Correlation between copy number variation genes (focal events) and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
04 October 2018  |  None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
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 110 focal events and 3 molecular subtypes across 100 patients, 97 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1p36.33 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_1q22 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_1q32.2 cnv correlated to 'METHYLATION_CNMF'.

  • amp_2p23.3 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_2q11.1 cnv correlated to 'METHYLATION_CNMF'.

  • amp_2q13 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_3p21.31 cnv correlated to 'METHYLATION_CNMF'.

  • amp_3q26.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_3q27.1 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_4p16.3 cnv correlated to 'METHYLATION_CNMF'.

  • amp_5q35.2 cnv correlated to 'METHYLATION_CNMF'.

  • amp_7p13 cnv correlated to 'METHYLATION_CNMF'.

  • amp_8q22.3 cnv correlated to 'MRNA_CHIERARCHICAL'.

  • amp_9q34.3 cnv correlated to 'METHYLATION_CNMF'.

  • amp_10q26.13 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_11p11.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_11q13.2 cnv correlated to 'METHYLATION_CNMF'.

  • amp_11q13.3 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_12p13.33 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

  • amp_12q13.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_13q12.11 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

  • amp_14q24.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_17q12 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_17q24.1 cnv correlated to 'METHYLATION_CNMF'.

  • amp_19p13.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_19p13.11 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_19q12 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_19q13.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • amp_20q13.33 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_1p36.12 cnv correlated to 'METHYLATION_CNMF'.

  • del_1p13.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_3p26.3 cnv correlated to 'METHYLATION_CNMF'.

  • del_3p21.1 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_4p15.31 cnv correlated to 'METHYLATION_CNMF'.

  • del_4q21.21 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

  • del_5q23.1 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_6q22.31 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_8p23.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_9p24.3 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

  • del_9p24.1 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_10q11.22 cnv correlated to 'METHYLATION_CNMF'.

  • del_11p15.5 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_11p15.3 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_11q24.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_12p13.33 cnv correlated to 'METHYLATION_CNMF'.

  • del_13q12.11 cnv correlated to 'MRNA_CHIERARCHICAL' and 'METHYLATION_CNMF'.

  • del_13q31.3 cnv correlated to 'METHYLATION_CNMF'.

  • del_15q11.2 cnv correlated to 'METHYLATION_CNMF'.

  • del_15q15.1 cnv correlated to 'MRNA_CHIERARCHICAL'.

  • del_15q24.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_16p13.3 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

  • del_16p11.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_16q22.1 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_16q22.2 cnv correlated to 'METHYLATION_CNMF'.

  • del_17p11.2 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_17q21.32 cnv correlated to 'METHYLATION_CNMF'.

  • del_18q22.1 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

  • del_19p13.3 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_19q13.33 cnv correlated to 'METHYLATION_CNMF'.

  • del_xp11.23 cnv correlated to 'METHYLATION_CHIERARCHICAL'.

  • del_xp11.23 cnv correlated to 'METHYLATION_CNMF' and 'METHYLATION_CHIERARCHICAL'.

  • del_xp11.22 cnv correlated to 'METHYLATION_CNMF'.

  • del_xq24 cnv correlated to 'METHYLATION_CNMF'.

  • del_xq27.3 cnv correlated to 'METHYLATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 110 focal events and 3 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 97 significant findings detected.

Clinical
Features 		MRNA
CHIERARCHICAL 		METHYLATION
CNMF 		METHYLATION
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test
amp 1p36 33 24 (24%) 76 0.29
(0.469) 		0.0203
(0.0985) 		0.0113
(0.0621)
amp 1q22 42 (42%) 58 0.156
(0.329) 		1e-05
(0.00165) 		5e-05
(0.00236)
amp 2p23 3 27 (27%) 73 0.769
(0.852) 		0.00447
(0.0321) 		0.00367
(0.0288)
amp 2q13 27 (27%) 73 0.807
(0.873) 		0.00288
(0.0264) 		0.00238
(0.0264)
amp 3q26 2 20 (20%) 80 0.132
(0.307) 		0.00265
(0.0264) 		0.00013
(0.00536)
amp 3q27 1 27 (27%) 73 0.371
(0.556) 		3e-05
(0.0022) 		2e-05
(0.0022)
amp 10q26 13 34 (34%) 66 0.486
(0.638) 		0.0329
(0.128) 		0.0453
(0.16)
amp 11p11 2 15 (15%) 85 0.874
(0.92) 		0.00526
(0.0362) 		0.00335
(0.0278)
amp 11q13 3 19 (19%) 81 0.646
(0.764) 		0.00019
(0.00627) 		0.00447
(0.0321)
amp 12q13 2 24 (24%) 76 0.0708
(0.215) 		0.0275
(0.118) 		0.00587
(0.0395)
amp 14q24 2 15 (15%) 85 0.429
(0.593) 		0.00034
(0.00935) 		0.00738
(0.046)
amp 17q12 21 (21%) 79 0.1
(0.267) 		4e-05
(0.0022) 		0.00267
(0.0264)
amp 19p13 2 20 (20%) 80 0.6
(0.731) 		0.00281
(0.0264) 		0.00615
(0.0406)
amp 19p13 11 22 (22%) 78 0.236
(0.416) 		0.03
(0.122) 		0.0443
(0.159)
amp 19q12 18 (18%) 82 0.604
(0.733) 		0.0257
(0.113) 		0.00384
(0.0293)
amp 19q13 2 18 (18%) 82 0.962
(0.977) 		0.013
(0.0692) 		0.00346
(0.0278)
amp 20q13 33 28 (28%) 72 0.473
(0.632) 		0.00061
(0.0144) 		0.00166
(0.0211)
del 1p13 2 12 (12%) 88 0.329
(0.512) 		0.00066
(0.0145) 		0.00205
(0.0251)
del 3p21 1 13 (13%) 87 0.867
(0.92) 		0.0244
(0.11) 		0.0289
(0.122)
del 5q23 1 13 (13%) 87 0.0847
(0.237) 		0.00146
(0.0201) 		0.0469
(0.161)
del 6q22 31 9 (9%) 91 0.128
(0.305) 		4e-05
(0.0022) 		0.00707
(0.0454)
del 8p23 2 11 (11%) 89 0.136
(0.313) 		0.00045
(0.0114) 		0.00021
(0.0063)
del 9p24 1 11 (11%) 89 0.138
(0.313) 		0.00099
(0.0156) 		0.00091
(0.015)
del 11p15 5 11 (11%) 89 0.633
(0.752) 		1e-05
(0.00165) 		0.00075
(0.0145)
del 11p15 3 15 (15%) 85 0.536
(0.691) 		0.0138
(0.0725) 		0.00251
(0.0264)
del 11q24 2 14 (14%) 86 1
(1.00) 		0.00716
(0.0454) 		0.00084
(0.0146)
del 13q12 11 14 (14%) 86 0.0268
(0.116) 		0.0324
(0.128) 		0.38
(0.562)
del 15q24 2 28 (28%) 72 0.18
(0.357) 		0.0296
(0.122) 		0.0298
(0.122)
del 16p11 2 21 (21%) 79 0.249
(0.428) 		0.00391
(0.0293) 		0.0219
(0.105)
del 16q22 1 11 (11%) 89 0.466
(0.627) 		0.00335
(0.0278) 		0.0463
(0.161)
del 17p11 2 17 (17%) 83 0.283
(0.465) 		0.00079
(0.0145) 		0.00077
(0.0145)
del 19p13 3 23 (23%) 77 0.759
(0.851) 		0.00016
(0.00587) 		0.00152
(0.0201)
del xp11 23 36 (36%) 64 0.761
(0.851) 		0.039
(0.146) 		0.00966
(0.0559)
amp 1q32 2 39 (39%) 61 0.104
(0.271) 		0.00143
(0.0201) 		0.357
(0.545)
amp 2q11 1 48 (48%) 52 0.583
(0.715) 		0.0342
(0.131) 		0.11
(0.282)
amp 3p21 31 27 (27%) 73 0.437
(0.596) 		0.0096
(0.0559) 		0.0885
(0.245)
amp 4p16 3 10 (10%) 90 0.424
(0.59) 		0.0187
(0.092) 		0.186
(0.365)
amp 5q35 2 10 (10%) 90 0.538
(0.691) 		0.0156
(0.0794) 		0.14
(0.313)
amp 7p13 29 (29%) 71 0.401
(0.576) 		0.00315
(0.0278) 		0.0971
(0.263)
amp 8q22 3 27 (27%) 73 0.00773
(0.0472) 		0.314
(0.495) 		0.654
(0.768)
amp 9q34 3 13 (13%) 87 0.404
(0.576) 		0.0255
(0.113) 		0.495
(0.648)
amp 11q13 2 22 (22%) 78 0.92
(0.954) 		0.00982
(0.0559) 		0.0548
(0.185)
amp 12p13 33 37 (37%) 63 0.664
(0.773) 		0.236
(0.416) 		0.0436
(0.159)
amp 13q12 11 14 (14%) 86 0.168
(0.341) 		0.335
(0.517) 		0.00113
(0.0169)
amp 17q24 1 18 (18%) 82 0.176
(0.353) 		0.0376
(0.143) 		0.172
(0.345)
del 1p36 12 16 (16%) 84 0.732
(0.827) 		0.00921
(0.0553) 		0.0771
(0.224)
del 3p26 3 15 (15%) 85 0.404
(0.576) 		0.0222
(0.105) 		0.071
(0.215)
del 4p15 31 13 (13%) 87 0.13
(0.306) 		0.0325
(0.128) 		0.0633
(0.201)
del 4q21 21 24 (24%) 76 0.203
(0.384) 		0.165
(0.336) 		0.0437
(0.159)
del 9p24 3 15 (15%) 85 0.571
(0.705) 		0.141
(0.313) 		0.0046
(0.0323)
del 10q11 22 6 (6%) 94 0.944
(0.973) 		0.0227
(0.105) 		0.369
(0.556)
del 12p13 33 4 (4%) 96 1
(1.00) 		0.016
(0.08) 		0.189
(0.368)
del 13q31 3 11 (11%) 89 0.82
(0.881) 		0.0233
(0.107) 		0.105
(0.273)
del 15q11 2 20 (20%) 80 0.221
(0.402) 		0.00288
(0.0264) 		0.157
(0.329)
del 15q15 1 26 (26%) 74 0.0106
(0.0593) 		0.211
(0.391) 		0.412
(0.578)
del 16p13 3 9 (9%) 91 0.797
(0.868) 		0.157
(0.329) 		0.044
(0.159)
del 16q22 2 16 (16%) 84 0.968
(0.98) 		0.0146
(0.0753) 		0.227
(0.407)
del 17q21 32 10 (10%) 90 0.546
(0.695) 		0.00266
(0.0264) 		0.162
(0.335)
del 18q22 1 16 (16%) 84 0.476
(0.632) 		0.0772
(0.224) 		0.0455
(0.16)
del 19q13 33 13 (13%) 87 1
(1.00) 		0.00268
(0.0264) 		0.309
(0.491)
del xp11 23 47 (47%) 53 0.303
(0.485) 		0.125
(0.304) 		0.0302
(0.122)
del xp11 22 29 (29%) 71 0.666
(0.773) 		0.0127
(0.0689) 		0.0796
(0.228)
del xq24 32 (32%) 68 0.132
(0.307) 		0.0493
(0.168) 		0.0819
(0.231)
del xq27 3 34 (34%) 66 0.415
(0.58) 		0.00337
(0.0278) 		0.0566
(0.187)
amp 1p36 13 14 (14%) 86 0.954
(0.973) 		0.444
(0.603) 		0.304
(0.485)
amp 6p21 32 44 (44%) 56 0.922
(0.954) 		0.119
(0.292) 		0.184
(0.364)
amp 6q25 1 17 (17%) 83 0.223
(0.404) 		0.374
(0.556) 		0.691
(0.797)
amp 7q11 23 35 (35%) 65 0.405
(0.576) 		0.155
(0.329) 		0.613
(0.741)
amp 7q22 1 32 (32%) 68 0.162
(0.335) 		0.064
(0.201) 		0.251
(0.429)
amp 9p24 3 38 (38%) 62 0.072
(0.216) 		0.102
(0.269) 		0.463
(0.627)
amp 10q23 2 30 (30%) 70 0.765
(0.852) 		0.8
(0.868) 		0.513
(0.669)
amp 11p15 2 5 (5%) 95 0.237
(0.416) 		0.114
(0.288) 		0.261
(0.44)
amp 12q24 31 21 (21%) 79 0.288
(0.468) 		0.0611
(0.198) 		0.119
(0.292)
amp 15q24 2 16 (16%) 84 0.429
(0.593) 		0.116
(0.29) 		0.391
(0.57)
amp 15q26 3 35 (35%) 65 0.622
(0.745) 		0.572
(0.705) 		0.623
(0.745)
amp 16p11 2 31 (31%) 69 0.0986
(0.264) 		0.14
(0.313) 		0.0619
(0.198)
amp 16q22 2 19 (19%) 81 0.954
(0.973) 		0.196
(0.374) 		0.359
(0.545)
amp 18p11 31 20 (20%) 80 0.0938
(0.256) 		0.253
(0.431) 		0.406
(0.576)
amp 22q13 2 19 (19%) 81 0.954
(0.973) 		0.219
(0.401) 		0.432
(0.594)
amp xp11 23 22 (22%) 78 0.769
(0.852) 		0.272
(0.451) 		0.531
(0.69)
amp xp11 23 31 (31%) 69 0.324
(0.507) 		0.56
(0.703) 		0.241
(0.416)
amp xq24 32 (32%) 68 0.874
(0.92) 		0.783
(0.862) 		0.206
(0.385)
amp xq28 40 (40%) 60 0.108
(0.279) 		0.469
(0.628) 		0.811
(0.875)
del 1p36 32 11 (11%) 89 0.759
(0.851) 		0.149
(0.322) 		0.477
(0.632)
del 1q32 2 13 (13%) 87 0.723
(0.822) 		0.559
(0.703) 		0.21
(0.391)
del 2q31 2 9 (9%) 91 0.862
(0.92) 		0.871
(0.92) 		0.292
(0.47)
del 3p12 2 22 (22%) 78 0.259
(0.438) 		0.485
(0.638) 		0.627
(0.747)
del 3q25 1 6 (6%) 94 0.697
(0.8) 		0.569
(0.705) 		0.145
(0.316)
del 3q25 33 5 (5%) 95 0.402
(0.576) 		0.0576
(0.188) 		0.164
(0.336)
del 4q13 2 25 (25%) 75 0.0566
(0.187) 		0.0702
(0.215) 		0.0811
(0.231)
del 7p22 1 9 (9%) 91 0.571
(0.705) 		0.317
(0.498) 		0.239
(0.416)
del 7q11 21 16 (16%) 84 0.65
(0.767) 		0.267
(0.447) 		0.789
(0.865)
del 7q11 23 6 (6%) 94 0.347
(0.533) 		0.875
(0.92) 		0.838
(0.898)
del 7q22 1 11 (11%) 89 0.798
(0.868) 		0.138
(0.313) 		0.237
(0.416)
del 7q22 1 7 (7%) 93 0.698
(0.8) 		0.396
(0.575) 		0.215
(0.397)
del 9q21 32 30 (30%) 70 0.332
(0.515) 		0.0648
(0.202) 		0.14
(0.313)
del 10q25 3 13 (13%) 87 0.0742
(0.219) 		0.0902
(0.248) 		0.126
(0.304)
del 11p11 12 17 (17%) 83 0.618
(0.744) 		0.144
(0.316) 		0.546
(0.695)
del 12p11 23 10 (10%) 90 0.538
(0.691) 		0.204
(0.384) 		0.196
(0.374)
del 12q21 32 18 (18%) 82 0.919
(0.954) 		0.196
(0.374) 		0.373
(0.556)
del 13q12 11 16 (16%) 84 0.41
(0.578) 		0.597
(0.73) 		0.274
(0.452)
del 14q32 31 20 (20%) 80 0.556
(0.703) 		0.227
(0.407) 		0.126
(0.304)
del 15q26 3 15 (15%) 85 0.286
(0.467) 		0.24
(0.416) 		0.39
(0.57)
del 16p13 3 24 (24%) 76 0.189
(0.368) 		0.658
(0.77) 		0.155
(0.329)
del 17q24 1 11 (11%) 89 0.901
(0.941) 		0.385
(0.567) 		0.37
(0.556)
del 19p13 2 17 (17%) 83 0.956
(0.973) 		0.129
(0.306) 		0.725
(0.822)
del 19p12 29 (29%) 71 0.985
(0.994) 		0.783
(0.862) 		0.548
(0.695)
del 20p13 9 (9%) 91 0.703
(0.802) 		0.115
(0.29) 		0.0738
(0.219)
del 20q13 13 6 (6%) 94 0.569
(0.705) 		0.686
(0.794) 		0.272
(0.451)
del 22q13 2 22 (22%) 78 0.887
(0.93) 		0.437
(0.596) 		0.147
(0.32)
'amp_1p36.33' versus 'METHYLATION_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.099

Table S1.  Gene #1: 'amp_1p36.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 1(1P36.33) MUTATED 6 5 8 5
AMP PEAK 1(1P36.33) WILD-TYPE 29 28 8 7

Figure S1.  Get High-res Image Gene #1: 'amp_1p36.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_1p36.33' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.062

Table S2.  Gene #1: 'amp_1p36.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 1(1P36.33) MUTATED 7 4 5 3 0 1 4
AMP PEAK 1(1P36.33) WILD-TYPE 27 7 4 4 6 19 5

Figure S2.  Get High-res Image Gene #1: 'amp_1p36.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_1q22' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S3.  Gene #3: 'amp_1q22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 3(1Q22) MUTATED 5 11 13 10
AMP PEAK 3(1Q22) WILD-TYPE 30 22 3 2

Figure S3.  Get High-res Image Gene #3: 'amp_1q22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_1q22' versus 'METHYLATION_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0024

Table S4.  Gene #3: 'amp_1q22' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 3(1Q22) MUTATED 9 9 2 6 6 5 2
AMP PEAK 3(1Q22) WILD-TYPE 25 2 7 1 0 15 7

Figure S4.  Get High-res Image Gene #3: 'amp_1q22' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_1q32.2' versus 'METHYLATION_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.02

Table S5.  Gene #4: 'amp_1q32.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 4(1Q32.2) MUTATED 10 8 8 10
AMP PEAK 4(1Q32.2) WILD-TYPE 25 25 8 2

Figure S5.  Get High-res Image Gene #4: 'amp_1q32.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_2p23.3' versus 'METHYLATION_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.032

Table S6.  Gene #5: 'amp_2p23.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 5(2P23.3) MUTATED 5 7 10 3
AMP PEAK 5(2P23.3) WILD-TYPE 30 26 6 9

Figure S6.  Get High-res Image Gene #5: 'amp_2p23.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_2p23.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00367 (Fisher's exact test), Q value = 0.029

Table S7.  Gene #5: 'amp_2p23.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 5(2P23.3) MUTATED 7 7 2 5 0 3 1
AMP PEAK 5(2P23.3) WILD-TYPE 27 4 7 2 6 17 8

Figure S7.  Get High-res Image Gene #5: 'amp_2p23.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_2q11.1' versus 'METHYLATION_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.13

Table S8.  Gene #6: 'amp_2q11.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 6(2Q11.1) MUTATED 11 20 11 6
AMP PEAK 6(2Q11.1) WILD-TYPE 24 13 5 6

Figure S8.  Get High-res Image Gene #6: 'amp_2q11.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_2q13' versus 'METHYLATION_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.026

Table S9.  Gene #7: 'amp_2q13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 7(2Q13) MUTATED 5 6 10 3
AMP PEAK 7(2Q13) WILD-TYPE 30 27 6 9

Figure S9.  Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_2q13' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00238 (Fisher's exact test), Q value = 0.026

Table S10.  Gene #7: 'amp_2q13' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 7(2Q13) MUTATED 6 7 2 5 0 3 1
AMP PEAK 7(2Q13) WILD-TYPE 28 4 7 2 6 17 8

Figure S10.  Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_3p21.31' versus 'METHYLATION_CNMF'

P value = 0.0096 (Fisher's exact test), Q value = 0.056

Table S11.  Gene #8: 'amp_3p21.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 8(3P21.31) MUTATED 7 6 10 3
AMP PEAK 8(3P21.31) WILD-TYPE 28 27 6 9

Figure S11.  Get High-res Image Gene #8: 'amp_3p21.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_3q26.2' versus 'METHYLATION_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.026

Table S12.  Gene #9: 'amp_3q26.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 9(3Q26.2) MUTATED 2 6 8 1
AMP PEAK 9(3Q26.2) WILD-TYPE 33 27 8 11

Figure S12.  Get High-res Image Gene #9: 'amp_3q26.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_3q26.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0054

Table S13.  Gene #9: 'amp_3q26.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 9(3Q26.2) MUTATED 4 8 0 3 0 2 0
AMP PEAK 9(3Q26.2) WILD-TYPE 30 3 9 4 6 18 9

Figure S13.  Get High-res Image Gene #9: 'amp_3q26.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_3q27.1' versus 'METHYLATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0022

Table S14.  Gene #10: 'amp_3q27.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 10(3Q27.1) MUTATED 3 7 12 2
AMP PEAK 10(3Q27.1) WILD-TYPE 32 26 4 10

Figure S14.  Get High-res Image Gene #10: 'amp_3q27.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_3q27.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S15.  Gene #10: 'amp_3q27.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 10(3Q27.1) MUTATED 6 9 0 5 1 2 1
AMP PEAK 10(3Q27.1) WILD-TYPE 28 2 9 2 5 18 8

Figure S15.  Get High-res Image Gene #10: 'amp_3q27.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_4p16.3' versus 'METHYLATION_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.092

Table S16.  Gene #11: 'amp_4p16.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 11(4P16.3) MUTATED 3 1 5 0
AMP PEAK 11(4P16.3) WILD-TYPE 32 32 11 12

Figure S16.  Get High-res Image Gene #11: 'amp_4p16.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_5q35.2' versus 'METHYLATION_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.079

Table S17.  Gene #12: 'amp_5q35.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 12(5Q35.2) MUTATED 1 3 5 0
AMP PEAK 12(5Q35.2) WILD-TYPE 34 30 11 12

Figure S17.  Get High-res Image Gene #12: 'amp_5q35.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_7p13' versus 'METHYLATION_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.028

Table S18.  Gene #15: 'amp_7p13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 15(7P13) MUTATED 8 6 11 3
AMP PEAK 15(7P13) WILD-TYPE 27 27 5 9

Figure S18.  Get High-res Image Gene #15: 'amp_7p13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_8q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00773 (Fisher's exact test), Q value = 0.047

Table S19.  Gene #18: 'amp_8q22.3' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
AMP PEAK 18(8Q22.3) MUTATED 10 2 0 10 5
AMP PEAK 18(8Q22.3) WILD-TYPE 18 18 11 10 16

Figure S19.  Get High-res Image Gene #18: 'amp_8q22.3' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'amp_9q34.3' versus 'METHYLATION_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.11

Table S20.  Gene #20: 'amp_9q34.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 20(9Q34.3) MUTATED 4 3 6 0
AMP PEAK 20(9Q34.3) WILD-TYPE 31 30 10 12

Figure S20.  Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_10q26.13' versus 'METHYLATION_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.13

Table S21.  Gene #22: 'amp_10q26.13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 22(10Q26.13) MUTATED 7 11 10 4
AMP PEAK 22(10Q26.13) WILD-TYPE 28 22 6 8

Figure S21.  Get High-res Image Gene #22: 'amp_10q26.13' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_10q26.13' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0453 (Fisher's exact test), Q value = 0.16

Table S22.  Gene #22: 'amp_10q26.13' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 22(10Q26.13) MUTATED 6 5 4 5 1 6 5
AMP PEAK 22(10Q26.13) WILD-TYPE 28 6 5 2 5 14 4

Figure S22.  Get High-res Image Gene #22: 'amp_10q26.13' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_11p11.2' versus 'METHYLATION_CNMF'

P value = 0.00526 (Fisher's exact test), Q value = 0.036

Table S23.  Gene #24: 'amp_11p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 24(11P11.2) MUTATED 3 3 7 0
AMP PEAK 24(11P11.2) WILD-TYPE 32 30 9 12

Figure S23.  Get High-res Image Gene #24: 'amp_11p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_11p11.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.028

Table S24.  Gene #24: 'amp_11p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 24(11P11.2) MUTATED 4 5 0 3 0 0 1
AMP PEAK 24(11P11.2) WILD-TYPE 30 6 9 4 6 20 8

Figure S24.  Get High-res Image Gene #24: 'amp_11p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_11q13.2' versus 'METHYLATION_CNMF'

P value = 0.00982 (Fisher's exact test), Q value = 0.056

Table S25.  Gene #25: 'amp_11q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 25(11Q13.2) MUTATED 7 3 8 1
AMP PEAK 25(11Q13.2) WILD-TYPE 28 30 8 11

Figure S25.  Get High-res Image Gene #25: 'amp_11q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_11q13.3' versus 'METHYLATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0063

Table S26.  Gene #26: 'amp_11q13.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 26(11Q13.3) MUTATED 6 2 9 0
AMP PEAK 26(11Q13.3) WILD-TYPE 29 31 7 12

Figure S26.  Get High-res Image Gene #26: 'amp_11q13.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_11q13.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00447 (Fisher's exact test), Q value = 0.032

Table S27.  Gene #26: 'amp_11q13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 26(11Q13.3) MUTATED 8 5 0 3 0 0 1
AMP PEAK 26(11Q13.3) WILD-TYPE 26 6 9 4 6 20 8

Figure S27.  Get High-res Image Gene #26: 'amp_11q13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_12p13.33' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0436 (Fisher's exact test), Q value = 0.16

Table S28.  Gene #27: 'amp_12p13.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 27(12P13.33) MUTATED 15 8 3 1 2 3 4
AMP PEAK 27(12P13.33) WILD-TYPE 19 3 6 6 4 17 5

Figure S28.  Get High-res Image Gene #27: 'amp_12p13.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_12q13.2' versus 'METHYLATION_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.12

Table S29.  Gene #28: 'amp_12q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 28(12Q13.2) MUTATED 4 8 8 2
AMP PEAK 28(12Q13.2) WILD-TYPE 31 25 8 10

Figure S29.  Get High-res Image Gene #28: 'amp_12q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_12q13.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00587 (Fisher's exact test), Q value = 0.04

Table S30.  Gene #28: 'amp_12q13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 28(12Q13.2) MUTATED 5 7 1 4 0 4 1
AMP PEAK 28(12Q13.2) WILD-TYPE 29 4 8 3 6 16 8

Figure S30.  Get High-res Image Gene #28: 'amp_12q13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_13q12.11' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00113 (Fisher's exact test), Q value = 0.017

Table S31.  Gene #30: 'amp_13q12.11' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 30(13Q12.11) MUTATED 0 2 4 2 0 5 0
AMP PEAK 30(13Q12.11) WILD-TYPE 34 9 5 5 6 15 9

Figure S31.  Get High-res Image Gene #30: 'amp_13q12.11' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_14q24.2' versus 'METHYLATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0093

Table S32.  Gene #31: 'amp_14q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 31(14Q24.2) MUTATED 2 2 8 1
AMP PEAK 31(14Q24.2) WILD-TYPE 33 31 8 11

Figure S32.  Get High-res Image Gene #31: 'amp_14q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_14q24.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00738 (Fisher's exact test), Q value = 0.046

Table S33.  Gene #31: 'amp_14q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 31(14Q24.2) MUTATED 4 3 0 4 1 0 1
AMP PEAK 31(14Q24.2) WILD-TYPE 30 8 9 3 5 20 8

Figure S33.  Get High-res Image Gene #31: 'amp_14q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_17q12' versus 'METHYLATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0022

Table S34.  Gene #36: 'amp_17q12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 36(17Q12) MUTATED 1 5 10 2
AMP PEAK 36(17Q12) WILD-TYPE 34 28 6 10

Figure S34.  Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_17q12' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.026

Table S35.  Gene #36: 'amp_17q12' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 36(17Q12) MUTATED 3 5 1 5 1 2 1
AMP PEAK 36(17Q12) WILD-TYPE 31 6 8 2 5 18 8

Figure S35.  Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_17q24.1' versus 'METHYLATION_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.14

Table S36.  Gene #37: 'amp_17q24.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 37(17Q24.1) MUTATED 2 6 5 4
AMP PEAK 37(17Q24.1) WILD-TYPE 33 27 11 8

Figure S36.  Get High-res Image Gene #37: 'amp_17q24.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_19p13.2' versus 'METHYLATION_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.026

Table S37.  Gene #39: 'amp_19p13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 39(19P13.2) MUTATED 4 5 9 1
AMP PEAK 39(19P13.2) WILD-TYPE 31 28 7 11

Figure S37.  Get High-res Image Gene #39: 'amp_19p13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_19p13.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00615 (Fisher's exact test), Q value = 0.041

Table S38.  Gene #39: 'amp_19p13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 39(19P13.2) MUTATED 5 6 0 4 1 2 1
AMP PEAK 39(19P13.2) WILD-TYPE 29 5 9 3 5 18 8

Figure S38.  Get High-res Image Gene #39: 'amp_19p13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_19p13.11' versus 'METHYLATION_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.12

Table S39.  Gene #40: 'amp_19p13.11' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 40(19P13.11) MUTATED 5 7 8 1
AMP PEAK 40(19P13.11) WILD-TYPE 30 26 8 11

Figure S39.  Get High-res Image Gene #40: 'amp_19p13.11' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_19p13.11' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0443 (Fisher's exact test), Q value = 0.16

Table S40.  Gene #40: 'amp_19p13.11' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 40(19P13.11) MUTATED 7 6 0 3 0 4 1
AMP PEAK 40(19P13.11) WILD-TYPE 27 5 9 4 6 16 8

Figure S40.  Get High-res Image Gene #40: 'amp_19p13.11' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_19q12' versus 'METHYLATION_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.11

Table S41.  Gene #41: 'amp_19q12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 41(19Q12) MUTATED 3 7 6 0
AMP PEAK 41(19Q12) WILD-TYPE 32 26 10 12

Figure S41.  Get High-res Image Gene #41: 'amp_19q12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_19q12' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.029

Table S42.  Gene #41: 'amp_19q12' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 41(19Q12) MUTATED 3 7 0 1 0 4 1
AMP PEAK 41(19Q12) WILD-TYPE 31 4 9 6 6 16 8

Figure S42.  Get High-res Image Gene #41: 'amp_19q12' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_19q13.2' versus 'METHYLATION_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.069

Table S43.  Gene #42: 'amp_19q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 42(19Q13.2) MUTATED 4 5 8 1
AMP PEAK 42(19Q13.2) WILD-TYPE 31 28 8 11

Figure S43.  Get High-res Image Gene #42: 'amp_19q13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_19q13.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00346 (Fisher's exact test), Q value = 0.028

Table S44.  Gene #42: 'amp_19q13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 42(19Q13.2) MUTATED 4 6 0 3 1 1 3
AMP PEAK 42(19Q13.2) WILD-TYPE 30 5 9 4 5 19 6

Figure S44.  Get High-res Image Gene #42: 'amp_19q13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'amp_20q13.33' versus 'METHYLATION_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.014

Table S45.  Gene #43: 'amp_20q13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AMP PEAK 43(20Q13.33) MUTATED 6 7 11 1
AMP PEAK 43(20Q13.33) WILD-TYPE 29 26 5 11

Figure S45.  Get High-res Image Gene #43: 'amp_20q13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'amp_20q13.33' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.021

Table S46.  Gene #43: 'amp_20q13.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AMP PEAK 43(20Q13.33) MUTATED 8 8 1 4 0 2 2
AMP PEAK 43(20Q13.33) WILD-TYPE 26 3 8 3 6 18 7

Figure S46.  Get High-res Image Gene #43: 'amp_20q13.33' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_1p36.12' versus 'METHYLATION_CNMF'

P value = 0.00921 (Fisher's exact test), Q value = 0.055

Table S47.  Gene #50: 'del_1p36.12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 2(1P36.12) MUTATED 4 2 7 1
DEL PEAK 2(1P36.12) WILD-TYPE 31 31 9 11

Figure S47.  Get High-res Image Gene #50: 'del_1p36.12' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_1p13.2' versus 'METHYLATION_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.014

Table S48.  Gene #51: 'del_1p13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 3(1P13.2) MUTATED 2 1 7 2
DEL PEAK 3(1P13.2) WILD-TYPE 33 32 9 10

Figure S48.  Get High-res Image Gene #51: 'del_1p13.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_1p13.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00205 (Fisher's exact test), Q value = 0.025

Table S49.  Gene #51: 'del_1p13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 3(1P13.2) MUTATED 3 5 1 3 0 0 0
DEL PEAK 3(1P13.2) WILD-TYPE 31 6 8 4 6 20 9

Figure S49.  Get High-res Image Gene #51: 'del_1p13.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_3p26.3' versus 'METHYLATION_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.1

Table S50.  Gene #54: 'del_3p26.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 7(3P26.3) MUTATED 3 2 6 2
DEL PEAK 7(3P26.3) WILD-TYPE 32 31 10 10

Figure S50.  Get High-res Image Gene #54: 'del_3p26.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_3p21.1' versus 'METHYLATION_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.11

Table S51.  Gene #55: 'del_3p21.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 8(3P21.1) MUTATED 3 2 6 1
DEL PEAK 8(3P21.1) WILD-TYPE 32 31 10 11

Figure S51.  Get High-res Image Gene #55: 'del_3p21.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_3p21.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.12

Table S52.  Gene #55: 'del_3p21.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 8(3P21.1) MUTATED 4 5 1 1 0 0 1
DEL PEAK 8(3P21.1) WILD-TYPE 30 6 8 6 6 20 8

Figure S52.  Get High-res Image Gene #55: 'del_3p21.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_4p15.31' versus 'METHYLATION_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.13

Table S53.  Gene #59: 'del_4p15.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 12(4P15.31) MUTATED 3 1 5 1
DEL PEAK 12(4P15.31) WILD-TYPE 32 32 11 11

Figure S53.  Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_4q21.21' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.16

Table S54.  Gene #61: 'del_4q21.21' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 14(4Q21.21) MUTATED 8 7 0 1 1 4 1
DEL PEAK 14(4Q21.21) WILD-TYPE 26 4 9 6 5 16 8

Figure S54.  Get High-res Image Gene #61: 'del_4q21.21' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_5q23.1' versus 'METHYLATION_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.02

Table S55.  Gene #62: 'del_5q23.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 15(5Q23.1) MUTATED 4 0 6 1
DEL PEAK 15(5Q23.1) WILD-TYPE 31 33 10 11

Figure S55.  Get High-res Image Gene #62: 'del_5q23.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_5q23.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.16

Table S56.  Gene #62: 'del_5q23.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 15(5Q23.1) MUTATED 4 4 2 1 0 0 0
DEL PEAK 15(5Q23.1) WILD-TYPE 30 7 7 6 6 20 9

Figure S56.  Get High-res Image Gene #62: 'del_5q23.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_6q22.31' versus 'METHYLATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0022

Table S57.  Gene #63: 'del_6q22.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 16(6Q22.31) MUTATED 0 0 6 2
DEL PEAK 16(6Q22.31) WILD-TYPE 35 33 10 10

Figure S57.  Get High-res Image Gene #63: 'del_6q22.31' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_6q22.31' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00707 (Fisher's exact test), Q value = 0.045

Table S58.  Gene #63: 'del_6q22.31' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 16(6Q22.31) MUTATED 1 4 2 1 0 0 0
DEL PEAK 16(6Q22.31) WILD-TYPE 33 7 7 6 6 20 9

Figure S58.  Get High-res Image Gene #63: 'del_6q22.31' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_8p23.2' versus 'METHYLATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.011

Table S59.  Gene #69: 'del_8p23.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 22(8P23.2) MUTATED 1 3 7 0
DEL PEAK 22(8P23.2) WILD-TYPE 34 30 9 12

Figure S59.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_8p23.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0063

Table S60.  Gene #69: 'del_8p23.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 22(8P23.2) MUTATED 2 7 0 1 0 1 0
DEL PEAK 22(8P23.2) WILD-TYPE 32 4 9 6 6 19 9

Figure S60.  Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_9p24.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.032

Table S61.  Gene #70: 'del_9p24.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 23(9P24.3) MUTATED 2 5 2 1 2 0 1
DEL PEAK 23(9P24.3) WILD-TYPE 32 6 7 6 4 20 8

Figure S61.  Get High-res Image Gene #70: 'del_9p24.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_9p24.1' versus 'METHYLATION_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.016

Table S62.  Gene #71: 'del_9p24.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 24(9P24.1) MUTATED 1 1 6 1
DEL PEAK 24(9P24.1) WILD-TYPE 34 32 10 11

Figure S62.  Get High-res Image Gene #71: 'del_9p24.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_9p24.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.015

Table S63.  Gene #71: 'del_9p24.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 24(9P24.1) MUTATED 1 5 1 2 0 0 0
DEL PEAK 24(9P24.1) WILD-TYPE 33 6 8 5 6 20 9

Figure S63.  Get High-res Image Gene #71: 'del_9p24.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_10q11.22' versus 'METHYLATION_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.11

Table S64.  Gene #73: 'del_10q11.22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 26(10Q11.22) MUTATED 1 0 3 0
DEL PEAK 26(10Q11.22) WILD-TYPE 34 33 13 12

Figure S64.  Get High-res Image Gene #73: 'del_10q11.22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_11p15.5' versus 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S65.  Gene #75: 'del_11p15.5' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 28(11P15.5) MUTATED 0 1 7 1
DEL PEAK 28(11P15.5) WILD-TYPE 35 32 9 11

Figure S65.  Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_11p15.5' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.014

Table S66.  Gene #75: 'del_11p15.5' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 28(11P15.5) MUTATED 1 5 1 2 0 0 0
DEL PEAK 28(11P15.5) WILD-TYPE 33 6 8 5 6 20 9

Figure S66.  Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_11p15.3' versus 'METHYLATION_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.072

Table S67.  Gene #76: 'del_11p15.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 29(11P15.3) MUTATED 2 4 6 0
DEL PEAK 29(11P15.3) WILD-TYPE 33 29 10 12

Figure S67.  Get High-res Image Gene #76: 'del_11p15.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_11p15.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.026

Table S68.  Gene #76: 'del_11p15.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 29(11P15.3) MUTATED 2 6 0 2 0 1 1
DEL PEAK 29(11P15.3) WILD-TYPE 32 5 9 5 6 19 8

Figure S68.  Get High-res Image Gene #76: 'del_11p15.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_11q24.2' versus 'METHYLATION_CNMF'

P value = 0.00716 (Fisher's exact test), Q value = 0.045

Table S69.  Gene #78: 'del_11q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 31(11Q24.2) MUTATED 4 3 7 0
DEL PEAK 31(11Q24.2) WILD-TYPE 31 30 9 12

Figure S69.  Get High-res Image Gene #78: 'del_11q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_11q24.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.015

Table S70.  Gene #78: 'del_11q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 31(11Q24.2) MUTATED 4 6 0 3 0 0 1
DEL PEAK 31(11Q24.2) WILD-TYPE 30 5 9 4 6 20 8

Figure S70.  Get High-res Image Gene #78: 'del_11q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_12p13.33' versus 'METHYLATION_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.08

Table S71.  Gene #79: 'del_12p13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 32(12P13.33) MUTATED 0 1 3 0
DEL PEAK 32(12P13.33) WILD-TYPE 35 32 13 12

Figure S71.  Get High-res Image Gene #79: 'del_12p13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_13q12.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.12

Table S72.  Gene #83: 'del_13q12.11' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DEL PEAK 36(13Q12.11) MUTATED 4 0 1 7 2
DEL PEAK 36(13Q12.11) WILD-TYPE 24 20 10 13 19

Figure S72.  Get High-res Image Gene #83: 'del_13q12.11' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_13q12.11' versus 'METHYLATION_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.13

Table S73.  Gene #83: 'del_13q12.11' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 36(13Q12.11) MUTATED 6 1 5 1
DEL PEAK 36(13Q12.11) WILD-TYPE 29 32 11 11

Figure S73.  Get High-res Image Gene #83: 'del_13q12.11' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_13q31.3' versus 'METHYLATION_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.11

Table S74.  Gene #84: 'del_13q31.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 37(13Q31.3) MUTATED 4 0 4 1
DEL PEAK 37(13Q31.3) WILD-TYPE 31 33 12 11

Figure S74.  Get High-res Image Gene #84: 'del_13q31.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_15q11.2' versus 'METHYLATION_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.026

Table S75.  Gene #86: 'del_15q11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 39(15Q11.2) MUTATED 6 2 8 1
DEL PEAK 39(15Q11.2) WILD-TYPE 29 31 8 11

Figure S75.  Get High-res Image Gene #86: 'del_15q11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_15q15.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.059

Table S76.  Gene #87: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DEL PEAK 40(15Q15.1) MUTATED 11 6 2 0 7
DEL PEAK 40(15Q15.1) WILD-TYPE 17 14 9 20 14

Figure S76.  Get High-res Image Gene #87: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'del_15q24.2' versus 'METHYLATION_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.12

Table S77.  Gene #88: 'del_15q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 41(15Q24.2) MUTATED 11 4 8 2
DEL PEAK 41(15Q24.2) WILD-TYPE 24 29 8 10

Figure S77.  Get High-res Image Gene #88: 'del_15q24.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_15q24.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.12

Table S78.  Gene #88: 'del_15q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 41(15Q24.2) MUTATED 10 4 4 4 0 1 2
DEL PEAK 41(15Q24.2) WILD-TYPE 24 7 5 3 6 19 7

Figure S78.  Get High-res Image Gene #88: 'del_15q24.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_16p13.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.16

Table S79.  Gene #91: 'del_16p13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 44(16P13.3) MUTATED 1 4 0 0 0 2 0
DEL PEAK 44(16P13.3) WILD-TYPE 33 7 9 7 6 18 9

Figure S79.  Get High-res Image Gene #91: 'del_16p13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_16p11.2' versus 'METHYLATION_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.029

Table S80.  Gene #92: 'del_16p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 45(16P11.2) MUTATED 14 2 3 1
DEL PEAK 45(16P11.2) WILD-TYPE 21 31 13 11

Figure S80.  Get High-res Image Gene #92: 'del_16p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_16p11.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.1

Table S81.  Gene #92: 'del_16p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 45(16P11.2) MUTATED 14 2 1 1 1 1 0
DEL PEAK 45(16P11.2) WILD-TYPE 20 9 8 6 5 19 9

Figure S81.  Get High-res Image Gene #92: 'del_16p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_16q22.1' versus 'METHYLATION_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.028

Table S82.  Gene #93: 'del_16q22.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 46(16Q22.1) MUTATED 3 1 6 0
DEL PEAK 46(16Q22.1) WILD-TYPE 32 32 10 12

Figure S82.  Get High-res Image Gene #93: 'del_16q22.1' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_16q22.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.16

Table S83.  Gene #93: 'del_16q22.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 46(16Q22.1) MUTATED 3 3 0 3 0 1 0
DEL PEAK 46(16Q22.1) WILD-TYPE 31 8 9 4 6 19 9

Figure S83.  Get High-res Image Gene #93: 'del_16q22.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_16q22.2' versus 'METHYLATION_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.075

Table S84.  Gene #94: 'del_16q22.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 47(16Q22.2) MUTATED 6 2 6 0
DEL PEAK 47(16Q22.2) WILD-TYPE 29 31 10 12

Figure S84.  Get High-res Image Gene #94: 'del_16q22.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_17p11.2' versus 'METHYLATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.014

Table S85.  Gene #95: 'del_17p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 48(17P11.2) MUTATED 2 6 8 0
DEL PEAK 48(17P11.2) WILD-TYPE 33 27 8 12

Figure S85.  Get High-res Image Gene #95: 'del_17p11.2' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_17p11.2' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.014

Table S86.  Gene #95: 'del_17p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 48(17P11.2) MUTATED 3 7 0 3 0 2 1
DEL PEAK 48(17P11.2) WILD-TYPE 31 4 9 4 6 18 8

Figure S86.  Get High-res Image Gene #95: 'del_17p11.2' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_17q21.32' versus 'METHYLATION_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.026

Table S87.  Gene #96: 'del_17q21.32' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 49(17Q21.32) MUTATED 3 0 5 0
DEL PEAK 49(17Q21.32) WILD-TYPE 32 33 11 12

Figure S87.  Get High-res Image Gene #96: 'del_17q21.32' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_18q22.1' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.16

Table S88.  Gene #98: 'del_18q22.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 51(18Q22.1) MUTATED 5 5 2 2 0 1 0
DEL PEAK 51(18Q22.1) WILD-TYPE 29 6 7 5 6 19 9

Figure S88.  Get High-res Image Gene #98: 'del_18q22.1' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_19p13.3' versus 'METHYLATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0059

Table S89.  Gene #99: 'del_19p13.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 52(19P13.3) MUTATED 3 8 10 0
DEL PEAK 52(19P13.3) WILD-TYPE 32 25 6 12

Figure S89.  Get High-res Image Gene #99: 'del_19p13.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_19p13.3' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00152 (Fisher's exact test), Q value = 0.02

Table S90.  Gene #99: 'del_19p13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 52(19P13.3) MUTATED 4 7 0 4 0 4 2
DEL PEAK 52(19P13.3) WILD-TYPE 30 4 9 3 6 16 7

Figure S90.  Get High-res Image Gene #99: 'del_19p13.3' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_19q13.33' versus 'METHYLATION_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.026

Table S91.  Gene #102: 'del_19q13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 55(19Q13.33) MUTATED 3 2 7 0
DEL PEAK 55(19Q13.33) WILD-TYPE 32 31 9 12

Figure S91.  Get High-res Image Gene #102: 'del_19q13.33' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_xp11.23' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.12

Table S92.  Gene #106: 'del_xp11.23' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 59(XP11.23) MUTATED 19 9 3 5 1 6 3
DEL PEAK 59(XP11.23) WILD-TYPE 15 2 6 2 5 14 6

Figure S92.  Get High-res Image Gene #106: 'del_xp11.23' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_xp11.23' versus 'METHYLATION_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.15

Table S93.  Gene #107: 'del_xp11.23' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 60(XP11.23) MUTATED 9 15 8 1
DEL PEAK 60(XP11.23) WILD-TYPE 26 18 8 11

Figure S93.  Get High-res Image Gene #107: 'del_xp11.23' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_xp11.23' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00966 (Fisher's exact test), Q value = 0.056

Table S94.  Gene #107: 'del_xp11.23' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DEL PEAK 60(XP11.23) MUTATED 10 9 1 3 0 7 3
DEL PEAK 60(XP11.23) WILD-TYPE 24 2 8 4 6 13 6

Figure S94.  Get High-res Image Gene #107: 'del_xp11.23' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'del_xp11.22' versus 'METHYLATION_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.069

Table S95.  Gene #108: 'del_xp11.22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 61(XP11.22) MUTATED 16 5 6 1
DEL PEAK 61(XP11.22) WILD-TYPE 19 28 10 11

Figure S95.  Get High-res Image Gene #108: 'del_xp11.22' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_xq24' versus 'METHYLATION_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 0.17

Table S96.  Gene #109: 'del_xq24' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 62(XQ24) MUTATED 9 10 9 1
DEL PEAK 62(XQ24) WILD-TYPE 26 23 7 11

Figure S96.  Get High-res Image Gene #109: 'del_xq24' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'del_xq27.3' versus 'METHYLATION_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.028

Table S97.  Gene #110: 'del_xq27.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DEL PEAK 63(XQ27.3) MUTATED 10 8 11 1
DEL PEAK 63(XQ27.3) WILD-TYPE 25 25 5 11

Figure S97.  Get High-res Image Gene #110: 'del_xq27.3' versus Molecular Subtype #2: 'METHYLATION_CNMF'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /cromwell_root/fc-8b2df640-93e1-40a2-b735-5b7a14ef6398/b8d03c5a-e1ed-4426-8834-af3b0ae152b6/correlate_genomic_events_all/b3a721d9-347a-4708-9fd3-f2507378733d/call-preprocess_genomic_event/transformed.cor.cli.txt

  • Molecular subtype file = /cromwell_root/fc-8b2df640-93e1-40a2-b735-5b7a14ef6398/10d02b45-07ea-40cc-ac82-013e5f89ebb2/aggregate_clusters_workflow/b0f8dcb2-0993-4424-ad42-552c0bd1a2d5/call-aggregate_clusters/CPTAC3-UCEC-TP.transposedmergedcluster.txt

  • Number of patients = 100

  • Number of significantly focal cnvs = 110

  • Number of molecular subtypes = 3

  • 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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