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

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

Summary

Testing the association between copy number variation 51 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',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 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 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

  • 18p gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • 18q gain cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • xq gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 1p loss cnv correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_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 'MIRSEQ_MATURE_CNMF'.

  • 4q loss cnv correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 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 'CN_CNMF',  '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 'MIRSEQ_MATURE_CNMF'.

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

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

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

  • 17q loss cnv correlated to '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 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  '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',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • xq loss cnv correlated to '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 51 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 23 (19%) 100 0.0004
(0.00234) 		1e-05
(0.000159) 		0.00043
(0.00249) 		1e-05
(0.000159) 		1e-05
(0.000159) 		1e-05
(0.000159) 		1e-05
(0.000159) 		1e-05
(0.000159) 		1e-05
(0.000159) 		1e-05
(0.000159)
7p gain 16 (13%) 107 0.0007
(0.00343) 		1e-05
(0.000159) 		0.0247
(0.049) 		0.00389
(0.0119) 		1e-05
(0.000159) 		1e-05
(0.000159) 		1e-05
(0.000159) 		8e-05
(0.00068) 		1e-05
(0.000159) 		3e-05
(0.000356)
7q gain 16 (13%) 107 0.00063
(0.00321) 		1e-05
(0.000159) 		0.0251
(0.0491) 		0.00413
(0.0125) 		3e-05
(0.000356) 		1e-05
(0.000159) 		1e-05
(0.000159) 		0.0001
(0.000797) 		1e-05
(0.000159) 		5e-05
(5e-04)
3p loss 12 (10%) 111 0.00369
(0.0115) 		1e-05
(0.000159) 		0.0381
(0.0666) 		1e-05
(0.000159) 		0.00106
(0.00454) 		0.00083
(0.00381) 		0.00045
(0.00255) 		0.00455
(0.0136) 		1e-05
(0.000159) 		0.00099
(0.00435)
6p loss 21 (17%) 102 0.00055
(0.00289) 		1e-05
(0.000159) 		6e-05
(0.000556) 		4e-05
(0.000425) 		1e-05
(0.000159) 		2e-05
(0.000283) 		1e-05
(0.000159) 		0.00015
(0.00112) 		1e-05
(0.000159) 		3e-05
(0.000356)
6q loss 20 (16%) 103 0.00027
(0.00177) 		1e-05
(0.000159) 		0.00024
(0.00161) 		7e-05
(0.000626) 		3e-05
(0.000356) 		0.00013
(0.00099) 		0.00029
(0.00187) 		0.0016
(0.00628) 		1e-05
(0.000159) 		0.00094
(0.00421)
14q gain 13 (11%) 110 0.00036
(0.00219) 		1e-05
(0.000159) 		0.268
(0.317) 		0.0298
(0.0556) 		2e-05
(0.000283) 		6e-05
(0.000556) 		4e-05
(0.000425) 		0.00011
(0.00085) 		1e-05
(0.000159) 		4e-05
(0.000425)
20p gain 10 (8%) 113 0.175
(0.223) 		0.00076
(0.00359) 		0.0051
(0.0147) 		0.00023
(0.00156) 		0.00151
(0.00597) 		0.0003
(0.00191) 		0.0284
(0.0539) 		0.0115
(0.0265) 		5e-05
(5e-04) 		0.0176
(0.0367)
20q gain 10 (8%) 113 0.173
(0.221) 		0.0006
(0.00309) 		0.00507
(0.0147) 		0.00019
(0.00133) 		0.00144
(0.00578) 		0.00039
(0.00231) 		0.0284
(0.0539) 		0.0102
(0.0245) 		5e-05
(5e-04) 		0.0174
(0.0364)
11p loss 9 (7%) 114 0.00978
(0.0236) 		0.00011
(0.00085) 		0.0162
(0.0354) 		0.00118
(0.00489) 		0.0091
(0.0225) 		0.00695
(0.0186) 		0.00369
(0.0115) 		0.0511
(0.0835) 		0.00017
(0.00122) 		0.0106
(0.0253)
11q loss 7 (6%) 116 0.0194
(0.04) 		0.00075
(0.00357) 		0.0475
(0.0801) 		0.00616
(0.0168) 		0.0358
(0.0637) 		0.0143
(0.0321) 		0.011
(0.0257) 		0.113
(0.16) 		0.00266
(0.00893) 		0.0261
(0.0508)
12p loss 8 (7%) 115 0.00287
(0.00926) 		0.00555
(0.0157) 		0.0171
(0.0361) 		0.00246
(0.00875) 		0.00883
(0.0221) 		0.014
(0.0318) 		0.00674
(0.0181) 		0.0531
(0.0852) 		0.00926
(0.0227) 		0.0159
(0.0348)
12q loss 7 (6%) 116 0.00798
(0.0202) 		0.00109
(0.00456) 		0.017
(0.0361) 		0.00282
(0.00925) 		0.00884
(0.0221) 		0.0135
(0.0306) 		0.0113
(0.0263) 		0.121
(0.167) 		0.00264
(0.00893) 		0.0364
(0.0641)
16q loss 13 (11%) 110 0.00084
(0.00382) 		1e-05
(0.000159) 		0.0783
(0.117) 		4e-05
(0.000425) 		3e-05
(0.000356) 		1e-05
(0.000159) 		0.0351
(0.0633) 		2e-05
(0.000283) 		0.00074
(0.00356) 		0.00166
(0.00646)
17p loss 14 (11%) 109 0.0098
(0.0236) 		0.00278
(0.00921) 		0.00482
(0.0142) 		0.00021
(0.00145) 		0.0192
(0.0398) 		0.00109
(0.00456) 		0.269
(0.318) 		0.00197
(0.00744) 		0.00236
(0.00848) 		0.0287
(0.0541)
21q loss 9 (7%) 114 0.00699
(0.0186) 		7e-05
(0.000626) 		0.0169
(0.0361) 		0.00256
(0.00893) 		0.00661
(0.0179) 		0.00711
(0.0187) 		0.00389
(0.0119) 		0.0518
(0.0842) 		0.00016
(0.00118) 		0.00776
(0.02)
5p gain 11 (9%) 112 0.0952
(0.138) 		2e-05
(0.000283) 		0.0656
(0.102) 		0.003
(0.00962) 		0.00185
(0.00709) 		0.00141
(0.00575) 		0.00036
(0.00219) 		0.013
(0.0298) 		1e-05
(0.000159) 		0.00224
(0.00822)
5q gain 9 (7%) 114 0.245
(0.292) 		8e-05
(0.00068) 		0.143
(0.191) 		0.00937
(0.0229) 		0.00898
(0.0223) 		0.00715
(0.0187) 		0.001
(0.00436) 		0.0163
(0.0354) 		6e-05
(0.000556) 		0.00591
(0.0166)
8p gain 12 (10%) 111 0.0995
(0.142) 		9e-05
(0.000752) 		0.4
(0.444) 		0.0043
(0.0129) 		0.00046
(0.00258) 		0.00017
(0.00122) 		0.00034
(0.00211) 		0.00185
(0.00709) 		0.0001
(0.000797) 		0.00077
(0.0036)
8q gain 12 (10%) 111 0.0993
(0.142) 		3e-05
(0.000356) 		0.404
(0.446) 		0.00407
(0.0124) 		0.0005
(0.00271) 		0.00019
(0.00133) 		0.00054
(0.00287) 		0.00195
(0.00742) 		6e-05
(0.000556) 		0.0007
(0.00343)
9p gain 11 (9%) 112 0.00027
(0.00177) 		0.00072
(0.0035) 		0.545
(0.59) 		0.384
(0.43) 		0.00039
(0.00231) 		0.00095
(0.00421) 		4e-05
(0.000425) 		0.00545
(0.0155) 		0.0001
(0.000797) 		0.00268
(0.00893)
9q gain 11 (9%) 112 0.00032
(0.00201) 		0.00057
(0.00297) 		0.542
(0.589) 		0.386
(0.431) 		0.00051
(0.00274) 		0.00078
(0.00362) 		1e-05
(0.000159) 		0.00609
(0.0168) 		8e-05
(0.00068) 		0.00283
(0.00925)
3q loss 7 (6%) 116 0.0361
(0.064) 		0.002
(0.0075) 		0.0872
(0.128) 		0.00107
(0.00455) 		0.0354
(0.0635) 		0.0317
(0.0578) 		0.0113
(0.0262) 		0.0851
(0.126) 		0.00259
(0.00893) 		0.0266
(0.0516)
18p loss 7 (6%) 116 0.0473
(0.0801) 		0.0358
(0.0637) 		0.0169
(0.0361) 		0.0974
(0.14) 		0.0347
(0.0628) 		0.0318
(0.0578) 		0.0037
(0.0115) 		0.0955
(0.138) 		0.00247
(0.00875) 		0.025
(0.049)
18q loss 7 (6%) 116 0.0486
(0.0809) 		0.0363
(0.0641) 		0.0174
(0.0364) 		0.0986
(0.142) 		0.0357
(0.0637) 		0.0319
(0.0578) 		0.00382
(0.0118) 		0.0961
(0.139) 		0.00217
(0.00802) 		0.0249
(0.049)
12p gain 4 (3%) 119 0.0282
(0.0538) 		0.00796
(0.0202) 		0.192
(0.24) 		0.0286
(0.0541) 		0.00489
(0.0143) 		0.00232
(0.00839) 		0.114
(0.161) 		0.0268
(0.0517) 		0.0491
(0.0814) 		0.147
(0.195)
12q gain 4 (3%) 119 0.0281
(0.0538) 		0.0078
(0.02) 		0.194
(0.242) 		0.0304
(0.0562) 		0.00471
(0.014) 		0.00226
(0.00823) 		0.116
(0.162) 		0.0274
(0.0527) 		0.0478
(0.0802) 		0.148
(0.195)
15q gain 12 (10%) 111 0.244
(0.292) 		0.00091
(0.00411) 		0.887
(0.93) 		0.666
(0.706) 		0.0213
(0.0432) 		0.00918
(0.0226) 		0.00266
(0.00893) 		0.0215
(0.0435) 		0.00069
(0.00343) 		0.0157
(0.0345)
1p loss 5 (4%) 118 0.151
(0.198) 		0.00712
(0.0187) 		0.374
(0.421) 		0.0144
(0.0321) 		0.00775
(0.02) 		0.0237
(0.0473) 		0.0399
(0.0693) 		0.231
(0.28) 		0.0317
(0.0578) 		0.126
(0.174)
xp loss 8 (7%) 115 0.14
(0.188) 		0.00574
(0.0162) 		0.521
(0.568) 		0.0249
(0.049) 		0.0197
(0.0406) 		0.0134
(0.0306) 		0.0171
(0.0361) 		0.137
(0.186) 		0.0005
(0.00271) 		0.109
(0.155)
1p gain 6 (5%) 117 0.0109
(0.0255) 		0.00738
(0.0192) 		0.095
(0.138) 		0.131
(0.179) 		0.0526
(0.0848) 		0.0212
(0.0432) 		0.0228
(0.0457) 		0.176
(0.223) 		0.00808
(0.0204) 		0.0643
(0.101)
13q loss 14 (11%) 109 0.00501
(0.0146) 		0.00068
(0.00343) 		0.00611
(0.0168) 		0.0407
(0.0701) 		0.0702
(0.108) 		0.0501
(0.0826) 		0.289
(0.339) 		0.58
(0.625) 		0.00203
(0.00756) 		0.345
(0.394)
19p loss 3 (2%) 120 0.00673
(0.0181) 		0.00268
(0.00893) 		0.00137
(0.00563) 		0.00047
(0.00261) 		0.234
(0.282) 		0.00962
(0.0234) 		0.0774
(0.116) 		0.0589
(0.0931)
19q loss 3 (2%) 120 0.00595
(0.0166) 		0.00287
(0.00926) 		0.00143
(0.00578) 		0.00045
(0.00255) 		0.231
(0.28) 		0.0105
(0.025) 		0.0754
(0.115) 		0.0593
(0.0934)
22q loss 13 (11%) 110 3e-05
(0.000356) 		0.0108
(0.0255) 		0.105
(0.149) 		0.0404
(0.0699) 		0.0896
(0.131) 		0.0431
(0.0741) 		0.325
(0.38) 		0.332
(0.384) 		0.006
(0.0166) 		0.331
(0.383)
xq loss 5 (4%) 118 0.147
(0.195) 		0.0157
(0.0345) 		0.14
(0.188) 		0.00263
(0.00893) 		0.0705
(0.108) 		0.0917
(0.134) 		0.0399
(0.0693) 		0.229
(0.28) 		0.0301
(0.056) 		0.13
(0.178)
3q gain 5 (4%) 118 0.755
(0.795) 		0.374
(0.421) 		0.0564
(0.0897) 		0.0142
(0.032) 		0.211
(0.261) 		0.0373
(0.0653) 		0.744
(0.786) 		0.00513
(0.0147) 		0.165
(0.214) 		0.243
(0.292)
9p loss 4 (3%) 119 0.00145
(0.00578) 		0.0752
(0.115) 		0.189
(0.237) 		0.201
(0.25) 		0.0217
(0.0436) 		0.00361
(0.0114) 		1
(1.00) 		0.0589
(0.0931) 		0.689
(0.729) 		0.336
(0.388)
10p loss 3 (2%) 120 0.0772
(0.116) 		0.109
(0.155) 		0.0212
(0.0432) 		0.0217
(0.0436) 		1
(1.00) 		0.0149
(0.0331) 		0.613
(0.655) 		0.554
(0.599)
17q gain 7 (6%) 116 0.00106
(0.00454) 		0.124
(0.171) 		0.0869
(0.128) 		0.138
(0.187) 		0.0504
(0.0826) 		0.00353
(0.0113) 		0.796
(0.837) 		0.0677
(0.105) 		0.182
(0.231) 		0.393
(0.437)
22q gain 4 (3%) 119 0.0816
(0.121) 		0.0166
(0.0357) 		0.137
(0.186) 		0.185
(0.234) 		0.115
(0.161) 		0.528
(0.574) 		0.0491
(0.0814) 		0.146
(0.195)
xq gain 4 (3%) 119 0.0812
(0.121) 		0.0166
(0.0357) 		0.138
(0.187) 		0.185
(0.234) 		0.0541
(0.0865) 		0.315
(0.369) 		0.0476
(0.0801) 		0.252
(0.3)
4q loss 4 (3%) 119 0.341
(0.392) 		0.388
(0.432) 		0.139
(0.187) 		0.186
(0.234) 		0.166
(0.214) 		0.118
(0.164) 		0.0482
(0.0806) 		0.0435
(0.0745)
16p loss 5 (4%) 118 0.124
(0.171) 		0.0452
(0.0771) 		0.374
(0.421) 		0.0144
(0.0322) 		0.213
(0.263) 		0.115
(0.162) 		0.158
(0.206) 		0.576
(0.621) 		0.165
(0.214) 		0.343
(0.392)
17q loss 6 (5%) 117 0.0761
(0.115) 		0.0455
(0.0774) 		0.139
(0.187) 		0.00257
(0.00893) 		0.343
(0.392) 		0.147
(0.195) 		0.216
(0.266) 		0.234
(0.282) 		0.116
(0.162) 		0.206
(0.255)
18p gain 3 (2%) 120 0.166
(0.214) 		0.0524
(0.0848) 		0.0663
(0.103) 		0.0293
(0.055) 		0.23
(0.28) 		0.285
(0.335) 		0.0756
(0.115) 		0.438
(0.482)
18q gain 3 (2%) 120 0.167
(0.214) 		0.0517
(0.0842) 		0.0656
(0.102) 		0.0302
(0.0561) 		0.231
(0.28) 		0.285
(0.335) 		0.0765
(0.115) 		0.44
(0.482)
4p loss 5 (4%) 118 0.404
(0.446) 		0.222
(0.272) 		0.0502
(0.0826) 		0.0653
(0.102) 		0.158
(0.206) 		0.385
(0.43) 		0.0309
(0.0569) 		0.228
(0.278)
19p gain 3 (2%) 120 0.256
(0.304) 		0.151
(0.198) 		0.354
(0.403) 		0.327
(0.381) 		0.0547
(0.0872) 		0.614
(0.655) 		0.0758
(0.115) 		0.439
(0.482)
19q gain 3 (2%) 120 0.256
(0.304) 		0.152
(0.199) 		0.355
(0.403) 		0.329
(0.382) 		0.0527
(0.0849) 		0.613
(0.655) 		0.0768
(0.116) 		0.441
(0.482)
21q gain 3 (2%) 120 0.168
(0.215) 		0.38
(0.427) 		0.369
(0.419) 		0.204
(0.253) 		0.493
(0.538) 		0.187
(0.235) 		0.658
(0.7) 		0.342
(0.392) 		0.614
(0.655) 		0.62
(0.66)
'1p gain' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
1P GAIN MUTATED 2 0 4 0 0
1P GAIN WILD-TYPE 34 27 15 31 10

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00738 (Fisher's exact test), Q value = 0.019

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
1P GAIN MUTATED 0 0 4 2 0 0 0 0
1P GAIN WILD-TYPE 37 23 15 8 18 8 2 6

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.043

Table S3.  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 4 0 0 2
1P GAIN WILD-TYPE 43 42 20 8

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.046

Table S4.  Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
1P GAIN MUTATED 5 0 1 0
1P GAIN WILD-TYPE 51 61 4 1

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00808 (Fisher's exact test), Q value = 0.02

Table S5.  Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
1P GAIN MUTATED 0 0 6 0
1P GAIN WILD-TYPE 28 51 37 1

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q gain' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
1Q GAIN MUTATED 12 0 6 2 3
1Q GAIN WILD-TYPE 24 27 13 29 7

Figure S6.  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 = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
1Q GAIN MUTATED 1 0 14 8 0 0 0 0
1Q GAIN WILD-TYPE 36 23 5 2 18 8 2 6

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

'1q gain' versus 'RPPA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0025

Table S8.  Gene #2: '1q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
1Q GAIN MUTATED 13 1 3
1Q GAIN WILD-TYPE 18 24 31

Figure S8.  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 = 0.00016

Table S9.  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 13
1Q GAIN WILD-TYPE 16 23 27 7

Figure S9.  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 = 0.00016

Table S10.  Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
1Q GAIN MUTATED 15 0 0 8
1Q GAIN WILD-TYPE 30 30 30 6

Figure S10.  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 = 0.00016

Table S11.  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 16 0 0 7
1Q GAIN WILD-TYPE 31 42 20 3

Figure S11.  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 = 0.00016

Table S12.  Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
1Q GAIN MUTATED 19 0 4 0
1Q GAIN WILD-TYPE 37 61 1 1

Figure S12.  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 = 0.00016

Table S13.  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 8 0 10 5 0 0
1Q GAIN WILD-TYPE 19 18 18 2 16 27

Figure S13.  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 = 0.00016

Table S14.  Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
1Q GAIN MUTATED 0 0 22 1
1Q GAIN WILD-TYPE 28 51 21 0

Figure S14.  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 = 0.00016

Table S15.  Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
1Q GAIN MUTATED 7 0 16 0
1Q GAIN WILD-TYPE 20 33 19 28

Figure S15.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.032

Table S16.  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 S16.  Get High-res Image Gene #3: '3q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.065

Table S17.  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 S17.  Get High-res Image Gene #3: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00513 (Fisher's exact test), Q value = 0.015

Table S18.  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 S18.  Get High-res Image Gene #3: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S19.  Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
5P GAIN MUTATED 0 0 8 2 0 0 0 1
5P GAIN WILD-TYPE 37 23 11 8 18 8 2 5

Figure S19.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.003 (Fisher's exact test), Q value = 0.0096

Table S20.  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 S20.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.0071

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
5P GAIN MUTATED 8 0 0 3
5P GAIN WILD-TYPE 37 30 30 11

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

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.0058

Table S22.  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 S22.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0022

Table S23.  Gene #4: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
5P GAIN MUTATED 9 0 2 0
5P GAIN WILD-TYPE 47 61 3 1

Figure S23.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.03

Table S24.  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 S24.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S25.  Gene #4: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
5P GAIN MUTATED 0 0 10 1
5P GAIN WILD-TYPE 28 51 33 0

Figure S25.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00224 (Fisher's exact test), Q value = 0.0082

Table S26.  Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
5P GAIN MUTATED 5 0 6 0
5P GAIN WILD-TYPE 22 33 29 28

Figure S26.  Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00068

Table S27.  Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
5Q GAIN MUTATED 0 0 7 1 0 0 0 1
5Q GAIN WILD-TYPE 37 23 12 9 18 8 2 5

Figure S27.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00937 (Fisher's exact test), Q value = 0.023

Table S28.  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 S28.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00898 (Fisher's exact test), Q value = 0.022

Table S29.  Gene #5: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
5Q GAIN MUTATED 7 0 0 2
5Q GAIN WILD-TYPE 38 30 30 12

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

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00715 (Fisher's exact test), Q value = 0.019

Table S30.  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 S30.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0044

Table S31.  Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
5Q GAIN MUTATED 7 0 2 0
5Q GAIN WILD-TYPE 49 61 3 1

Figure S31.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.035

Table S32.  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 S32.  Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00056

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
5Q GAIN MUTATED 0 0 8 1
5Q GAIN WILD-TYPE 28 51 35 0

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

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00591 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
5Q GAIN MUTATED 5 0 4 0
5Q GAIN WILD-TYPE 22 33 31 28

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

'7p gain' versus 'CN_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0034

Table S35.  Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
7P GAIN MUTATED 12 0 2 2 0
7P GAIN WILD-TYPE 24 27 17 29 10

Figure S35.  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 = 0.00016

Table S36.  Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
7P GAIN MUTATED 1 0 13 1 0 0 0 1
7P GAIN WILD-TYPE 36 23 6 9 18 8 2 5

Figure S36.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'RPPA_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.049

Table S37.  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 S37.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00389 (Fisher's exact test), Q value = 0.012

Table S38.  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 S38.  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 = 0.00016

Table S39.  Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
7P GAIN MUTATED 16 0 0 0
7P GAIN WILD-TYPE 29 30 30 14

Figure S39.  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 = 0.00016

Table S40.  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 S40.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
7P GAIN MUTATED 12 0 4 0
7P GAIN WILD-TYPE 44 61 1 1

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

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00068

Table S42.  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 S42.  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 = 0.00016

Table S43.  Gene #6: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
7P GAIN MUTATED 0 0 15 1
7P GAIN WILD-TYPE 28 51 28 0

Figure S43.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S44.  Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
7P GAIN MUTATED 8 0 8 0
7P GAIN WILD-TYPE 19 33 27 28

Figure S44.  Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0032

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
7Q GAIN MUTATED 12 0 2 2 0
7Q GAIN WILD-TYPE 24 27 17 29 10

Figure S45.  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 = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
7Q GAIN MUTATED 1 0 13 1 0 0 0 1
7Q GAIN WILD-TYPE 36 23 6 9 18 8 2 5

Figure S46.  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 = 0.049

Table S47.  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 S47.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00413 (Fisher's exact test), Q value = 0.012

Table S48.  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 S48.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
7Q GAIN MUTATED 16 0 0 0
7Q GAIN WILD-TYPE 29 30 30 14

Figure S49.  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 = 0.00016

Table S50.  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 S50.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
7Q GAIN MUTATED 12 0 4 0
7Q GAIN WILD-TYPE 44 61 1 1

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

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 8e-04

Table S52.  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 S52.  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 = 0.00016

Table S53.  Gene #7: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
7Q GAIN MUTATED 0 0 15 1
7Q GAIN WILD-TYPE 28 51 28 0

Figure S53.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 5e-04

Table S54.  Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
7Q GAIN MUTATED 8 0 8 0
7Q GAIN WILD-TYPE 19 33 27 28

Figure S54.  Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00075

Table S55.  Gene #8: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
8P GAIN MUTATED 1 0 7 4 0 0 0 0
8P GAIN WILD-TYPE 36 23 12 6 18 8 2 6

Figure S55.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0043 (Fisher's exact test), Q value = 0.013

Table S56.  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 S56.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0026

Table S57.  Gene #8: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
8P GAIN MUTATED 8 0 0 4
8P GAIN WILD-TYPE 37 30 30 10

Figure S57.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0012

Table S58.  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 S58.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0021

Table S59.  Gene #8: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
8P GAIN MUTATED 11 0 1 0
8P GAIN WILD-TYPE 45 61 4 1

Figure S59.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00185 (Fisher's exact test), Q value = 0.0071

Table S60.  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 S60.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 8e-04

Table S61.  Gene #8: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
8P GAIN MUTATED 1 0 11 0
8P GAIN WILD-TYPE 27 51 32 1

Figure S61.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0036

Table S62.  Gene #8: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
8P GAIN MUTATED 4 0 8 0
8P GAIN WILD-TYPE 23 33 27 28

Figure S62.  Get High-res Image Gene #8: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S63.  Gene #9: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
8Q GAIN MUTATED 1 0 7 4 0 0 0 0
8Q GAIN WILD-TYPE 36 23 12 6 18 8 2 6

Figure S63.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00407 (Fisher's exact test), Q value = 0.012

Table S64.  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 S64.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0027

Table S65.  Gene #9: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
8Q GAIN MUTATED 8 0 0 4
8Q GAIN WILD-TYPE 37 30 30 10

Figure S65.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0013

Table S66.  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 S66.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0029

Table S67.  Gene #9: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
8Q GAIN MUTATED 11 0 1 0
8Q GAIN WILD-TYPE 45 61 4 1

Figure S67.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.0074

Table S68.  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 S68.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00056

Table S69.  Gene #9: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
8Q GAIN MUTATED 1 0 11 0
8Q GAIN WILD-TYPE 27 51 32 1

Figure S69.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0034

Table S70.  Gene #9: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
8Q GAIN MUTATED 4 0 8 0
8Q GAIN WILD-TYPE 23 33 27 28

Figure S70.  Get High-res Image Gene #9: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0018

Table S71.  Gene #10: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
9P GAIN MUTATED 10 0 0 1 0
9P GAIN WILD-TYPE 26 27 19 30 10

Figure S71.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0035

Table S72.  Gene #10: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
9P GAIN MUTATED 1 0 8 1 1 0 0 0
9P GAIN WILD-TYPE 36 23 11 9 17 8 2 6

Figure S72.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0023

Table S73.  Gene #10: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
9P GAIN MUTATED 10 0 0 0
9P GAIN WILD-TYPE 35 30 30 14

Figure S73.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0042

Table S74.  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 S74.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00042

Table S75.  Gene #10: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
9P GAIN MUTATED 6 1 4 0
9P GAIN WILD-TYPE 50 60 1 1

Figure S75.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.016

Table S76.  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 S76.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 8e-04

Table S77.  Gene #10: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
9P GAIN MUTATED 0 1 9 1
9P GAIN WILD-TYPE 28 50 34 0

Figure S77.  Get High-res Image Gene #10: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00268 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
9P GAIN MUTATED 7 0 3 1
9P GAIN WILD-TYPE 20 33 32 27

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

'9q gain' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.002

Table S79.  Gene #11: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
9Q GAIN MUTATED 10 0 0 1 0
9Q GAIN WILD-TYPE 26 27 19 30 10

Figure S79.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.003

Table S80.  Gene #11: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
9Q GAIN MUTATED 1 0 8 1 1 0 0 0
9Q GAIN WILD-TYPE 36 23 11 9 17 8 2 6

Figure S80.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0027

Table S81.  Gene #11: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
9Q GAIN MUTATED 10 0 0 0
9Q GAIN WILD-TYPE 35 30 30 14

Figure S81.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0036

Table S82.  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 S82.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S83.  Gene #11: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
9Q GAIN MUTATED 6 1 4 0
9Q GAIN WILD-TYPE 50 60 1 1

Figure S83.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00609 (Fisher's exact test), Q value = 0.017

Table S84.  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 S84.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00068

Table S85.  Gene #11: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
9Q GAIN MUTATED 0 1 9 1
9Q GAIN WILD-TYPE 28 50 34 0

Figure S85.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00283 (Fisher's exact test), Q value = 0.0093

Table S86.  Gene #11: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
9Q GAIN MUTATED 7 0 3 1
9Q GAIN WILD-TYPE 20 33 32 27

Figure S86.  Get High-res Image Gene #11: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.054

Table S87.  Gene #12: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
12P GAIN MUTATED 0 0 3 1 0
12P GAIN WILD-TYPE 36 27 16 30 10

Figure S87.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 0.00796 (Fisher's exact test), Q value = 0.02

Table S88.  Gene #12: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
12P GAIN MUTATED 0 0 1 3 0 0 0 0
12P GAIN WILD-TYPE 37 23 18 7 18 8 2 6

Figure S88.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0286 (Fisher's exact test), Q value = 0.054

Table S89.  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 S89.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.014

Table S90.  Gene #12: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
12P GAIN MUTATED 1 0 0 3
12P GAIN WILD-TYPE 44 30 30 11

Figure S90.  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 = 0.0084

Table S91.  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 S91.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.052

Table S92.  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 S92.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.081

Table S93.  Gene #12: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
12P GAIN MUTATED 0 0 4 0
12P GAIN WILD-TYPE 28 51 39 1

Figure S93.  Get High-res Image Gene #12: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.054

Table S94.  Gene #13: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
12Q GAIN MUTATED 0 0 3 1 0
12Q GAIN WILD-TYPE 36 27 16 30 10

Figure S94.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0078 (Fisher's exact test), Q value = 0.02

Table S95.  Gene #13: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
12Q GAIN MUTATED 0 0 1 3 0 0 0 0
12Q GAIN WILD-TYPE 37 23 18 7 18 8 2 6

Figure S95.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.056

Table S96.  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 S96.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 0.014

Table S97.  Gene #13: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
12Q GAIN MUTATED 1 0 0 3
12Q GAIN WILD-TYPE 44 30 30 11

Figure S97.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00226 (Fisher's exact test), Q value = 0.0082

Table S98.  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 S98.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.053

Table S99.  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 S99.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.08

Table S100.  Gene #13: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
12Q GAIN MUTATED 0 0 4 0
12Q GAIN WILD-TYPE 28 51 39 1

Figure S100.  Get High-res Image Gene #13: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0022

Table S101.  Gene #14: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
14Q GAIN MUTATED 11 0 1 1 0
14Q GAIN WILD-TYPE 25 27 18 30 10

Figure S101.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S102.  Gene #14: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
14Q GAIN MUTATED 2 0 10 0 0 0 0 1
14Q GAIN WILD-TYPE 35 23 9 10 18 8 2 5

Figure S102.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.056

Table S103.  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 S103.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S104.  Gene #14: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
14Q GAIN MUTATED 13 0 0 0
14Q GAIN WILD-TYPE 32 30 30 14

Figure S104.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00056

Table S105.  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 S105.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00042

Table S106.  Gene #14: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
14Q GAIN MUTATED 10 0 3 0
14Q GAIN WILD-TYPE 46 61 2 1

Figure S106.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00085

Table S107.  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 S107.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S108.  Gene #14: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
14Q GAIN MUTATED 0 0 12 1
14Q GAIN WILD-TYPE 28 51 31 0

Figure S108.  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 = 0.00042

Table S109.  Gene #14: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
14Q GAIN MUTATED 9 0 4 0
14Q GAIN WILD-TYPE 18 33 31 28

Figure S109.  Get High-res Image Gene #14: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0041

Table S110.  Gene #15: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
15Q GAIN MUTATED 1 1 8 1 0 0 0 1
15Q GAIN WILD-TYPE 36 22 11 9 18 8 2 5

Figure S110.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.043

Table S111.  Gene #15: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
15Q GAIN MUTATED 8 0 1 2
15Q GAIN WILD-TYPE 37 30 29 12

Figure S111.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00918 (Fisher's exact test), Q value = 0.023

Table S112.  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 S112.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.0089

Table S113.  Gene #15: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
15Q GAIN MUTATED 9 1 2 0
15Q GAIN WILD-TYPE 47 60 3 1

Figure S113.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.043

Table S114.  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 S114.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0034

Table S115.  Gene #15: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
15Q GAIN MUTATED 1 1 9 1
15Q GAIN WILD-TYPE 27 50 34 0

Figure S115.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.035

Table S116.  Gene #15: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
15Q GAIN MUTATED 5 1 6 0
15Q GAIN WILD-TYPE 22 32 29 28

Figure S116.  Get High-res Image Gene #15: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0045

Table S117.  Gene #16: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
17Q GAIN MUTATED 0 2 5 0 0
17Q GAIN WILD-TYPE 36 25 14 31 10

Figure S117.  Get High-res Image Gene #16: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S118.  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 S118.  Get High-res Image Gene #16: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.055

Table S119.  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 S119.  Get High-res Image Gene #17: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.056

Table S120.  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 S120.  Get High-res Image Gene #18: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0036

Table S121.  Gene #21: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
20P GAIN MUTATED 1 0 5 4 0 0 0 0
20P GAIN WILD-TYPE 36 23 14 6 18 8 2 6

Figure S121.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0051 (Fisher's exact test), Q value = 0.015

Table S122.  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 S122.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0016

Table S123.  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 S123.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.006

Table S124.  Gene #21: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
20P GAIN MUTATED 6 0 0 4
20P GAIN WILD-TYPE 39 30 30 10

Figure S124.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0019

Table S125.  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 S125.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.054

Table S126.  Gene #21: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
20P GAIN MUTATED 9 1 0 0
20P GAIN WILD-TYPE 47 60 5 1

Figure S126.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.027

Table S127.  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 S127.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 5e-04

Table S128.  Gene #21: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
20P GAIN MUTATED 0 0 10 0
20P GAIN WILD-TYPE 28 51 33 1

Figure S128.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.037

Table S129.  Gene #21: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
20P GAIN MUTATED 2 1 7 0
20P GAIN WILD-TYPE 25 32 28 28

Figure S129.  Get High-res Image Gene #21: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'METHLYATION_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0031

Table S130.  Gene #22: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
20Q GAIN MUTATED 1 0 5 4 0 0 0 0
20Q GAIN WILD-TYPE 36 23 14 6 18 8 2 6

Figure S130.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.00507 (Fisher's exact test), Q value = 0.015

Table S131.  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 S131.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0013

Table S132.  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 S132.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.0058

Table S133.  Gene #22: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
20Q GAIN MUTATED 6 0 0 4
20Q GAIN WILD-TYPE 39 30 30 10

Figure S133.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0023

Table S134.  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 S134.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.054

Table S135.  Gene #22: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
20Q GAIN MUTATED 9 1 0 0
20Q GAIN WILD-TYPE 47 60 5 1

Figure S135.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S136.  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 S136.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 5e-04

Table S137.  Gene #22: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
20Q GAIN MUTATED 0 0 10 0
20Q GAIN WILD-TYPE 28 51 33 1

Figure S137.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.036

Table S138.  Gene #22: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
20Q GAIN MUTATED 2 1 7 0
20Q GAIN WILD-TYPE 25 32 28 28

Figure S138.  Get High-res Image Gene #22: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.036

Table S139.  Gene #24: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
22Q GAIN MUTATED 0 0 4 0 0 0 0 0
22Q GAIN WILD-TYPE 37 23 15 10 18 8 2 6

Figure S139.  Get High-res Image Gene #24: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.081

Table S140.  Gene #24: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
22Q GAIN MUTATED 0 0 4 0
22Q GAIN WILD-TYPE 28 51 39 1

Figure S140.  Get High-res Image Gene #24: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.036

Table S141.  Gene #25: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
XQ GAIN MUTATED 0 0 4 0 0 0 0 0
XQ GAIN WILD-TYPE 37 23 15 10 18 8 2 6

Figure S141.  Get High-res Image Gene #25: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.08

Table S142.  Gene #25: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
XQ GAIN MUTATED 0 0 4 0
XQ GAIN WILD-TYPE 28 51 39 1

Figure S142.  Get High-res Image Gene #25: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00712 (Fisher's exact test), Q value = 0.019

Table S143.  Gene #26: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
1P LOSS MUTATED 0 0 2 3 0 0 0 0
1P LOSS WILD-TYPE 37 23 17 7 18 8 2 6

Figure S143.  Get High-res Image Gene #26: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.032

Table S144.  Gene #26: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

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

Figure S144.  Get High-res Image Gene #26: '1p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00775 (Fisher's exact test), Q value = 0.02

Table S145.  Gene #26: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
1P LOSS MUTATED 2 0 0 3
1P LOSS WILD-TYPE 43 30 30 11

Figure S145.  Get High-res Image Gene #26: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.047

Table S146.  Gene #26: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
1P LOSS MUTATED 3 0 0 2
1P LOSS WILD-TYPE 44 42 20 8

Figure S146.  Get High-res Image Gene #26: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.069

Table S147.  Gene #26: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
1P LOSS MUTATED 4 0 1 0
1P LOSS WILD-TYPE 52 61 4 1

Figure S147.  Get High-res Image Gene #26: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.058

Table S148.  Gene #26: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
1P LOSS MUTATED 0 0 5 0
1P LOSS WILD-TYPE 28 51 38 1

Figure S148.  Get High-res Image Gene #26: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'CN_CNMF'

P value = 0.00369 (Fisher's exact test), Q value = 0.012

Table S149.  Gene #27: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
3P LOSS MUTATED 7 0 4 0 1
3P LOSS WILD-TYPE 29 27 15 31 9

Figure S149.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S150.  Gene #27: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
3P LOSS MUTATED 0 0 9 3 0 0 0 0
3P LOSS WILD-TYPE 37 23 10 7 18 8 2 6

Figure S150.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.067

Table S151.  Gene #27: '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 S151.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S152.  Gene #27: '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 S152.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0045

Table S153.  Gene #27: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
3P LOSS MUTATED 9 0 0 3
3P LOSS WILD-TYPE 36 30 30 11

Figure S153.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0038

Table S154.  Gene #27: '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 S154.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0025

Table S155.  Gene #27: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
3P LOSS MUTATED 11 0 1 0
3P LOSS WILD-TYPE 45 61 4 1

Figure S155.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00455 (Fisher's exact test), Q value = 0.014

Table S156.  Gene #27: '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 S156.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S157.  Gene #27: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
3P LOSS MUTATED 0 0 12 0
3P LOSS WILD-TYPE 28 51 31 1

Figure S157.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0044

Table S158.  Gene #27: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
3P LOSS MUTATED 6 0 6 0
3P LOSS WILD-TYPE 21 33 29 28

Figure S158.  Get High-res Image Gene #27: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.064

Table S159.  Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
3Q LOSS MUTATED 4 0 3 0 0
3Q LOSS WILD-TYPE 32 27 16 31 10

Figure S159.  Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.0075

Table S160.  Gene #28: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
3Q LOSS MUTATED 0 0 5 2 0 0 0 0
3Q LOSS WILD-TYPE 37 23 14 8 18 8 2 6

Figure S160.  Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0045

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

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.064

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
3Q LOSS MUTATED 6 0 0 1
3Q LOSS WILD-TYPE 39 30 30 13

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

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.058

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

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
3Q LOSS MUTATED 6 0 1 0
3Q LOSS WILD-TYPE 50 61 4 1

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

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00259 (Fisher's exact test), Q value = 0.0089

Table S165.  Gene #28: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
3Q LOSS MUTATED 0 0 7 0
3Q LOSS WILD-TYPE 28 51 36 1

Figure S165.  Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.052

Table S166.  Gene #28: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
3Q LOSS MUTATED 4 0 3 0
3Q LOSS WILD-TYPE 23 33 32 28

Figure S166.  Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0309 (Fisher's exact test), Q value = 0.057

Table S167.  Gene #29: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
4P LOSS MUTATED 0 0 5 0
4P LOSS WILD-TYPE 28 51 38 1

Figure S167.  Get High-res Image Gene #29: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.081

Table S168.  Gene #30: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
4Q LOSS MUTATED 0 0 4 0
4Q LOSS WILD-TYPE 28 51 39 1

Figure S168.  Get High-res Image Gene #30: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.074

Table S169.  Gene #30: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
4Q LOSS MUTATED 3 1 0 0
4Q LOSS WILD-TYPE 24 32 35 28

Figure S169.  Get High-res Image Gene #30: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0029

Table S170.  Gene #31: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
6P LOSS MUTATED 12 0 6 2 1
6P LOSS WILD-TYPE 24 27 13 29 9

Figure S170.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S171.  Gene #31: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
6P LOSS MUTATED 1 0 13 6 1 0 0 0
6P LOSS WILD-TYPE 36 23 6 4 17 8 2 6

Figure S171.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00056

Table S172.  Gene #31: '6p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
6P LOSS MUTATED 13 2 1
6P LOSS WILD-TYPE 18 23 33

Figure S172.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00042

Table S173.  Gene #31: '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 3 0 2 11
6P LOSS WILD-TYPE 13 23 29 9

Figure S173.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S174.  Gene #31: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
6P LOSS MUTATED 14 1 0 6
6P LOSS WILD-TYPE 31 29 30 8

Figure S174.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S175.  Gene #31: '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 1 0 5
6P LOSS WILD-TYPE 32 41 20 5

Figure S175.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S176.  Gene #31: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
6P LOSS MUTATED 18 1 2 0
6P LOSS WILD-TYPE 38 60 3 1

Figure S176.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0011

Table S177.  Gene #31: '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 1
6P LOSS WILD-TYPE 18 18 20 4 16 26

Figure S177.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S178.  Gene #31: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
6P LOSS MUTATED 0 1 20 0
6P LOSS WILD-TYPE 28 50 23 1

Figure S178.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S179.  Gene #31: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
6P LOSS MUTATED 8 0 12 1
6P LOSS WILD-TYPE 19 33 23 27

Figure S179.  Get High-res Image Gene #31: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
6Q LOSS MUTATED 11 0 7 2 0
6Q LOSS WILD-TYPE 25 27 12 29 10

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

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
6Q LOSS MUTATED 1 0 11 6 1 0 0 1
6Q LOSS WILD-TYPE 36 23 8 4 17 8 2 5

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

'6q loss' versus 'RPPA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0016

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

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

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

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00063

Table S183.  Gene #32: '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 3 1 1 10
6Q LOSS WILD-TYPE 13 22 30 10

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

'6q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
6Q LOSS MUTATED 12 1 0 7
6Q LOSS WILD-TYPE 33 29 30 7

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

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00099

Table S185.  Gene #32: '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 1 1 5
6Q LOSS WILD-TYPE 34 41 19 5

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

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0019

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
6Q LOSS MUTATED 16 2 2 0
6Q LOSS WILD-TYPE 40 59 3 1

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

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0016 (Fisher's exact test), Q value = 0.0063

Table S187.  Gene #32: '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 1
6Q LOSS WILD-TYPE 18 18 22 4 15 26

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

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
6Q LOSS MUTATED 0 1 19 0
6Q LOSS WILD-TYPE 28 50 24 1

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

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0042

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
6Q LOSS MUTATED 8 1 10 1
6Q LOSS WILD-TYPE 19 32 25 27

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

'9p loss' versus 'CN_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0058

Table S190.  Gene #33: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
9P LOSS MUTATED 0 0 4 0 0
9P LOSS WILD-TYPE 36 27 15 31 10

Figure S190.  Get High-res Image Gene #33: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.044

Table S191.  Gene #33: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
9P LOSS MUTATED 0 0 2 2
9P LOSS WILD-TYPE 45 30 28 12

Figure S191.  Get High-res Image Gene #33: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.011

Table S192.  Gene #33: '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 S192.  Get High-res Image Gene #33: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.043

Table S193.  Gene #34: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
10P LOSS MUTATED 0 0 1 2
10P LOSS WILD-TYPE 45 30 29 12

Figure S193.  Get High-res Image Gene #34: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.044

Table S194.  Gene #34: '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 S194.  Get High-res Image Gene #34: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.033

Table S195.  Gene #34: '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 S195.  Get High-res Image Gene #34: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00978 (Fisher's exact test), Q value = 0.024

Table S196.  Gene #35: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
11P LOSS MUTATED 6 0 3 0 0
11P LOSS WILD-TYPE 30 27 16 31 10

Figure S196.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00085

Table S197.  Gene #35: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
11P LOSS MUTATED 0 0 7 2 0 0 0 0
11P LOSS WILD-TYPE 37 23 12 8 18 8 2 6

Figure S197.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.035

Table S198.  Gene #35: '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 S198.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0049

Table S199.  Gene #35: '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 S199.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.0091 (Fisher's exact test), Q value = 0.023

Table S200.  Gene #35: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
11P LOSS MUTATED 7 0 0 2
11P LOSS WILD-TYPE 38 30 30 12

Figure S200.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00695 (Fisher's exact test), Q value = 0.019

Table S201.  Gene #35: '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 S201.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.00369 (Fisher's exact test), Q value = 0.012

Table S202.  Gene #35: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
11P LOSS MUTATED 8 0 1 0
11P LOSS WILD-TYPE 48 61 4 1

Figure S202.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0012

Table S203.  Gene #35: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
11P LOSS MUTATED 0 0 9 0
11P LOSS WILD-TYPE 28 51 34 1

Figure S203.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.025

Table S204.  Gene #35: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
11P LOSS MUTATED 4 0 5 0
11P LOSS WILD-TYPE 23 33 30 28

Figure S204.  Get High-res Image Gene #35: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.04

Table S205.  Gene #36: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
11Q LOSS MUTATED 6 0 1 0 0
11Q LOSS WILD-TYPE 30 27 18 31 10

Figure S205.  Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0036

Table S206.  Gene #36: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
11Q LOSS MUTATED 0 0 6 1 0 0 0 0
11Q LOSS WILD-TYPE 37 23 13 9 18 8 2 6

Figure S206.  Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.08

Table S207.  Gene #36: '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 S207.  Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00616 (Fisher's exact test), Q value = 0.017

Table S208.  Gene #36: '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 S208.  Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.064

Table S209.  Gene #36: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
11Q LOSS MUTATED 6 0 0 1
11Q LOSS WILD-TYPE 39 30 30 13

Figure S209.  Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.032

Table S210.  Gene #36: '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 S210.  Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.026

Table S211.  Gene #36: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
11Q LOSS MUTATED 6 0 1 0
11Q LOSS WILD-TYPE 50 61 4 1

Figure S211.  Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.0089

Table S212.  Gene #36: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
11Q LOSS MUTATED 0 0 7 0
11Q LOSS WILD-TYPE 28 51 36 1

Figure S212.  Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.051

Table S213.  Gene #36: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
11Q LOSS MUTATED 4 0 3 0
11Q LOSS WILD-TYPE 23 33 32 28

Figure S213.  Get High-res Image Gene #36: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.0093

Table S214.  Gene #37: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
12P LOSS MUTATED 7 0 0 0 1
12P LOSS WILD-TYPE 29 27 19 31 9

Figure S214.  Get High-res Image Gene #37: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

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

Table S215.  Gene #37: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
12P LOSS MUTATED 1 0 6 1 0 0 0 0
12P LOSS WILD-TYPE 36 23 13 9 18 8 2 6

Figure S215.  Get High-res Image Gene #37: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.036

Table S216.  Gene #37: '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 S216.  Get High-res Image Gene #37: '12p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.0087

Table S217.  Gene #37: '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 S217.  Get High-res Image Gene #37: '12p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 0.00883 (Fisher's exact test), Q value = 0.022

Table S218.  Gene #37: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
12P LOSS MUTATED 7 0 0 0
12P LOSS WILD-TYPE 38 30 30 14

Figure S218.  Get High-res Image Gene #37: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.032

Table S219.  Gene #37: '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 S219.  Get High-res Image Gene #37: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 0.00674 (Fisher's exact test), Q value = 0.018

Table S220.  Gene #37: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
12P LOSS MUTATED 7 0 1 0
12P LOSS WILD-TYPE 49 61 4 1

Figure S220.  Get High-res Image Gene #37: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.023

Table S221.  Gene #37: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
12P LOSS MUTATED 1 0 7 0
12P LOSS WILD-TYPE 27 51 36 1

Figure S221.  Get High-res Image Gene #37: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.035

Table S222.  Gene #37: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
12P LOSS MUTATED 3 0 5 0
12P LOSS WILD-TYPE 24 33 30 28

Figure S222.  Get High-res Image Gene #37: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 0.00798 (Fisher's exact test), Q value = 0.02

Table S223.  Gene #38: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
12Q LOSS MUTATED 6 0 0 0 1
12Q LOSS WILD-TYPE 30 27 19 31 9

Figure S223.  Get High-res Image Gene #38: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0046

Table S224.  Gene #38: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
12Q LOSS MUTATED 0 0 6 1 0 0 0 0
12Q LOSS WILD-TYPE 37 23 13 9 18 8 2 6

Figure S224.  Get High-res Image Gene #38: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.036

Table S225.  Gene #38: '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 S225.  Get High-res Image Gene #38: '12q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 0.0093

Table S226.  Gene #38: '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 S226.  Get High-res Image Gene #38: '12q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 0.00884 (Fisher's exact test), Q value = 0.022

Table S227.  Gene #38: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
12Q LOSS MUTATED 7 0 0 0
12Q LOSS WILD-TYPE 38 30 30 14

Figure S227.  Get High-res Image Gene #38: '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 S228.  Gene #38: '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 S228.  Get High-res Image Gene #38: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.026

Table S229.  Gene #38: '12q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
12Q LOSS MUTATED 6 0 1 0
12Q LOSS WILD-TYPE 50 61 4 1

Figure S229.  Get High-res Image Gene #38: '12q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00264 (Fisher's exact test), Q value = 0.0089

Table S230.  Gene #38: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
12Q LOSS MUTATED 0 0 7 0
12Q LOSS WILD-TYPE 28 51 36 1

Figure S230.  Get High-res Image Gene #38: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.064

Table S231.  Gene #38: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
12Q LOSS MUTATED 3 0 4 0
12Q LOSS WILD-TYPE 24 33 31 28

Figure S231.  Get High-res Image Gene #38: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00501 (Fisher's exact test), Q value = 0.015

Table S232.  Gene #39: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
13Q LOSS MUTATED 6 2 6 0 0
13Q LOSS WILD-TYPE 30 25 13 31 10

Figure S232.  Get High-res Image Gene #39: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0034

Table S233.  Gene #39: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
13Q LOSS MUTATED 1 0 8 2 3 0 0 0
13Q LOSS WILD-TYPE 36 23 11 8 15 8 2 6

Figure S233.  Get High-res Image Gene #39: '13q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.00611 (Fisher's exact test), Q value = 0.017

Table S234.  Gene #39: '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 S234.  Get High-res Image Gene #39: '13q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.07

Table S235.  Gene #39: '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 S235.  Get High-res Image Gene #39: '13q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.0076

Table S236.  Gene #39: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
13Q LOSS MUTATED 0 3 11 0
13Q LOSS WILD-TYPE 28 48 32 1

Figure S236.  Get High-res Image Gene #39: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.077

Table S237.  Gene #40: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
16P LOSS MUTATED 1 0 1 3 0 0 0 0
16P LOSS WILD-TYPE 36 23 18 7 18 8 2 6

Figure S237.  Get High-res Image Gene #40: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.032

Table S238.  Gene #40: '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 S238.  Get High-res Image Gene #40: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0038

Table S239.  Gene #41: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
16Q LOSS MUTATED 3 0 6 1 3
16Q LOSS WILD-TYPE 33 27 13 30 7

Figure S239.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S240.  Gene #41: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
16Q LOSS MUTATED 1 1 2 9 0 0 0 0
16Q LOSS WILD-TYPE 36 22 17 1 18 8 2 6

Figure S240.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00042

Table S241.  Gene #41: '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 S241.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S242.  Gene #41: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
16Q LOSS MUTATED 3 1 1 8
16Q LOSS WILD-TYPE 42 29 29 6

Figure S242.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

Table S243.  Gene #41: '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 S243.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.063

Table S244.  Gene #41: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
16Q LOSS MUTATED 10 2 1 0
16Q LOSS WILD-TYPE 46 59 4 1

Figure S244.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00028

Table S245.  Gene #41: '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 S245.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0036

Table S246.  Gene #41: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
16Q LOSS MUTATED 0 2 11 0
16Q LOSS WILD-TYPE 28 49 32 1

Figure S246.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.0065

Table S247.  Gene #41: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
16Q LOSS MUTATED 1 1 10 1
16Q LOSS WILD-TYPE 26 32 25 27

Figure S247.  Get High-res Image Gene #41: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.0098 (Fisher's exact test), Q value = 0.024

Table S248.  Gene #42: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
17P LOSS MUTATED 5 2 6 0 1
17P LOSS WILD-TYPE 31 25 13 31 9

Figure S248.  Get High-res Image Gene #42: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00278 (Fisher's exact test), Q value = 0.0092

Table S249.  Gene #42: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
17P LOSS MUTATED 1 3 6 4 0 0 0 0
17P LOSS WILD-TYPE 36 20 13 6 18 8 2 6

Figure S249.  Get High-res Image Gene #42: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

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

Table S250.  Gene #42: '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 S250.  Get High-res Image Gene #42: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0014

Table S251.  Gene #42: '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 S251.  Get High-res Image Gene #42: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.04

Table S252.  Gene #42: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
17P LOSS MUTATED 7 0 3 4
17P LOSS WILD-TYPE 38 30 27 10

Figure S252.  Get High-res Image Gene #42: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0046

Table S253.  Gene #42: '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 S253.  Get High-res Image Gene #42: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00197 (Fisher's exact test), Q value = 0.0074

Table S254.  Gene #42: '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 S254.  Get High-res Image Gene #42: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.0085

Table S255.  Gene #42: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
17P LOSS MUTATED 0 3 11 0
17P LOSS WILD-TYPE 28 48 32 1

Figure S255.  Get High-res Image Gene #42: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.054

Table S256.  Gene #42: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
17P LOSS MUTATED 2 4 8 0
17P LOSS WILD-TYPE 25 29 27 28

Figure S256.  Get High-res Image Gene #42: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.077

Table S257.  Gene #43: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
17Q LOSS MUTATED 0 1 4 1 0 0 0 0
17Q LOSS WILD-TYPE 37 22 15 9 18 8 2 6

Figure S257.  Get High-res Image Gene #43: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00257 (Fisher's exact test), Q value = 0.0089

Table S258.  Gene #43: '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 S258.  Get High-res Image Gene #43: '17q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.08

Table S259.  Gene #44: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
18P LOSS MUTATED 5 0 1 0 1
18P LOSS WILD-TYPE 31 27 18 31 9

Figure S259.  Get High-res Image Gene #44: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.064

Table S260.  Gene #44: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
18P LOSS MUTATED 1 0 4 2 0 0 0 0
18P LOSS WILD-TYPE 36 23 15 8 18 8 2 6

Figure S260.  Get High-res Image Gene #44: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.036

Table S261.  Gene #44: '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 S261.  Get High-res Image Gene #44: '18p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

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

Table S262.  Gene #44: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
18P LOSS MUTATED 6 0 0 1
18P LOSS WILD-TYPE 39 30 30 13

Figure S262.  Get High-res Image Gene #44: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.058

Table S263.  Gene #44: '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 S263.  Get High-res Image Gene #44: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.012

Table S264.  Gene #44: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
18P LOSS MUTATED 5 0 2 0
18P LOSS WILD-TYPE 51 61 3 1

Figure S264.  Get High-res Image Gene #44: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.0087

Table S265.  Gene #44: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
18P LOSS MUTATED 0 0 7 0
18P LOSS WILD-TYPE 28 51 36 1

Figure S265.  Get High-res Image Gene #44: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.049

Table S266.  Gene #44: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
18P LOSS MUTATED 2 0 5 0
18P LOSS WILD-TYPE 25 33 30 28

Figure S266.  Get High-res Image Gene #44: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.081

Table S267.  Gene #45: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
18Q LOSS MUTATED 5 0 1 0 1
18Q LOSS WILD-TYPE 31 27 18 31 9

Figure S267.  Get High-res Image Gene #45: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.064

Table S268.  Gene #45: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
18Q LOSS MUTATED 1 0 4 2 0 0 0 0
18Q LOSS WILD-TYPE 36 23 15 8 18 8 2 6

Figure S268.  Get High-res Image Gene #45: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.036

Table S269.  Gene #45: '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 S269.  Get High-res Image Gene #45: '18q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.064

Table S270.  Gene #45: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
18Q LOSS MUTATED 6 0 0 1
18Q LOSS WILD-TYPE 39 30 30 13

Figure S270.  Get High-res Image Gene #45: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.058

Table S271.  Gene #45: '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 S271.  Get High-res Image Gene #45: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00382 (Fisher's exact test), Q value = 0.012

Table S272.  Gene #45: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
18Q LOSS MUTATED 5 0 2 0
18Q LOSS WILD-TYPE 51 61 3 1

Figure S272.  Get High-res Image Gene #45: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.008

Table S273.  Gene #45: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
18Q LOSS MUTATED 0 0 7 0
18Q LOSS WILD-TYPE 28 51 36 1

Figure S273.  Get High-res Image Gene #45: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.049

Table S274.  Gene #45: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
18Q LOSS MUTATED 2 0 5 0
18Q LOSS WILD-TYPE 25 33 30 28

Figure S274.  Get High-res Image Gene #45: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 0.00673 (Fisher's exact test), Q value = 0.018

Table S275.  Gene #46: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
19P LOSS MUTATED 0 0 3 0 0
19P LOSS WILD-TYPE 36 27 16 31 10

Figure S275.  Get High-res Image Gene #46: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.0089

Table S276.  Gene #46: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
19P LOSS MUTATED 0 0 0 3 0 0 0 0
19P LOSS WILD-TYPE 37 23 19 7 18 8 2 6

Figure S276.  Get High-res Image Gene #46: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0056

Table S277.  Gene #46: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
19P LOSS MUTATED 0 0 0 3
19P LOSS WILD-TYPE 45 30 30 11

Figure S277.  Get High-res Image Gene #46: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0026

Table S278.  Gene #46: '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 S278.  Get High-res Image Gene #46: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00962 (Fisher's exact test), Q value = 0.023

Table S279.  Gene #46: '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 S279.  Get High-res Image Gene #46: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 0.00595 (Fisher's exact test), Q value = 0.017

Table S280.  Gene #47: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
19Q LOSS MUTATED 0 0 3 0 0
19Q LOSS WILD-TYPE 36 27 16 31 10

Figure S280.  Get High-res Image Gene #47: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.0093

Table S281.  Gene #47: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
19Q LOSS MUTATED 0 0 0 3 0 0 0 0
19Q LOSS WILD-TYPE 37 23 19 7 18 8 2 6

Figure S281.  Get High-res Image Gene #47: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0058

Table S282.  Gene #47: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
19Q LOSS MUTATED 0 0 0 3
19Q LOSS WILD-TYPE 45 30 30 11

Figure S282.  Get High-res Image Gene #47: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0025

Table S283.  Gene #47: '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 S283.  Get High-res Image Gene #47: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.025

Table S284.  Gene #47: '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 S284.  Get High-res Image Gene #47: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 0.00699 (Fisher's exact test), Q value = 0.019

Table S285.  Gene #48: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
21Q LOSS MUTATED 7 0 2 0 0
21Q LOSS WILD-TYPE 29 27 17 31 10

Figure S285.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00063

Table S286.  Gene #48: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
21Q LOSS MUTATED 0 0 7 2 0 0 0 0
21Q LOSS WILD-TYPE 37 23 12 8 18 8 2 6

Figure S286.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.036

Table S287.  Gene #48: '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 S287.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00256 (Fisher's exact test), Q value = 0.0089

Table S288.  Gene #48: '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 S288.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.00661 (Fisher's exact test), Q value = 0.018

Table S289.  Gene #48: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
21Q LOSS MUTATED 8 0 0 1
21Q LOSS WILD-TYPE 37 30 30 13

Figure S289.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00711 (Fisher's exact test), Q value = 0.019

Table S290.  Gene #48: '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 S290.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.00389 (Fisher's exact test), Q value = 0.012

Table S291.  Gene #48: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
21Q LOSS MUTATED 8 0 1 0
21Q LOSS WILD-TYPE 48 61 4 1

Figure S291.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0012

Table S292.  Gene #48: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
21Q LOSS MUTATED 0 0 9 0
21Q LOSS WILD-TYPE 28 51 34 1

Figure S292.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00776 (Fisher's exact test), Q value = 0.02

Table S293.  Gene #48: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
21Q LOSS MUTATED 3 0 6 0
21Q LOSS WILD-TYPE 24 33 29 28

Figure S293.  Get High-res Image Gene #48: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00036

Table S294.  Gene #49: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
22Q LOSS MUTATED 2 2 9 0 0
22Q LOSS WILD-TYPE 34 25 10 31 10

Figure S294.  Get High-res Image Gene #49: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.026

Table S295.  Gene #49: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
22Q LOSS MUTATED 1 1 2 4 2 2 1 0
22Q LOSS WILD-TYPE 36 22 17 6 16 6 1 6

Figure S295.  Get High-res Image Gene #49: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0404 (Fisher's exact test), Q value = 0.07

Table S296.  Gene #49: '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 S296.  Get High-res Image Gene #49: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0431 (Fisher's exact test), Q value = 0.074

Table S297.  Gene #49: '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 S297.  Get High-res Image Gene #49: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.006 (Fisher's exact test), Q value = 0.017

Table S298.  Gene #49: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
22Q LOSS MUTATED 0 3 10 0
22Q LOSS WILD-TYPE 28 48 33 1

Figure S298.  Get High-res Image Gene #49: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00574 (Fisher's exact test), Q value = 0.016

Table S299.  Gene #50: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
XP LOSS MUTATED 1 0 6 1 0 0 0 0
XP LOSS WILD-TYPE 36 23 13 9 18 8 2 6

Figure S299.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.049

Table S300.  Gene #50: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
XP LOSS MUTATED 0 0 1 4
XP LOSS WILD-TYPE 16 23 30 16

Figure S300.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.041

Table S301.  Gene #50: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
XP LOSS MUTATED 6 0 0 2
XP LOSS WILD-TYPE 39 30 30 12

Figure S301.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S302.  Gene #50: '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 7 0 0 1
XP LOSS WILD-TYPE 40 42 20 9

Figure S302.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.036

Table S303.  Gene #50: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
XP LOSS MUTATED 5 1 2 0
XP LOSS WILD-TYPE 51 60 3 1

Figure S303.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0027

Table S304.  Gene #50: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
XP LOSS MUTATED 0 0 8 0
XP LOSS WILD-TYPE 28 51 35 1

Figure S304.  Get High-res Image Gene #50: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.035

Table S305.  Gene #51: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
XQ LOSS MUTATED 0 0 4 1 0 0 0 0
XQ LOSS WILD-TYPE 37 23 15 9 18 8 2 6

Figure S305.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00263 (Fisher's exact test), Q value = 0.0089

Table S306.  Gene #51: '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 4
XQ LOSS WILD-TYPE 16 23 31 16

Figure S306.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.069

Table S307.  Gene #51: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
XQ LOSS MUTATED 4 0 1 0
XQ LOSS WILD-TYPE 52 61 4 1

Figure S307.  Get High-res Image Gene #51: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.056

Table S308.  Gene #51: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
XQ LOSS MUTATED 0 0 5 0
XQ LOSS WILD-TYPE 28 51 38 1

Figure S308.  Get High-res Image Gene #51: '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/22516316/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/22541006/THYM-TP.transferedmergedcluster.txt

  • Number of patients = 123

  • Number of significantly arm-level cnvs = 51

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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