Correlation between copy number variation genes (focal events) and molecular subtypes
Pheochromocytoma and Paraganglioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1F76BM0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1F76BM0
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 28 focal events and 10 molecular subtypes across 162 patients, 94 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'CN_CNMF'.

  • amp_4q31.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • amp_12q13.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • amp_14q24.3 cnv correlated to 'CN_CNMF'.

  • amp_17q21.31 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_1p12 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'.

  • del_1q42.13 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_3p24.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q26.1 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q28.3 cnv correlated to 'MRNASEQ_CNMF'.

  • del_6p12.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • del_6q16.1 cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • del_8p22 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_8q23.3 cnv correlated to 'CN_CNMF'.

  • del_9q21.12 cnv correlated to 'CN_CNMF'.

  • del_11p15.4 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q22.1 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q21 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_17p13.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_17q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_22q13.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xp21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 28 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 94 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
del 1p12 113 (70%) 49 1e-05
(0.000215) 		2e-05
(0.00035) 		0.033
(0.104) 		0.00131
(0.0108) 		2e-05
(0.00035) 		4e-05
(0.000589) 		0.00046
(0.00477) 		0.0167
(0.07) 		0.00763
(0.0427) 		0.015
(0.0665)
del 3p24 1 64 (40%) 98 0.00151
(0.0121) 		0.00763
(0.0427) 		0.0338
(0.104) 		0.0862
(0.203) 		4e-05
(0.000589) 		3e-05
(0.000494) 		1e-05
(0.000215) 		0.00032
(0.0039) 		1e-05
(0.000215) 		1e-05
(0.000215)
del 3q26 1 93 (57%) 69 2e-05
(0.00035) 		0.516
(0.681) 		0.0216
(0.0804) 		0.0141
(0.0639) 		0.0245
(0.0872) 		1e-05
(0.000215) 		0.0183
(0.0743) 		0.00941
(0.0488) 		0.0114
(0.0532) 		0.0105
(0.0523)
del 11p15 4 58 (36%) 104 1e-05
(0.000215) 		1e-05
(0.000215) 		0.00167
(0.0126) 		0.112
(0.247) 		0.00044
(0.00477) 		1e-05
(0.000215) 		8e-05
(0.00112) 		1e-05
(0.000215) 		1e-05
(0.000215) 		0.00031
(0.0039)
del 11q22 1 48 (30%) 114 1e-05
(0.000215) 		0.21
(0.377) 		0.0135
(0.0619) 		0.0614
(0.17) 		0.00076
(0.00665) 		0.00977
(0.0497) 		0.00333
(0.0239) 		0.00075
(0.00665) 		0.00034
(0.00397) 		0.0323
(0.104)
del 22q13 31 65 (40%) 97 1e-05
(0.000215) 		0.0211
(0.0803) 		0.432
(0.611) 		0.0579
(0.167) 		0.0194
(0.0766) 		0.00056
(0.00541) 		0.0114
(0.0532) 		0.0266
(0.0913) 		0.0165
(0.0698) 		0.0212
(0.0803)
del 17p13 2 64 (40%) 98 0.00014
(0.00187) 		0.00048
(0.0048) 		0.45
(0.621) 		0.0659
(0.177) 		0.0154
(0.0665) 		0.00619
(0.0377) 		0.0271
(0.0913) 		0.00778
(0.0427) 		0.17
(0.326) 		0.0175
(0.0721)
del xp21 1 46 (28%) 116 0.00084
(0.00713) 		0.00605
(0.0377) 		0.077
(0.189) 		0.243
(0.415) 		0.0339
(0.104) 		0.00388
(0.0265) 		0.00069
(0.00644) 		0.0452
(0.136) 		0.183
(0.342) 		0.0327
(0.104)
del 6q16 1 24 (15%) 138 0.135
(0.282) 		0.0744
(0.186) 		0.0536
(0.156) 		0.218
(0.39) 		0.0265
(0.0913) 		0.00702
(0.0409) 		0.0153
(0.0665) 		0.0062
(0.0377) 		0.0826
(0.198) 		0.0937
(0.213)
del 8p22 25 (15%) 137 0.00159
(0.0124) 		0.0825
(0.198) 		0.258
(0.433) 		0.646
(0.773) 		0.00668
(0.0398) 		0.00818
(0.0432) 		0.207
(0.377) 		0.238
(0.415) 		0.027
(0.0913) 		0.241
(0.415)
del 17q11 2 42 (26%) 120 1e-05
(0.000215) 		0.00344
(0.0241) 		0.0678
(0.179) 		0.131
(0.276) 		0.0246
(0.0872) 		0.00284
(0.0209) 		0.103
(0.231) 		0.0705
(0.183) 		0.369
(0.543) 		0.14
(0.285)
amp 4q31 1 13 (8%) 149 0.00569
(0.0371) 		0.0683
(0.179) 		0.568
(0.73) 		0.0641
(0.176) 		0.614
(0.751) 		0.00806
(0.0432) 		0.408
(0.586) 		0.228
(0.401) 		0.11
(0.245) 		0.322
(0.497)
amp 12q13 3 16 (10%) 146 0.0442
(0.134) 		0.138
(0.283) 		0.777
(0.885) 		0.322
(0.497) 		0.613
(0.751) 		0.623
(0.756) 		0.0481
(0.143) 		0.273
(0.447) 		0.131
(0.276) 		0.323
(0.497)
del 1q42 13 18 (11%) 144 0.0218
(0.0804) 		0.136
(0.282) 		0.276
(0.447) 		0.0597
(0.167) 		0.0244
(0.0872) 		0.178
(0.335) 		0.33
(0.501) 		0.532
(0.692) 		0.0722
(0.184) 		0.245
(0.416)
del 6p12 3 10 (6%) 152 0.0108
(0.0523) 		0.269
(0.447) 		0.0206
(0.0803) 		0.0864
(0.203) 		0.199
(0.365) 		0.162
(0.318) 		0.927
(0.967) 		0.052
(0.153)
amp 1q21 3 30 (19%) 132 0.0047
(0.0313) 		0.607
(0.751) 		0.979
(1.00) 		0.795
(0.894) 		0.638
(0.767) 		0.942
(0.977) 		0.904
(0.956) 		0.445
(0.621) 		0.69
(0.819) 		0.822
(0.914)
amp 14q24 3 10 (6%) 152 0.029
(0.0956) 		0.198
(0.364) 		0.85
(0.932) 		0.163
(0.318) 		0.852
(0.932) 		0.177
(0.335) 		0.457
(0.621) 		0.714
(0.837) 		0.438
(0.617) 		0.859
(0.932)
amp 17q21 31 16 (10%) 146 0.631
(0.761) 		0.888
(0.948) 		0.596
(0.745) 		0.351
(0.52) 		0.53
(0.692) 		0.00046
(0.00477) 		0.755
(0.87) 		0.145
(0.295) 		0.0672
(0.179) 		0.456
(0.621)
del 4q28 3 10 (6%) 152 0.0734
(0.185) 		0.241
(0.415) 		0.501
(0.667) 		0.163
(0.318) 		0.019
(0.076) 		0.339
(0.508) 		0.456
(0.621) 		0.713
(0.837) 		0.328
(0.501) 		0.323
(0.497)
del 8q23 3 13 (8%) 149 0.0327
(0.104) 		0.866
(0.937) 		0.149
(0.301) 		1
(1.00) 		0.274
(0.447) 		0.523
(0.687) 		0.0711
(0.183) 		0.466
(0.631) 		0.928
(0.967) 		0.302
(0.475)
del 9q21 12 14 (9%) 148 0.0108
(0.0523) 		0.546
(0.707) 		0.154
(0.307) 		0.0593
(0.167) 		0.373
(0.547) 		0.39
(0.565) 		0.722
(0.839) 		0.114
(0.247) 		0.581
(0.74) 		0.345
(0.514)
del 16q21 5 (3%) 157 0.065
(0.177) 		0.114
(0.247) 		0.746
(0.863) 		0.788
(0.89) 		0.553
(0.714) 		0.0279
(0.0931) 		0.209
(0.377) 		0.592
(0.745) 		0.0915
(0.212) 		0.83
(0.918)
amp 4q25 6 (4%) 156 0.882
(0.946) 		0.759
(0.871) 		1
(1.00) 		0.451
(0.621) 		0.13
(0.276) 		0.385
(0.561) 		0.764
(0.873) 		0.624
(0.756) 		0.292
(0.467) 		0.503
(0.667)
amp 11p15 2 8 (5%) 154 0.0937
(0.213) 		0.0791
(0.193) 		0.572
(0.732) 		0.223
(0.395) 		0.332
(0.502) 		0.103
(0.231) 		0.411
(0.587) 		0.396
(0.571) 		0.457
(0.621) 		0.811
(0.905)
del 5q15 12 (7%) 150 0.595
(0.745) 		1
(1.00) 		0.165
(0.318) 		0.805
(0.902) 		0.974
(1.00) 		1
(1.00) 		0.929
(0.967) 		0.188
(0.348) 		0.242
(0.415) 		0.296
(0.471)
del 9p24 2 15 (9%) 147 0.291
(0.467) 		0.339
(0.508) 		0.276
(0.447) 		0.164
(0.318) 		0.0911
(0.212) 		0.173
(0.33) 		0.481
(0.647) 		0.0762
(0.189) 		0.484
(0.649) 		0.302
(0.475)
del 12q21 33 8 (5%) 154 0.0594
(0.167) 		0.892
(0.948) 		0.668
(0.796) 		0.608
(0.751) 		0.914
(0.963) 		0.875
(0.942) 		0.593
(0.745) 		0.697
(0.824) 		0.835
(0.92) 		1
(1.00)
del 13q22 3 8 (5%) 154 0.247
(0.417) 		0.894
(0.948) 		0.128
(0.275) 		0.786
(0.89) 		0.271
(0.447) 		0.429
(0.609) 		1
(1.00) 		0.613
(0.751) 		0.72
(0.839) 		0.857
(0.932)
'amp_1q21.3' versus 'CN_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.031

Table S1.  Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
AMP PEAK 1(1Q21.3) MUTATED 10 6 14
AMP PEAK 1(1Q21.3) WILD-TYPE 50 57 25

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q31.1' versus 'CN_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.037

Table S2.  Gene #3: 'amp_4q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
AMP PEAK 3(4Q31.1) MUTATED 10 3 0
AMP PEAK 3(4Q31.1) WILD-TYPE 50 60 39

Figure S2.  Get High-res Image Gene #3: 'amp_4q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_4q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00806 (Fisher's exact test), Q value = 0.043

Table S3.  Gene #3: 'amp_4q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
AMP PEAK 3(4Q31.1) MUTATED 7 5 0 1
AMP PEAK 3(4Q31.1) WILD-TYPE 27 59 43 20

Figure S3.  Get High-res Image Gene #3: 'amp_4q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.3' versus 'CN_CNMF'

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

Table S4.  Gene #5: 'amp_12q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
AMP PEAK 5(12Q13.3) MUTATED 3 5 8
AMP PEAK 5(12Q13.3) WILD-TYPE 57 58 31

Figure S4.  Get High-res Image Gene #5: 'amp_12q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.14

Table S5.  Gene #5: 'amp_12q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
AMP PEAK 5(12Q13.3) MUTATED 11 4 1
AMP PEAK 5(12Q13.3) WILD-TYPE 54 54 38

Figure S5.  Get High-res Image Gene #5: 'amp_12q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_14q24.3' versus 'CN_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.096

Table S6.  Gene #6: 'amp_14q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
AMP PEAK 6(14Q24.3) MUTATED 1 3 6
AMP PEAK 6(14Q24.3) WILD-TYPE 59 60 33

Figure S6.  Get High-res Image Gene #6: 'amp_14q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0048

Table S7.  Gene #7: 'amp_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
AMP PEAK 7(17Q21.31) MUTATED 10 5 1 0
AMP PEAK 7(17Q21.31) WILD-TYPE 24 59 42 21

Figure S7.  Get High-res Image Gene #7: 'amp_17q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S8.  Gene #8: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 1(1P12) MUTATED 54 27 32
DEL PEAK 1(1P12) WILD-TYPE 6 36 7

Figure S8.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p12' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

Table S9.  Gene #8: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
DEL PEAK 1(1P12) MUTATED 24 68 21
DEL PEAK 1(1P12) WILD-TYPE 16 10 23

Figure S9.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p12' versus 'RPPA_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.1

Table S10.  Gene #8: 'del_1p12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 13 9 20 5 17 13
DEL PEAK 1(1P12) MUTATED 11 7 18 3 9 6
DEL PEAK 1(1P12) WILD-TYPE 2 2 2 2 8 7

Figure S10.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.011

Table S11.  Gene #8: 'del_1p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 18 28
DEL PEAK 1(1P12) MUTATED 15 17 22
DEL PEAK 1(1P12) WILD-TYPE 16 1 6

Figure S11.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p12' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

Table S12.  Gene #8: 'del_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 1(1P12) MUTATED 24 58 21 10
DEL PEAK 1(1P12) WILD-TYPE 9 6 23 11

Figure S12.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00059

Table S13.  Gene #8: 'del_1p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 1(1P12) MUTATED 19 58 27 9
DEL PEAK 1(1P12) WILD-TYPE 15 6 16 12

Figure S13.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p12' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0048

Table S14.  Gene #8: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 1(1P12) MUTATED 39 51 23
DEL PEAK 1(1P12) WILD-TYPE 26 7 16

Figure S14.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.07

Table S15.  Gene #8: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 1(1P12) MUTATED 41 46 12 14
DEL PEAK 1(1P12) WILD-TYPE 25 8 6 10

Figure S15.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.043

Table S16.  Gene #8: 'del_1p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
DEL PEAK 1(1P12) MUTATED 22 50 8 21 12
DEL PEAK 1(1P12) WILD-TYPE 12 8 3 14 11

Figure S16.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.066

Table S17.  Gene #8: 'del_1p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
DEL PEAK 1(1P12) MUTATED 58 34 12 9
DEL PEAK 1(1P12) WILD-TYPE 13 19 6 10

Figure S17.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q42.13' versus 'CN_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.08

Table S18.  Gene #9: 'del_1q42.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 2(1Q42.13) MUTATED 2 8 8
DEL PEAK 2(1Q42.13) WILD-TYPE 58 55 31

Figure S18.  Get High-res Image Gene #9: 'del_1q42.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q42.13' versus 'MRNASEQ_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.087

Table S19.  Gene #9: 'del_1q42.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 2(1Q42.13) MUTATED 8 3 6 1
DEL PEAK 2(1Q42.13) WILD-TYPE 25 61 38 20

Figure S19.  Get High-res Image Gene #9: 'del_1q42.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p24.1' versus 'CN_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.012

Table S20.  Gene #10: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 3(3P24.1) MUTATED 15 25 24
DEL PEAK 3(3P24.1) WILD-TYPE 45 38 15

Figure S20.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p24.1' versus 'METHLYATION_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.043

Table S21.  Gene #10: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
DEL PEAK 3(3P24.1) MUTATED 23 22 19
DEL PEAK 3(3P24.1) WILD-TYPE 17 56 25

Figure S21.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p24.1' versus 'RPPA_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.1

Table S22.  Gene #10: 'del_3p24.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 13 9 20 5 17 13
DEL PEAK 3(3P24.1) MUTATED 2 2 9 3 4 9
DEL PEAK 3(3P24.1) WILD-TYPE 11 7 11 2 13 4

Figure S22.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3p24.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00059

Table S23.  Gene #10: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 3(3P24.1) MUTATED 18 15 27 4
DEL PEAK 3(3P24.1) WILD-TYPE 15 49 17 17

Figure S23.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00049

Table S24.  Gene #10: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 3(3P24.1) MUTATED 12 17 31 4
DEL PEAK 3(3P24.1) WILD-TYPE 22 47 12 17

Figure S24.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S25.  Gene #10: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 3(3P24.1) MUTATED 39 19 6
DEL PEAK 3(3P24.1) WILD-TYPE 26 39 33

Figure S25.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0039

Table S26.  Gene #10: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 3(3P24.1) MUTATED 39 15 6 4
DEL PEAK 3(3P24.1) WILD-TYPE 27 39 12 20

Figure S26.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S27.  Gene #10: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
DEL PEAK 3(3P24.1) MUTATED 12 15 2 29 6
DEL PEAK 3(3P24.1) WILD-TYPE 22 43 9 6 17

Figure S27.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S28.  Gene #10: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
DEL PEAK 3(3P24.1) MUTATED 18 36 6 4
DEL PEAK 3(3P24.1) WILD-TYPE 53 17 12 15

Figure S28.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00035

Table S29.  Gene #11: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 4(3Q26.1) MUTATED 40 22 31
DEL PEAK 4(3Q26.1) WILD-TYPE 20 41 8

Figure S29.  Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.1' versus 'RPPA_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.08

Table S30.  Gene #11: 'del_3q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 13 9 20 5 17 13
DEL PEAK 4(3Q26.1) MUTATED 8 7 15 4 4 8
DEL PEAK 4(3Q26.1) WILD-TYPE 5 2 5 1 13 5

Figure S30.  Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3q26.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.064

Table S31.  Gene #11: 'del_3q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 18 28
DEL PEAK 4(3Q26.1) MUTATED 13 15 18
DEL PEAK 4(3Q26.1) WILD-TYPE 18 3 10

Figure S31.  Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3q26.1' versus 'MRNASEQ_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.087

Table S32.  Gene #11: 'del_3q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 4(3Q26.1) MUTATED 20 44 22 7
DEL PEAK 4(3Q26.1) WILD-TYPE 13 20 22 14

Figure S32.  Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S33.  Gene #11: 'del_3q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 4(3Q26.1) MUTATED 6 47 33 7
DEL PEAK 4(3Q26.1) WILD-TYPE 28 17 10 14

Figure S33.  Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.1' versus 'MIRSEQ_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.074

Table S34.  Gene #11: 'del_3q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 4(3Q26.1) MUTATED 39 39 15
DEL PEAK 4(3Q26.1) WILD-TYPE 26 19 24

Figure S34.  Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00941 (Fisher's exact test), Q value = 0.049

Table S35.  Gene #11: 'del_3q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 4(3Q26.1) MUTATED 39 38 5 11
DEL PEAK 4(3Q26.1) WILD-TYPE 27 16 13 13

Figure S35.  Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.053

Table S36.  Gene #11: 'del_3q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
DEL PEAK 4(3Q26.1) MUTATED 12 41 5 23 12
DEL PEAK 4(3Q26.1) WILD-TYPE 22 17 6 12 11

Figure S36.  Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.052

Table S37.  Gene #11: 'del_3q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
DEL PEAK 4(3Q26.1) MUTATED 44 36 5 8
DEL PEAK 4(3Q26.1) WILD-TYPE 27 17 13 11

Figure S37.  Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q28.3' versus 'MRNASEQ_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.076

Table S38.  Gene #12: 'del_4q28.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 5(4Q28.3) MUTATED 0 2 7 1
DEL PEAK 5(4Q28.3) WILD-TYPE 33 62 37 20

Figure S38.  Get High-res Image Gene #12: 'del_4q28.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p12.3' versus 'CN_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.052

Table S39.  Gene #14: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 7(6P12.3) MUTATED 0 5 5
DEL PEAK 7(6P12.3) WILD-TYPE 60 58 34

Figure S39.  Get High-res Image Gene #14: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p12.3' versus 'MRNASEQ_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.08

Table S40.  Gene #14: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 7(6P12.3) MUTATED 1 1 4 4
DEL PEAK 7(6P12.3) WILD-TYPE 32 63 40 17

Figure S40.  Get High-res Image Gene #14: 'del_6p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q16.1' versus 'MRNASEQ_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.091

Table S41.  Gene #15: 'del_6q16.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 8(6Q16.1) MUTATED 1 15 4 4
DEL PEAK 8(6Q16.1) WILD-TYPE 32 49 40 17

Figure S41.  Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00702 (Fisher's exact test), Q value = 0.041

Table S42.  Gene #15: 'del_6q16.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 8(6Q16.1) MUTATED 1 16 3 4
DEL PEAK 8(6Q16.1) WILD-TYPE 33 48 40 17

Figure S42.  Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q16.1' versus 'MIRSEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.066

Table S43.  Gene #15: 'del_6q16.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 8(6Q16.1) MUTATED 4 14 6
DEL PEAK 8(6Q16.1) WILD-TYPE 61 44 33

Figure S43.  Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q16.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0062 (Fisher's exact test), Q value = 0.038

Table S44.  Gene #15: 'del_6q16.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 8(6Q16.1) MUTATED 4 15 1 4
DEL PEAK 8(6Q16.1) WILD-TYPE 62 39 17 20

Figure S44.  Get High-res Image Gene #15: 'del_6q16.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p22' versus 'CN_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.012

Table S45.  Gene #16: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 9(8P22) MUTATED 10 3 12
DEL PEAK 9(8P22) WILD-TYPE 50 60 27

Figure S45.  Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p22' versus 'MRNASEQ_CNMF'

P value = 0.00668 (Fisher's exact test), Q value = 0.04

Table S46.  Gene #16: 'del_8p22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 9(8P22) MUTATED 3 18 3 1
DEL PEAK 9(8P22) WILD-TYPE 30 46 41 20

Figure S46.  Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00818 (Fisher's exact test), Q value = 0.043

Table S47.  Gene #16: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 9(8P22) MUTATED 5 17 2 1
DEL PEAK 9(8P22) WILD-TYPE 29 47 41 20

Figure S47.  Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.091

Table S48.  Gene #16: 'del_8p22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
DEL PEAK 9(8P22) MUTATED 5 16 0 3 1
DEL PEAK 9(8P22) WILD-TYPE 29 42 11 32 22

Figure S48.  Get High-res Image Gene #16: 'del_8p22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8q23.3' versus 'CN_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.1

Table S49.  Gene #17: 'del_8q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 10(8Q23.3) MUTATED 7 1 5
DEL PEAK 10(8Q23.3) WILD-TYPE 53 62 34

Figure S49.  Get High-res Image Gene #17: 'del_8q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.12' versus 'CN_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.052

Table S50.  Gene #19: 'del_9q21.12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 12(9Q21.12) MUTATED 4 2 8
DEL PEAK 12(9Q21.12) WILD-TYPE 56 61 31

Figure S50.  Get High-res Image Gene #19: 'del_9q21.12' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S51.  Gene #20: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 13(11P15.4) MUTATED 2 39 17
DEL PEAK 13(11P15.4) WILD-TYPE 58 24 22

Figure S51.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S52.  Gene #20: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
DEL PEAK 13(11P15.4) MUTATED 23 14 21
DEL PEAK 13(11P15.4) WILD-TYPE 17 64 23

Figure S52.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.4' versus 'RPPA_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.013

Table S53.  Gene #20: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 13 9 20 5 17 13
DEL PEAK 13(11P15.4) MUTATED 3 1 3 3 8 10
DEL PEAK 13(11P15.4) WILD-TYPE 10 8 17 2 9 3

Figure S53.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.4' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0048

Table S54.  Gene #20: 'del_11p15.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 13(11P15.4) MUTATED 13 13 26 6
DEL PEAK 13(11P15.4) WILD-TYPE 20 51 18 15

Figure S54.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S55.  Gene #20: 'del_11p15.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 13(11P15.4) MUTATED 11 10 31 6
DEL PEAK 13(11P15.4) WILD-TYPE 23 54 12 15

Figure S55.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0011

Table S56.  Gene #20: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 13(11P15.4) MUTATED 36 12 10
DEL PEAK 13(11P15.4) WILD-TYPE 29 46 29

Figure S56.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.4' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S57.  Gene #20: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 13(11P15.4) MUTATED 39 8 5 6
DEL PEAK 13(11P15.4) WILD-TYPE 27 46 13 18

Figure S57.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S58.  Gene #20: 'del_11p15.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
DEL PEAK 13(11P15.4) MUTATED 12 8 2 24 11
DEL PEAK 13(11P15.4) WILD-TYPE 22 50 9 11 12

Figure S58.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0039

Table S59.  Gene #20: 'del_11p15.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
DEL PEAK 13(11P15.4) MUTATED 16 31 5 5
DEL PEAK 13(11P15.4) WILD-TYPE 55 22 13 14

Figure S59.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S60.  Gene #21: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 14(11Q22.1) MUTATED 4 26 18
DEL PEAK 14(11Q22.1) WILD-TYPE 56 37 21

Figure S60.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.1' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.062

Table S61.  Gene #21: 'del_11q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 13 9 20 5 17 13
DEL PEAK 14(11Q22.1) MUTATED 4 1 5 2 9 10
DEL PEAK 14(11Q22.1) WILD-TYPE 9 8 15 3 8 3

Figure S61.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0066

Table S62.  Gene #21: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 14(11Q22.1) MUTATED 9 10 23 6
DEL PEAK 14(11Q22.1) WILD-TYPE 24 54 21 15

Figure S62.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00977 (Fisher's exact test), Q value = 0.05

Table S63.  Gene #21: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 14(11Q22.1) MUTATED 10 12 21 5
DEL PEAK 14(11Q22.1) WILD-TYPE 24 52 22 16

Figure S63.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00333 (Fisher's exact test), Q value = 0.024

Table S64.  Gene #21: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 14(11Q22.1) MUTATED 28 9 11
DEL PEAK 14(11Q22.1) WILD-TYPE 37 49 28

Figure S64.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0066

Table S65.  Gene #21: 'del_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 14(11Q22.1) MUTATED 30 8 2 8
DEL PEAK 14(11Q22.1) WILD-TYPE 36 46 16 16

Figure S65.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.004

Table S66.  Gene #21: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
DEL PEAK 14(11Q22.1) MUTATED 10 8 2 20 8
DEL PEAK 14(11Q22.1) WILD-TYPE 24 50 9 15 15

Figure S66.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.1

Table S67.  Gene #21: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
DEL PEAK 14(11Q22.1) MUTATED 17 23 2 6
DEL PEAK 14(11Q22.1) WILD-TYPE 54 30 16 13

Figure S67.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.093

Table S68.  Gene #24: 'del_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 17(16Q21) MUTATED 4 1 0 0
DEL PEAK 17(16Q21) WILD-TYPE 30 63 43 21

Figure S68.  Get High-res Image Gene #24: 'del_16q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.2' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0019

Table S69.  Gene #25: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 18(17P13.2) MUTATED 22 16 26
DEL PEAK 18(17P13.2) WILD-TYPE 38 47 13

Figure S69.  Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0048

Table S70.  Gene #25: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
DEL PEAK 18(17P13.2) MUTATED 9 43 12
DEL PEAK 18(17P13.2) WILD-TYPE 31 35 32

Figure S70.  Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.2' versus 'MRNASEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.066

Table S71.  Gene #25: 'del_17p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 18(17P13.2) MUTATED 10 35 14 5
DEL PEAK 18(17P13.2) WILD-TYPE 23 29 30 16

Figure S71.  Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00619 (Fisher's exact test), Q value = 0.038

Table S72.  Gene #25: 'del_17p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 18(17P13.2) MUTATED 10 36 13 5
DEL PEAK 18(17P13.2) WILD-TYPE 24 28 30 16

Figure S72.  Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.2' versus 'MIRSEQ_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.091

Table S73.  Gene #25: 'del_17p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 18(17P13.2) MUTATED 21 31 12
DEL PEAK 18(17P13.2) WILD-TYPE 44 27 27

Figure S73.  Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00778 (Fisher's exact test), Q value = 0.043

Table S74.  Gene #25: 'del_17p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 18(17P13.2) MUTATED 18 30 9 7
DEL PEAK 18(17P13.2) WILD-TYPE 48 24 9 17

Figure S74.  Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.072

Table S75.  Gene #25: 'del_17p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
DEL PEAK 18(17P13.2) MUTATED 36 13 9 6
DEL PEAK 18(17P13.2) WILD-TYPE 35 40 9 13

Figure S75.  Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S76.  Gene #26: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 19(17Q11.2) MUTATED 13 4 25
DEL PEAK 19(17Q11.2) WILD-TYPE 47 59 14

Figure S76.  Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00344 (Fisher's exact test), Q value = 0.024

Table S77.  Gene #26: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
DEL PEAK 19(17Q11.2) MUTATED 4 29 9
DEL PEAK 19(17Q11.2) WILD-TYPE 36 49 35

Figure S77.  Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.087

Table S78.  Gene #26: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 19(17Q11.2) MUTATED 5 25 9 3
DEL PEAK 19(17Q11.2) WILD-TYPE 28 39 35 18

Figure S78.  Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00284 (Fisher's exact test), Q value = 0.021

Table S79.  Gene #26: 'del_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 19(17Q11.2) MUTATED 6 27 6 3
DEL PEAK 19(17Q11.2) WILD-TYPE 28 37 37 18

Figure S79.  Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00022

Table S80.  Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 20(22Q13.31) MUTATED 40 9 16
DEL PEAK 20(22Q13.31) WILD-TYPE 20 54 23

Figure S80.  Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.08

Table S81.  Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
DEL PEAK 20(22Q13.31) MUTATED 11 40 14
DEL PEAK 20(22Q13.31) WILD-TYPE 29 38 30

Figure S81.  Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.077

Table S82.  Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 20(22Q13.31) MUTATED 9 35 13 8
DEL PEAK 20(22Q13.31) WILD-TYPE 24 29 31 13

Figure S82.  Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0054

Table S83.  Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 20(22Q13.31) MUTATED 13 37 8 7
DEL PEAK 20(22Q13.31) WILD-TYPE 21 27 35 14

Figure S83.  Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.053

Table S84.  Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 20(22Q13.31) MUTATED 17 29 19
DEL PEAK 20(22Q13.31) WILD-TYPE 48 29 20

Figure S84.  Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.091

Table S85.  Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 20(22Q13.31) MUTATED 18 29 7 11
DEL PEAK 20(22Q13.31) WILD-TYPE 48 25 11 13

Figure S85.  Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.07

Table S86.  Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
DEL PEAK 20(22Q13.31) MUTATED 13 33 4 8 7
DEL PEAK 20(22Q13.31) WILD-TYPE 21 25 7 27 16

Figure S86.  Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.08

Table S87.  Gene #27: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
DEL PEAK 20(22Q13.31) MUTATED 37 13 7 8
DEL PEAK 20(22Q13.31) WILD-TYPE 34 40 11 11

Figure S87.  Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0071

Table S88.  Gene #28: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 21(XP21.1) MUTATED 21 8 17
DEL PEAK 21(XP21.1) WILD-TYPE 39 55 22

Figure S88.  Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00605 (Fisher's exact test), Q value = 0.038

Table S89.  Gene #28: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
DEL PEAK 21(XP21.1) MUTATED 9 31 6
DEL PEAK 21(XP21.1) WILD-TYPE 31 47 38

Figure S89.  Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.1

Table S90.  Gene #28: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 21(XP21.1) MUTATED 10 25 9 2
DEL PEAK 21(XP21.1) WILD-TYPE 23 39 35 19

Figure S90.  Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00388 (Fisher's exact test), Q value = 0.026

Table S91.  Gene #28: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 21(XP21.1) MUTATED 7 27 11 1
DEL PEAK 21(XP21.1) WILD-TYPE 27 37 32 20

Figure S91.  Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0064

Table S92.  Gene #28: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 21(XP21.1) MUTATED 13 27 6
DEL PEAK 21(XP21.1) WILD-TYPE 52 31 33

Figure S92.  Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 0.14

Table S93.  Gene #28: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 21(XP21.1) MUTATED 15 21 7 3
DEL PEAK 21(XP21.1) WILD-TYPE 51 33 11 21

Figure S93.  Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 0.1

Table S94.  Gene #28: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
DEL PEAK 21(XP21.1) MUTATED 25 13 7 1
DEL PEAK 21(XP21.1) WILD-TYPE 46 40 11 18

Figure S94.  Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_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/PCPG-TP/15096462/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/15107813/PCPG-TP.transferedmergedcluster.txt

  • Number of patients = 162

  • Number of significantly focal cnvs = 28

  • Number of molecular subtypes = 10

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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