Correlation between copy number variations of arm-level result and molecular subtypes
Thymoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C13X85ZZ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13X85ZZ
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 52 arm-level events and 10 molecular subtypes across 123 patients, 308 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • 3q gain cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

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

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

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

  • xp gain cnv correlated to 'CN_CNMF'.

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

  • 1p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 3p 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'.

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

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

  • 4q loss cnv correlated to 'CN_CNMF'.

  • 6p 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'.

  • 6q 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'.

  • 9p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

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

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

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

  • 12q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • 16p loss cnv correlated to 'RPPA_CHIERARCHICAL'.

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

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

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

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

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

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

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

  • 21q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 52 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, 308 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
1q gain 22 (18%) 101 1e-05
(0.000106) 		1e-05
(0.000106) 		0.00116
(0.00475) 		1e-05
(0.000106) 		1e-05
(0.000106) 		1e-05
(0.000106) 		1e-05
(0.000106) 		1e-05
(0.000106) 		1e-05
(0.000106) 		1e-05
(0.000106)
7p gain 16 (13%) 107 1e-05
(0.000106) 		1e-05
(0.000106) 		0.0252
(0.0503) 		0.00412
(0.0127) 		1e-05
(0.000106) 		1e-05
(0.000106) 		2e-05
(0.000182) 		0.00016
(0.00108) 		1e-05
(0.000106) 		1e-05
(0.000106)
7q gain 16 (13%) 107 1e-05
(0.000106) 		1e-05
(0.000106) 		0.0251
(0.0503) 		0.00411
(0.0127) 		1e-05
(0.000106) 		1e-05
(0.000106) 		2e-05
(0.000182) 		0.0002
(0.0012) 		1e-05
(0.000106) 		2e-05
(0.000182)
3p loss 12 (10%) 111 1e-05
(0.000106) 		1e-05
(0.000106) 		0.0367
(0.0656) 		3e-05
(0.000233) 		0.00104
(0.00436) 		0.00079
(0.00351) 		0.00067
(0.0032) 		0.00482
(0.0144) 		1e-05
(0.000106) 		0.00046
(0.00232)
6p loss 20 (16%) 103 1e-05
(0.000106) 		1e-05
(0.000106) 		0.00018
(0.00111) 		2e-05
(0.000182) 		1e-05
(0.000106) 		1e-05
(0.000106) 		1e-05
(0.000106) 		3e-05
(0.000233) 		1e-05
(0.000106) 		1e-05
(0.000106)
6q loss 19 (15%) 104 1e-05
(0.000106) 		1e-05
(0.000106) 		0.00069
(0.00326) 		3e-05
(0.000233) 		1e-05
(0.000106) 		1e-05
(0.000106) 		2e-05
(0.000182) 		0.00026
(0.00147) 		1e-05
(0.000106) 		9e-05
(0.00065)
1p gain 8 (7%) 115 0.00023
(0.00134) 		0.0216
(0.0449) 		0.275
(0.337) 		0.0349
(0.0633) 		0.00875
(0.0221) 		0.00347
(0.0111) 		0.0206
(0.0437) 		0.0213
(0.0444) 		0.00353
(0.0113) 		0.00698
(0.0191)
5p gain 11 (9%) 112 1e-05
(0.000106) 		1e-05
(0.000106) 		0.0647
(0.102) 		0.00271
(0.00909) 		0.00183
(0.00673) 		0.0014
(0.00547) 		0.00083
(0.00366) 		0.0134
(0.031) 		2e-05
(0.000182) 		0.00207
(0.00741)
5q gain 9 (7%) 114 3e-05
(0.000233) 		1e-05
(0.000106) 		0.14
(0.193) 		0.00973
(0.0239) 		0.00933
(0.023) 		0.00688
(0.0189) 		0.00362
(0.0114) 		0.0166
(0.0366) 		0.00025
(0.00144) 		0.00324
(0.0106)
8p gain 12 (10%) 111 0.00041
(0.00215) 		0.0212
(0.0444) 		0.402
(0.448) 		0.00392
(0.0123) 		0.0007
(0.00328) 		0.00018
(0.00111) 		0.00071
(0.00328) 		0.0018
(0.00673) 		0.00017
(0.00109) 		0.00046
(0.00232)
8q gain 12 (10%) 111 0.00026
(0.00147) 		0.021
(0.0442) 		0.401
(0.448) 		0.00396
(0.0123) 		0.00072
(0.00328) 		0.00017
(0.00109) 		0.0005
(0.00245) 		0.00182
(0.00673) 		0.00014
(0.000958) 		0.00055
(0.00267)
14q gain 13 (11%) 110 1e-05
(0.000106) 		3e-05
(0.000233) 		0.269
(0.333) 		0.0296
(0.0564) 		3e-05
(0.000233) 		3e-05
(0.000233) 		0.00019
(0.00115) 		0.00017
(0.00109) 		2e-05
(0.000182) 		4e-05
(0.000301)
11p loss 9 (7%) 114 1e-05
(0.000106) 		2e-05
(0.000182) 		0.0166
(0.0366) 		0.00121
(0.00488) 		0.00926
(0.0229) 		0.00705
(0.0192) 		0.00916
(0.0228) 		0.0522
(0.0875) 		0.00021
(0.00124) 		0.00844
(0.0218)
11q loss 7 (6%) 116 8e-05
(0.000586) 		3e-05
(0.000233) 		0.0473
(0.0812) 		0.00625
(0.0173) 		0.0321
(0.0593) 		0.0135
(0.031) 		0.0335
(0.0612) 		0.112
(0.16) 		0.00208
(0.00741) 		0.00815
(0.0213)
12p loss 8 (7%) 115 0.00448
(0.0137) 		7e-05
(0.00052) 		0.0175
(0.0378) 		0.00253
(0.00854) 		0.00854
(0.0218) 		0.0138
(0.0315) 		0.0226
(0.0464) 		0.0539
(0.0885) 		0.00326
(0.0106) 		0.0198
(0.0424)
12q loss 7 (6%) 116 0.0016
(0.00607) 		1e-05
(0.000106) 		0.0177
(0.0381) 		0.00245
(0.00838) 		0.0076
(0.0204) 		0.0135
(0.031) 		0.0329
(0.0603) 		0.123
(0.173) 		0.00229
(0.00794) 		0.0363
(0.0654)
21q loss 9 (7%) 114 1e-05
(0.000106) 		1e-05
(0.000106) 		0.0172
(0.0374) 		0.00302
(0.00994) 		0.00565
(0.0161) 		0.00736
(0.0199) 		0.0089
(0.0222) 		0.0515
(0.0866) 		0.00018
(0.00111) 		0.00873
(0.0221)
9p gain 11 (9%) 112 1e-05
(0.000106) 		0.00013
(0.000914) 		0.543
(0.595) 		0.384
(0.434) 		0.00045
(0.00232) 		0.00097
(0.00417) 		0.0102
(0.0247) 		0.00555
(0.0159) 		0.00532
(0.0155) 		0.00103
(0.00435)
9q gain 11 (9%) 112 1e-05
(0.000106) 		0.00014
(0.000958) 		0.547
(0.597) 		0.385
(0.434) 		0.00039
(0.00207) 		0.00098
(0.00418) 		0.0101
(0.0247) 		0.00593
(0.0167) 		0.00482
(0.0144) 		0.00094
(0.00407)
15q gain 12 (10%) 111 0.00013
(0.000914) 		4e-05
(0.000301) 		0.888
(0.933) 		0.665
(0.71) 		0.0205
(0.0437) 		0.0089
(0.0222) 		0.0141
(0.032) 		0.0209
(0.0442) 		0.0015
(0.00577) 		0.00584
(0.0165)
20p gain 10 (8%) 113 0.00046
(0.00232) 		0.0236
(0.0483) 		0.00486
(0.0144) 		0.0003
(0.00162) 		0.0014
(0.00547) 		0.00032
(0.00172) 		0.0532
(0.088) 		0.0109
(0.026) 		0.00049
(0.00245) 		0.0533
(0.088)
20q gain 10 (8%) 113 0.00062
(0.00299) 		0.0247
(0.0499) 		0.00555
(0.0159) 		0.00017
(0.00109) 		0.00123
(0.00492) 		0.0003
(0.00162) 		0.0528
(0.088) 		0.0109
(0.026) 		0.0005
(0.00245) 		0.0531
(0.088)
3q loss 7 (6%) 116 0.00078
(0.00351) 		0.00027
(0.00149) 		0.0863
(0.133) 		0.00111
(0.00458) 		0.0315
(0.0585) 		0.0322
(0.0593) 		0.0347
(0.0632) 		0.0846
(0.131) 		0.0021
(0.00743) 		0.00818
(0.0213)
17p loss 14 (11%) 109 0.0219
(0.0454) 		0.00119
(0.00483) 		0.00501
(0.0147) 		0.00019
(0.00115) 		0.0172
(0.0374) 		0.00085
(0.00371) 		0.37
(0.423) 		0.00185
(0.00673) 		0.0279
(0.0549) 		0.0594
(0.0948)
18p loss 7 (6%) 116 0.00185
(0.00673) 		0.00854
(0.0218) 		0.0176
(0.038) 		0.0959
(0.145) 		0.0308
(0.0583) 		0.0312
(0.0584) 		0.013
(0.0301) 		0.0951
(0.145) 		0.002
(0.00722) 		0.0432
(0.0756)
18q loss 7 (6%) 116 0.00183
(0.00673) 		0.008
(0.0212) 		0.017
(0.0373) 		0.0989
(0.149) 		0.0313
(0.0584) 		0.0313
(0.0584) 		0.0129
(0.03) 		0.0957
(0.145) 		0.00217
(0.00757) 		0.0421
(0.074)
16q loss 13 (11%) 110 0.0563
(0.0921) 		0.00551
(0.0159) 		0.0776
(0.12) 		3e-05
(0.000233) 		1e-05
(0.000106) 		1e-05
(0.000106) 		0.0587
(0.094) 		1e-05
(0.000106) 		0.00146
(0.00567) 		0.00079
(0.00351)
12p gain 4 (3%) 119 0.0281
(0.0552) 		0.144
(0.198) 		0.192
(0.251) 		0.0296
(0.0564) 		0.00476
(0.0144) 		0.00232
(0.00799) 		0.172
(0.231) 		0.027
(0.0534) 		0.0448
(0.0779) 		0.17
(0.23)
12q gain 4 (3%) 119 0.0286
(0.0558) 		0.146
(0.201) 		0.191
(0.251) 		0.0288
(0.0559) 		0.00466
(0.0142) 		0.00253
(0.00854) 		0.173
(0.231) 		0.0264
(0.0524) 		0.0453
(0.0783) 		0.171
(0.231)
13q loss 14 (11%) 109 3e-05
(0.000233) 		0.00611
(0.0171) 		0.0062
(0.0172) 		0.0407
(0.072) 		0.0662
(0.103) 		0.0495
(0.0841) 		0.37
(0.423) 		0.578
(0.629) 		0.0605
(0.096) 		0.354
(0.409)
xp loss 7 (6%) 116 0.00291
(0.0097) 		0.0082
(0.0213) 		0.829
(0.873) 		0.0976
(0.148) 		0.0299
(0.0568) 		0.0323
(0.0594) 		0.0569
(0.0928) 		0.104
(0.153) 		0.00753
(0.0203) 		0.136
(0.19)
xq loss 4 (3%) 119 0.0293
(0.0564) 		0.0362
(0.0653) 		0.372
(0.423) 		0.0143
(0.0323) 		0.0574
(0.0933) 		0.119
(0.169) 		0.0256
(0.051) 		0.251
(0.313) 		0.0447
(0.0779) 		0.304
(0.367)
xq gain 5 (4%) 118 0.00106
(0.00441) 		0.00808
(0.0213) 		0.631
(0.677) 		0.333
(0.392) 		0.0487
(0.0833) 		0.0638
(0.101) 		0.148
(0.202) 		0.274
(0.337) 		0.012
(0.0281) 		0.102
(0.151)
3q gain 5 (4%) 118 0.261
(0.324) 		0.141
(0.194) 		0.0579
(0.0938) 		0.0147
(0.0329) 		0.166
(0.227) 		0.0384
(0.0684) 		0.724
(0.769) 		0.00493
(0.0146) 		0.356
(0.409) 		0.17
(0.23)
1p loss 4 (3%) 119 0.00524
(0.0153) 		0.00214
(0.00752) 		0.0588
(0.094) 		0.121
(0.17) 		0.172
(0.231) 		0.53
(0.582) 		0.0451
(0.0781) 		0.305
(0.367)
4p loss 5 (4%) 118 0.00778
(0.0207) 		0.012
(0.0282) 		0.0493
(0.0841) 		0.0656
(0.103) 		0.322
(0.386) 		0.385
(0.434) 		0.0527
(0.088) 		0.269
(0.333)
10p loss 3 (2%) 120 0.6
(0.651) 		0.35
(0.407) 		0.0115
(0.0271) 		0.0222
(0.0459) 		1
(1.00) 		0.0151
(0.0338) 		0.74
(0.782) 		0.619
(0.666)
17q loss 6 (5%) 117 0.0104
(0.0249) 		0.00847
(0.0218) 		0.139
(0.193) 		0.00295
(0.00977) 		0.301
(0.365) 		0.148
(0.202) 		0.272
(0.335) 		0.237
(0.297) 		0.1
(0.151) 		0.44
(0.488)
19p loss 3 (2%) 120 0.101
(0.151) 		0.348
(0.406) 		0.00151
(0.00577) 		0.00072
(0.00328) 		0.196
(0.253) 		0.0102
(0.0247) 		0.107
(0.155) 		0.0586
(0.094)
19q loss 3 (2%) 120 0.102
(0.151) 		0.351
(0.407) 		0.00133
(0.00528) 		0.00027
(0.00149) 		0.197
(0.253) 		0.0102
(0.0247) 		0.107
(0.155) 		0.0585
(0.094)
22q loss 13 (11%) 110 1e-05
(0.000106) 		0.115
(0.163) 		0.104
(0.153) 		0.0409
(0.0721) 		0.0945
(0.144) 		0.0455
(0.0783) 		0.114
(0.162) 		0.332
(0.392) 		0.054
(0.0885) 		0.337
(0.396)
17q gain 7 (6%) 116 0.392
(0.441) 		0.221
(0.28) 		0.0857
(0.132) 		0.137
(0.191) 		0.0404
(0.0718) 		0.00362
(0.0114) 		0.773
(0.816) 		0.0683
(0.106) 		0.439
(0.488) 		0.397
(0.445)
18p gain 3 (2%) 120 0.102
(0.151) 		0.175
(0.234) 		0.0498
(0.0841) 		0.0295
(0.0564) 		0.197
(0.253) 		0.286
(0.348) 		0.107
(0.155) 		0.499
(0.551)
18q gain 3 (2%) 120 0.1
(0.151) 		0.177
(0.235) 		0.0497
(0.0841) 		0.0284
(0.0555) 		0.197
(0.253) 		0.285
(0.348) 		0.106
(0.155) 		0.505
(0.556)
22q gain 5 (4%) 118 0.0366
(0.0656) 		0.0313
(0.0584) 		0.374
(0.423) 		0.203
(0.257) 		0.274
(0.337) 		0.228
(0.286) 		0.325
(0.388) 		0.605
(0.655) 		0.224
(0.282) 		0.682
(0.726)
9p loss 4 (3%) 119 0.25
(0.313) 		0.108
(0.155) 		0.189
(0.248) 		0.203
(0.257) 		0.0161
(0.0357) 		0.00331
(0.0107) 		1
(1.00) 		0.0605
(0.096) 		1
(1.00) 		0.335
(0.395)
19p gain 3 (2%) 120 0.0244
(0.0498) 		0.179
(0.237) 		0.357
(0.41) 		0.327
(0.388) 		0.195
(0.253) 		0.612
(0.661) 		0.105
(0.154) 		0.303
(0.367)
19q gain 3 (2%) 120 0.0246
(0.0499) 		0.176
(0.235) 		0.356
(0.409) 		0.33
(0.391) 		0.196
(0.253) 		0.613
(0.662) 		0.106
(0.154) 		0.304
(0.367)
xp gain 3 (2%) 120 0.0247
(0.0499) 		0.177
(0.235) 		0.353
(0.409) 		0.327
(0.388) 		0.198
(0.254) 		0.682
(0.726) 		0.107
(0.155) 		0.505
(0.556)
4q loss 4 (3%) 119 0.0295
(0.0564) 		0.0611
(0.0966) 		0.139
(0.193) 		0.183
(0.242) 		0.435
(0.484) 		0.116
(0.164) 		0.105
(0.154) 		0.0872
(0.134)
16p loss 5 (4%) 118 0.13
(0.182) 		0.202
(0.257) 		0.372
(0.423) 		0.0143
(0.0323) 		0.196
(0.253) 		0.114
(0.162) 		0.324
(0.388) 		0.577
(0.629) 		0.228
(0.286) 		0.308
(0.369)
21q gain 3 (2%) 120 0.278
(0.34) 		0.347
(0.406) 		0.372
(0.423) 		0.203
(0.257) 		0.488
(0.54) 		0.188
(0.248) 		0.649
(0.694) 		0.344
(0.403) 		0.74
(0.782) 		0.62
(0.666)
'1p gain' versus 'CN_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0013

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
1P GAIN MUTATED 0 7 1
1P GAIN WILD-TYPE 65 24 26

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.045

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
1P GAIN MUTATED 1 2 5 0
1P GAIN WILD-TYPE 38 34 19 24

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0349 (Fisher's exact test), Q value = 0.063

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
1P GAIN MUTATED 0 0 2 4
1P GAIN WILD-TYPE 16 23 29 16

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00875 (Fisher's exact test), Q value = 0.022

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
1P GAIN MUTATED 5 0 0 3
1P GAIN WILD-TYPE 40 31 29 11

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00347 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
1P GAIN MUTATED 5 0 0 3
1P GAIN WILD-TYPE 42 42 20 7

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.044

Table S6.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
1P GAIN MUTATED 8 0 0 0 0
1P GAIN WILD-TYPE 50 61 1 2 1

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.044

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
1P GAIN MUTATED 2 0 4 2 0 0
1P GAIN WILD-TYPE 25 18 24 5 16 27

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

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.011

Table S8.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
1P GAIN MUTATED 1 0 7
1P GAIN WILD-TYPE 17 59 39

Figure S8.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00698 (Fisher's exact test), Q value = 0.019

Table S9.  Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
1P GAIN MUTATED 2 0 6 0
1P GAIN WILD-TYPE 27 33 27 28

Figure S9.  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 = 0.00011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
1Q GAIN MUTATED 3 18 1
1Q GAIN WILD-TYPE 62 13 26

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

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
1Q GAIN MUTATED 2 6 14 0
1Q GAIN WILD-TYPE 37 30 10 24

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

'1q gain' versus 'RPPA_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0047

Table S12.  Gene #2: '1q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
1Q GAIN MUTATED 12 1 3
1Q GAIN WILD-TYPE 19 24 31

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

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
1Q GAIN MUTATED 0 0 4 12
1Q GAIN WILD-TYPE 16 23 27 8

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S14.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
1Q GAIN MUTATED 15 0 0 7
1Q GAIN WILD-TYPE 30 31 29 7

Figure S14.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S15.  Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
1Q GAIN MUTATED 15 0 0 7
1Q GAIN WILD-TYPE 32 42 20 3

Figure S15.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S16.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
1Q GAIN MUTATED 21 0 0 1 0
1Q GAIN WILD-TYPE 37 61 1 1 1

Figure S16.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S17.  Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
1Q GAIN MUTATED 7 0 10 5 0 0
1Q GAIN WILD-TYPE 20 18 18 2 16 27

Figure S17.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S18.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
1Q GAIN MUTATED 1 0 21
1Q GAIN WILD-TYPE 17 59 25

Figure S18.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S19.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
1Q GAIN MUTATED 7 0 15 0
1Q GAIN WILD-TYPE 22 33 18 28

Figure S19.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.033

Table S20.  Gene #3: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
3Q GAIN MUTATED 0 0 0 3
3Q GAIN WILD-TYPE 16 23 31 17

Figure S20.  Get High-res Image Gene #3: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0384 (Fisher's exact test), Q value = 0.068

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
3Q GAIN MUTATED 2 0 1 2
3Q GAIN WILD-TYPE 45 42 19 8

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

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00493 (Fisher's exact test), Q value = 0.015

Table S22.  Gene #3: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
3Q GAIN MUTATED 0 0 1 2 2 0
3Q GAIN WILD-TYPE 27 18 27 5 14 27

Figure S22.  Get High-res Image Gene #3: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S23.  Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
5P GAIN MUTATED 0 11 0
5P GAIN WILD-TYPE 65 20 27

Figure S23.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S24.  Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
5P GAIN MUTATED 0 2 9 0
5P GAIN WILD-TYPE 39 34 15 24

Figure S24.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00271 (Fisher's exact test), Q value = 0.0091

Table S25.  Gene #4: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
5P GAIN MUTATED 1 0 1 6
5P GAIN WILD-TYPE 15 23 30 14

Figure S25.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0067

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
5P GAIN MUTATED 8 0 0 3
5P GAIN WILD-TYPE 37 31 29 11

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

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.0055

Table S27.  Gene #4: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
5P GAIN MUTATED 9 0 0 2
5P GAIN WILD-TYPE 38 42 20 8

Figure S27.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0037

Table S28.  Gene #4: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
5P GAIN MUTATED 10 0 0 1 0
5P GAIN WILD-TYPE 48 61 1 1 1

Figure S28.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.031

Table S29.  Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
5P GAIN MUTATED 6 0 4 1 0 0
5P GAIN WILD-TYPE 21 18 24 6 16 27

Figure S29.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S30.  Gene #4: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
5P GAIN MUTATED 0 0 11
5P GAIN WILD-TYPE 18 59 35

Figure S30.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.0074

Table S31.  Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
5P GAIN MUTATED 6 0 5 0
5P GAIN WILD-TYPE 23 33 28 28

Figure S31.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
5Q GAIN MUTATED 0 9 0
5Q GAIN WILD-TYPE 65 22 27

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

'5q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S33.  Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
5Q GAIN MUTATED 0 1 8 0
5Q GAIN WILD-TYPE 39 35 16 24

Figure S33.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00973 (Fisher's exact test), Q value = 0.024

Table S34.  Gene #5: '5q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
5Q GAIN MUTATED 1 0 1 5
5Q GAIN WILD-TYPE 15 23 30 15

Figure S34.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00933 (Fisher's exact test), Q value = 0.023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
5Q GAIN MUTATED 7 0 0 2
5Q GAIN WILD-TYPE 38 31 29 12

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

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00688 (Fisher's exact test), Q value = 0.019

Table S36.  Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
5Q GAIN MUTATED 8 0 0 1
5Q GAIN WILD-TYPE 39 42 20 9

Figure S36.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.00362 (Fisher's exact test), Q value = 0.011

Table S37.  Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
5Q GAIN MUTATED 8 0 0 1 0
5Q GAIN WILD-TYPE 50 61 1 1 1

Figure S37.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.037

Table S38.  Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
5Q GAIN MUTATED 6 0 3 0 0 0
5Q GAIN WILD-TYPE 21 18 25 7 16 27

Figure S38.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0014

Table S39.  Gene #5: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
5Q GAIN MUTATED 0 0 9
5Q GAIN WILD-TYPE 18 59 37

Figure S39.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
5Q GAIN MUTATED 6 0 3 0
5Q GAIN WILD-TYPE 23 33 30 28

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

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S41.  Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
7P GAIN MUTATED 0 16 0
7P GAIN WILD-TYPE 65 15 27

Figure S41.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S42.  Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
7P GAIN MUTATED 1 1 14 0
7P GAIN WILD-TYPE 38 35 10 24

Figure S42.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.05

Table S43.  Gene #6: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
7P GAIN MUTATED 8 1 2
7P GAIN WILD-TYPE 23 24 32

Figure S43.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00412 (Fisher's exact test), Q value = 0.013

Table S44.  Gene #6: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
7P GAIN MUTATED 1 0 3 7
7P GAIN WILD-TYPE 15 23 28 13

Figure S44.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S45.  Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
7P GAIN MUTATED 16 0 0 0
7P GAIN WILD-TYPE 29 31 29 14

Figure S45.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S46.  Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
7P GAIN MUTATED 16 0 0 0
7P GAIN WILD-TYPE 31 42 20 10

Figure S46.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S47.  Gene #6: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
7P GAIN MUTATED 15 0 0 1 0
7P GAIN WILD-TYPE 43 61 1 1 1

Figure S47.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0011

Table S48.  Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
7P GAIN MUTATED 9 0 7 0 0 0
7P GAIN WILD-TYPE 18 18 21 7 16 27

Figure S48.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S49.  Gene #6: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
7P GAIN MUTATED 0 0 16
7P GAIN WILD-TYPE 18 59 30

Figure S49.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S50.  Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
7P GAIN MUTATED 10 0 6 0
7P GAIN WILD-TYPE 19 33 27 28

Figure S50.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S51.  Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
7Q GAIN MUTATED 0 16 0
7Q GAIN WILD-TYPE 65 15 27

Figure S51.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S52.  Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
7Q GAIN MUTATED 1 1 14 0
7Q GAIN WILD-TYPE 38 35 10 24

Figure S52.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.05

Table S53.  Gene #7: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
7Q GAIN MUTATED 8 1 2
7Q GAIN WILD-TYPE 23 24 32

Figure S53.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00411 (Fisher's exact test), Q value = 0.013

Table S54.  Gene #7: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
7Q GAIN MUTATED 1 0 3 7
7Q GAIN WILD-TYPE 15 23 28 13

Figure S54.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S55.  Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
7Q GAIN MUTATED 16 0 0 0
7Q GAIN WILD-TYPE 29 31 29 14

Figure S55.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S56.  Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
7Q GAIN MUTATED 16 0 0 0
7Q GAIN WILD-TYPE 31 42 20 10

Figure S56.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S57.  Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
7Q GAIN MUTATED 15 0 0 1 0
7Q GAIN WILD-TYPE 43 61 1 1 1

Figure S57.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.0012

Table S58.  Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
7Q GAIN MUTATED 9 0 7 0 0 0
7Q GAIN WILD-TYPE 18 18 21 7 16 27

Figure S58.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S59.  Gene #7: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
7Q GAIN MUTATED 0 0 16
7Q GAIN WILD-TYPE 18 59 30

Figure S59.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S60.  Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
7Q GAIN MUTATED 10 0 6 0
7Q GAIN WILD-TYPE 19 33 27 28

Figure S60.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0022

Table S61.  Gene #8: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
8P GAIN MUTATED 2 9 1
8P GAIN WILD-TYPE 63 22 26

Figure S61.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.044

Table S62.  Gene #8: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
8P GAIN MUTATED 2 4 6 0
8P GAIN WILD-TYPE 37 32 18 24

Figure S62.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00392 (Fisher's exact test), Q value = 0.012

Table S63.  Gene #8: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
8P GAIN MUTATED 1 0 3 7
8P GAIN WILD-TYPE 15 23 28 13

Figure S63.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0033

Table S64.  Gene #8: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
8P GAIN MUTATED 8 0 0 4
8P GAIN WILD-TYPE 37 31 29 10

Figure S64.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0011

Table S65.  Gene #8: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
8P GAIN MUTATED 8 0 0 4
8P GAIN WILD-TYPE 39 42 20 6

Figure S65.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0033

Table S66.  Gene #8: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
8P GAIN MUTATED 12 0 0 0 0
8P GAIN WILD-TYPE 46 61 1 2 1

Figure S66.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.0067

Table S67.  Gene #8: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
8P GAIN MUTATED 4 0 5 3 0 0
8P GAIN WILD-TYPE 23 18 23 4 16 27

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

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0011

Table S68.  Gene #8: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
8P GAIN MUTATED 2 0 10
8P GAIN WILD-TYPE 16 59 36

Figure S68.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0023

Table S69.  Gene #8: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
8P GAIN MUTATED 4 0 8 0
8P GAIN WILD-TYPE 25 33 25 28

Figure S69.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0015

Table S70.  Gene #9: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
8Q GAIN MUTATED 2 9 1
8Q GAIN WILD-TYPE 63 22 26

Figure S70.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.044

Table S71.  Gene #9: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
8Q GAIN MUTATED 2 4 6 0
8Q GAIN WILD-TYPE 37 32 18 24

Figure S71.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00396 (Fisher's exact test), Q value = 0.012

Table S72.  Gene #9: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
8Q GAIN MUTATED 1 0 3 7
8Q GAIN WILD-TYPE 15 23 28 13

Figure S72.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0033

Table S73.  Gene #9: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
8Q GAIN MUTATED 8 0 0 4
8Q GAIN WILD-TYPE 37 31 29 10

Figure S73.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0011

Table S74.  Gene #9: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
8Q GAIN MUTATED 8 0 0 4
8Q GAIN WILD-TYPE 39 42 20 6

Figure S74.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0025

Table S75.  Gene #9: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
8Q GAIN MUTATED 12 0 0 0 0
8Q GAIN WILD-TYPE 46 61 1 2 1

Figure S75.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00182 (Fisher's exact test), Q value = 0.0067

Table S76.  Gene #9: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
8Q GAIN MUTATED 4 0 5 3 0 0
8Q GAIN WILD-TYPE 23 18 23 4 16 27

Figure S76.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00096

Table S77.  Gene #9: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
8Q GAIN MUTATED 2 0 10
8Q GAIN WILD-TYPE 16 59 36

Figure S77.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0027

Table S78.  Gene #9: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
8Q GAIN MUTATED 4 0 8 0
8Q GAIN WILD-TYPE 25 33 25 28

Figure S78.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S79.  Gene #10: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
9P GAIN MUTATED 0 11 0
9P GAIN WILD-TYPE 65 20 27

Figure S79.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00091

Table S80.  Gene #10: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
9P GAIN MUTATED 2 0 8 1
9P GAIN WILD-TYPE 37 36 16 23

Figure S80.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0023

Table S81.  Gene #10: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
9P GAIN MUTATED 10 0 0 0
9P GAIN WILD-TYPE 35 31 29 14

Figure S81.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0042

Table S82.  Gene #10: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
9P GAIN MUTATED 10 0 0 0
9P GAIN WILD-TYPE 37 42 20 10

Figure S82.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.025

Table S83.  Gene #10: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
9P GAIN MUTATED 9 1 0 1 0
9P GAIN WILD-TYPE 49 60 1 1 1

Figure S83.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00555 (Fisher's exact test), Q value = 0.016

Table S84.  Gene #10: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
9P GAIN MUTATED 8 0 2 0 0 1
9P GAIN WILD-TYPE 19 18 26 7 16 26

Figure S84.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00532 (Fisher's exact test), Q value = 0.015

Table S85.  Gene #10: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
9P GAIN MUTATED 1 1 9
9P GAIN WILD-TYPE 17 58 37

Figure S85.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.0044

Table S86.  Gene #10: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
9P GAIN MUTATED 8 0 2 1
9P GAIN WILD-TYPE 21 33 31 27

Figure S86.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S87.  Gene #11: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
9Q GAIN MUTATED 0 11 0
9Q GAIN WILD-TYPE 65 20 27

Figure S87.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00096

Table S88.  Gene #11: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
9Q GAIN MUTATED 2 0 8 1
9Q GAIN WILD-TYPE 37 36 16 23

Figure S88.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0021

Table S89.  Gene #11: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
9Q GAIN MUTATED 10 0 0 0
9Q GAIN WILD-TYPE 35 31 29 14

Figure S89.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0042

Table S90.  Gene #11: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
9Q GAIN MUTATED 10 0 0 0
9Q GAIN WILD-TYPE 37 42 20 10

Figure S90.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.025

Table S91.  Gene #11: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
9Q GAIN MUTATED 9 1 0 1 0
9Q GAIN WILD-TYPE 49 60 1 1 1

Figure S91.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00593 (Fisher's exact test), Q value = 0.017

Table S92.  Gene #11: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
9Q GAIN MUTATED 8 0 2 0 0 1
9Q GAIN WILD-TYPE 19 18 26 7 16 26

Figure S92.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00482 (Fisher's exact test), Q value = 0.014

Table S93.  Gene #11: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
9Q GAIN MUTATED 1 1 9
9Q GAIN WILD-TYPE 17 58 37

Figure S93.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0041

Table S94.  Gene #11: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
9Q GAIN MUTATED 8 0 2 1
9Q GAIN WILD-TYPE 21 33 31 27

Figure S94.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.055

Table S95.  Gene #12: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
12P GAIN MUTATED 0 3 1
12P GAIN WILD-TYPE 65 28 26

Figure S95.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.056

Table S96.  Gene #12: '12p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
12P GAIN MUTATED 1 0 0 3
12P GAIN WILD-TYPE 15 23 31 17

Figure S96.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00476 (Fisher's exact test), Q value = 0.014

Table S97.  Gene #12: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
12P GAIN MUTATED 1 0 0 3
12P GAIN WILD-TYPE 44 31 29 11

Figure S97.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00232 (Fisher's exact test), Q value = 0.008

Table S98.  Gene #12: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
12P GAIN MUTATED 1 0 0 3
12P GAIN WILD-TYPE 46 42 20 7

Figure S98.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.053

Table S99.  Gene #12: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
12P GAIN MUTATED 1 0 1 2 0 0
12P GAIN WILD-TYPE 26 18 27 5 16 27

Figure S99.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.078

Table S100.  Gene #12: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
12P GAIN MUTATED 0 0 4
12P GAIN WILD-TYPE 18 59 42

Figure S100.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.056

Table S101.  Gene #13: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
12Q GAIN MUTATED 0 3 1
12Q GAIN WILD-TYPE 65 28 26

Figure S101.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.056

Table S102.  Gene #13: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
12Q GAIN MUTATED 1 0 0 3
12Q GAIN WILD-TYPE 15 23 31 17

Figure S102.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.014

Table S103.  Gene #13: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
12Q GAIN MUTATED 1 0 0 3
12Q GAIN WILD-TYPE 44 31 29 11

Figure S103.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00253 (Fisher's exact test), Q value = 0.0085

Table S104.  Gene #13: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
12Q GAIN MUTATED 1 0 0 3
12Q GAIN WILD-TYPE 46 42 20 7

Figure S104.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.052

Table S105.  Gene #13: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
12Q GAIN MUTATED 1 0 1 2 0 0
12Q GAIN WILD-TYPE 26 18 27 5 16 27

Figure S105.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.078

Table S106.  Gene #13: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
12Q GAIN MUTATED 0 0 4
12Q GAIN WILD-TYPE 18 59 42

Figure S106.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S107.  Gene #14: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
14Q GAIN MUTATED 0 13 0
14Q GAIN WILD-TYPE 65 18 27

Figure S107.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S108.  Gene #14: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
14Q GAIN MUTATED 2 1 10 0
14Q GAIN WILD-TYPE 37 35 14 24

Figure S108.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.056

Table S109.  Gene #14: '14q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
14Q GAIN MUTATED 1 0 2 5
14Q GAIN WILD-TYPE 15 23 29 15

Figure S109.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S110.  Gene #14: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
14Q GAIN MUTATED 13 0 0 0
14Q GAIN WILD-TYPE 32 31 29 14

Figure S110.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S111.  Gene #14: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
14Q GAIN MUTATED 13 0 0 0
14Q GAIN WILD-TYPE 34 42 20 10

Figure S111.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0011

Table S112.  Gene #14: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
14Q GAIN MUTATED 12 0 0 1 0
14Q GAIN WILD-TYPE 46 61 1 1 1

Figure S112.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0011

Table S113.  Gene #14: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
14Q GAIN MUTATED 10 0 3 0 0 0
14Q GAIN WILD-TYPE 17 18 25 7 16 27

Figure S113.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S114.  Gene #14: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
14Q GAIN MUTATED 0 0 13
14Q GAIN WILD-TYPE 18 59 33

Figure S114.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 3e-04

Table S115.  Gene #14: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
14Q GAIN MUTATED 10 0 3 0
14Q GAIN WILD-TYPE 19 33 30 28

Figure S115.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00091

Table S116.  Gene #15: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
15Q GAIN MUTATED 1 9 2
15Q GAIN WILD-TYPE 64 22 25

Figure S116.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 3e-04

Table S117.  Gene #15: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
15Q GAIN MUTATED 2 1 9 0
15Q GAIN WILD-TYPE 37 35 15 24

Figure S117.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.044

Table S118.  Gene #15: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
15Q GAIN MUTATED 8 0 1 2
15Q GAIN WILD-TYPE 37 31 28 12

Figure S118.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0089 (Fisher's exact test), Q value = 0.022

Table S119.  Gene #15: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
15Q GAIN MUTATED 9 0 1 1
15Q GAIN WILD-TYPE 38 42 19 9

Figure S119.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.032

Table S120.  Gene #15: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
15Q GAIN MUTATED 11 1 0 0 0
15Q GAIN WILD-TYPE 47 60 1 2 1

Figure S120.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.044

Table S121.  Gene #15: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
15Q GAIN MUTATED 6 0 5 0 1 0
15Q GAIN WILD-TYPE 21 18 23 7 15 27

Figure S121.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0058

Table S122.  Gene #15: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
15Q GAIN MUTATED 1 1 10
15Q GAIN WILD-TYPE 17 58 36

Figure S122.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00584 (Fisher's exact test), Q value = 0.017

Table S123.  Gene #15: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
15Q GAIN MUTATED 7 1 4 0
15Q GAIN WILD-TYPE 22 32 29 28

Figure S123.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.072

Table S124.  Gene #16: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
17Q GAIN MUTATED 2 0 2 3
17Q GAIN WILD-TYPE 43 31 27 11

Figure S124.  Get High-res Image Gene #16: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00362 (Fisher's exact test), Q value = 0.011

Table S125.  Gene #16: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
17Q GAIN MUTATED 2 0 2 3
17Q GAIN WILD-TYPE 45 42 18 7

Figure S125.  Get High-res Image Gene #16: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.084

Table S126.  Gene #17: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
18P GAIN MUTATED 1 0 0 2
18P GAIN WILD-TYPE 44 31 29 12

Figure S126.  Get High-res Image Gene #17: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.056

Table S127.  Gene #17: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
18P GAIN MUTATED 1 0 0 2
18P GAIN WILD-TYPE 46 42 20 8

Figure S127.  Get High-res Image Gene #17: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.084

Table S128.  Gene #18: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
18Q GAIN MUTATED 1 0 0 2
18Q GAIN WILD-TYPE 44 31 29 12

Figure S128.  Get High-res Image Gene #18: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.056

Table S129.  Gene #18: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
18Q GAIN MUTATED 1 0 0 2
18Q GAIN WILD-TYPE 46 42 20 8

Figure S129.  Get High-res Image Gene #18: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.05

Table S130.  Gene #19: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
19P GAIN MUTATED 0 3 0
19P GAIN WILD-TYPE 65 28 27

Figure S130.  Get High-res Image Gene #19: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.05

Table S131.  Gene #20: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
19Q GAIN MUTATED 0 3 0
19Q GAIN WILD-TYPE 65 28 27

Figure S131.  Get High-res Image Gene #20: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0023

Table S132.  Gene #21: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
20P GAIN MUTATED 1 8 1
20P GAIN WILD-TYPE 64 23 26

Figure S132.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.048

Table S133.  Gene #21: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
20P GAIN MUTATED 1 4 5 0
20P GAIN WILD-TYPE 38 32 19 24

Figure S133.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.00486 (Fisher's exact test), Q value = 0.014

Table S134.  Gene #21: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
20P GAIN MUTATED 6 1 0
20P GAIN WILD-TYPE 25 24 34

Figure S134.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0016

Table S135.  Gene #21: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
20P GAIN MUTATED 1 0 0 6
20P GAIN WILD-TYPE 15 23 31 14

Figure S135.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0055

Table S136.  Gene #21: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
20P GAIN MUTATED 6 0 0 4
20P GAIN WILD-TYPE 39 31 29 10

Figure S136.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0017

Table S137.  Gene #21: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
20P GAIN MUTATED 6 0 0 4
20P GAIN WILD-TYPE 41 42 20 6

Figure S137.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.026

Table S138.  Gene #21: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
20P GAIN MUTATED 3 0 3 3 1 0
20P GAIN WILD-TYPE 24 18 25 4 15 27

Figure S138.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0024

Table S139.  Gene #21: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
20P GAIN MUTATED 1 0 9
20P GAIN WILD-TYPE 17 59 37

Figure S139.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.003

Table S140.  Gene #22: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
20Q GAIN MUTATED 1 8 1
20Q GAIN WILD-TYPE 64 23 26

Figure S140.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.05

Table S141.  Gene #22: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
20Q GAIN MUTATED 1 4 5 0
20Q GAIN WILD-TYPE 38 32 19 24

Figure S141.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.00555 (Fisher's exact test), Q value = 0.016

Table S142.  Gene #22: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
20Q GAIN MUTATED 6 1 0
20Q GAIN WILD-TYPE 25 24 34

Figure S142.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0011

Table S143.  Gene #22: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
20Q GAIN MUTATED 1 0 0 6
20Q GAIN WILD-TYPE 15 23 31 14

Figure S143.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0049

Table S144.  Gene #22: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
20Q GAIN MUTATED 6 0 0 4
20Q GAIN WILD-TYPE 39 31 29 10

Figure S144.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0016

Table S145.  Gene #22: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
20Q GAIN MUTATED 6 0 0 4
20Q GAIN WILD-TYPE 41 42 20 6

Figure S145.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.026

Table S146.  Gene #22: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
20Q GAIN MUTATED 3 0 3 3 1 0
20Q GAIN WILD-TYPE 24 18 25 4 15 27

Figure S146.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0025

Table S147.  Gene #22: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
20Q GAIN MUTATED 1 0 9
20Q GAIN WILD-TYPE 17 59 37

Figure S147.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.066

Table S148.  Gene #24: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
22Q GAIN MUTATED 1 4 0
22Q GAIN WILD-TYPE 64 27 27

Figure S148.  Get High-res Image Gene #24: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.058

Table S149.  Gene #24: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
22Q GAIN MUTATED 0 2 3 0
22Q GAIN WILD-TYPE 39 34 21 24

Figure S149.  Get High-res Image Gene #24: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.05

Table S150.  Gene #25: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
XP GAIN MUTATED 0 3 0
XP GAIN WILD-TYPE 65 28 27

Figure S150.  Get High-res Image Gene #25: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0044

Table S151.  Gene #26: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
XQ GAIN MUTATED 0 5 0
XQ GAIN WILD-TYPE 65 26 27

Figure S151.  Get High-res Image Gene #26: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.00808 (Fisher's exact test), Q value = 0.021

Table S152.  Gene #26: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
XQ GAIN MUTATED 0 1 4 0
XQ GAIN WILD-TYPE 39 35 20 24

Figure S152.  Get High-res Image Gene #26: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.083

Table S153.  Gene #26: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
XQ GAIN MUTATED 5 0 0 0
XQ GAIN WILD-TYPE 40 31 29 14

Figure S153.  Get High-res Image Gene #26: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.028

Table S154.  Gene #26: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
XQ GAIN MUTATED 0 0 5
XQ GAIN WILD-TYPE 18 59 41

Figure S154.  Get High-res Image Gene #26: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.00524 (Fisher's exact test), Q value = 0.015

Table S155.  Gene #27: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
1P LOSS MUTATED 0 4 0
1P LOSS WILD-TYPE 65 27 27

Figure S155.  Get High-res Image Gene #27: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.0075

Table S156.  Gene #27: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
1P LOSS MUTATED 0 0 4 0
1P LOSS WILD-TYPE 39 36 20 24

Figure S156.  Get High-res Image Gene #27: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.078

Table S157.  Gene #27: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
1P LOSS MUTATED 0 0 4
1P LOSS WILD-TYPE 18 59 42

Figure S157.  Get High-res Image Gene #27: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S158.  Gene #28: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
3P LOSS MUTATED 1 10 1
3P LOSS WILD-TYPE 64 21 26

Figure S158.  Get High-res Image Gene #28: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S159.  Gene #28: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
3P LOSS MUTATED 0 2 10 0
3P LOSS WILD-TYPE 39 34 14 24

Figure S159.  Get High-res Image Gene #28: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.066

Table S160.  Gene #28: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
3P LOSS MUTATED 7 2 1
3P LOSS WILD-TYPE 24 23 33

Figure S160.  Get High-res Image Gene #28: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S161.  Gene #28: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
3P LOSS MUTATED 2 0 0 8
3P LOSS WILD-TYPE 14 23 31 12

Figure S161.  Get High-res Image Gene #28: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0044

Table S162.  Gene #28: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
3P LOSS MUTATED 9 0 0 3
3P LOSS WILD-TYPE 36 31 29 11

Figure S162.  Get High-res Image Gene #28: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0035

Table S163.  Gene #28: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
3P LOSS MUTATED 10 0 0 2
3P LOSS WILD-TYPE 37 42 20 8

Figure S163.  Get High-res Image Gene #28: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0032

Table S164.  Gene #28: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
3P LOSS MUTATED 12 0 0 0 0
3P LOSS WILD-TYPE 46 61 1 2 1

Figure S164.  Get High-res Image Gene #28: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00482 (Fisher's exact test), Q value = 0.014

Table S165.  Gene #28: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
3P LOSS MUTATED 6 0 4 2 0 0
3P LOSS WILD-TYPE 21 18 24 5 16 27

Figure S165.  Get High-res Image Gene #28: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S166.  Gene #28: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
3P LOSS MUTATED 0 0 12
3P LOSS WILD-TYPE 18 59 34

Figure S166.  Get High-res Image Gene #28: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0023

Table S167.  Gene #28: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
3P LOSS MUTATED 7 0 5 0
3P LOSS WILD-TYPE 22 33 28 28

Figure S167.  Get High-res Image Gene #28: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0035

Table S168.  Gene #29: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
3Q LOSS MUTATED 0 6 1
3Q LOSS WILD-TYPE 65 25 26

Figure S168.  Get High-res Image Gene #29: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0015

Table S169.  Gene #29: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
3Q LOSS MUTATED 0 1 6 0
3Q LOSS WILD-TYPE 39 35 18 24

Figure S169.  Get High-res Image Gene #29: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0046

Table S170.  Gene #29: '3q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
3Q LOSS MUTATED 1 0 0 5
3Q LOSS WILD-TYPE 15 23 31 15

Figure S170.  Get High-res Image Gene #29: '3q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 0.059

Table S171.  Gene #29: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
3Q LOSS MUTATED 6 0 0 1
3Q LOSS WILD-TYPE 39 31 29 13

Figure S171.  Get High-res Image Gene #29: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.059

Table S172.  Gene #29: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
3Q LOSS MUTATED 6 0 0 1
3Q LOSS WILD-TYPE 41 42 20 9

Figure S172.  Get High-res Image Gene #29: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.063

Table S173.  Gene #29: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
3Q LOSS MUTATED 7 0 0 0 0
3Q LOSS WILD-TYPE 51 61 1 2 1

Figure S173.  Get High-res Image Gene #29: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.0074

Table S174.  Gene #29: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
3Q LOSS MUTATED 0 0 7
3Q LOSS WILD-TYPE 18 59 39

Figure S174.  Get High-res Image Gene #29: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00818 (Fisher's exact test), Q value = 0.021

Table S175.  Gene #29: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
3Q LOSS MUTATED 5 0 2 0
3Q LOSS WILD-TYPE 24 33 31 28

Figure S175.  Get High-res Image Gene #29: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 0.00778 (Fisher's exact test), Q value = 0.021

Table S176.  Gene #30: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
4P LOSS MUTATED 0 4 1
4P LOSS WILD-TYPE 65 27 26

Figure S176.  Get High-res Image Gene #30: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.028

Table S177.  Gene #30: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
4P LOSS MUTATED 1 0 4 0
4P LOSS WILD-TYPE 38 36 20 24

Figure S177.  Get High-res Image Gene #30: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 0.084

Table S178.  Gene #30: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
4P LOSS MUTATED 5 0 0 0
4P LOSS WILD-TYPE 40 31 29 14

Figure S178.  Get High-res Image Gene #30: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'CN_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.056

Table S179.  Gene #31: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
4Q LOSS MUTATED 0 3 1
4Q LOSS WILD-TYPE 65 28 26

Figure S179.  Get High-res Image Gene #31: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S180.  Gene #32: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
6P LOSS MUTATED 1 18 1
6P LOSS WILD-TYPE 64 13 26

Figure S180.  Get High-res Image Gene #32: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S181.  Gene #32: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
6P LOSS MUTATED 2 3 15 0
6P LOSS WILD-TYPE 37 33 9 24

Figure S181.  Get High-res Image Gene #32: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0011

Table S182.  Gene #32: '6p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
6P LOSS MUTATED 12 2 1
6P LOSS WILD-TYPE 19 23 33

Figure S182.  Get High-res Image Gene #32: '6p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S183.  Gene #32: '6p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
6P LOSS MUTATED 2 0 2 11
6P LOSS WILD-TYPE 14 23 29 9

Figure S183.  Get High-res Image Gene #32: '6p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S184.  Gene #32: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
6P LOSS MUTATED 14 0 0 6
6P LOSS WILD-TYPE 31 31 29 8

Figure S184.  Get High-res Image Gene #32: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S185.  Gene #32: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
6P LOSS MUTATED 15 0 0 5
6P LOSS WILD-TYPE 32 42 20 5

Figure S185.  Get High-res Image Gene #32: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S186.  Gene #32: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
6P LOSS MUTATED 19 0 0 1 0
6P LOSS WILD-TYPE 39 61 1 1 1

Figure S186.  Get High-res Image Gene #32: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S187.  Gene #32: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
6P LOSS MUTATED 9 0 8 3 0 0
6P LOSS WILD-TYPE 18 18 20 4 16 27

Figure S187.  Get High-res Image Gene #32: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S188.  Gene #32: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
6P LOSS MUTATED 1 0 19
6P LOSS WILD-TYPE 17 59 27

Figure S188.  Get High-res Image Gene #32: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S189.  Gene #32: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
6P LOSS MUTATED 10 0 10 0
6P LOSS WILD-TYPE 19 33 23 28

Figure S189.  Get High-res Image Gene #32: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S190.  Gene #33: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
6Q LOSS MUTATED 0 17 2
6Q LOSS WILD-TYPE 65 14 25

Figure S190.  Get High-res Image Gene #33: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S191.  Gene #33: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
6Q LOSS MUTATED 1 3 15 0
6Q LOSS WILD-TYPE 38 33 9 24

Figure S191.  Get High-res Image Gene #33: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0033

Table S192.  Gene #33: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
6Q LOSS MUTATED 11 2 1
6Q LOSS WILD-TYPE 20 23 33

Figure S192.  Get High-res Image Gene #33: '6q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S193.  Gene #33: '6q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
6Q LOSS MUTATED 2 1 1 10
6Q LOSS WILD-TYPE 14 22 30 10

Figure S193.  Get High-res Image Gene #33: '6q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S194.  Gene #33: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
6Q LOSS MUTATED 12 0 0 7
6Q LOSS WILD-TYPE 33 31 29 7

Figure S194.  Get High-res Image Gene #33: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S195.  Gene #33: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
6Q LOSS MUTATED 13 0 1 5
6Q LOSS WILD-TYPE 34 42 19 5

Figure S195.  Get High-res Image Gene #33: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S196.  Gene #33: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
6Q LOSS MUTATED 17 1 0 1 0
6Q LOSS WILD-TYPE 41 60 1 1 1

Figure S196.  Get High-res Image Gene #33: '6q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0015

Table S197.  Gene #33: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
6Q LOSS MUTATED 9 0 6 3 1 0
6Q LOSS WILD-TYPE 18 18 22 4 15 27

Figure S197.  Get High-res Image Gene #33: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S198.  Gene #33: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
6Q LOSS MUTATED 0 0 19
6Q LOSS WILD-TYPE 18 59 27

Figure S198.  Get High-res Image Gene #33: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00065

Table S199.  Gene #33: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
6Q LOSS MUTATED 10 1 8 0
6Q LOSS WILD-TYPE 19 32 25 28

Figure S199.  Get High-res Image Gene #33: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.036

Table S200.  Gene #34: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
9P LOSS MUTATED 0 0 2 2
9P LOSS WILD-TYPE 45 31 27 12

Figure S200.  Get High-res Image Gene #34: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00331 (Fisher's exact test), Q value = 0.011

Table S201.  Gene #34: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
9P LOSS MUTATED 0 0 2 2
9P LOSS WILD-TYPE 47 42 18 8

Figure S201.  Get High-res Image Gene #34: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.027

Table S202.  Gene #35: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
10P LOSS MUTATED 0 0 1 2
10P LOSS WILD-TYPE 45 31 28 12

Figure S202.  Get High-res Image Gene #35: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.046

Table S203.  Gene #35: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
10P LOSS MUTATED 0 0 2 1
10P LOSS WILD-TYPE 47 42 18 9

Figure S203.  Get High-res Image Gene #35: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.034

Table S204.  Gene #35: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
10P LOSS MUTATED 0 0 0 1 2 0
10P LOSS WILD-TYPE 27 18 28 6 14 27

Figure S204.  Get High-res Image Gene #35: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S205.  Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
11P LOSS MUTATED 0 9 0
11P LOSS WILD-TYPE 65 22 27

Figure S205.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00018

Table S206.  Gene #36: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
11P LOSS MUTATED 0 1 8 0
11P LOSS WILD-TYPE 39 35 16 24

Figure S206.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.037

Table S207.  Gene #36: '11p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
11P LOSS MUTATED 5 1 0
11P LOSS WILD-TYPE 26 24 34

Figure S207.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0049

Table S208.  Gene #36: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
11P LOSS MUTATED 1 0 0 5
11P LOSS WILD-TYPE 15 23 31 15

Figure S208.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.023

Table S209.  Gene #36: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
11P LOSS MUTATED 7 0 0 2
11P LOSS WILD-TYPE 38 31 29 12

Figure S209.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00705 (Fisher's exact test), Q value = 0.019

Table S210.  Gene #36: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
11P LOSS MUTATED 8 0 0 1
11P LOSS WILD-TYPE 39 42 20 9

Figure S210.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00916 (Fisher's exact test), Q value = 0.023

Table S211.  Gene #36: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
11P LOSS MUTATED 9 0 0 0 0
11P LOSS WILD-TYPE 49 61 1 2 1

Figure S211.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0012

Table S212.  Gene #36: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
11P LOSS MUTATED 0 0 9
11P LOSS WILD-TYPE 18 59 37

Figure S212.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00844 (Fisher's exact test), Q value = 0.022

Table S213.  Gene #36: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
11P LOSS MUTATED 5 0 4 0
11P LOSS WILD-TYPE 24 33 29 28

Figure S213.  Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00059

Table S214.  Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
11Q LOSS MUTATED 0 7 0
11Q LOSS WILD-TYPE 65 24 27

Figure S214.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S215.  Gene #37: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
11Q LOSS MUTATED 0 0 7 0
11Q LOSS WILD-TYPE 39 36 17 24

Figure S215.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.081

Table S216.  Gene #37: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
11Q LOSS MUTATED 4 1 0
11Q LOSS WILD-TYPE 27 24 34

Figure S216.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00625 (Fisher's exact test), Q value = 0.017

Table S217.  Gene #37: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
11Q LOSS MUTATED 1 0 0 4
11Q LOSS WILD-TYPE 15 23 31 16

Figure S217.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.059

Table S218.  Gene #37: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
11Q LOSS MUTATED 6 0 0 1
11Q LOSS WILD-TYPE 39 31 29 13

Figure S218.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.031

Table S219.  Gene #37: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
11Q LOSS MUTATED 7 0 0 0
11Q LOSS WILD-TYPE 40 42 20 10

Figure S219.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.061

Table S220.  Gene #37: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
11Q LOSS MUTATED 7 0 0 0 0
11Q LOSS WILD-TYPE 51 61 1 2 1

Figure S220.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00208 (Fisher's exact test), Q value = 0.0074

Table S221.  Gene #37: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
11Q LOSS MUTATED 0 0 7
11Q LOSS WILD-TYPE 18 59 39

Figure S221.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00815 (Fisher's exact test), Q value = 0.021

Table S222.  Gene #37: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
11Q LOSS MUTATED 5 0 2 0
11Q LOSS WILD-TYPE 24 33 31 28

Figure S222.  Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.014

Table S223.  Gene #38: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
12P LOSS MUTATED 1 6 1
12P LOSS WILD-TYPE 64 25 26

Figure S223.  Get High-res Image Gene #38: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00052

Table S224.  Gene #38: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
12P LOSS MUTATED 1 0 7 0
12P LOSS WILD-TYPE 38 36 17 24

Figure S224.  Get High-res Image Gene #38: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.038

Table S225.  Gene #38: '12p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
12P LOSS MUTATED 4 0 0
12P LOSS WILD-TYPE 27 25 34

Figure S225.  Get High-res Image Gene #38: '12p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00253 (Fisher's exact test), Q value = 0.0085

Table S226.  Gene #38: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
12P LOSS MUTATED 0 0 0 4
12P LOSS WILD-TYPE 16 23 31 16

Figure S226.  Get High-res Image Gene #38: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.00854 (Fisher's exact test), Q value = 0.022

Table S227.  Gene #38: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
12P LOSS MUTATED 7 0 0 0
12P LOSS WILD-TYPE 38 31 29 14

Figure S227.  Get High-res Image Gene #38: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.031

Table S228.  Gene #38: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
12P LOSS MUTATED 7 0 0 0
12P LOSS WILD-TYPE 40 42 20 10

Figure S228.  Get High-res Image Gene #38: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.046

Table S229.  Gene #38: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
12P LOSS MUTATED 8 0 0 0 0
12P LOSS WILD-TYPE 50 61 1 2 1

Figure S229.  Get High-res Image Gene #38: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.011

Table S230.  Gene #38: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
12P LOSS MUTATED 1 0 7
12P LOSS WILD-TYPE 17 59 39

Figure S230.  Get High-res Image Gene #38: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.042

Table S231.  Gene #38: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
12P LOSS MUTATED 4 0 4 0
12P LOSS WILD-TYPE 25 33 29 28

Figure S231.  Get High-res Image Gene #38: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.0061

Table S232.  Gene #39: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
12Q LOSS MUTATED 1 6 0
12Q LOSS WILD-TYPE 64 25 27

Figure S232.  Get High-res Image Gene #39: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S233.  Gene #39: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
12Q LOSS MUTATED 0 0 7 0
12Q LOSS WILD-TYPE 39 36 17 24

Figure S233.  Get High-res Image Gene #39: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.038

Table S234.  Gene #39: '12q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
12Q LOSS MUTATED 4 0 0
12Q LOSS WILD-TYPE 27 25 34

Figure S234.  Get High-res Image Gene #39: '12q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00245 (Fisher's exact test), Q value = 0.0084

Table S235.  Gene #39: '12q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
12Q LOSS MUTATED 0 0 0 4
12Q LOSS WILD-TYPE 16 23 31 16

Figure S235.  Get High-res Image Gene #39: '12q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.0076 (Fisher's exact test), Q value = 0.02

Table S236.  Gene #39: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
12Q LOSS MUTATED 7 0 0 0
12Q LOSS WILD-TYPE 38 31 29 14

Figure S236.  Get High-res Image Gene #39: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.031

Table S237.  Gene #39: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
12Q LOSS MUTATED 7 0 0 0
12Q LOSS WILD-TYPE 40 42 20 10

Figure S237.  Get High-res Image Gene #39: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.06

Table S238.  Gene #39: '12q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
12Q LOSS MUTATED 7 0 0 0 0
12Q LOSS WILD-TYPE 51 61 1 2 1

Figure S238.  Get High-res Image Gene #39: '12q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.0079

Table S239.  Gene #39: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
12Q LOSS MUTATED 0 0 7
12Q LOSS WILD-TYPE 18 59 39

Figure S239.  Get High-res Image Gene #39: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.065

Table S240.  Gene #39: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
12Q LOSS MUTATED 4 0 3 0
12Q LOSS WILD-TYPE 25 33 30 28

Figure S240.  Get High-res Image Gene #39: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S241.  Gene #40: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
13Q LOSS MUTATED 0 9 5
13Q LOSS WILD-TYPE 65 22 22

Figure S241.  Get High-res Image Gene #40: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00611 (Fisher's exact test), Q value = 0.017

Table S242.  Gene #40: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
13Q LOSS MUTATED 2 2 8 2
13Q LOSS WILD-TYPE 37 34 16 22

Figure S242.  Get High-res Image Gene #40: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.0062 (Fisher's exact test), Q value = 0.017

Table S243.  Gene #40: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
13Q LOSS MUTATED 7 4 0
13Q LOSS WILD-TYPE 24 21 34

Figure S243.  Get High-res Image Gene #40: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.072

Table S244.  Gene #40: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
13Q LOSS MUTATED 2 2 1 6
13Q LOSS WILD-TYPE 14 21 30 14

Figure S244.  Get High-res Image Gene #40: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0495 (Fisher's exact test), Q value = 0.084

Table S245.  Gene #40: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
13Q LOSS MUTATED 10 3 0 1
13Q LOSS WILD-TYPE 37 39 20 9

Figure S245.  Get High-res Image Gene #40: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.032

Table S246.  Gene #41: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
16P LOSS MUTATED 0 0 0 3
16P LOSS WILD-TYPE 16 23 31 17

Figure S246.  Get High-res Image Gene #41: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.016

Table S247.  Gene #42: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
16Q LOSS MUTATED 1 7 5 0
16Q LOSS WILD-TYPE 38 29 19 24

Figure S247.  Get High-res Image Gene #42: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00023

Table S248.  Gene #42: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
16Q LOSS MUTATED 0 1 0 8
16Q LOSS WILD-TYPE 16 22 31 12

Figure S248.  Get High-res Image Gene #42: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S249.  Gene #42: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
16Q LOSS MUTATED 3 1 1 8
16Q LOSS WILD-TYPE 42 30 28 6

Figure S249.  Get High-res Image Gene #42: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S250.  Gene #42: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
16Q LOSS MUTATED 3 1 1 8
16Q LOSS WILD-TYPE 44 41 19 2

Figure S250.  Get High-res Image Gene #42: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S251.  Gene #42: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
16Q LOSS MUTATED 1 0 4 6 1 1
16Q LOSS WILD-TYPE 26 18 24 1 15 26

Figure S251.  Get High-res Image Gene #42: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.0057

Table S252.  Gene #42: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
16Q LOSS MUTATED 0 2 11
16Q LOSS WILD-TYPE 18 57 35

Figure S252.  Get High-res Image Gene #42: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0035

Table S253.  Gene #42: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
16Q LOSS MUTATED 1 1 10 1
16Q LOSS WILD-TYPE 28 32 23 27

Figure S253.  Get High-res Image Gene #42: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.045

Table S254.  Gene #43: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
17P LOSS MUTATED 3 7 4
17P LOSS WILD-TYPE 62 24 23

Figure S254.  Get High-res Image Gene #43: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0048

Table S255.  Gene #43: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
17P LOSS MUTATED 1 6 7 0
17P LOSS WILD-TYPE 38 30 17 24

Figure S255.  Get High-res Image Gene #43: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.00501 (Fisher's exact test), Q value = 0.015

Table S256.  Gene #43: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
17P LOSS MUTATED 7 2 0
17P LOSS WILD-TYPE 24 23 34

Figure S256.  Get High-res Image Gene #43: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0011

Table S257.  Gene #43: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
17P LOSS MUTATED 0 2 0 7
17P LOSS WILD-TYPE 16 21 31 13

Figure S257.  Get High-res Image Gene #43: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.037

Table S258.  Gene #43: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
17P LOSS MUTATED 7 0 3 4
17P LOSS WILD-TYPE 38 31 26 10

Figure S258.  Get High-res Image Gene #43: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0037

Table S259.  Gene #43: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
17P LOSS MUTATED 7 0 3 4
17P LOSS WILD-TYPE 40 42 17 6

Figure S259.  Get High-res Image Gene #43: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00185 (Fisher's exact test), Q value = 0.0067

Table S260.  Gene #43: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
17P LOSS MUTATED 2 0 5 3 4 0
17P LOSS WILD-TYPE 25 18 23 4 12 27

Figure S260.  Get High-res Image Gene #43: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.055

Table S261.  Gene #43: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
17P LOSS MUTATED 1 3 10
17P LOSS WILD-TYPE 17 56 36

Figure S261.  Get High-res Image Gene #43: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.025

Table S262.  Gene #44: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
17Q LOSS MUTATED 0 4 2
17Q LOSS WILD-TYPE 65 27 25

Figure S262.  Get High-res Image Gene #44: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.00847 (Fisher's exact test), Q value = 0.022

Table S263.  Gene #44: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
17Q LOSS MUTATED 0 2 4 0
17Q LOSS WILD-TYPE 39 34 20 24

Figure S263.  Get High-res Image Gene #44: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00295 (Fisher's exact test), Q value = 0.0098

Table S264.  Gene #44: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
17Q LOSS MUTATED 0 0 0 4
17Q LOSS WILD-TYPE 16 23 31 16

Figure S264.  Get High-res Image Gene #44: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.0067

Table S265.  Gene #45: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
18P LOSS MUTATED 1 6 0
18P LOSS WILD-TYPE 64 25 27

Figure S265.  Get High-res Image Gene #45: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.00854 (Fisher's exact test), Q value = 0.022

Table S266.  Gene #45: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
18P LOSS MUTATED 1 1 5 0
18P LOSS WILD-TYPE 38 35 19 24

Figure S266.  Get High-res Image Gene #45: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.038

Table S267.  Gene #45: '18p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
18P LOSS MUTATED 4 0 0
18P LOSS WILD-TYPE 27 25 34

Figure S267.  Get High-res Image Gene #45: '18p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.058

Table S268.  Gene #45: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
18P LOSS MUTATED 6 0 0 1
18P LOSS WILD-TYPE 39 31 29 13

Figure S268.  Get High-res Image Gene #45: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.058

Table S269.  Gene #45: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
18P LOSS MUTATED 6 0 0 1
18P LOSS WILD-TYPE 41 42 20 9

Figure S269.  Get High-res Image Gene #45: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.03

Table S270.  Gene #45: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
18P LOSS MUTATED 6 0 0 1 0
18P LOSS WILD-TYPE 52 61 1 1 1

Figure S270.  Get High-res Image Gene #45: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.0072

Table S271.  Gene #45: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
18P LOSS MUTATED 0 0 7
18P LOSS WILD-TYPE 18 59 39

Figure S271.  Get High-res Image Gene #45: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.076

Table S272.  Gene #45: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
18P LOSS MUTATED 3 0 4 0
18P LOSS WILD-TYPE 26 33 29 28

Figure S272.  Get High-res Image Gene #45: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.0067

Table S273.  Gene #46: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
18Q LOSS MUTATED 1 6 0
18Q LOSS WILD-TYPE 64 25 27

Figure S273.  Get High-res Image Gene #46: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.008 (Fisher's exact test), Q value = 0.021

Table S274.  Gene #46: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
18Q LOSS MUTATED 1 1 5 0
18Q LOSS WILD-TYPE 38 35 19 24

Figure S274.  Get High-res Image Gene #46: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.037

Table S275.  Gene #46: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
18Q LOSS MUTATED 4 0 0
18Q LOSS WILD-TYPE 27 25 34

Figure S275.  Get High-res Image Gene #46: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.058

Table S276.  Gene #46: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
18Q LOSS MUTATED 6 0 0 1
18Q LOSS WILD-TYPE 39 31 29 13

Figure S276.  Get High-res Image Gene #46: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.058

Table S277.  Gene #46: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
18Q LOSS MUTATED 6 0 0 1
18Q LOSS WILD-TYPE 41 42 20 9

Figure S277.  Get High-res Image Gene #46: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.03

Table S278.  Gene #46: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
18Q LOSS MUTATED 6 0 0 1 0
18Q LOSS WILD-TYPE 52 61 1 1 1

Figure S278.  Get High-res Image Gene #46: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0076

Table S279.  Gene #46: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
18Q LOSS MUTATED 0 0 7
18Q LOSS WILD-TYPE 18 59 39

Figure S279.  Get High-res Image Gene #46: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.074

Table S280.  Gene #46: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
18Q LOSS MUTATED 3 0 4 0
18Q LOSS WILD-TYPE 26 33 29 28

Figure S280.  Get High-res Image Gene #46: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0058

Table S281.  Gene #47: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
19P LOSS MUTATED 0 0 0 3
19P LOSS WILD-TYPE 45 31 29 11

Figure S281.  Get High-res Image Gene #47: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.0033

Table S282.  Gene #47: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
19P LOSS MUTATED 0 0 0 3
19P LOSS WILD-TYPE 47 42 20 7

Figure S282.  Get High-res Image Gene #47: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.025

Table S283.  Gene #47: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
19P LOSS MUTATED 0 0 1 2 0 0
19P LOSS WILD-TYPE 27 18 27 5 16 27

Figure S283.  Get High-res Image Gene #47: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0053

Table S284.  Gene #48: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
19Q LOSS MUTATED 0 0 0 3
19Q LOSS WILD-TYPE 45 31 29 11

Figure S284.  Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.0015

Table S285.  Gene #48: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
19Q LOSS MUTATED 0 0 0 3
19Q LOSS WILD-TYPE 47 42 20 7

Figure S285.  Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.025

Table S286.  Gene #48: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
19Q LOSS MUTATED 0 0 1 2 0 0
19Q LOSS WILD-TYPE 27 18 27 5 16 27

Figure S286.  Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S287.  Gene #49: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
21Q LOSS MUTATED 0 9 0
21Q LOSS WILD-TYPE 65 22 27

Figure S287.  Get High-res Image Gene #49: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S288.  Gene #49: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
21Q LOSS MUTATED 0 1 8 0
21Q LOSS WILD-TYPE 39 35 16 24

Figure S288.  Get High-res Image Gene #49: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.037

Table S289.  Gene #49: '21q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
21Q LOSS MUTATED 4 0 0
21Q LOSS WILD-TYPE 27 25 34

Figure S289.  Get High-res Image Gene #49: '21q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00302 (Fisher's exact test), Q value = 0.0099

Table S290.  Gene #49: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
21Q LOSS MUTATED 0 0 0 4
21Q LOSS WILD-TYPE 16 23 31 16

Figure S290.  Get High-res Image Gene #49: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00565 (Fisher's exact test), Q value = 0.016

Table S291.  Gene #49: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
21Q LOSS MUTATED 8 0 0 1
21Q LOSS WILD-TYPE 37 31 29 13

Figure S291.  Get High-res Image Gene #49: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00736 (Fisher's exact test), Q value = 0.02

Table S292.  Gene #49: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
21Q LOSS MUTATED 8 0 0 1
21Q LOSS WILD-TYPE 39 42 20 9

Figure S292.  Get High-res Image Gene #49: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.0089 (Fisher's exact test), Q value = 0.022

Table S293.  Gene #49: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
21Q LOSS MUTATED 9 0 0 0 0
21Q LOSS WILD-TYPE 49 61 1 2 1

Figure S293.  Get High-res Image Gene #49: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0011

Table S294.  Gene #49: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
21Q LOSS MUTATED 0 0 9
21Q LOSS WILD-TYPE 18 59 37

Figure S294.  Get High-res Image Gene #49: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00873 (Fisher's exact test), Q value = 0.022

Table S295.  Gene #49: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
21Q LOSS MUTATED 5 0 4 0
21Q LOSS WILD-TYPE 24 33 29 28

Figure S295.  Get High-res Image Gene #49: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S296.  Gene #50: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
22Q LOSS MUTATED 0 4 9
22Q LOSS WILD-TYPE 65 27 18

Figure S296.  Get High-res Image Gene #50: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0409 (Fisher's exact test), Q value = 0.072

Table S297.  Gene #50: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
22Q LOSS MUTATED 4 1 1 4
22Q LOSS WILD-TYPE 12 22 30 16

Figure S297.  Get High-res Image Gene #50: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.078

Table S298.  Gene #50: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
22Q LOSS MUTATED 3 4 2 4
22Q LOSS WILD-TYPE 44 38 18 6

Figure S298.  Get High-res Image Gene #50: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 0.00291 (Fisher's exact test), Q value = 0.0097

Table S299.  Gene #51: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
XP LOSS MUTATED 0 5 2
XP LOSS WILD-TYPE 65 26 25

Figure S299.  Get High-res Image Gene #51: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.0082 (Fisher's exact test), Q value = 0.021

Table S300.  Gene #51: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
XP LOSS MUTATED 1 1 5 0
XP LOSS WILD-TYPE 38 35 19 24

Figure S300.  Get High-res Image Gene #51: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.057

Table S301.  Gene #51: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
XP LOSS MUTATED 5 0 0 2
XP LOSS WILD-TYPE 40 31 29 12

Figure S301.  Get High-res Image Gene #51: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.059

Table S302.  Gene #51: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
XP LOSS MUTATED 6 0 0 1
XP LOSS WILD-TYPE 41 42 20 9

Figure S302.  Get High-res Image Gene #51: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00753 (Fisher's exact test), Q value = 0.02

Table S303.  Gene #51: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
XP LOSS MUTATED 1 0 6
XP LOSS WILD-TYPE 17 59 40

Figure S303.  Get High-res Image Gene #51: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.056

Table S304.  Gene #52: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
XQ LOSS MUTATED 0 3 1
XQ LOSS WILD-TYPE 65 28 26

Figure S304.  Get High-res Image Gene #52: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.065

Table S305.  Gene #52: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
XQ LOSS MUTATED 0 1 3 0
XQ LOSS WILD-TYPE 39 35 21 24

Figure S305.  Get High-res Image Gene #52: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.032

Table S306.  Gene #52: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
XQ LOSS MUTATED 0 0 0 3
XQ LOSS WILD-TYPE 16 23 31 17

Figure S306.  Get High-res Image Gene #52: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.051

Table S307.  Gene #52: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
XQ LOSS MUTATED 3 0 0 1 0
XQ LOSS WILD-TYPE 55 61 1 1 1

Figure S307.  Get High-res Image Gene #52: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0447 (Fisher's exact test), Q value = 0.078

Table S308.  Gene #52: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
XQ LOSS MUTATED 0 0 4
XQ LOSS WILD-TYPE 18 59 42

Figure S308.  Get High-res Image Gene #52: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THYM-TP/19781935/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/20140903/THYM-TP.transferedmergedcluster.txt

  • Number of patients = 123

  • Number of significantly arm-level cnvs = 52

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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