Correlation between copy number variation genes (focal events) and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 30 focal events and 12 molecular subtypes across 528 patients, 221 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q24.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_1q32.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_3q26.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • amp_4q32.1 cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_5q35.1 cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_7q36.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_8q24.22 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'.

  • amp_10p14 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_xp22.2 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_xp11.4 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • amp_xq11.2 cnv correlated to 'RPPA_CHIERARCHICAL'.

  • amp_xq28 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_1p36.23 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_1p31.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_1q43 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_2q37.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_3p26.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p22.2 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p14.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_3p12.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_3q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_4q34.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q26 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_6q26 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_8p23.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_9p23 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_9p21.3 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_10q23.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_13q14.2 cnv correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_14q31.1 cnv correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 30 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 221 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		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 Fisher's exact test Fisher's exact test
del 3p26 3 455 (86%) 73 1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		3e-05
(0.000112) 		0.0332
(0.0577) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		0.00011
(0.000354) 		5e-05
(0.000173) 		0.00287
(0.00689) 		0.00971
(0.0199)
del 9p21 3 159 (30%) 369 0.00147
(0.00375) 		0.0165
(0.0306) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		2e-05
(8e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		0.00129
(0.00339) 		0.0126
(0.0247)
del 3p22 2 465 (88%) 63 1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		2e-05
(8e-05) 		0.0707
(0.11) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		0.00616
(0.0133) 		0.0305
(0.0535)
del 9p23 152 (29%) 376 0.00363
(0.00838) 		0.0361
(0.0619) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		0.00291
(0.00694) 		0.124
(0.179)
amp 8q24 22 79 (15%) 449 0.227
(0.292) 		0.105
(0.154) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		2e-05
(8e-05) 		0.0242
(0.0435)
del 1p36 23 103 (20%) 425 0.00015
(0.000466) 		0.00094
(0.00258) 		1e-05
(4.5e-05) 		0.0787
(0.122) 		2e-05
(8e-05) 		3e-05
(0.000112) 		8e-05
(0.000264) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		0.00437
(0.01) 		0.0209
(0.0378) 		0.314
(0.383)
del 1p31 1 77 (15%) 451 0.00182
(0.00452) 		0.00624
(0.0134) 		1e-05
(4.5e-05) 		0.0947
(0.143) 		0.00024
(0.000726) 		0.00144
(0.0037) 		0.0147
(0.028) 		2e-05
(8e-05) 		1e-05
(4.5e-05) 		0.00267
(0.00645) 		0.00518
(0.0117) 		0.618
(0.684)
del 6q26 151 (29%) 377 0.0153
(0.0286) 		0.0985
(0.147) 		1e-05
(4.5e-05) 		0.0123
(0.0244) 		4e-05
(0.000144) 		2e-05
(8e-05) 		0.00107
(0.0029) 		0.00032
(0.000937) 		1e-05
(4.5e-05) 		0.00015
(0.000466) 		0.0293
(0.0522) 		0.133
(0.188)
del 6q26 151 (29%) 377 0.0149
(0.0283) 		0.0969
(0.145) 		1e-05
(4.5e-05) 		0.0126
(0.0247) 		2e-05
(8e-05) 		3e-05
(0.000112) 		0.00029
(0.000856) 		0.00021
(0.000646) 		1e-05
(4.5e-05) 		0.00015
(0.000466) 		0.0294
(0.0522) 		0.133
(0.188)
del 14q31 1 228 (43%) 300 6e-05
(2e-04) 		0.0004
(0.00115) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		4e-05
(0.000144) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		0.092
(0.14) 		0.952
(0.957)
amp 3q26 32 87 (16%) 441 0.0575
(0.092) 		0.119
(0.172) 		1e-05
(4.5e-05) 		3e-05
(0.000112) 		0.00324
(0.00762) 		2e-05
(8e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		0.00126
(0.00334) 		0.00467
(0.0106) 		0.128
(0.183)
del 13q14 2 82 (16%) 446 0.014
(0.0272) 		0.0845
(0.129) 		1e-05
(4.5e-05) 		0.0001
(0.000324) 		1e-05
(4.5e-05) 		5e-05
(0.000173) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		0.096
(0.144) 		0.151
(0.208)
amp 7q36 3 176 (33%) 352 0.452
(0.524) 		0.86
(0.887) 		1e-05
(4.5e-05) 		0.00581
(0.0128) 		0.00049
(0.0014) 		0.00312
(0.00739) 		1e-05
(4.5e-05) 		0.00615
(0.0133) 		0.00671
(0.0142) 		0.0145
(0.0278) 		0.148
(0.204) 		0.787
(0.829)
del 4q34 3 78 (15%) 450 0.238
(0.302) 		0.493
(0.563) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		0.0399
(0.0671) 		0.00547
(0.0122) 		0.00014
(0.000446) 		1e-05
(4.5e-05) 		0.154
(0.211) 		0.00855
(0.0177) 		0.18
(0.239) 		0.0168
(0.0311)
del 8p23 2 154 (29%) 374 0.504
(0.572) 		0.245
(0.308) 		1e-05
(4.5e-05) 		0.0405
(0.0676) 		0.0055
(0.0122) 		0.0108
(0.0218) 		0.00143
(0.0037) 		6e-05
(2e-04) 		0.00111
(0.00298) 		0.00094
(0.00258) 		0.14
(0.195) 		0.339
(0.407)
del 1q43 42 (8%) 486 0.0105
(0.0213) 		0.0114
(0.0227) 		5e-05
(0.000173) 		0.356
(0.424) 		0.0198
(0.0361) 		0.064
(0.101) 		0.0056
(0.0124) 		4e-05
(0.000144) 		0.0998
(0.148) 		0.016
(0.0299) 		0.293
(0.36) 		0.824
(0.857)
del 3p14 1 373 (71%) 155 0.00334
(0.00781) 		0.0104
(0.0211) 		1e-05
(4.5e-05) 		0.00613
(0.0133) 		0.0911
(0.139) 		0.0556
(0.0893) 		1e-05
(4.5e-05) 		1e-05
(4.5e-05) 		0.0927
(0.14) 		0.00702
(0.0148) 		0.335
(0.403) 		0.88
(0.898)
del 10q23 31 96 (18%) 432 0.44
(0.511) 		0.543
(0.607) 		1e-05
(4.5e-05) 		0.00132
(0.00344) 		0.915
(0.928) 		0.00665
(0.0142) 		0.0473
(0.0777) 		0.00028
(0.00084) 		0.0143
(0.0276) 		2e-05
(8e-05) 		0.802
(0.837) 		0.436
(0.508)
amp 1q32 1 62 (12%) 466 0.408
(0.478) 		0.901
(0.916) 		1e-05
(4.5e-05) 		0.0403
(0.0675) 		0.0648
(0.102) 		0.0503
(0.0816) 		1e-05
(4.5e-05) 		0.00173
(0.00432) 		1e-05
(4.5e-05) 		0.00064
(0.00181) 		0.278
(0.342) 		0.749
(0.805)
amp 5q35 1 332 (63%) 196 0.0635
(0.101) 		0.0484
(0.0791) 		0.00035
(0.00102) 		0.335
(0.403) 		0.0398
(0.0671) 		0.00945
(0.0194) 		0.00105
(0.00286) 		5e-05
(0.000173) 		0.129
(0.184) 		0.407
(0.478) 		0.62
(0.684) 		0.741
(0.799)
amp xp11 4 33 (6%) 495 0.845
(0.877) 		0.8
(0.837) 		0.00207
(0.0051) 		0.116
(0.168) 		0.00069
(0.00194) 		0.00211
(0.00517) 		0.0301
(0.0532) 		0.00029
(0.000856) 		0.0487
(0.0793) 		0.246
(0.308) 		0.792
(0.831) 		1
(1.00)
del 3p12 2 305 (58%) 223 0.0399
(0.0671) 		0.0654
(0.102) 		1e-05
(4.5e-05) 		0.0192
(0.0354) 		0.349
(0.416) 		0.562
(0.626) 		0.00085
(0.00237) 		2e-05
(8e-05) 		0.258
(0.32) 		0.0455
(0.0752) 		0.524
(0.59) 		0.737
(0.796)
amp 1q24 1 62 (12%) 466 0.26
(0.321) 		0.787
(0.829) 		1e-05
(4.5e-05) 		0.147
(0.203) 		0.166
(0.223) 		0.135
(0.189) 		1e-05
(4.5e-05) 		0.00339
(0.00787) 		3e-05
(0.000112) 		0.00714
(0.0149) 		0.584
(0.649) 		0.925
(0.935)
amp 10p14 20 (4%) 508 0.19
(0.248) 		0.775
(0.821) 		3e-05
(0.000112) 		0.18
(0.238) 		0.328
(0.397) 		0.203
(0.262) 		0.00221
(0.00538) 		4e-05
(0.000144) 		0.0321
(0.0561) 		0.0349
(0.0601) 		0.863
(0.887) 		0.37
(0.438)
amp xp22 2 31 (6%) 497 1
(1.00) 		0.522
(0.589) 		0.00836
(0.0174) 		0.236
(0.302) 		0.00114
(0.00304) 		0.0152
(0.0286) 		0.0553
(0.0893) 		0.00457
(0.0104) 		0.0371
(0.0633) 		0.348
(0.416) 		0.943
(0.951) 		0.879
(0.898)
del 2q37 3 50 (9%) 478 0.00168
(0.00423) 		0.00023
(0.000702) 		0.767
(0.817) 		0.621
(0.684) 		0.241
(0.305) 		0.114
(0.166) 		9e-05
(0.000295) 		6e-05
(2e-04) 		0.0123
(0.0244) 		0.0675
(0.105) 		0.253
(0.316) 		0.134
(0.188)
amp 4q32 1 16 (3%) 512 0.19
(0.248) 		0.775
(0.821) 		0.238
(0.302) 		0.707
(0.769) 		0.632
(0.693) 		0.219
(0.282) 		0.0201
(0.0366) 		0.0127
(0.0247) 		0.00154
(0.0039) 		0.102
(0.15) 		0.235
(0.302) 		0.495
(0.564)
del 3q11 2 161 (30%) 367 0.186
(0.244) 		0.165
(0.223) 		1e-05
(4.5e-05) 		0.0408
(0.0677) 		0.866
(0.888) 		0.471
(0.544) 		0.517
(0.586) 		6e-05
(2e-04) 		0.539
(0.605) 		0.0615
(0.0979) 		0.752
(0.805) 		0.76
(0.812)
amp xq11 2 29 (5%) 499 0.172
(0.229) 		0.163
(0.222) 		0.164
(0.222) 		0.255
(0.318) 		0.171
(0.229) 		0.0282
(0.0506) 		0.195
(0.253) 		0.309
(0.378) 		0.145
(0.202) 		0.424
(0.496) 		0.393
(0.464) 		0.853
(0.883)
amp xq28 37 (7%) 491 0.489
(0.561) 		0.7
(0.763) 		0.164
(0.222) 		0.636
(0.696) 		0.184
(0.242) 		0.107
(0.156) 		0.0792
(0.122) 		0.0341
(0.0591) 		0.105
(0.154) 		0.326
(0.397) 		0.73
(0.791) 		0.487
(0.561)
'amp_1q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S1.  Gene #1: 'amp_1q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 1(1Q24.1) MUTATED 12 3 47
AMP PEAK 1(1Q24.1) WILD-TYPE 226 132 108

Figure S1.  Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S2.  Gene #1: 'amp_1q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
AMP PEAK 1(1Q24.1) MUTATED 3 19 38
AMP PEAK 1(1Q24.1) WILD-TYPE 108 202 155

Figure S2.  Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00339 (Fisher's exact test), Q value = 0.0079

Table S3.  Gene #1: 'amp_1q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
AMP PEAK 1(1Q24.1) MUTATED 7 3 18 25 7 0
AMP PEAK 1(1Q24.1) WILD-TYPE 110 30 165 107 28 25

Figure S3.  Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q24.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S4.  Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 1(1Q24.1) MUTATED 4 19 37
AMP PEAK 1(1Q24.1) WILD-TYPE 120 185 145

Figure S4.  Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00714 (Fisher's exact test), Q value = 0.015

Table S5.  Gene #1: 'amp_1q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
AMP PEAK 1(1Q24.1) MUTATED 15 20 15 10
AMP PEAK 1(1Q24.1) WILD-TYPE 129 114 180 27

Figure S5.  Get High-res Image Gene #1: 'amp_1q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S6.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 2(1Q32.1) MUTATED 9 3 50
AMP PEAK 2(1Q32.1) WILD-TYPE 229 132 105

Figure S6.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q32.1' versus 'METHLYATION_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.067

Table S7.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
AMP PEAK 2(1Q32.1) MUTATED 6 11 12
AMP PEAK 2(1Q32.1) WILD-TYPE 122 65 98

Figure S7.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S8.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
AMP PEAK 2(1Q32.1) MUTATED 2 19 39
AMP PEAK 2(1Q32.1) WILD-TYPE 109 202 154

Figure S8.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.0043

Table S9.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
AMP PEAK 2(1Q32.1) MUTATED 7 2 18 26 7 0
AMP PEAK 2(1Q32.1) WILD-TYPE 110 31 165 106 28 25

Figure S9.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S10.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 2(1Q32.1) MUTATED 4 18 38
AMP PEAK 2(1Q32.1) WILD-TYPE 120 186 144

Figure S10.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0018

Table S11.  Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
AMP PEAK 2(1Q32.1) MUTATED 12 20 16 12
AMP PEAK 2(1Q32.1) WILD-TYPE 132 114 179 25

Figure S11.  Get High-res Image Gene #2: 'amp_1q32.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S12.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 3(3Q26.32) MUTATED 14 19 54
AMP PEAK 3(3Q26.32) WILD-TYPE 224 116 101

Figure S12.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.32' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S13.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
AMP PEAK 3(3Q26.32) MUTATED 7 14 30
AMP PEAK 3(3Q26.32) WILD-TYPE 121 62 80

Figure S13.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'RPPA_CNMF'

P value = 0.00324 (Fisher's exact test), Q value = 0.0076

Table S14.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
AMP PEAK 3(3Q26.32) MUTATED 11 18 15 21 9 4
AMP PEAK 3(3Q26.32) WILD-TYPE 97 44 60 59 70 39

Figure S14.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S15.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
AMP PEAK 3(3Q26.32) MUTATED 14 22 42
AMP PEAK 3(3Q26.32) WILD-TYPE 107 174 88

Figure S15.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S16.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
AMP PEAK 3(3Q26.32) MUTATED 14 18 55
AMP PEAK 3(3Q26.32) WILD-TYPE 97 203 138

Figure S16.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S17.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
AMP PEAK 3(3Q26.32) MUTATED 14 4 14 43 8 4
AMP PEAK 3(3Q26.32) WILD-TYPE 103 29 169 89 27 21

Figure S17.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S18.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 3(3Q26.32) MUTATED 13 16 55
AMP PEAK 3(3Q26.32) WILD-TYPE 111 188 127

Figure S18.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0033

Table S19.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
AMP PEAK 3(3Q26.32) MUTATED 29 32 17 6
AMP PEAK 3(3Q26.32) WILD-TYPE 115 102 178 31

Figure S19.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00467 (Fisher's exact test), Q value = 0.011

Table S20.  Gene #3: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
AMP PEAK 3(3Q26.32) MUTATED 3 1 3 11
AMP PEAK 3(3Q26.32) WILD-TYPE 35 20 45 24

Figure S20.  Get High-res Image Gene #3: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4q32.1' versus 'MRNASEQ_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.037

Table S21.  Gene #4: 'amp_4q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
AMP PEAK 4(4Q32.1) MUTATED 7 2 6
AMP PEAK 4(4Q32.1) WILD-TYPE 104 219 187

Figure S21.  Get High-res Image Gene #4: 'amp_4q32.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.025

Table S22.  Gene #4: 'amp_4q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
AMP PEAK 4(4Q32.1) MUTATED 4 0 2 5 0 4
AMP PEAK 4(4Q32.1) WILD-TYPE 113 33 181 127 35 21

Figure S22.  Get High-res Image Gene #4: 'amp_4q32.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q32.1' versus 'MIRSEQ_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0039

Table S23.  Gene #4: 'amp_4q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 4(4Q32.1) MUTATED 3 1 12
AMP PEAK 4(4Q32.1) WILD-TYPE 121 203 170

Figure S23.  Get High-res Image Gene #4: 'amp_4q32.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0484 (Fisher's exact test), Q value = 0.079

Table S24.  Gene #5: 'amp_5q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
AMP PEAK 5(5Q35.1) MUTATED 8 5 0 9 7 5 3
AMP PEAK 5(5Q35.1) WILD-TYPE 3 7 4 2 6 4 7

Figure S24.  Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5q35.1' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.001

Table S25.  Gene #5: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 5(5Q35.1) MUTATED 162 65 105
AMP PEAK 5(5Q35.1) WILD-TYPE 76 70 50

Figure S25.  Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q35.1' versus 'RPPA_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.067

Table S26.  Gene #5: 'amp_5q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
AMP PEAK 5(5Q35.1) MUTATED 73 35 58 48 44 30
AMP PEAK 5(5Q35.1) WILD-TYPE 35 27 17 32 35 13

Figure S26.  Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00945 (Fisher's exact test), Q value = 0.019

Table S27.  Gene #5: 'amp_5q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
AMP PEAK 5(5Q35.1) MUTATED 88 129 71
AMP PEAK 5(5Q35.1) WILD-TYPE 33 67 59

Figure S27.  Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5q35.1' versus 'MRNASEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0029

Table S28.  Gene #5: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
AMP PEAK 5(5Q35.1) MUTATED 53 149 128
AMP PEAK 5(5Q35.1) WILD-TYPE 58 72 65

Figure S28.  Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S29.  Gene #5: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
AMP PEAK 5(5Q35.1) MUTATED 79 15 121 84 26 5
AMP PEAK 5(5Q35.1) WILD-TYPE 38 18 62 48 9 20

Figure S29.  Get High-res Image Gene #5: 'amp_5q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S30.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 6(7Q36.3) MUTATED 39 48 89
AMP PEAK 6(7Q36.3) WILD-TYPE 199 87 66

Figure S30.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q36.3' versus 'METHLYATION_CNMF'

P value = 0.00581 (Fisher's exact test), Q value = 0.013

Table S31.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
AMP PEAK 6(7Q36.3) MUTATED 32 16 45
AMP PEAK 6(7Q36.3) WILD-TYPE 96 60 65

Figure S31.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q36.3' versus 'RPPA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0014

Table S32.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
AMP PEAK 6(7Q36.3) MUTATED 23 30 31 35 23 10
AMP PEAK 6(7Q36.3) WILD-TYPE 85 32 44 45 56 33

Figure S32.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7q36.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00312 (Fisher's exact test), Q value = 0.0074

Table S33.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
AMP PEAK 6(7Q36.3) MUTATED 40 53 59
AMP PEAK 6(7Q36.3) WILD-TYPE 81 143 71

Figure S33.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7q36.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S34.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
AMP PEAK 6(7Q36.3) MUTATED 33 53 88
AMP PEAK 6(7Q36.3) WILD-TYPE 78 168 105

Figure S34.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00615 (Fisher's exact test), Q value = 0.013

Table S35.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
AMP PEAK 6(7Q36.3) MUTATED 39 11 45 60 13 6
AMP PEAK 6(7Q36.3) WILD-TYPE 78 22 138 72 22 19

Figure S35.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q36.3' versus 'MIRSEQ_CNMF'

P value = 0.00671 (Fisher's exact test), Q value = 0.014

Table S36.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 6(7Q36.3) MUTATED 37 58 78
AMP PEAK 6(7Q36.3) WILD-TYPE 87 146 104

Figure S36.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.028

Table S37.  Gene #6: 'amp_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
AMP PEAK 6(7Q36.3) MUTATED 48 57 52 16
AMP PEAK 6(7Q36.3) WILD-TYPE 96 77 143 21

Figure S37.  Get High-res Image Gene #6: 'amp_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S38.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 7(8Q24.22) MUTATED 6 17 56
AMP PEAK 7(8Q24.22) WILD-TYPE 232 118 99

Figure S38.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S39.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
AMP PEAK 7(8Q24.22) MUTATED 6 14 33
AMP PEAK 7(8Q24.22) WILD-TYPE 122 62 77

Figure S39.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.22' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S40.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
AMP PEAK 7(8Q24.22) MUTATED 5 24 15 15 10 2
AMP PEAK 7(8Q24.22) WILD-TYPE 103 38 60 65 69 41

Figure S40.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.22' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S41.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
AMP PEAK 7(8Q24.22) MUTATED 15 18 38
AMP PEAK 7(8Q24.22) WILD-TYPE 106 178 92

Figure S41.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S42.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
AMP PEAK 7(8Q24.22) MUTATED 8 9 61
AMP PEAK 7(8Q24.22) WILD-TYPE 103 212 132

Figure S42.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S43.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
AMP PEAK 7(8Q24.22) MUTATED 9 2 8 54 4 1
AMP PEAK 7(8Q24.22) WILD-TYPE 108 31 175 78 31 24

Figure S43.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S44.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 7(8Q24.22) MUTATED 13 11 53
AMP PEAK 7(8Q24.22) WILD-TYPE 111 193 129

Figure S44.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S45.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
AMP PEAK 7(8Q24.22) MUTATED 29 24 11 13
AMP PEAK 7(8Q24.22) WILD-TYPE 115 110 184 24

Figure S45.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S46.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
AMP PEAK 7(8Q24.22) MUTATED 3 1 1 14
AMP PEAK 7(8Q24.22) WILD-TYPE 35 20 47 21

Figure S46.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.043

Table S47.  Gene #7: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
AMP PEAK 7(8Q24.22) MUTATED 3 13 3
AMP PEAK 7(8Q24.22) WILD-TYPE 36 43 44

Figure S47.  Get High-res Image Gene #7: 'amp_8q24.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p14' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S48.  Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 8(10P14) MUTATED 1 5 14
AMP PEAK 8(10P14) WILD-TYPE 237 130 141

Figure S48.  Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p14' versus 'MRNASEQ_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0054

Table S49.  Gene #8: 'amp_10p14' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
AMP PEAK 8(10P14) MUTATED 4 2 14
AMP PEAK 8(10P14) WILD-TYPE 107 219 179

Figure S49.  Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S50.  Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
AMP PEAK 8(10P14) MUTATED 2 2 0 14 2 0
AMP PEAK 8(10P14) WILD-TYPE 115 31 183 118 33 25

Figure S50.  Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p14' versus 'MIRSEQ_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.056

Table S51.  Gene #8: 'amp_10p14' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 8(10P14) MUTATED 5 3 12
AMP PEAK 8(10P14) WILD-TYPE 119 201 170

Figure S51.  Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p14' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0349 (Fisher's exact test), Q value = 0.06

Table S52.  Gene #8: 'amp_10p14' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
AMP PEAK 8(10P14) MUTATED 7 6 3 4
AMP PEAK 8(10P14) WILD-TYPE 137 128 192 33

Figure S52.  Get High-res Image Gene #8: 'amp_10p14' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xp22.2' versus 'CN_CNMF'

P value = 0.00836 (Fisher's exact test), Q value = 0.017

Table S53.  Gene #9: 'amp_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 9(XP22.2) MUTATED 8 6 17
AMP PEAK 9(XP22.2) WILD-TYPE 230 129 138

Figure S53.  Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp22.2' versus 'RPPA_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.003

Table S54.  Gene #9: 'amp_xp22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
AMP PEAK 9(XP22.2) MUTATED 0 4 7 10 3 1
AMP PEAK 9(XP22.2) WILD-TYPE 108 58 68 70 76 42

Figure S54.  Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.029

Table S55.  Gene #9: 'amp_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
AMP PEAK 9(XP22.2) MUTATED 4 7 14
AMP PEAK 9(XP22.2) WILD-TYPE 117 189 116

Figure S55.  Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00457 (Fisher's exact test), Q value = 0.01

Table S56.  Gene #9: 'amp_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
AMP PEAK 9(XP22.2) MUTATED 3 4 6 16 2 0
AMP PEAK 9(XP22.2) WILD-TYPE 114 29 177 116 33 25

Figure S56.  Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp22.2' versus 'MIRSEQ_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.063

Table S57.  Gene #9: 'amp_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 9(XP22.2) MUTATED 5 8 18
AMP PEAK 9(XP22.2) WILD-TYPE 119 196 164

Figure S57.  Get High-res Image Gene #9: 'amp_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp11.4' versus 'CN_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.0051

Table S58.  Gene #10: 'amp_xp11.4' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
AMP PEAK 10(XP11.4) MUTATED 8 6 19
AMP PEAK 10(XP11.4) WILD-TYPE 230 129 136

Figure S58.  Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.4' versus 'RPPA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0019

Table S59.  Gene #10: 'amp_xp11.4' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
AMP PEAK 10(XP11.4) MUTATED 0 5 5 10 5 0
AMP PEAK 10(XP11.4) WILD-TYPE 108 57 70 70 74 43

Figure S59.  Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_xp11.4' versus 'RPPA_CHIERARCHICAL'

P value = 0.00211 (Fisher's exact test), Q value = 0.0052

Table S60.  Gene #10: 'amp_xp11.4' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
AMP PEAK 10(XP11.4) MUTATED 2 8 15
AMP PEAK 10(XP11.4) WILD-TYPE 119 188 115

Figure S60.  Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xp11.4' versus 'MRNASEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.053

Table S61.  Gene #10: 'amp_xp11.4' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
AMP PEAK 10(XP11.4) MUTATED 9 7 17
AMP PEAK 10(XP11.4) WILD-TYPE 102 214 176

Figure S61.  Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00086

Table S62.  Gene #10: 'amp_xp11.4' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
AMP PEAK 10(XP11.4) MUTATED 2 4 7 19 1 0
AMP PEAK 10(XP11.4) WILD-TYPE 115 29 176 113 34 25

Figure S62.  Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.4' versus 'MIRSEQ_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.079

Table S63.  Gene #10: 'amp_xp11.4' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
AMP PEAK 10(XP11.4) MUTATED 6 8 18
AMP PEAK 10(XP11.4) WILD-TYPE 118 196 164

Figure S63.  Get High-res Image Gene #10: 'amp_xp11.4' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.051

Table S64.  Gene #11: 'amp_xq11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
AMP PEAK 11(XQ11.2) MUTATED 2 9 12
AMP PEAK 11(XQ11.2) WILD-TYPE 119 187 118

Figure S64.  Get High-res Image Gene #11: 'amp_xq11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.059

Table S65.  Gene #12: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
AMP PEAK 12(XQ28) MUTATED 5 2 9 14 6 0
AMP PEAK 12(XQ28) WILD-TYPE 112 31 174 118 29 25

Figure S65.  Get High-res Image Gene #12: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00047

Table S66.  Gene #13: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 1(1P36.23) MUTATED 2 8 8
DEL PEAK 1(1P36.23) WILD-TYPE 31 16 5

Figure S66.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.23' versus 'MRNA_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0026

Table S67.  Gene #13: 'del_1p36.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 1(1P36.23) MUTATED 0 2 2 5 1 1 7
DEL PEAK 1(1P36.23) WILD-TYPE 11 10 2 6 12 8 3

Figure S67.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S68.  Gene #13: 'del_1p36.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 1(1P36.23) MUTATED 13 37 53
DEL PEAK 1(1P36.23) WILD-TYPE 225 98 102

Figure S68.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.23' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S69.  Gene #13: 'del_1p36.23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 1(1P36.23) MUTATED 10 20 20 26 7 6
DEL PEAK 1(1P36.23) WILD-TYPE 98 42 55 54 72 37

Figure S69.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.23' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S70.  Gene #13: 'del_1p36.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 1(1P36.23) MUTATED 26 22 41
DEL PEAK 1(1P36.23) WILD-TYPE 95 174 89

Figure S70.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00026

Table S71.  Gene #13: 'del_1p36.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 1(1P36.23) MUTATED 21 26 56
DEL PEAK 1(1P36.23) WILD-TYPE 90 195 137

Figure S71.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S72.  Gene #13: 'del_1p36.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 1(1P36.23) MUTATED 11 6 23 41 10 12
DEL PEAK 1(1P36.23) WILD-TYPE 106 27 160 91 25 13

Figure S72.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S73.  Gene #13: 'del_1p36.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 1(1P36.23) MUTATED 19 23 61
DEL PEAK 1(1P36.23) WILD-TYPE 105 181 121

Figure S73.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00437 (Fisher's exact test), Q value = 0.01

Table S74.  Gene #13: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 1(1P36.23) MUTATED 32 34 25 12
DEL PEAK 1(1P36.23) WILD-TYPE 112 100 170 25

Figure S74.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.038

Table S75.  Gene #13: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
DEL PEAK 1(1P36.23) MUTATED 8 3 3 11
DEL PEAK 1(1P36.23) WILD-TYPE 30 18 45 24

Figure S75.  Get High-res Image Gene #13: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p31.1' versus 'MRNA_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.0045

Table S76.  Gene #14: 'del_1p31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 2(1P31.1) MUTATED 2 5 7
DEL PEAK 2(1P31.1) WILD-TYPE 31 19 6

Figure S76.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p31.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00624 (Fisher's exact test), Q value = 0.013

Table S77.  Gene #14: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 2(1P31.1) MUTATED 0 3 2 1 1 1 6
DEL PEAK 2(1P31.1) WILD-TYPE 11 9 2 10 12 8 4

Figure S77.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S78.  Gene #14: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 2(1P31.1) MUTATED 8 29 40
DEL PEAK 2(1P31.1) WILD-TYPE 230 106 115

Figure S78.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p31.1' versus 'RPPA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00073

Table S79.  Gene #14: 'del_1p31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 2(1P31.1) MUTATED 9 16 12 21 4 5
DEL PEAK 2(1P31.1) WILD-TYPE 99 46 63 59 75 38

Figure S79.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p31.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.0037

Table S80.  Gene #14: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 2(1P31.1) MUTATED 20 17 30
DEL PEAK 2(1P31.1) WILD-TYPE 101 179 100

Figure S80.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p31.1' versus 'MRNASEQ_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.028

Table S81.  Gene #14: 'del_1p31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 2(1P31.1) MUTATED 20 21 36
DEL PEAK 2(1P31.1) WILD-TYPE 91 200 157

Figure S81.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S82.  Gene #14: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 2(1P31.1) MUTATED 11 6 16 28 4 12
DEL PEAK 2(1P31.1) WILD-TYPE 106 27 167 104 31 13

Figure S82.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S83.  Gene #14: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 2(1P31.1) MUTATED 10 20 47
DEL PEAK 2(1P31.1) WILD-TYPE 114 184 135

Figure S83.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.0065

Table S84.  Gene #14: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 2(1P31.1) MUTATED 17 33 20 7
DEL PEAK 2(1P31.1) WILD-TYPE 127 101 175 30

Figure S84.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00518 (Fisher's exact test), Q value = 0.012

Table S85.  Gene #14: 'del_1p31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
DEL PEAK 2(1P31.1) MUTATED 6 0 2 9
DEL PEAK 2(1P31.1) WILD-TYPE 32 21 46 26

Figure S85.  Get High-res Image Gene #14: 'del_1p31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1q43' versus 'MRNA_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.021

Table S86.  Gene #15: 'del_1q43' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 3(1Q43) MUTATED 2 1 5
DEL PEAK 3(1Q43) WILD-TYPE 31 23 8

Figure S86.  Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1q43' versus 'MRNA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.023

Table S87.  Gene #15: 'del_1q43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 3(1Q43) MUTATED 0 1 0 0 1 1 5
DEL PEAK 3(1Q43) WILD-TYPE 11 11 4 11 12 8 5

Figure S87.  Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1q43' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S88.  Gene #15: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 3(1Q43) MUTATED 7 22 13
DEL PEAK 3(1Q43) WILD-TYPE 231 113 142

Figure S88.  Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #3: 'CN_CNMF'

'del_1q43' versus 'RPPA_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.036

Table S89.  Gene #15: 'del_1q43' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 3(1Q43) MUTATED 9 5 4 13 1 3
DEL PEAK 3(1Q43) WILD-TYPE 99 57 71 67 78 40

Figure S89.  Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1q43' versus 'MRNASEQ_CNMF'

P value = 0.0056 (Fisher's exact test), Q value = 0.012

Table S90.  Gene #15: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 3(1Q43) MUTATED 17 16 9
DEL PEAK 3(1Q43) WILD-TYPE 94 205 184

Figure S90.  Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1q43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S91.  Gene #15: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 3(1Q43) MUTATED 6 1 13 9 2 11
DEL PEAK 3(1Q43) WILD-TYPE 111 32 170 123 33 14

Figure S91.  Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1q43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.03

Table S92.  Gene #15: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 3(1Q43) MUTATED 10 19 13 0
DEL PEAK 3(1Q43) WILD-TYPE 134 115 182 37

Figure S92.  Get High-res Image Gene #15: 'del_1q43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.0042

Table S93.  Gene #16: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 4(2Q37.3) MUTATED 1 4 6
DEL PEAK 4(2Q37.3) WILD-TYPE 32 20 7

Figure S93.  Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 7e-04

Table S94.  Gene #16: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 4(2Q37.3) MUTATED 0 4 0 0 1 0 6
DEL PEAK 4(2Q37.3) WILD-TYPE 11 8 4 11 12 9 4

Figure S94.  Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00029

Table S95.  Gene #16: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 4(2Q37.3) MUTATED 21 9 19
DEL PEAK 4(2Q37.3) WILD-TYPE 90 212 174

Figure S95.  Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S96.  Gene #16: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 4(2Q37.3) MUTATED 13 1 7 18 1 9
DEL PEAK 4(2Q37.3) WILD-TYPE 104 32 176 114 34 16

Figure S96.  Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.024

Table S97.  Gene #16: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 4(2Q37.3) MUTATED 11 11 26
DEL PEAK 4(2Q37.3) WILD-TYPE 113 193 156

Figure S97.  Get High-res Image Gene #16: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S98.  Gene #17: 'del_3p26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 5(3P26.3) MUTATED 32 22 3
DEL PEAK 5(3P26.3) WILD-TYPE 1 2 10

Figure S98.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p26.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S99.  Gene #17: 'del_3p26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 5(3P26.3) MUTATED 11 11 1 11 12 9 2
DEL PEAK 5(3P26.3) WILD-TYPE 0 1 3 0 1 0 8

Figure S99.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S100.  Gene #17: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 5(3P26.3) MUTATED 236 69 150
DEL PEAK 5(3P26.3) WILD-TYPE 2 66 5

Figure S100.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S101.  Gene #17: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 5(3P26.3) MUTATED 118 50 103
DEL PEAK 5(3P26.3) WILD-TYPE 10 26 7

Figure S101.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p26.3' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S102.  Gene #17: 'del_3p26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 5(3P26.3) MUTATED 106 54 67 60 64 39
DEL PEAK 5(3P26.3) WILD-TYPE 2 8 8 20 15 4

Figure S102.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.058

Table S103.  Gene #17: 'del_3p26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 5(3P26.3) MUTATED 112 172 106
DEL PEAK 5(3P26.3) WILD-TYPE 9 24 24

Figure S103.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S104.  Gene #17: 'del_3p26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 5(3P26.3) MUTATED 70 211 171
DEL PEAK 5(3P26.3) WILD-TYPE 41 10 22

Figure S104.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S105.  Gene #17: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 5(3P26.3) MUTATED 108 20 175 114 33 2
DEL PEAK 5(3P26.3) WILD-TYPE 9 13 8 18 2 23

Figure S105.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00035

Table S106.  Gene #17: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 5(3P26.3) MUTATED 103 191 144
DEL PEAK 5(3P26.3) WILD-TYPE 21 13 38

Figure S106.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S107.  Gene #17: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 5(3P26.3) MUTATED 112 108 184 34
DEL PEAK 5(3P26.3) WILD-TYPE 32 26 11 3

Figure S107.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.0069

Table S108.  Gene #17: 'del_3p26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
DEL PEAK 5(3P26.3) MUTATED 27 14 46 28
DEL PEAK 5(3P26.3) WILD-TYPE 11 7 2 7

Figure S108.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00971 (Fisher's exact test), Q value = 0.02

Table S109.  Gene #17: 'del_3p26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
DEL PEAK 5(3P26.3) MUTATED 27 44 44
DEL PEAK 5(3P26.3) WILD-TYPE 12 12 3

Figure S109.  Get High-res Image Gene #17: 'del_3p26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p22.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S110.  Gene #18: 'del_3p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 6(3P22.2) MUTATED 32 22 3
DEL PEAK 6(3P22.2) WILD-TYPE 1 2 10

Figure S110.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p22.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S111.  Gene #18: 'del_3p22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 6(3P22.2) MUTATED 11 11 1 11 12 9 2
DEL PEAK 6(3P22.2) WILD-TYPE 0 1 3 0 1 0 8

Figure S111.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S112.  Gene #18: 'del_3p22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 6(3P22.2) MUTATED 238 75 152
DEL PEAK 6(3P22.2) WILD-TYPE 0 60 3

Figure S112.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S113.  Gene #18: 'del_3p22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 6(3P22.2) MUTATED 119 52 106
DEL PEAK 6(3P22.2) WILD-TYPE 9 24 4

Figure S113.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p22.2' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S114.  Gene #18: 'del_3p22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 6(3P22.2) MUTATED 107 59 66 63 65 40
DEL PEAK 6(3P22.2) WILD-TYPE 1 3 9 17 14 3

Figure S114.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S115.  Gene #18: 'del_3p22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 6(3P22.2) MUTATED 70 216 176
DEL PEAK 6(3P22.2) WILD-TYPE 41 5 17

Figure S115.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S116.  Gene #18: 'del_3p22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 6(3P22.2) MUTATED 110 19 179 116 35 3
DEL PEAK 6(3P22.2) WILD-TYPE 7 14 4 16 0 22

Figure S116.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S117.  Gene #18: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 6(3P22.2) MUTATED 103 197 148
DEL PEAK 6(3P22.2) WILD-TYPE 21 7 34

Figure S117.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S118.  Gene #18: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 6(3P22.2) MUTATED 114 111 187 36
DEL PEAK 6(3P22.2) WILD-TYPE 30 23 8 1

Figure S118.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00616 (Fisher's exact test), Q value = 0.013

Table S119.  Gene #18: 'del_3p22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
DEL PEAK 6(3P22.2) MUTATED 29 14 46 28
DEL PEAK 6(3P22.2) WILD-TYPE 9 7 2 7

Figure S119.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.053

Table S120.  Gene #18: 'del_3p22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
DEL PEAK 6(3P22.2) MUTATED 29 44 44
DEL PEAK 6(3P22.2) WILD-TYPE 10 12 3

Figure S120.  Get High-res Image Gene #18: 'del_3p22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.1' versus 'MRNA_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.0078

Table S121.  Gene #19: 'del_3p14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 7(3P14.1) MUTATED 22 19 3
DEL PEAK 7(3P14.1) WILD-TYPE 11 5 10

Figure S121.  Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p14.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.021

Table S122.  Gene #19: 'del_3p14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 7(3P14.1) MUTATED 8 9 1 10 7 7 2
DEL PEAK 7(3P14.1) WILD-TYPE 3 3 3 1 6 2 8

Figure S122.  Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S123.  Gene #19: 'del_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 7(3P14.1) MUTATED 199 32 142
DEL PEAK 7(3P14.1) WILD-TYPE 39 103 13

Figure S123.  Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p14.1' versus 'METHLYATION_CNMF'

P value = 0.00613 (Fisher's exact test), Q value = 0.013

Table S124.  Gene #19: 'del_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 7(3P14.1) MUTATED 98 44 86
DEL PEAK 7(3P14.1) WILD-TYPE 30 32 24

Figure S124.  Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S125.  Gene #19: 'del_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 7(3P14.1) MUTATED 49 175 147
DEL PEAK 7(3P14.1) WILD-TYPE 62 46 46

Figure S125.  Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S126.  Gene #19: 'del_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 7(3P14.1) MUTATED 90 14 140 100 25 2
DEL PEAK 7(3P14.1) WILD-TYPE 27 19 43 32 10 23

Figure S126.  Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00702 (Fisher's exact test), Q value = 0.015

Table S127.  Gene #19: 'del_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 7(3P14.1) MUTATED 89 91 149 31
DEL PEAK 7(3P14.1) WILD-TYPE 55 43 46 6

Figure S127.  Get High-res Image Gene #19: 'del_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.2' versus 'MRNA_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.067

Table S128.  Gene #20: 'del_3p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 8(3P12.2) MUTATED 18 13 2
DEL PEAK 8(3P12.2) WILD-TYPE 15 11 11

Figure S128.  Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S129.  Gene #20: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 8(3P12.2) MUTATED 160 22 123
DEL PEAK 8(3P12.2) WILD-TYPE 78 113 32

Figure S129.  Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.2' versus 'METHLYATION_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.035

Table S130.  Gene #20: 'del_3p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 8(3P12.2) MUTATED 82 35 71
DEL PEAK 8(3P12.2) WILD-TYPE 46 41 39

Figure S130.  Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.2' versus 'MRNASEQ_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0024

Table S131.  Gene #20: 'del_3p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 8(3P12.2) MUTATED 47 134 123
DEL PEAK 8(3P12.2) WILD-TYPE 64 87 70

Figure S131.  Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S132.  Gene #20: 'del_3p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 8(3P12.2) MUTATED 75 13 109 84 21 2
DEL PEAK 8(3P12.2) WILD-TYPE 42 20 74 48 14 23

Figure S132.  Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.075

Table S133.  Gene #20: 'del_3p12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 8(3P12.2) MUTATED 70 80 118 26
DEL PEAK 8(3P12.2) WILD-TYPE 74 54 77 11

Figure S133.  Get High-res Image Gene #20: 'del_3p12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S134.  Gene #21: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 9(3Q11.2) MUTATED 83 13 65
DEL PEAK 9(3Q11.2) WILD-TYPE 155 122 90

Figure S134.  Get High-res Image Gene #21: 'del_3q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q11.2' versus 'METHLYATION_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.068

Table S135.  Gene #21: 'del_3q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 9(3Q11.2) MUTATED 45 15 38
DEL PEAK 9(3Q11.2) WILD-TYPE 83 61 72

Figure S135.  Get High-res Image Gene #21: 'del_3q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S136.  Gene #21: 'del_3q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 9(3Q11.2) MUTATED 49 6 50 50 5 1
DEL PEAK 9(3Q11.2) WILD-TYPE 68 27 133 82 30 24

Figure S136.  Get High-res Image Gene #21: 'del_3q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S137.  Gene #22: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 10(4Q34.3) MUTATED 10 17 51
DEL PEAK 10(4Q34.3) WILD-TYPE 228 118 104

Figure S137.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S138.  Gene #22: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 10(4Q34.3) MUTATED 10 9 34
DEL PEAK 10(4Q34.3) WILD-TYPE 118 67 76

Figure S138.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.067

Table S139.  Gene #22: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 10(4Q34.3) MUTATED 16 20 12 10 10 6
DEL PEAK 10(4Q34.3) WILD-TYPE 92 42 63 70 69 37

Figure S139.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00547 (Fisher's exact test), Q value = 0.012

Table S140.  Gene #22: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 10(4Q34.3) MUTATED 22 21 31
DEL PEAK 10(4Q34.3) WILD-TYPE 99 175 99

Figure S140.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00045

Table S141.  Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 10(4Q34.3) MUTATED 8 25 45
DEL PEAK 10(4Q34.3) WILD-TYPE 103 196 148

Figure S141.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S142.  Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 10(4Q34.3) MUTATED 15 1 18 38 6 0
DEL PEAK 10(4Q34.3) WILD-TYPE 102 32 165 94 29 25

Figure S142.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00855 (Fisher's exact test), Q value = 0.018

Table S143.  Gene #22: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 10(4Q34.3) MUTATED 23 15 26 13
DEL PEAK 10(4Q34.3) WILD-TYPE 121 119 169 24

Figure S143.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.031

Table S144.  Gene #22: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
DEL PEAK 10(4Q34.3) MUTATED 3 15 4
DEL PEAK 10(4Q34.3) WILD-TYPE 36 41 43

Figure S144.  Get High-res Image Gene #22: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.029

Table S145.  Gene #23: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 11(6Q26) MUTATED 7 12 8
DEL PEAK 11(6Q26) WILD-TYPE 26 12 5

Figure S145.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S146.  Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 11(6Q26) MUTATED 37 26 88
DEL PEAK 11(6Q26) WILD-TYPE 201 109 67

Figure S146.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.024

Table S147.  Gene #23: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 11(6Q26) MUTATED 27 14 39
DEL PEAK 11(6Q26) WILD-TYPE 101 62 71

Figure S147.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S148.  Gene #23: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 11(6Q26) MUTATED 35 30 25 23 9 8
DEL PEAK 11(6Q26) WILD-TYPE 73 32 50 57 70 35

Figure S148.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S149.  Gene #23: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 11(6Q26) MUTATED 39 36 55
DEL PEAK 11(6Q26) WILD-TYPE 82 160 75

Figure S149.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0029

Table S150.  Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 11(6Q26) MUTATED 22 54 73
DEL PEAK 11(6Q26) WILD-TYPE 89 167 120

Figure S150.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.00094

Table S151.  Gene #23: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 11(6Q26) MUTATED 26 6 40 58 10 9
DEL PEAK 11(6Q26) WILD-TYPE 91 27 143 74 25 16

Figure S151.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S152.  Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 11(6Q26) MUTATED 25 43 79
DEL PEAK 11(6Q26) WILD-TYPE 99 161 103

Figure S152.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00047

Table S153.  Gene #23: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 11(6Q26) MUTATED 38 50 40 19
DEL PEAK 11(6Q26) WILD-TYPE 106 84 155 18

Figure S153.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.052

Table S154.  Gene #23: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
DEL PEAK 11(6Q26) MUTATED 7 2 12 15
DEL PEAK 11(6Q26) WILD-TYPE 31 19 36 20

Figure S154.  Get High-res Image Gene #23: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MRNA_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.028

Table S155.  Gene #24: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 12(6Q26) MUTATED 7 12 8
DEL PEAK 12(6Q26) WILD-TYPE 26 12 5

Figure S155.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S156.  Gene #24: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 12(6Q26) MUTATED 37 26 88
DEL PEAK 12(6Q26) WILD-TYPE 201 109 67

Figure S156.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.025

Table S157.  Gene #24: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 12(6Q26) MUTATED 27 14 39
DEL PEAK 12(6Q26) WILD-TYPE 101 62 71

Figure S157.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S158.  Gene #24: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 12(6Q26) MUTATED 34 31 25 23 9 8
DEL PEAK 12(6Q26) WILD-TYPE 74 31 50 57 70 35

Figure S158.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S159.  Gene #24: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 12(6Q26) MUTATED 39 36 55
DEL PEAK 12(6Q26) WILD-TYPE 82 160 75

Figure S159.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00086

Table S160.  Gene #24: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 12(6Q26) MUTATED 21 54 74
DEL PEAK 12(6Q26) WILD-TYPE 90 167 119

Figure S160.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00065

Table S161.  Gene #24: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 12(6Q26) MUTATED 26 6 40 59 9 9
DEL PEAK 12(6Q26) WILD-TYPE 91 27 143 73 26 16

Figure S161.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S162.  Gene #24: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 12(6Q26) MUTATED 24 43 80
DEL PEAK 12(6Q26) WILD-TYPE 100 161 102

Figure S162.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00047

Table S163.  Gene #24: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 12(6Q26) MUTATED 38 50 40 19
DEL PEAK 12(6Q26) WILD-TYPE 106 84 155 18

Figure S163.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.052

Table S164.  Gene #24: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
DEL PEAK 12(6Q26) MUTATED 7 2 12 15
DEL PEAK 12(6Q26) WILD-TYPE 31 19 36 20

Figure S164.  Get High-res Image Gene #24: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S165.  Gene #25: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 13(8P23.2) MUTATED 43 37 74
DEL PEAK 13(8P23.2) WILD-TYPE 195 98 81

Figure S165.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.068

Table S166.  Gene #25: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 13(8P23.2) MUTATED 28 19 40
DEL PEAK 13(8P23.2) WILD-TYPE 100 57 70

Figure S166.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 0.0055 (Fisher's exact test), Q value = 0.012

Table S167.  Gene #25: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 13(8P23.2) MUTATED 22 29 26 24 24 8
DEL PEAK 13(8P23.2) WILD-TYPE 86 33 49 56 55 35

Figure S167.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.022

Table S168.  Gene #25: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 13(8P23.2) MUTATED 32 49 52
DEL PEAK 13(8P23.2) WILD-TYPE 89 147 78

Figure S168.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0037

Table S169.  Gene #25: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 13(8P23.2) MUTATED 23 56 74
DEL PEAK 13(8P23.2) WILD-TYPE 88 165 119

Figure S169.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S170.  Gene #25: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 13(8P23.2) MUTATED 31 3 48 60 6 5
DEL PEAK 13(8P23.2) WILD-TYPE 86 30 135 72 29 20

Figure S170.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.003

Table S171.  Gene #25: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 13(8P23.2) MUTATED 36 44 71
DEL PEAK 13(8P23.2) WILD-TYPE 88 160 111

Figure S171.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0026

Table S172.  Gene #25: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 13(8P23.2) MUTATED 51 39 42 19
DEL PEAK 13(8P23.2) WILD-TYPE 93 95 153 18

Figure S172.  Get High-res Image Gene #25: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.0084

Table S173.  Gene #26: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 14(9P23) MUTATED 5 12 1
DEL PEAK 14(9P23) WILD-TYPE 28 12 12

Figure S173.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.062

Table S174.  Gene #26: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 14(9P23) MUTATED 2 7 0 5 1 2 1
DEL PEAK 14(9P23) WILD-TYPE 9 5 4 6 12 7 9

Figure S174.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S175.  Gene #26: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 14(9P23) MUTATED 9 34 109
DEL PEAK 14(9P23) WILD-TYPE 229 101 46

Figure S175.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S176.  Gene #26: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 14(9P23) MUTATED 6 21 68
DEL PEAK 14(9P23) WILD-TYPE 122 55 42

Figure S176.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S177.  Gene #26: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 14(9P23) MUTATED 17 38 31 21 19 10
DEL PEAK 14(9P23) WILD-TYPE 91 24 44 59 60 33

Figure S177.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S178.  Gene #26: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 14(9P23) MUTATED 34 42 60
DEL PEAK 14(9P23) WILD-TYPE 87 154 70

Figure S178.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S179.  Gene #26: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 14(9P23) MUTATED 16 25 110
DEL PEAK 14(9P23) WILD-TYPE 95 196 83

Figure S179.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S180.  Gene #26: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 14(9P23) MUTATED 32 3 15 84 13 4
DEL PEAK 14(9P23) WILD-TYPE 85 30 168 48 22 21

Figure S180.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S181.  Gene #26: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 14(9P23) MUTATED 26 25 96
DEL PEAK 14(9P23) WILD-TYPE 98 179 86

Figure S181.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S182.  Gene #26: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 14(9P23) MUTATED 44 56 23 24
DEL PEAK 14(9P23) WILD-TYPE 100 78 172 13

Figure S182.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00291 (Fisher's exact test), Q value = 0.0069

Table S183.  Gene #26: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
DEL PEAK 14(9P23) MUTATED 8 4 5 16
DEL PEAK 14(9P23) WILD-TYPE 30 17 43 19

Figure S183.  Get High-res Image Gene #26: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0038

Table S184.  Gene #27: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 15(9P21.3) MUTATED 5 13 1
DEL PEAK 15(9P21.3) WILD-TYPE 28 11 12

Figure S184.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.031

Table S185.  Gene #27: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 15(9P21.3) MUTATED 2 7 0 6 1 2 1
DEL PEAK 15(9P21.3) WILD-TYPE 9 5 4 5 12 7 9

Figure S185.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S186.  Gene #27: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 15(9P21.3) MUTATED 12 35 112
DEL PEAK 15(9P21.3) WILD-TYPE 226 100 43

Figure S186.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S187.  Gene #27: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 15(9P21.3) MUTATED 6 24 68
DEL PEAK 15(9P21.3) WILD-TYPE 122 52 42

Figure S187.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S188.  Gene #27: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 15(9P21.3) MUTATED 18 40 31 22 22 10
DEL PEAK 15(9P21.3) WILD-TYPE 90 22 44 58 57 33

Figure S188.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S189.  Gene #27: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 15(9P21.3) MUTATED 34 45 64
DEL PEAK 15(9P21.3) WILD-TYPE 87 151 66

Figure S189.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S190.  Gene #27: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 15(9P21.3) MUTATED 18 27 113
DEL PEAK 15(9P21.3) WILD-TYPE 93 194 80

Figure S190.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S191.  Gene #27: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 15(9P21.3) MUTATED 32 2 16 90 14 4
DEL PEAK 15(9P21.3) WILD-TYPE 85 31 167 42 21 21

Figure S191.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S192.  Gene #27: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 15(9P21.3) MUTATED 29 26 98
DEL PEAK 15(9P21.3) WILD-TYPE 95 178 84

Figure S192.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S193.  Gene #27: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 15(9P21.3) MUTATED 48 55 24 26
DEL PEAK 15(9P21.3) WILD-TYPE 96 79 171 11

Figure S193.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.0034

Table S194.  Gene #27: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 21 48 35
DEL PEAK 15(9P21.3) MUTATED 8 5 5 17
DEL PEAK 15(9P21.3) WILD-TYPE 30 16 43 18

Figure S194.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.025

Table S195.  Gene #27: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 39 56 47
DEL PEAK 15(9P21.3) MUTATED 8 21 6
DEL PEAK 15(9P21.3) WILD-TYPE 31 35 41

Figure S195.  Get High-res Image Gene #27: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S196.  Gene #28: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 16(10Q23.31) MUTATED 17 29 50
DEL PEAK 16(10Q23.31) WILD-TYPE 221 106 105

Figure S196.  Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0034

Table S197.  Gene #28: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 16(10Q23.31) MUTATED 17 9 33
DEL PEAK 16(10Q23.31) WILD-TYPE 111 67 77

Figure S197.  Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00665 (Fisher's exact test), Q value = 0.014

Table S198.  Gene #28: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 16(10Q23.31) MUTATED 20 27 36
DEL PEAK 16(10Q23.31) WILD-TYPE 101 169 94

Figure S198.  Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.078

Table S199.  Gene #28: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 16(10Q23.31) MUTATED 21 30 44
DEL PEAK 16(10Q23.31) WILD-TYPE 90 191 149

Figure S199.  Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00084

Table S200.  Gene #28: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 16(10Q23.31) MUTATED 22 3 21 37 3 9
DEL PEAK 16(10Q23.31) WILD-TYPE 95 30 162 95 32 16

Figure S200.  Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.028

Table S201.  Gene #28: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 16(10Q23.31) MUTATED 22 27 45
DEL PEAK 16(10Q23.31) WILD-TYPE 102 177 137

Figure S201.  Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 8e-05

Table S202.  Gene #28: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 16(10Q23.31) MUTATED 21 35 23 15
DEL PEAK 16(10Q23.31) WILD-TYPE 123 99 172 22

Figure S202.  Get High-res Image Gene #28: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.027

Table S203.  Gene #29: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 17(13Q14.2) MUTATED 1 7 3
DEL PEAK 17(13Q14.2) WILD-TYPE 32 17 10

Figure S203.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S204.  Gene #29: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 17(13Q14.2) MUTATED 11 23 48
DEL PEAK 17(13Q14.2) WILD-TYPE 227 112 107

Figure S204.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00032

Table S205.  Gene #29: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 17(13Q14.2) MUTATED 8 16 27
DEL PEAK 17(13Q14.2) WILD-TYPE 120 60 83

Figure S205.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S206.  Gene #29: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 17(13Q14.2) MUTATED 3 22 15 14 11 7
DEL PEAK 17(13Q14.2) WILD-TYPE 105 40 60 66 68 36

Figure S206.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S207.  Gene #29: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 17(13Q14.2) MUTATED 15 20 37
DEL PEAK 17(13Q14.2) WILD-TYPE 106 176 93

Figure S207.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S208.  Gene #29: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 17(13Q14.2) MUTATED 13 19 50
DEL PEAK 17(13Q14.2) WILD-TYPE 98 202 143

Figure S208.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S209.  Gene #29: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 17(13Q14.2) MUTATED 7 2 15 43 8 7
DEL PEAK 17(13Q14.2) WILD-TYPE 110 31 168 89 27 18

Figure S209.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S210.  Gene #29: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 17(13Q14.2) MUTATED 14 16 50
DEL PEAK 17(13Q14.2) WILD-TYPE 110 188 132

Figure S210.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S211.  Gene #29: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 17(13Q14.2) MUTATED 20 33 14 13
DEL PEAK 17(13Q14.2) WILD-TYPE 124 101 181 24

Figure S211.  Get High-res Image Gene #29: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S212.  Gene #30: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 24 13
DEL PEAK 18(14Q31.1) MUTATED 10 19 2
DEL PEAK 18(14Q31.1) WILD-TYPE 23 5 11

Figure S212.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.1' versus 'MRNA_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0012

Table S213.  Gene #30: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 4 11 13 9 10
DEL PEAK 18(14Q31.1) MUTATED 4 7 1 11 5 1 2
DEL PEAK 18(14Q31.1) WILD-TYPE 7 5 3 0 8 8 8

Figure S213.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S214.  Gene #30: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 238 135 155
DEL PEAK 18(14Q31.1) MUTATED 70 47 111
DEL PEAK 18(14Q31.1) WILD-TYPE 168 88 44

Figure S214.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S215.  Gene #30: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 128 76 110
DEL PEAK 18(14Q31.1) MUTATED 32 36 65
DEL PEAK 18(14Q31.1) WILD-TYPE 96 40 45

Figure S215.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q31.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S216.  Gene #30: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 108 62 75 80 79 43
DEL PEAK 18(14Q31.1) MUTATED 37 41 56 27 26 13
DEL PEAK 18(14Q31.1) WILD-TYPE 71 21 19 53 53 30

Figure S216.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S217.  Gene #30: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 121 196 130
DEL PEAK 18(14Q31.1) MUTATED 69 64 67
DEL PEAK 18(14Q31.1) WILD-TYPE 52 132 63

Figure S217.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S218.  Gene #30: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 111 221 193
DEL PEAK 18(14Q31.1) MUTATED 21 73 131
DEL PEAK 18(14Q31.1) WILD-TYPE 90 148 62

Figure S218.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S219.  Gene #30: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 117 33 183 132 35 25
DEL PEAK 18(14Q31.1) MUTATED 45 7 57 81 33 2
DEL PEAK 18(14Q31.1) WILD-TYPE 72 26 126 51 2 23

Figure S219.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S220.  Gene #30: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 204 182
DEL PEAK 18(14Q31.1) MUTATED 38 66 118
DEL PEAK 18(14Q31.1) WILD-TYPE 86 138 64

Figure S220.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 4.5e-05

Table S221.  Gene #30: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 144 134 195 37
DEL PEAK 18(14Q31.1) MUTATED 52 84 62 24
DEL PEAK 18(14Q31.1) WILD-TYPE 92 50 133 13

Figure S221.  Get High-res Image Gene #30: 'del_14q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/15087097/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/15107132/KIRC-TP.transferedmergedcluster.txt

  • Number of patients = 528

  • Number of significantly focal cnvs = 30

  • Number of molecular subtypes = 12

  • Exclude genes that fewer than K tumors have alterations, 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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