		0.116
(0.251) 		0.00171
(0.0129) 		0.01
(0.0481)
1p gain 90 (22%) 318 1e-05
(0.000178) 		0.0225
(0.0865) 		0.571
(0.708) 		0.492
(0.64) 		0.85
(0.903) 		0.685
(0.791) 		0.894
(0.931) 		0.382
(0.552) 		0.751
(0.831) 		0.0286
(0.104)
5q gain 53 (13%) 355 0.00557
(0.0313) 		0.0833
(0.203) 		0.00894
(0.0441) 		0.119
(0.254) 		0.401
(0.568) 		0.268
(0.443) 		0.344
(0.517) 		0.123
(0.257) 		0.486
(0.637) 		0.0362
(0.118)
6q gain 41 (10%) 367 0.184
(0.341) 		0.863
(0.911) 		0.975
(0.982) 		0.0414
(0.129) 		0.39
(0.557) 		0.393
(0.561) 		0.508
(0.654) 		0.505
(0.652) 		0.0442
(0.135) 		0.0242
(0.0912)
8p gain 90 (22%) 318 1e-05
(0.000178) 		0.283
(0.458) 		0.0683
(0.177) 		0.0194
(0.0807) 		0.334
(0.511) 		0.952
(0.965) 		0.119
(0.254) 		0.016
(0.0706) 		0.35
(0.525) 		0.177
(0.334)
9p gain 68 (17%) 340 1e-05
(0.000178) 		0.116
(0.251) 		0.933
(0.958) 		0.423
(0.586) 		0.101
(0.23) 		0.0638
(0.172) 		0.321
(0.496) 		0.219
(0.384) 		4e-05
(0.000538) 		1e-05
(0.000178)
10q gain 45 (11%) 363 0.00037
(0.00357) 		0.0522
(0.151) 		0.482
(0.634) 		0.432
(0.596) 		0.521
(0.661) 		0.0298
(0.104) 		0.44
(0.605) 		0.974
(0.982) 		0.255
(0.429) 		0.0291
(0.104)
11q gain 48 (12%) 360 0.00592
(0.033) 		0.319
(0.494) 		0.171
(0.327) 		0.0297
(0.104) 		0.278
(0.455) 		0.141
(0.285) 		0.94
(0.959) 		0.905
(0.937) 		0.0326
(0.111) 		0.154
(0.302)
18q gain 63 (15%) 345 0.00428
(0.0254) 		0.246
(0.42) 		0.123
(0.257) 		0.134
(0.273) 		0.585
(0.721) 		0.366
(0.542) 		0.0386
(0.123) 		0.426
(0.59) 		0.325
(0.5) 		0.00704
(0.0377)
19q gain 134 (33%) 274 1e-05
(0.000178) 		0.00401
(0.0242) 		0.484
(0.636) 		0.681
(0.789) 		0.301
(0.477) 		0.29
(0.463) 		0.48
(0.634) 		0.0205
(0.0818) 		0.163
(0.315) 		0.183
(0.34)
20p gain 201 (49%) 207 1e-05
(0.000178) 		0.063
(0.172) 		0.535
(0.675) 		0.0134
(0.0612) 		0.604
(0.738) 		0.0428
(0.132) 		0.51
(0.656) 		0.138
(0.28) 		0.0641
(0.172) 		0.0553
(0.158)
20q gain 229 (56%) 179 2e-05
(0.000309) 		0.0294
(0.104) 		0.471
(0.629) 		0.0759
(0.189) 		0.497
(0.644) 		0.108
(0.238) 		0.376
(0.549) 		0.191
(0.35) 		0.518
(0.661) 		0.0239
(0.0908)
10q loss 128 (31%) 280 1e-05
(0.000178) 		0.00025
(0.00259) 		0.561
(0.699) 		0.687
(0.791) 		0.0123
(0.0567) 		0.722
(0.814) 		0.122
(0.257) 		0.0535
(0.154) 		0.288
(0.463) 		0.0646
(0.172)
11q loss 131 (32%) 277 1e-05
(0.000178) 		0.022
(0.0855) 		0.0285
(0.104) 		0.118
(0.253) 		0.336
(0.511) 		0.253
(0.428) 		0.701
(0.8) 		0.536
(0.675) 		0.663
(0.779) 		0.284
(0.458)
16q loss 103 (25%) 305 1e-05
(0.000178) 		0.0201
(0.081) 		0.702
(0.801) 		0.987
(0.989) 		0.612
(0.743) 		0.356
(0.531) 		0.709
(0.806) 		0.1
(0.23) 		0.453
(0.616) 		0.00354
(0.022)
17p loss 180 (44%) 228 0.00024
(0.00252) 		0.265
(0.441) 		0.831
(0.887) 		0.886
(0.926) 		0.305
(0.479) 		0.0696
(0.178) 		0.763
(0.84) 		0.036
(0.118) 		0.162
(0.315) 		0.00384
(0.0235)
19p loss 94 (23%) 314 3e-05
(0.000424) 		0.046
(0.138) 		0.641
(0.764) 		0.491
(0.639) 		0.0961
(0.223) 		0.00723
(0.0385) 		0.255
(0.429) 		0.304
(0.479) 		0.342
(0.517) 		0.068
(0.177)
2q gain 57 (14%) 351 1e-05
(0.000178) 		0.00184
(0.0136) 		0.306
(0.48) 		0.353
(0.529) 		0.654
(0.776) 		0.243
(0.416) 		0.0646
(0.172) 		0.249
(0.423) 		0.501
(0.649) 		0.277
(0.455)
4q gain 26 (6%) 382 0.00187
(0.0137) 		0.101
(0.23) 		0.46
(0.622) 		0.163
(0.315) 		0.0946
(0.222) 		0.112
(0.244) 		0.0199
(0.0807) 		0.494
(0.641) 		0.323
(0.499) 		0.412
(0.579)
7q gain 150 (37%) 258 1e-05
(0.000178) 		0.12
(0.255) 		0.279
(0.455) 		0.815
(0.876) 		0.931
(0.958) 		0.662
(0.779) 		0.234
(0.402) 		0.208
(0.37) 		0.803
(0.869) 		0.0024
(0.0166)
12p gain 115 (28%) 293 0.00466
(0.0269) 		0.0647
(0.172) 		0.757
(0.837) 		0.53
(0.67) 		0.705
(0.803) 		0.828
(0.884) 		0.728
(0.819) 		0.0235
(0.0898) 		0.303
(0.479) 		0.129
(0.268)
12q gain 92 (23%) 316 0.0707
(0.179) 		0.227
(0.397) 		0.0737
(0.185) 		0.0218
(0.0854) 		0.382
(0.552) 		0.127
(0.265) 		0.674
(0.786) 		0.0885
(0.212) 		0.964
(0.974) 		0.0304
(0.106)
13q gain 100 (25%) 308 0.0298
(0.104) 		0.658
(0.777) 		0.951
(0.965) 		0.812
(0.873) 		0.319
(0.494) 		0.469
(0.627) 		0.775
(0.847) 		0.824
(0.881) 		0.376
(0.549) 		0.025
(0.0936)
15q gain 35 (9%) 373 0.0579
(0.162) 		0.00011
(0.00125) 		0.707
(0.804) 		0.579
(0.716) 		0.336
(0.511) 		0.0318
(0.109) 		0.0743
(0.186) 		0.616
(0.748) 		0.146
(0.29) 		0.0557
(0.159)
7p loss 21 (5%) 387 0.0862
(0.207) 		0.464
(0.625) 		0.685
(0.791) 		0.637
(0.762) 		0.409
(0.578) 		0.157
(0.308) 		0.0981
(0.227) 		0.0436
(0.133) 		0.0477
(0.141) 		0.0685
(0.177)
8q loss 38 (9%) 370 0.00282
(0.0186) 		0.617
(0.748) 		0.52
(0.661) 		0.276
(0.455) 		0.0366
(0.118) 		0.782
(0.852) 		0.12
(0.255) 		0.28
(0.455) 		0.368
(0.543) 		0.384
(0.552)
10p loss 74 (18%) 334 0.0199
(0.0807) 		0.069
(0.177) 		0.867
(0.912) 		0.443
(0.606) 		0.00319
(0.0201) 		0.204
(0.366) 		0.409
(0.578) 		0.108
(0.238) 		0.193
(0.351) 		0.398
(0.565)
16p loss 107 (26%) 301 1e-05
(0.000178) 		0.0569
(0.16) 		0.73
(0.821) 		0.817
(0.876) 		0.254
(0.429) 		0.201
(0.363) 		0.518
(0.661) 		0.137
(0.278) 		0.0776
(0.191) 		0.0196
(0.0807)
18p loss 99 (24%) 309 0.0183
(0.0786) 		0.0899
(0.214) 		0.344
(0.517) 		0.297
(0.471) 		0.978
(0.982) 		0.028
(0.103) 		0.0747
(0.186) 		0.655
(0.776) 		0.0698
(0.178) 		0.175
(0.331)
19q loss 57 (14%) 351 0.00075
(0.00654) 		0.336
(0.511) 		0.204
(0.366) 		0.0936
(0.221) 		0.416
(0.583) 		0.137
(0.278) 		0.0729
(0.184) 		0.628
(0.759) 		0.266
(0.442) 		0.019
(0.0801)
1q gain 128 (31%) 280 1e-05
(0.000178) 		0.687
(0.791) 		0.644
(0.767) 		0.909
(0.94) 		0.782
(0.852) 		0.863
(0.911) 		0.375
(0.549) 		0.77
(0.846) 		0.49
(0.639) 		0.538
(0.675)
6p gain 78 (19%) 330 0.00065
(0.00573) 		0.481
(0.634) 		0.807
(0.871) 		0.335
(0.511) 		0.871
(0.915) 		0.638
(0.762) 		0.786
(0.854) 		0.881
(0.923) 		0.19
(0.349) 		0.172
(0.327)
16p gain 74 (18%) 334 0.0488
(0.143) 		0.129
(0.267) 		0.609
(0.742) 		0.14
(0.282) 		0.396
(0.564) 		0.153
(0.302) 		0.514
(0.66) 		0.206
(0.368) 		0.675
(0.786) 		0.384
(0.552)
16q gain 83 (20%) 325 0.0363
(0.118) 		0.0518
(0.15) 		0.478
(0.634) 		0.096
(0.223) 		0.377
(0.549) 		0.111
(0.243) 		0.147
(0.292) 		0.0745
(0.186) 		0.453
(0.616) 		0.125
(0.263)
17p gain 58 (14%) 350 0.00096
(0.00812) 		0.0559
(0.159) 		0.429
(0.593) 		0.417
(0.583) 		0.629
(0.759) 		0.163
(0.315) 		0.324
(0.499) 		0.71
(0.806) 		0.532
(0.672) 		0.181
(0.339)
19p gain 87 (21%) 321 0.00295
(0.019) 		0.0969
(0.224) 		0.543
(0.68) 		0.599
(0.732) 		0.107
(0.238) 		0.0955
(0.223) 		0.508
(0.654) 		0.378
(0.55) 		0.182
(0.34) 		0.864
(0.911)
22q gain 49 (12%) 359 0.102
(0.232) 		0.0571
(0.16) 		0.488
(0.637) 		0.524
(0.665) 		0.00884
(0.0439) 		0.132
(0.272) 		0.146
(0.29) 		0.572
(0.708) 		0.18
(0.338) 		0.235
(0.404)
1p loss 34 (8%) 374 0.132
(0.272) 		0.0449
(0.136) 		0.516
(0.661) 		0.733
(0.823) 		0.444
(0.607) 		0.168
(0.322) 		0.233
(0.402) 		0.666
(0.779) 		0.29
(0.463) 		0.481
(0.634)
2p loss 45 (11%) 363 0.0769
(0.19) 		0.0861
(0.207) 		1
(1.00) 		0.888
(0.928) 		0.292
(0.465) 		0.0279
(0.103) 		0.519
(0.661) 		0.933
(0.958) 		0.191
(0.35) 		0.214
(0.376)
3q loss 24 (6%) 384 0.101
(0.23) 		0.263
(0.44) 		0.28
(0.455) 		0.418
(0.583) 		0.376
(0.549) 		0.48
(0.634) 		0.767
(0.843) 		0.13
(0.269) 		0.00112
(0.009) 		0.117
(0.252)
7q loss 27 (7%) 381 0.00154
(0.0118) 		0.479
(0.634) 		0.632
(0.76) 		0.611
(0.743) 		0.937
(0.958) 		0.82
(0.878) 		0.103
(0.232) 		0.084
(0.204) 		0.36
(0.535) 		0.119
(0.254)
12q loss 60 (15%) 348 2e-05
(0.000309) 		0.566
(0.704) 		0.684
(0.791) 		0.775
(0.847) 		0.667
(0.779) 		0.52
(0.661) 		0.803
(0.869) 		0.547
(0.685) 		0.667
(0.779) 		0.127
(0.265)
17q loss 43 (11%) 365 0.0407
(0.128) 		0.487
(0.637) 		0.952
(0.965) 		0.979
(0.982) 		0.731
(0.821) 		0.937
(0.958) 		0.746
(0.829) 		0.912
(0.941) 		0.646
(0.767) 		0.56
(0.699)
20p loss 33 (8%) 375 0.209
(0.37) 		0.103
(0.232) 		0.251
(0.426) 		0.0365
(0.118) 		0.945
(0.961) 		0.718
(0.81) 		0.797
(0.864) 		0.956
(0.967) 		0.4
(0.568) 		0.308
(0.48)
xp loss 71 (17%) 337 0.186
(0.344) 		0.0607
(0.167) 		0.655
(0.776) 		0.675
(0.786) 		0.107
(0.238) 		0.717
(0.81) 		0.311
(0.484) 		0.447
(0.61) 		0.278
(0.455) 		0.0454
(0.137)
xq gain 47 (12%) 361 0.068
(0.177) 		0.381
(0.552) 		0.691
(0.791) 		0.599
(0.732) 		0.0561
(0.159) 		0.784
(0.853) 		0.228
(0.397) 		0.192
(0.35) 		0.411
(0.579) 		0.421
(0.586)
1q loss 34 (8%) 374 0.233
(0.402) 		0.0797
(0.196) 		0.665
(0.779) 		0.744
(0.829) 		0.441
(0.605) 		0.221
(0.387) 		0.894
(0.931) 		0.209
(0.37) 		0.712
(0.807) 		0.165
(0.317)
20q loss 14 (3%) 394 0.0919
(0.218) 		0.474
(0.631) 		0.739
(0.825) 		0.462
(0.625) 		0.783
(0.853) 		0.941
(0.959) 		0.466
(0.626) 		0.343
(0.517) 		0.595
(0.73) 		0.937
(0.958)
'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
1P GAIN MUTATED 15 50 13 12
1P GAIN WILD-TYPE 154 90 46 28

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.087

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
1P GAIN MUTATED 27 35 8 20
1P GAIN WILD-TYPE 111 81 61 65

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.1

Table S3.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
1P GAIN MUTATED 16 11 28 12 1 22
1P GAIN WILD-TYPE 58 35 65 54 30 62

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
1Q GAIN MUTATED 32 62 16 18
1Q GAIN WILD-TYPE 137 78 43 22

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S5.  Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
2P GAIN MUTATED 14 64 12 21
2P GAIN WILD-TYPE 155 76 47 19

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
2P GAIN MUTATED 27 56 11 17
2P GAIN WILD-TYPE 111 60 58 68

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

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.081

Table S7.  Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
2P GAIN MUTATED 44 26 41
2P GAIN WILD-TYPE 74 86 133

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00812 (Fisher's exact test), Q value = 0.042

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
2P GAIN MUTATED 23 32 15 28 12
2P GAIN WILD-TYPE 66 67 78 42 42

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

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.011

Table S9.  Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
2P GAIN MUTATED 17 19 35 18 2 17
2P GAIN WILD-TYPE 57 27 58 48 29 67

Figure S9.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S10.  Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
2Q GAIN MUTATED 9 31 5 12
2Q GAIN WILD-TYPE 160 109 54 28

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
2Q GAIN MUTATED 12 29 7 9
2Q GAIN WILD-TYPE 126 87 62 76

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

'3p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
3P GAIN MUTATED 40 63 18 21
3P GAIN WILD-TYPE 129 77 41 19

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
3P GAIN MUTATED 39 52 24 27
3P GAIN WILD-TYPE 99 64 45 58

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

'3p gain' versus 'MRNASEQ_CNMF'

P value = 0.00869 (Fisher's exact test), Q value = 0.044

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
3P GAIN MUTATED 42 73 25
3P GAIN WILD-TYPE 74 107 83

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

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.081

Table S15.  Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
3P GAIN MUTATED 51 41 48
3P GAIN WILD-TYPE 67 71 126

Figure S15.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

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

Table S16.  Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
3P GAIN MUTATED 40 44 57
3P GAIN WILD-TYPE 80 52 132

Figure S16.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.086

Table S17.  Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
3P GAIN MUTATED 28 23 41 45
3P GAIN WILD-TYPE 70 20 93 74

Figure S17.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0036

Table S18.  Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
3P GAIN MUTATED 27 24 37 24 2 23
3P GAIN WILD-TYPE 47 22 56 42 29 61

Figure S18.  Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S19.  Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
3Q GAIN MUTATED 50 81 22 25
3Q GAIN WILD-TYPE 119 59 37 15

Figure S19.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.11

Table S20.  Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
3Q GAIN MUTATED 49 53 75
3Q GAIN WILD-TYPE 71 43 114

Figure S20.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.1

Table S21.  Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
3Q GAIN MUTATED 39 52 28 32 26
3Q GAIN WILD-TYPE 50 47 65 38 28

Figure S21.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.11

Table S22.  Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
3Q GAIN MUTATED 37 27 53 54
3Q GAIN WILD-TYPE 61 16 81 65

Figure S22.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S23.  Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
3Q GAIN MUTATED 30 28 49 32 3 29
3Q GAIN WILD-TYPE 44 18 44 34 28 55

Figure S23.  Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 0.00241 (Fisher's exact test), Q value = 0.017

Table S24.  Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
4P GAIN MUTATED 7 23 4 4
4P GAIN WILD-TYPE 162 117 55 36

Figure S24.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00873 (Fisher's exact test), Q value = 0.044

Table S25.  Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
4P GAIN MUTATED 7 20 4 7
4P GAIN WILD-TYPE 131 96 65 78

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

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00797 (Fisher's exact test), Q value = 0.041

Table S26.  Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
4P GAIN MUTATED 7 26 5
4P GAIN WILD-TYPE 109 154 103

Figure S26.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.048

Table S27.  Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
4P GAIN MUTATED 11 18 9
4P GAIN WILD-TYPE 107 94 165

Figure S27.  Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.057

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
4P GAIN MUTATED 4 13 21
4P GAIN WILD-TYPE 116 83 168

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

'4q gain' versus 'CN_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.014

Table S29.  Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
4Q GAIN MUTATED 6 17 0 3
4Q GAIN WILD-TYPE 163 123 59 37

Figure S29.  Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.081

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
4Q GAIN MUTATED 2 9 15
4Q GAIN WILD-TYPE 118 87 174

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

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S31.  Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
5P GAIN MUTATED 36 73 36 21
5P GAIN WILD-TYPE 133 67 23 19

Figure S31.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.13

Table S32.  Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
5P GAIN MUTATED 65 44 19 38
5P GAIN WILD-TYPE 73 72 50 47

Figure S32.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 34 5 19
5P GAIN MUTATED 11 7 18 0 9
5P GAIN WILD-TYPE 26 22 16 5 10

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

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.004

Table S34.  Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
5P GAIN MUTATED 34 41 89
5P GAIN WILD-TYPE 84 71 85

Figure S34.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.019

Table S35.  Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
5P GAIN MUTATED 40 49 22 32 22
5P GAIN WILD-TYPE 49 50 71 38 32

Figure S35.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00462 (Fisher's exact test), Q value = 0.027

Table S36.  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 74 46 93 66 31 84
5P GAIN MUTATED 23 20 39 31 5 44
5P GAIN WILD-TYPE 51 26 54 35 26 40

Figure S36.  Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00557 (Fisher's exact test), Q value = 0.031

Table S37.  Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
5Q GAIN MUTATED 12 20 11 10
5Q GAIN WILD-TYPE 157 120 48 30

Figure S37.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'RPPA_CNMF'

P value = 0.00894 (Fisher's exact test), Q value = 0.044

Table S38.  Gene #10: '5q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 34 5 19
5Q GAIN MUTATED 4 1 10 0 0
5Q GAIN WILD-TYPE 33 28 24 5 19

Figure S38.  Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.12

Table S39.  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 74 46 93 66 31 84
5Q GAIN MUTATED 7 5 11 13 0 16
5Q GAIN WILD-TYPE 67 41 82 53 31 68

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

'6p gain' versus 'CN_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0057

Table S40.  Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
6P GAIN MUTATED 17 35 17 9
6P GAIN WILD-TYPE 152 105 42 31

Figure S40.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 0.13

Table S41.  Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 38 26 18
6Q GAIN MUTATED 1 1 4 3
6Q GAIN WILD-TYPE 41 37 22 15

Figure S41.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.13

Table S42.  Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
6Q GAIN MUTATED 13 4 18 5
6Q GAIN WILD-TYPE 85 39 116 114

Figure S42.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.091

Table S43.  Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
6Q GAIN MUTATED 3 5 15 2 3 12
6Q GAIN WILD-TYPE 71 41 78 64 28 72

Figure S43.  Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
7P GAIN MUTATED 36 76 32 27
7P GAIN WILD-TYPE 133 64 27 13

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

'7p gain' versus 'RPPA_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.11

Table S45.  Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 34 5 19
7P GAIN MUTATED 19 6 17 1 5
7P GAIN WILD-TYPE 18 23 17 4 14

Figure S45.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0402 (Fisher's exact test), Q value = 0.13

Table S46.  Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
7P GAIN MUTATED 43 44 28 35 19
7P GAIN WILD-TYPE 46 55 65 35 35

Figure S46.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S47.  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 74 46 93 66 31 84
7P GAIN MUTATED 24 16 45 32 3 44
7P GAIN WILD-TYPE 50 30 48 34 28 40

Figure S47.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S48.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
7Q GAIN MUTATED 39 63 23 25
7Q GAIN WILD-TYPE 130 77 36 15

Figure S48.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0024 (Fisher's exact test), Q value = 0.017

Table S49.  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 74 46 93 66 31 84
7Q GAIN MUTATED 21 15 42 28 3 35
7Q GAIN WILD-TYPE 53 31 51 38 28 49

Figure S49.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S50.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
8P GAIN MUTATED 28 27 11 24
8P GAIN WILD-TYPE 141 113 48 16

Figure S50.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.081

Table S51.  Gene #15: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 38 26 18
8P GAIN MUTATED 9 4 11 2
8P GAIN WILD-TYPE 33 34 15 16

Figure S51.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.071

Table S52.  Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
8P GAIN MUTATED 26 16 19 22 6
8P GAIN WILD-TYPE 63 83 74 48 48

Figure S52.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S53.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
8Q GAIN MUTATED 64 73 31 35
8Q GAIN WILD-TYPE 105 67 28 5

Figure S53.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.045

Table S54.  Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
8Q GAIN MUTATED 67 70 24 42
8Q GAIN WILD-TYPE 71 46 45 43

Figure S54.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.1

Table S55.  Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 34 5 19
8Q GAIN MUTATED 17 6 18 4 7
8Q GAIN WILD-TYPE 20 23 16 1 12

Figure S55.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
8Q GAIN MUTATED 47 47 43 45 20
8Q GAIN WILD-TYPE 42 52 50 25 34

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

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 0.13

Table S57.  Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
8Q GAIN MUTATED 31 21 54 36 9 46
8Q GAIN WILD-TYPE 43 25 39 30 22 38

Figure S57.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S58.  Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
9P GAIN MUTATED 11 24 25 8
9P GAIN WILD-TYPE 158 116 34 32

Figure S58.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00054

Table S59.  Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
9P GAIN MUTATED 32 4 14 15
9P GAIN WILD-TYPE 66 39 120 104

Figure S59.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S60.  Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
9P GAIN MUTATED 14 5 13 2 1 30
9P GAIN WILD-TYPE 60 41 80 64 30 54

Figure S60.  Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0022

Table S61.  Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
9Q GAIN MUTATED 12 21 18 5
9Q GAIN WILD-TYPE 157 119 41 35

Figure S61.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.084

Table S62.  Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
9Q GAIN MUTATED 28 12 4 12
9Q GAIN WILD-TYPE 110 104 65 73

Figure S62.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00682 (Fisher's exact test), Q value = 0.037

Table S63.  Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 38 26 18
9Q GAIN MUTATED 1 6 5 6
9Q GAIN WILD-TYPE 41 32 21 12

Figure S63.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.016

Table S64.  Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
9Q GAIN MUTATED 16 14 24
9Q GAIN WILD-TYPE 100 166 84

Figure S64.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S65.  Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
9Q GAIN MUTATED 7 10 37
9Q GAIN WILD-TYPE 111 102 137

Figure S65.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0032

Table S66.  Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
9Q GAIN MUTATED 26 3 10 14
9Q GAIN WILD-TYPE 72 40 124 105

Figure S66.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S67.  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 74 46 93 66 31 84
9Q GAIN MUTATED 10 5 10 2 0 26
9Q GAIN WILD-TYPE 64 41 83 64 31 58

Figure S67.  Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S68.  Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
10P GAIN MUTATED 15 60 19 22
10P GAIN WILD-TYPE 154 80 40 18

Figure S68.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 0.029

Table S69.  Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
10P GAIN MUTATED 34 48 15 19
10P GAIN WILD-TYPE 104 68 54 66

Figure S69.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00245 (Fisher's exact test), Q value = 0.017

Table S70.  Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
10P GAIN MUTATED 48 24 44
10P GAIN WILD-TYPE 70 88 130

Figure S70.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.048

Table S71.  Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
10P GAIN MUTATED 23 14 30 23 1 21
10P GAIN WILD-TYPE 51 32 63 43 30 63

Figure S71.  Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0036

Table S72.  Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
10Q GAIN MUTATED 7 24 6 8
10Q GAIN WILD-TYPE 162 116 53 32

Figure S72.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.1

Table S73.  Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
10Q GAIN MUTATED 21 10 14
10Q GAIN WILD-TYPE 97 102 160

Figure S73.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.1

Table S74.  Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
10Q GAIN MUTATED 9 7 13 11 0 4
10Q GAIN WILD-TYPE 65 39 80 55 31 80

Figure S74.  Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00076

Table S75.  Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
11P GAIN MUTATED 6 5 12 5
11P GAIN WILD-TYPE 163 135 47 35

Figure S75.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00662 (Fisher's exact test), Q value = 0.036

Table S76.  Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
11P GAIN MUTATED 5 3 20
11P GAIN WILD-TYPE 113 109 154

Figure S76.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.016

Table S77.  Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
11P GAIN MUTATED 16 1 6 5
11P GAIN WILD-TYPE 82 42 128 114

Figure S77.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.076

Table S78.  Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
11P GAIN MUTATED 3 1 4 5 1 14
11P GAIN WILD-TYPE 71 45 89 61 30 70

Figure S78.  Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.00592 (Fisher's exact test), Q value = 0.033

Table S79.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
11Q GAIN MUTATED 10 19 11 8
11Q GAIN WILD-TYPE 159 121 48 32

Figure S79.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

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

Table S80.  Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 38 26 18
11Q GAIN MUTATED 4 2 2 6
11Q GAIN WILD-TYPE 38 36 24 12

Figure S80.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.11

Table S81.  Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
11Q GAIN MUTATED 20 6 11 11
11Q GAIN WILD-TYPE 78 37 123 108

Figure S81.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.027

Table S82.  Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
12P GAIN MUTATED 32 50 19 14
12P GAIN WILD-TYPE 137 90 40 26

Figure S82.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.09

Table S83.  Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
12P GAIN MUTATED 27 29 17 29 13
12P GAIN WILD-TYPE 62 70 76 41 41

Figure S83.  Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.085

Table S84.  Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 38 26 18
12Q GAIN MUTATED 15 3 7 5
12Q GAIN WILD-TYPE 27 35 19 13

Figure S84.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.11

Table S85.  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 74 46 93 66 31 84
12Q GAIN MUTATED 11 12 26 23 6 13
12Q GAIN WILD-TYPE 63 34 67 43 25 71

Figure S85.  Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.1

Table S86.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
13Q GAIN MUTATED 29 41 18 12
13Q GAIN WILD-TYPE 140 99 41 28

Figure S86.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.094

Table S87.  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 74 46 93 66 31 84
13Q GAIN MUTATED 20 10 32 18 2 16
13Q GAIN WILD-TYPE 54 36 61 48 29 68

Figure S87.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00087

Table S88.  Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
14Q GAIN MUTATED 14 16 14 14
14Q GAIN WILD-TYPE 155 124 45 26

Figure S88.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.14

Table S89.  Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
14Q GAIN MUTATED 21 20 3 14
14Q GAIN WILD-TYPE 117 96 66 71

Figure S89.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.13

Table S90.  Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
14Q GAIN MUTATED 18 17 21
14Q GAIN WILD-TYPE 98 163 87

Figure S90.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.13

Table S91.  Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
14Q GAIN MUTATED 12 11 33
14Q GAIN WILD-TYPE 106 101 141

Figure S91.  Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'METHLYATION_CNMF'

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

Table S92.  Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
15Q GAIN MUTATED 4 6 14 11
15Q GAIN WILD-TYPE 134 110 55 74

Figure S92.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S93.  Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
15Q GAIN MUTATED 14 13 8
15Q GAIN WILD-TYPE 104 99 166

Figure S93.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.14

Table S94.  Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
16P GAIN MUTATED 24 36 9 5
16P GAIN WILD-TYPE 145 104 50 35

Figure S94.  Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.12

Table S95.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
16Q GAIN MUTATED 27 40 10 6
16Q GAIN WILD-TYPE 142 100 49 34

Figure S95.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0081

Table S96.  Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
17P GAIN MUTATED 12 31 11 4
17P GAIN WILD-TYPE 157 109 48 36

Figure S96.  Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.02

Table S97.  Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
17Q GAIN MUTATED 42 58 17 19
17Q GAIN WILD-TYPE 127 82 42 21

Figure S97.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.11

Table S98.  Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
17Q GAIN MUTATED 36 50 20 30
17Q GAIN WILD-TYPE 102 66 49 55

Figure S98.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.13

Table S99.  Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
17Q GAIN MUTATED 31 72 32
17Q GAIN WILD-TYPE 85 108 76

Figure S99.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00279 (Fisher's exact test), Q value = 0.019

Table S100.  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 74 46 93 66 31 84
17Q GAIN MUTATED 18 21 42 22 4 25
17Q GAIN WILD-TYPE 56 25 51 44 27 59

Figure S100.  Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S101.  Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
18P GAIN MUTATED 16 54 31 16
18P GAIN WILD-TYPE 153 86 28 24

Figure S101.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.023

Table S102.  Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
18P GAIN MUTATED 42 43 9 23
18P GAIN WILD-TYPE 96 73 60 62

Figure S102.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.082

Table S103.  Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
18P GAIN MUTATED 29 25 63
18P GAIN WILD-TYPE 89 87 111

Figure S103.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00054

Table S104.  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 74 46 93 66 31 84
18P GAIN MUTATED 15 10 36 21 0 30
18P GAIN WILD-TYPE 59 36 57 45 31 54

Figure S104.  Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00428 (Fisher's exact test), Q value = 0.025

Table S105.  Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
18Q GAIN MUTATED 14 26 14 9
18Q GAIN WILD-TYPE 155 114 45 31

Figure S105.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.12

Table S106.  Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
18Q GAIN MUTATED 15 9 38
18Q GAIN WILD-TYPE 105 87 151

Figure S106.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00704 (Fisher's exact test), Q value = 0.038

Table S107.  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 74 46 93 66 31 84
18Q GAIN MUTATED 7 4 17 16 0 15
18Q GAIN WILD-TYPE 67 42 76 50 31 69

Figure S107.  Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.00295 (Fisher's exact test), Q value = 0.019

Table S108.  Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
19P GAIN MUTATED 24 44 11 8
19P GAIN WILD-TYPE 145 96 48 32

Figure S108.  Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S109.  Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
19Q GAIN MUTATED 34 68 15 17
19Q GAIN WILD-TYPE 135 72 44 23

Figure S109.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.00401 (Fisher's exact test), Q value = 0.024

Table S110.  Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
19Q GAIN MUTATED 32 52 23 27
19Q GAIN WILD-TYPE 106 64 46 58

Figure S110.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.082

Table S111.  Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
19Q GAIN MUTATED 27 34 20 31 22
19Q GAIN WILD-TYPE 62 65 73 39 32

Figure S111.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S112.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
20P GAIN MUTATED 59 79 36 27
20P GAIN WILD-TYPE 110 61 23 13

Figure S112.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.061

Table S113.  Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 38 26 18
20P GAIN MUTATED 14 26 14 11
20P GAIN WILD-TYPE 28 12 12 7

Figure S113.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
20P GAIN MUTATED 69 47 84
20P GAIN WILD-TYPE 49 65 90

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

'20q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S115.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
20Q GAIN MUTATED 69 92 39 29
20Q GAIN WILD-TYPE 100 48 20 11

Figure S115.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.1

Table S116.  Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
20Q GAIN MUTATED 71 77 32 49
20Q GAIN WILD-TYPE 67 39 37 36

Figure S116.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.091

Table S117.  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 74 46 93 66 31 84
20Q GAIN MUTATED 42 28 61 38 9 47
20Q GAIN WILD-TYPE 32 18 32 28 22 37

Figure S117.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S118.  Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
21Q GAIN MUTATED 19 70 15 11
21Q GAIN WILD-TYPE 150 70 44 29

Figure S118.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S119.  Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
21Q GAIN MUTATED 25 54 16 20
21Q GAIN WILD-TYPE 113 62 53 65

Figure S119.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00263 (Fisher's exact test), Q value = 0.018

Table S120.  Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
21Q GAIN MUTATED 31 65 19
21Q GAIN WILD-TYPE 85 115 89

Figure S120.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00164 (Fisher's exact test), Q value = 0.012

Table S121.  Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
21Q GAIN MUTATED 48 30 37
21Q GAIN WILD-TYPE 70 82 137

Figure S121.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.00754 (Fisher's exact test), Q value = 0.04

Table S122.  Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
21Q GAIN MUTATED 28 39 46
21Q GAIN WILD-TYPE 92 57 143

Figure S122.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00783 (Fisher's exact test), Q value = 0.041

Table S123.  Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
21Q GAIN MUTATED 15 34 20 27 17
21Q GAIN WILD-TYPE 74 65 73 43 37

Figure S123.  Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 0.00884 (Fisher's exact test), Q value = 0.044

Table S124.  Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
22Q GAIN MUTATED 9 32 8
22Q GAIN WILD-TYPE 107 148 100

Figure S124.  Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0049

Table S125.  Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
XP GAIN MUTATED 16 37 6 7
XP GAIN WILD-TYPE 153 103 53 33

Figure S125.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00101 (Fisher's exact test), Q value = 0.0083

Table S126.  Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
XP GAIN MUTATED 10 29 10 17
XP GAIN WILD-TYPE 128 87 59 68

Figure S126.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.00804 (Fisher's exact test), Q value = 0.041

Table S127.  Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
XP GAIN MUTATED 12 41 13
XP GAIN WILD-TYPE 104 139 95

Figure S127.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.085

Table S128.  Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
XP GAIN MUTATED 12 9 32 13
XP GAIN WILD-TYPE 86 34 102 106

Figure S128.  Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

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

Table S129.  Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
1P LOSS MUTATED 8 15 8 3
1P LOSS WILD-TYPE 130 101 61 82

Figure S129.  Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.1

Table S130.  Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
2P LOSS MUTATED 14 18 11
2P LOSS WILD-TYPE 104 94 163

Figure S130.  Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.0094

Table S131.  Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
2Q LOSS MUTATED 22 40 19 10
2Q LOSS WILD-TYPE 147 100 40 30

Figure S131.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.09

Table S132.  Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
2Q LOSS MUTATED 22 36 12 21
2Q LOSS WILD-TYPE 116 80 57 64

Figure S132.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 0.11

Table S133.  Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
2Q LOSS MUTATED 29 32 28
2Q LOSS WILD-TYPE 89 80 146

Figure S133.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.051

Table S134.  Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
2Q LOSS MUTATED 12 13 38 23
2Q LOSS WILD-TYPE 86 30 96 96

Figure S134.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00519 (Fisher's exact test), Q value = 0.029

Table S135.  Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
2Q LOSS MUTATED 14 15 30 13 2 12
2Q LOSS WILD-TYPE 60 31 63 53 29 72

Figure S135.  Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'METHLYATION_CNMF'

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

Table S136.  Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
3P LOSS MUTATED 27 10 5 11
3P LOSS WILD-TYPE 111 106 64 74

Figure S136.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.14

Table S137.  Gene #46: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 34 5 19
3P LOSS MUTATED 2 4 10 0 5
3P LOSS WILD-TYPE 35 25 24 5 14

Figure S137.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S138.  Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
3P LOSS MUTATED 5 13 34
3P LOSS WILD-TYPE 111 167 74

Figure S138.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S139.  Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
3P LOSS MUTATED 5 8 39
3P LOSS WILD-TYPE 113 104 135

Figure S139.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00424 (Fisher's exact test), Q value = 0.025

Table S140.  Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
3P LOSS MUTATED 22 9 7 11 4
3P LOSS WILD-TYPE 67 90 86 59 50

Figure S140.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0036

Table S141.  Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
3P LOSS MUTATED 25 3 15 8
3P LOSS WILD-TYPE 73 40 119 111

Figure S141.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.012

Table S142.  Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
3P LOSS MUTATED 2 4 15 10 1 19
3P LOSS WILD-TYPE 72 42 78 56 30 65

Figure S142.  Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.009

Table S143.  Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
3Q LOSS MUTATED 13 3 7 1
3Q LOSS WILD-TYPE 85 40 127 118

Figure S143.  Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S144.  Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
4P LOSS MUTATED 28 60 33 22
4P LOSS WILD-TYPE 141 80 26 18

Figure S144.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.00615 (Fisher's exact test), Q value = 0.034

Table S145.  Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
4P LOSS MUTATED 46 48 47
4P LOSS WILD-TYPE 70 132 61

Figure S145.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

Table S146.  Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
4P LOSS MUTATED 49 21 71
4P LOSS WILD-TYPE 69 91 103

Figure S146.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.11

Table S147.  Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
4P LOSS MUTATED 48 40 54
4P LOSS WILD-TYPE 72 56 135

Figure S147.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00945 (Fisher's exact test), Q value = 0.046

Table S148.  Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
4P LOSS MUTATED 37 42 19 25 19
4P LOSS WILD-TYPE 52 57 74 45 35

Figure S148.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.064

Table S149.  Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
4P LOSS MUTATED 42 18 33 45
4P LOSS WILD-TYPE 56 25 101 74

Figure S149.  Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S150.  Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
4Q LOSS MUTATED 25 57 35 19
4Q LOSS WILD-TYPE 144 83 24 21

Figure S150.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

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

Table S151.  Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
4Q LOSS MUTATED 40 49 45
4Q LOSS WILD-TYPE 76 131 63

Figure S151.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0083

Table S152.  Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
4Q LOSS MUTATED 46 22 66
4Q LOSS WILD-TYPE 72 90 108

Figure S152.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.13

Table S153.  Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
4Q LOSS MUTATED 37 35 20 27 17
4Q LOSS WILD-TYPE 52 64 73 43 37

Figure S153.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.014

Table S154.  Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
4Q LOSS MUTATED 43 13 29 45
4Q LOSS WILD-TYPE 55 30 105 74

Figure S154.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00287 (Fisher's exact test), Q value = 0.019

Table S155.  Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
4Q LOSS MUTATED 22 15 28 28 2 35
4Q LOSS WILD-TYPE 52 31 65 38 29 49

Figure S155.  Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'METHLYATION_CNMF'

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

Table S156.  Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
5P LOSS MUTATED 15 29 9 3
5P LOSS WILD-TYPE 123 87 60 82

Figure S156.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S157.  Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
5P LOSS MUTATED 29 14 13
5P LOSS WILD-TYPE 89 98 161

Figure S157.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.076

Table S158.  Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
5P LOSS MUTATED 8 11 14 21
5P LOSS WILD-TYPE 90 32 120 98

Figure S158.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.048

Table S159.  Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
5P LOSS MUTATED 15 11 13 8 0 7
5P LOSS WILD-TYPE 59 35 80 58 31 77

Figure S159.  Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S160.  Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
5Q LOSS MUTATED 37 77 26 19
5Q LOSS WILD-TYPE 132 63 33 21

Figure S160.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.011

Table S161.  Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
5Q LOSS MUTATED 52 61 17 29
5Q LOSS WILD-TYPE 86 55 52 56

Figure S161.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.073

Table S162.  Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
5Q LOSS MUTATED 59 39 60
5Q LOSS WILD-TYPE 59 73 114

Figure S162.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.08

Table S163.  Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
5Q LOSS MUTATED 33 44 24 34 24
5Q LOSS WILD-TYPE 56 55 69 36 30

Figure S163.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00785 (Fisher's exact test), Q value = 0.041

Table S164.  Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
5Q LOSS MUTATED 27 24 42 31 5 27
5Q LOSS WILD-TYPE 47 22 51 35 26 57

Figure S164.  Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00065

Table S165.  Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
6P LOSS MUTATED 24 51 12 13
6P LOSS WILD-TYPE 145 89 47 27

Figure S165.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.079

Table S166.  Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
6P LOSS MUTATED 23 39 18 20
6P LOSS WILD-TYPE 115 77 51 65

Figure S166.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.12

Table S167.  Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
6P LOSS MUTATED 36 31 32
6P LOSS WILD-TYPE 82 81 142

Figure S167.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 0.14

Table S168.  Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
6P LOSS MUTATED 26 33 41
6P LOSS WILD-TYPE 94 63 148

Figure S168.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00463 (Fisher's exact test), Q value = 0.027

Table S169.  Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
6P LOSS MUTATED 17 32 13 25 13
6P LOSS WILD-TYPE 72 67 80 45 41

Figure S169.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00096

Table S170.  Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
6P LOSS MUTATED 15 19 32 19 1 12
6P LOSS WILD-TYPE 59 27 61 47 30 72

Figure S170.  Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S171.  Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
6Q LOSS MUTATED 34 83 20 22
6Q LOSS WILD-TYPE 135 57 39 18

Figure S171.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.061

Table S172.  Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
6Q LOSS MUTATED 43 59 25 32
6Q LOSS WILD-TYPE 95 57 44 53

Figure S172.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.14

Table S173.  Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
6Q LOSS MUTATED 57 42 59
6Q LOSS WILD-TYPE 61 70 115

Figure S173.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00286 (Fisher's exact test), Q value = 0.019

Table S174.  Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
6Q LOSS MUTATED 30 48 23 34 23
6Q LOSS WILD-TYPE 59 51 70 36 31

Figure S174.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00065

Table S175.  Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
6Q LOSS MUTATED 26 25 46 31 2 26
6Q LOSS WILD-TYPE 48 21 47 35 29 58

Figure S175.  Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.13

Table S176.  Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
7P LOSS MUTATED 2 9 4 6 0
7P LOSS WILD-TYPE 87 90 89 64 54

Figure S176.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.14

Table S177.  Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
7P LOSS MUTATED 4 6 8 3
7P LOSS WILD-TYPE 94 37 126 116

Figure S177.  Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'CN_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.012

Table S178.  Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
7Q LOSS MUTATED 3 16 6 2
7Q LOSS WILD-TYPE 166 124 53 38

Figure S178.  Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S179.  Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
8P LOSS MUTATED 48 94 38 8
8P LOSS WILD-TYPE 121 46 21 32

Figure S179.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 0.00596 (Fisher's exact test), Q value = 0.033

Table S180.  Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
8P LOSS MUTATED 67 66 24 31
8P LOSS WILD-TYPE 71 50 45 54

Figure S180.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.085

Table S181.  Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
8P LOSS MUTATED 62 40 86
8P LOSS WILD-TYPE 56 72 88

Figure S181.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.1

Table S182.  Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
8P LOSS MUTATED 35 57 34 33 27
8P LOSS WILD-TYPE 54 42 59 37 27

Figure S182.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00342 (Fisher's exact test), Q value = 0.021

Table S183.  Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
8P LOSS MUTATED 34 27 48 26 5 42
8P LOSS WILD-TYPE 40 19 45 40 26 42

Figure S183.  Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00282 (Fisher's exact test), Q value = 0.019

Table S184.  Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
8Q LOSS MUTATED 10 22 6 0
8Q LOSS WILD-TYPE 159 118 53 40

Figure S184.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.12

Table S185.  Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
8Q LOSS MUTATED 18 13 7
8Q LOSS WILD-TYPE 98 167 101

Figure S185.  Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S186.  Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
9P LOSS MUTATED 79 73 3 20
9P LOSS WILD-TYPE 90 67 56 20

Figure S186.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

Table S187.  Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
9P LOSS MUTATED 37 61 34 43
9P LOSS WILD-TYPE 101 55 35 42

Figure S187.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0077

Table S188.  Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
9P LOSS MUTATED 44 96 35
9P LOSS WILD-TYPE 72 84 73

Figure S188.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S189.  Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
9P LOSS MUTATED 63 60 52
9P LOSS WILD-TYPE 55 52 122

Figure S189.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.1

Table S190.  Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
9P LOSS MUTATED 42 51 82
9P LOSS WILD-TYPE 78 45 107

Figure S190.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0083

Table S191.  Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
9P LOSS MUTATED 26 48 37 43 21
9P LOSS WILD-TYPE 63 51 56 27 33

Figure S191.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S192.  Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
9P LOSS MUTATED 23 25 70 53
9P LOSS WILD-TYPE 75 18 64 66

Figure S192.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S193.  Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
9P LOSS MUTATED 24 25 43 39 21 19
9P LOSS WILD-TYPE 50 21 50 27 10 65

Figure S193.  Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S194.  Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
9Q LOSS MUTATED 79 65 4 22
9Q LOSS WILD-TYPE 90 75 55 18

Figure S194.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S195.  Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
9Q LOSS MUTATED 33 57 37 43
9Q LOSS WILD-TYPE 105 59 32 42

Figure S195.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.067

Table S196.  Gene #59: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 34 5 19
9Q LOSS MUTATED 21 12 8 3 4
9Q LOSS WILD-TYPE 16 17 26 2 15

Figure S196.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00499 (Fisher's exact test), Q value = 0.029

Table S197.  Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 38 26 18
9Q LOSS MUTATED 24 14 8 2
9Q LOSS WILD-TYPE 18 24 18 16

Figure S197.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S198.  Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
9Q LOSS MUTATED 39 100 31
9Q LOSS WILD-TYPE 77 80 77

Figure S198.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S199.  Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
9Q LOSS MUTATED 62 65 43
9Q LOSS WILD-TYPE 56 47 131

Figure S199.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.081

Table S200.  Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
9Q LOSS MUTATED 39 49 82
9Q LOSS WILD-TYPE 81 47 107

Figure S200.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S201.  Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
9Q LOSS MUTATED 22 43 40 41 24
9Q LOSS WILD-TYPE 67 56 53 29 30

Figure S201.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S202.  Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
9Q LOSS MUTATED 17 25 76 49
9Q LOSS WILD-TYPE 81 18 58 70

Figure S202.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S203.  Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
9Q LOSS MUTATED 28 24 43 35 25 12
9Q LOSS WILD-TYPE 46 22 50 31 6 72

Figure S203.  Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.081

Table S204.  Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
10P LOSS MUTATED 20 34 14 6
10P LOSS WILD-TYPE 149 106 45 34

Figure S204.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00319 (Fisher's exact test), Q value = 0.02

Table S205.  Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
10P LOSS MUTATED 10 35 27
10P LOSS WILD-TYPE 106 145 81

Figure S205.  Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S206.  Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
10Q LOSS MUTATED 23 68 24 13
10Q LOSS WILD-TYPE 146 72 35 27

Figure S206.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0026

Table S207.  Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
10Q LOSS MUTATED 30 52 16 30
10Q LOSS WILD-TYPE 108 64 53 55

Figure S207.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.057

Table S208.  Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
10Q LOSS MUTATED 24 66 35
10Q LOSS WILD-TYPE 92 114 73

Figure S208.  Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S209.  Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
11P LOSS MUTATED 58 90 11 22
11P LOSS WILD-TYPE 111 50 48 18

Figure S209.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S210.  Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
11P LOSS MUTATED 33 67 39 42
11P LOSS WILD-TYPE 105 49 30 43

Figure S210.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00054

Table S211.  Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
11P LOSS MUTATED 41 101 37
11P LOSS WILD-TYPE 75 79 71

Figure S211.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S212.  Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
11P LOSS MUTATED 64 62 53
11P LOSS WILD-TYPE 54 50 121

Figure S212.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S213.  Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
11P LOSS MUTATED 25 23 70 57
11P LOSS WILD-TYPE 73 20 64 62

Figure S213.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.0046

Table S214.  Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
11P LOSS MUTATED 29 24 49 37 15 21
11P LOSS WILD-TYPE 45 22 44 29 16 63

Figure S214.  Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S215.  Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
11Q LOSS MUTATED 36 63 12 20
11Q LOSS WILD-TYPE 133 77 47 20

Figure S215.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.086

Table S216.  Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
11Q LOSS MUTATED 32 44 21 34
11Q LOSS WILD-TYPE 106 72 48 51

Figure S216.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.1

Table S217.  Gene #63: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 34 5 19
11Q LOSS MUTATED 16 6 15 1 2
11Q LOSS WILD-TYPE 21 23 19 4 17

Figure S217.  Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p loss' versus 'CN_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.027

Table S218.  Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
12P LOSS MUTATED 12 29 9 6
12P LOSS WILD-TYPE 157 111 50 34

Figure S218.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 0.00317 (Fisher's exact test), Q value = 0.02

Table S219.  Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
12P LOSS MUTATED 10 25 13 8
12P LOSS WILD-TYPE 128 91 56 77

Figure S219.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.071

Table S220.  Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
12P LOSS MUTATED 25 14 16
12P LOSS WILD-TYPE 93 98 158

Figure S220.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.1

Table S221.  Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
12P LOSS MUTATED 7 11 21 16
12P LOSS WILD-TYPE 91 32 113 103

Figure S221.  Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S222.  Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
12Q LOSS MUTATED 10 25 16 9
12Q LOSS WILD-TYPE 159 115 43 31

Figure S222.  Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S223.  Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
13Q LOSS MUTATED 15 42 17 12
13Q LOSS WILD-TYPE 154 98 42 28

Figure S223.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.065

Table S224.  Gene #66: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 34 5 19
13Q LOSS MUTATED 8 5 16 0 2
13Q LOSS WILD-TYPE 29 24 18 5 17

Figure S224.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.079

Table S225.  Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
13Q LOSS MUTATED 20 31 33
13Q LOSS WILD-TYPE 96 149 75

Figure S225.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S226.  Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
13Q LOSS MUTATED 28 29 8 18 3
13Q LOSS WILD-TYPE 61 70 85 52 51

Figure S226.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.051

Table S227.  Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
13Q LOSS MUTATED 32 11 24 18
13Q LOSS WILD-TYPE 66 32 110 101

Figure S227.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0072

Table S228.  Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
13Q LOSS MUTATED 6 14 21 13 3 28
13Q LOSS WILD-TYPE 68 32 72 53 28 56

Figure S228.  Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S229.  Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
14Q LOSS MUTATED 29 75 11 7
14Q LOSS WILD-TYPE 140 65 48 33

Figure S229.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S230.  Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
14Q LOSS MUTATED 34 53 24 11
14Q LOSS WILD-TYPE 104 63 45 74

Figure S230.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.15

Table S231.  Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 34 5 19
14Q LOSS MUTATED 13 2 9 2 6
14Q LOSS WILD-TYPE 24 27 25 3 13

Figure S231.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.068

Table S232.  Gene #67: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 38 26 18
14Q LOSS MUTATED 16 4 5 7
14Q LOSS WILD-TYPE 26 34 21 11

Figure S232.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0016

Table S233.  Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
14Q LOSS MUTATED 53 31 37
14Q LOSS WILD-TYPE 65 81 137

Figure S233.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0056

Table S234.  Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
14Q LOSS MUTATED 32 44 45
14Q LOSS WILD-TYPE 88 52 144

Figure S234.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 0.091

Table S235.  Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
14Q LOSS MUTATED 21 39 19 25 17
14Q LOSS WILD-TYPE 68 60 74 45 37

Figure S235.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.017

Table S236.  Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
14Q LOSS MUTATED 23 22 32 42
14Q LOSS WILD-TYPE 75 21 102 77

Figure S236.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

Table S237.  Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
14Q LOSS MUTATED 19 22 33 28 1 16
14Q LOSS WILD-TYPE 55 24 60 38 30 68

Figure S237.  Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S238.  Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
15Q LOSS MUTATED 23 76 32 14
15Q LOSS WILD-TYPE 146 64 27 26

Figure S238.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S239.  Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
15Q LOSS MUTATED 59 57 9 20
15Q LOSS WILD-TYPE 79 59 60 65

Figure S239.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.00899 (Fisher's exact test), Q value = 0.044

Table S240.  Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
15Q LOSS MUTATED 40 47 58
15Q LOSS WILD-TYPE 80 49 131

Figure S240.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S241.  Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
15Q LOSS MUTATED 29 50 17 34 15
15Q LOSS WILD-TYPE 60 49 76 36 39

Figure S241.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00646 (Fisher's exact test), Q value = 0.035

Table S242.  Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
15Q LOSS MUTATED 41 24 40 36
15Q LOSS WILD-TYPE 57 19 94 83

Figure S242.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S243.  Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
15Q LOSS MUTATED 23 24 37 21 1 35
15Q LOSS WILD-TYPE 51 22 56 45 30 49

Figure S243.  Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S244.  Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
16P LOSS MUTATED 16 41 36 14
16P LOSS WILD-TYPE 153 99 23 26

Figure S244.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.081

Table S245.  Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
16P LOSS MUTATED 16 11 25 14 3 33
16P LOSS WILD-TYPE 58 35 68 52 28 51

Figure S245.  Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S246.  Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
16Q LOSS MUTATED 9 44 32 18
16Q LOSS WILD-TYPE 160 96 27 22

Figure S246.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.081

Table S247.  Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
16Q LOSS MUTATED 31 41 11 20
16Q LOSS WILD-TYPE 107 75 58 65

Figure S247.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00354 (Fisher's exact test), Q value = 0.022

Table S248.  Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
16Q LOSS MUTATED 11 14 29 13 2 28
16Q LOSS WILD-TYPE 63 32 64 53 29 56

Figure S248.  Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0025

Table S249.  Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
17P LOSS MUTATED 58 72 23 27
17P LOSS WILD-TYPE 111 68 36 13

Figure S249.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S250.  Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
17P LOSS MUTATED 44 40 30 38 26
17P LOSS WILD-TYPE 45 59 63 32 28

Figure S250.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.023

Table S251.  Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
17P LOSS MUTATED 28 20 45 40 6 35
17P LOSS WILD-TYPE 46 26 48 26 25 49

Figure S251.  Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.13

Table S252.  Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
17Q LOSS MUTATED 10 22 7 4
17Q LOSS WILD-TYPE 159 118 52 36

Figure S252.  Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

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

Table S253.  Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
18P LOSS MUTATED 36 46 8 9
18P LOSS WILD-TYPE 133 94 51 31

Figure S253.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.1

Table S254.  Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
18P LOSS MUTATED 38 27 32
18P LOSS WILD-TYPE 80 85 142

Figure S254.  Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.013

Table S255.  Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
18Q LOSS MUTATED 44 66 21 15
18Q LOSS WILD-TYPE 125 74 38 25

Figure S255.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.14

Table S256.  Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
18Q LOSS MUTATED 53 37 54
18Q LOSS WILD-TYPE 65 75 120

Figure S256.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

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

Table S257.  Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
18Q LOSS MUTATED 42 51 53
18Q LOSS WILD-TYPE 78 45 136

Figure S257.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0044

Table S258.  Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
18Q LOSS MUTATED 24 53 26 27 16
18Q LOSS WILD-TYPE 65 46 67 43 38

Figure S258.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

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

Table S259.  Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
18Q LOSS MUTATED 29 23 45 49
18Q LOSS WILD-TYPE 69 20 89 70

Figure S259.  Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00042

Table S260.  Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
19P LOSS MUTATED 22 44 10 18
19P LOSS WILD-TYPE 147 96 49 22

Figure S260.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.14

Table S261.  Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
19P LOSS MUTATED 35 33 8 18
19P LOSS WILD-TYPE 103 83 61 67

Figure S261.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00723 (Fisher's exact test), Q value = 0.038

Table S262.  Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
19P LOSS MUTATED 32 14 46
19P LOSS WILD-TYPE 86 98 128

Figure S262.  Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0065

Table S263.  Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
19Q LOSS MUTATED 11 25 10 11
19Q LOSS WILD-TYPE 158 115 49 29

Figure S263.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.08

Table S264.  Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
19Q LOSS MUTATED 8 6 17 5 0 17
19Q LOSS WILD-TYPE 66 40 76 61 31 67

Figure S264.  Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 0.12

Table S265.  Gene #77: '20p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 38 26 18
20P LOSS MUTATED 6 0 2 3
20P LOSS WILD-TYPE 36 38 24 15

Figure S265.  Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.014

Table S266.  Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
21Q LOSS MUTATED 17 28 34
21Q LOSS WILD-TYPE 99 152 74

Figure S266.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.05

Table S267.  Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
21Q LOSS MUTATED 14 20 45
21Q LOSS WILD-TYPE 104 92 129

Figure S267.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00824 (Fisher's exact test), Q value = 0.042

Table S268.  Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
21Q LOSS MUTATED 31 6 21 18
21Q LOSS WILD-TYPE 67 37 113 101

Figure S268.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.1

Table S269.  Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
21Q LOSS MUTATED 12 8 15 12 2 27
21Q LOSS WILD-TYPE 62 38 78 54 29 57

Figure S269.  Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S270.  Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 169 140 59 40
22Q LOSS MUTATED 24 73 44 18
22Q LOSS WILD-TYPE 145 67 15 22

Figure S270.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.081

Table S271.  Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
22Q LOSS MUTATED 62 48 16 33
22Q LOSS WILD-TYPE 76 68 53 52

Figure S271.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.073

Table S272.  Gene #80: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 38 26 18
22Q LOSS MUTATED 12 22 6 7
22Q LOSS WILD-TYPE 30 16 20 11

Figure S272.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00879 (Fisher's exact test), Q value = 0.044

Table S273.  Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 180 108
22Q LOSS MUTATED 50 55 51
22Q LOSS WILD-TYPE 66 125 57

Figure S273.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.0084

Table S274.  Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 118 112 174
22Q LOSS MUTATED 44 29 83
22Q LOSS WILD-TYPE 74 83 91

Figure S274.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.024

Table S275.  Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 99 93 70 54
22Q LOSS MUTATED 39 47 21 29 22
22Q LOSS WILD-TYPE 50 52 72 41 32

Figure S275.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S276.  Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
22Q LOSS MUTATED 23 13 45 30 1 42
22Q LOSS WILD-TYPE 51 33 48 36 30 42

Figure S276.  Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 0.14

Table S277.  Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
XP LOSS MUTATED 8 4 21 16 8 11
XP LOSS WILD-TYPE 66 42 72 50 23 73

Figure S277.  Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00076

Table S278.  Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 138 116 69 85
XQ LOSS MUTATED 12 32 12 24
XQ LOSS WILD-TYPE 126 84 57 61

Figure S278.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

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

Table S279.  Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 96 189
XQ LOSS MUTATED 15 19 46
XQ LOSS WILD-TYPE 105 77 143

Figure S279.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.013

Table S280.  Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 43 134 119
XQ LOSS MUTATED 10 10 39 18
XQ LOSS WILD-TYPE 88 33 95 101

Figure S280.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.048

Table S281.  Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 46 93 66 31 84
XQ LOSS MUTATED 8 9 28 13 9 10
XQ LOSS WILD-TYPE 66 37 65 53 22 74

Figure S281.  Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/15082909/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/15111049/BLCA-TP.transferedmergedcluster.txt

  • Number of patients = 408

  • Number of significantly arm-level cnvs = 82

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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