Correlation between copy number variation genes (focal events) and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C18G8JM3
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 31 focal events and 10 molecular subtypes across 288 patients, 100 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_2p23.2 cnv correlated to 'CN_CNMF'.

  • amp_2q32.1 cnv correlated to 'CN_CNMF'.

  • amp_3q27.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_5q35.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • amp_7q31.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q25.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_19p13.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_1p36.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_2q22.1 cnv correlated to 'MRNASEQ_CNMF'.

  • del_3p22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_5q35.2 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6p12.3 cnv correlated to 'CN_CNMF'.

  • del_6q22.31 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_6q25.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_10q21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_11q22.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_11q23.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_14q11.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_14q24.2 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_15q13.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_16q24.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • del_19p13.3 cnv correlated to 'CN_CNMF'.

  • del_19q13.42 cnv correlated to 'CN_CNMF'.

  • del_22q12.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_xp11.4 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_xq28 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 31 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, 100 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
amp 7q31 2 177 (61%) 111 1e-05
(0.0031)
1e-05
(0.0031)
0.0134
(1.00)
5e-05
(0.0121)
1e-05
(0.0031)
1e-05
(0.0031)
0.0508
(1.00)
1e-05
(0.0031)
3e-05
(0.00756)
1e-05
(0.0031)
del 9p21 3 40 (14%) 248 1e-05
(0.0031)
1e-05
(0.0031)
0.37
(1.00)
0.00073
(0.159)
1e-05
(0.0031)
1e-05
(0.0031)
0.00038
(0.0844)
0.0302
(1.00)
0.0001
(0.0233)
3e-05
(0.00756)
amp 17q25 2 201 (70%) 87 1e-05
(0.0031)
3e-05
(0.00756)
0.0804
(1.00)
0.00011
(0.0255)
1e-05
(0.0031)
1e-05
(0.0031)
0.0702
(1.00)
0.00103
(0.218)
0.00161
(0.328)
0.00105
(0.222)
del 4q34 3 32 (11%) 256 1e-05
(0.0031)
1e-05
(0.0031)
0.572
(1.00)
0.00593
(1.00)
1e-05
(0.0031)
5e-05
(0.0121)
0.423
(1.00)
0.367
(1.00)
0.00893
(1.00)
3e-05
(0.00756)
del xp11 4 34 (12%) 254 1e-05
(0.0031)
1e-05
(0.0031)
0.373
(1.00)
0.00274
(0.535)
1e-05
(0.0031)
2e-05
(0.00508)
0.704
(1.00)
0.264
(1.00)
0.00138
(0.286)
0.0004
(0.0884)
amp 3q27 1 100 (35%) 188 1e-05
(0.0031)
0.0576
(1.00)
0.256
(1.00)
0.0117
(1.00)
1e-05
(0.0031)
0.00085
(0.184)
0.0336
(1.00)
0.00019
(0.0431)
0.761
(1.00)
0.0174
(1.00)
amp 5q35 2 37 (13%) 251 1e-05
(0.0031)
0.00016
(0.0365)
0.256
(1.00)
0.321
(1.00)
0.00065
(0.142)
8e-05
(0.0188)
0.051
(1.00)
0.00537
(0.967)
0.41
(1.00)
0.0548
(1.00)
del 1p36 31 55 (19%) 233 1e-05
(0.0031)
6e-05
(0.0144)
0.662
(1.00)
0.0521
(1.00)
1e-05
(0.0031)
1e-05
(0.0031)
0.771
(1.00)
0.855
(1.00)
0.0244
(1.00)
0.00554
(0.988)
del 3p22 1 25 (9%) 263 1e-05
(0.0031)
1e-05
(0.0031)
0.472
(1.00)
0.00168
(0.339)
1e-05
(0.0031)
1e-05
(0.0031)
0.202
(1.00)
0.00572
(1.00)
0.0256
(1.00)
0.00446
(0.834)
del 5q35 2 11 (4%) 277 0.028
(1.00)
4e-05
(0.00984)
0.414
(1.00)
0.00632
(1.00)
6e-05
(0.0144)
6e-05
(0.0144)
0.00712
(1.00)
0.00301
(0.581)
0.00166
(0.337)
1e-05
(0.0031)
del 6q25 3 32 (11%) 256 1e-05
(0.0031)
0.00044
(0.0968)
0.857
(1.00)
0.104
(1.00)
1e-05
(0.0031)
6e-05
(0.0144)
0.342
(1.00)
0.743
(1.00)
0.0414
(1.00)
0.0653
(1.00)
del 10q21 1 19 (7%) 269 1e-05
(0.0031)
4e-05
(0.00984)
0.332
(1.00)
0.00408
(0.767)
8e-05
(0.0188)
0.00078
(0.169)
0.636
(1.00)
0.975
(1.00)
0.0374
(1.00)
0.00616
(1.00)
del 11q23 3 29 (10%) 259 1e-05
(0.0031)
0.00015
(0.0345)
0.418
(1.00)
0.192
(1.00)
6e-05
(0.0144)
0.00028
(0.0627)
0.323
(1.00)
0.333
(1.00)
0.00598
(1.00)
0.00513
(0.939)
del 15q13 3 35 (12%) 253 1e-05
(0.0031)
4e-05
(0.00984)
0.135
(1.00)
0.00947
(1.00)
1e-05
(0.0031)
1e-05
(0.0031)
0.0766
(1.00)
0.601
(1.00)
0.0409
(1.00)
0.0033
(0.634)
del 22q12 2 63 (22%) 225 1e-05
(0.0031)
1e-05
(0.0031)
0.742
(1.00)
0.00595
(1.00)
1e-05
(0.0031)
1e-05
(0.0031)
1
(1.00)
0.4
(1.00)
0.0379
(1.00)
0.00525
(0.95)
amp 19p13 2 31 (11%) 257 1e-05
(0.0031)
0.00816
(1.00)
0.00467
(0.864)
0.00448
(0.834)
0.0009
(0.193)
0.00096
(0.204)
0.122
(1.00)
0.564
(1.00)
0.0612
(1.00)
0.0078
(1.00)
del 6q22 31 29 (10%) 259 1e-05
(0.0031)
0.00755
(1.00)
0.96
(1.00)
0.0379
(1.00)
2e-05
(0.00508)
3e-05
(0.00756)
0.418
(1.00)
0.266
(1.00)
0.0138
(1.00)
0.0376
(1.00)
del 11q22 3 31 (11%) 257 1e-05
(0.0031)
0.00144
(0.297)
0.738
(1.00)
0.234
(1.00)
0.00015
(0.0345)
0.0002
(0.0452)
0.239
(1.00)
0.191
(1.00)
0.00281
(0.545)
0.0024
(0.475)
del 14q11 2 51 (18%) 237 1e-05
(0.0031)
0.0141
(1.00)
0.0777
(1.00)
0.00398
(0.752)
1e-05
(0.0031)
1e-05
(0.0031)
0.523
(1.00)
0.561
(1.00)
0.0238
(1.00)
0.0286
(1.00)
del 14q24 2 50 (17%) 238 1e-05
(0.0031)
0.00134
(0.279)
0.0384
(1.00)
0.00266
(0.524)
1e-05
(0.0031)
1e-05
(0.0031)
0.54
(1.00)
0.573
(1.00)
0.00657
(1.00)
0.0081
(1.00)
del 16q24 1 12 (4%) 276 0.00026
(0.0585)
4e-05
(0.00984)
0.307
(1.00)
0.548
(1.00)
0.00089
(0.191)
0.0183
(1.00)
1
(1.00)
0.054
(1.00)
0.0103
(1.00)
0.0499
(1.00)
del xq28 28 (10%) 260 1e-05
(0.0031)
0.00012
(0.0277)
0.903
(1.00)
0.078
(1.00)
1e-05
(0.0031)
0.0017
(0.342)
0.75
(1.00)
0.794
(1.00)
0.00725
(1.00)
0.00509
(0.937)
amp 2p23 2 45 (16%) 243 1e-05
(0.0031)
0.0109
(1.00)
0.804
(1.00)
0.051
(1.00)
0.66
(1.00)
0.0655
(1.00)
0.152
(1.00)
0.062
(1.00)
0.437
(1.00)
0.079
(1.00)
amp 2q32 1 53 (18%) 235 1e-05
(0.0031)
0.0645
(1.00)
0.811
(1.00)
0.0839
(1.00)
0.435
(1.00)
0.029
(1.00)
0.302
(1.00)
0.127
(1.00)
0.975
(1.00)
0.511
(1.00)
del 2q22 1 10 (3%) 278 0.0033
(0.634)
0.00552
(0.988)
0.541
(1.00)
0.313
(1.00)
0.00031
(0.0691)
0.0518
(1.00)
0.671
(1.00)
0.808
(1.00)
0.178
(1.00)
0.426
(1.00)
del 6p12 3 26 (9%) 262 1e-05
(0.0031)
0.00905
(1.00)
1
(1.00)
0.631
(1.00)
0.00133
(0.278)
0.00124
(0.26)
0.131
(1.00)
0.506
(1.00)
0.264
(1.00)
0.22
(1.00)
del 19p13 3 23 (8%) 265 1e-05
(0.0031)
0.0449
(1.00)
0.779
(1.00)
0.294
(1.00)
0.0376
(1.00)
0.00519
(0.945)
0.238
(1.00)
0.313
(1.00)
0.0873
(1.00)
0.0363
(1.00)
del 19q13 42 19 (7%) 269 3e-05
(0.00756)
0.0453
(1.00)
0.888
(1.00)
0.134
(1.00)
0.01
(1.00)
0.00273
(0.535)
0.398
(1.00)
0.304
(1.00)
0.229
(1.00)
0.346
(1.00)
del 2p12 8 (3%) 280 0.0844
(1.00)
0.122
(1.00)
0.129
(1.00)
0.103
(1.00)
0.25
(1.00)
0.238
(1.00)
0.176
(1.00)
0.283
(1.00)
0.694
(1.00)
1
(1.00)
del 2q37 3 12 (4%) 276 0.0947
(1.00)
0.00188
(0.376)
0.00727
(1.00)
0.0478
(1.00)
0.00706
(1.00)
0.0214
(1.00)
0.144
(1.00)
0.151
(1.00)
0.0455
(1.00)
0.235
(1.00)
del 5p15 33 13 (5%) 275 0.26
(1.00)
0.00233
(0.464)
0.854
(1.00)
0.0138
(1.00)
0.0198
(1.00)
0.00352
(0.669)
0.559
(1.00)
0.203
(1.00)
0.332
(1.00)
0.00159
(0.326)
'amp_2p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S1.  Gene #1: 'amp_2p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
AMP PEAK 1(2P23.2) MUTATED 2 3 14 26
AMP PEAK 1(2P23.2) WILD-TYPE 112 73 32 26

Figure S1.  Get High-res Image Gene #1: 'amp_2p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S2.  Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
AMP PEAK 2(2Q32.1) MUTATED 4 4 15 30
AMP PEAK 2(2Q32.1) WILD-TYPE 110 72 31 22

Figure S2.  Get High-res Image Gene #2: 'amp_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q27.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S3.  Gene #3: 'amp_3q27.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
AMP PEAK 3(3Q27.1) MUTATED 20 17 45 18
AMP PEAK 3(3Q27.1) WILD-TYPE 94 59 1 34

Figure S3.  Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q27.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S4.  Gene #3: 'amp_3q27.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
AMP PEAK 3(3Q27.1) MUTATED 39 48 13
AMP PEAK 3(3Q27.1) WILD-TYPE 39 66 82

Figure S4.  Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q27.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.18

Table S5.  Gene #3: 'amp_3q27.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
AMP PEAK 3(3Q27.1) MUTATED 39 39 12 10
AMP PEAK 3(3Q27.1) WILD-TYPE 86 33 32 36

Figure S5.  Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q27.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.043

Table S6.  Gene #3: 'amp_3q27.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
AMP PEAK 3(3Q27.1) MUTATED 20 18 43 19
AMP PEAK 3(3Q27.1) WILD-TYPE 35 48 38 67

Figure S6.  Get High-res Image Gene #3: 'amp_3q27.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S7.  Gene #4: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
AMP PEAK 4(5Q35.2) MUTATED 19 2 0 16
AMP PEAK 4(5Q35.2) WILD-TYPE 95 74 46 36

Figure S7.  Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.2' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.036

Table S8.  Gene #4: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
AMP PEAK 4(5Q35.2) MUTATED 11 15 4
AMP PEAK 4(5Q35.2) WILD-TYPE 52 43 99

Figure S8.  Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5q35.2' versus 'MRNASEQ_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.14

Table S9.  Gene #4: 'amp_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
AMP PEAK 4(5Q35.2) MUTATED 12 5 20
AMP PEAK 4(5Q35.2) WILD-TYPE 66 109 75

Figure S9.  Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S10.  Gene #4: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
AMP PEAK 4(5Q35.2) MUTATED 29 3 1 4
AMP PEAK 4(5Q35.2) WILD-TYPE 96 69 43 42

Figure S10.  Get High-res Image Gene #4: 'amp_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S11.  Gene #5: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
AMP PEAK 5(7Q31.2) MUTATED 32 75 43 27
AMP PEAK 5(7Q31.2) WILD-TYPE 82 1 3 25

Figure S11.  Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S12.  Gene #5: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
AMP PEAK 5(7Q31.2) MUTATED 34 19 85
AMP PEAK 5(7Q31.2) WILD-TYPE 29 39 18

Figure S12.  Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S13.  Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 17 22 29 22 27 39 25 25
AMP PEAK 5(7Q31.2) MUTATED 14 17 27 9 12 18 18 14
AMP PEAK 5(7Q31.2) WILD-TYPE 3 5 2 13 15 21 7 11

Figure S13.  Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S14.  Gene #5: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
AMP PEAK 5(7Q31.2) MUTATED 50 97 29
AMP PEAK 5(7Q31.2) WILD-TYPE 28 17 66

Figure S14.  Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S15.  Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
AMP PEAK 5(7Q31.2) MUTATED 59 68 32 17
AMP PEAK 5(7Q31.2) WILD-TYPE 66 4 12 29

Figure S15.  Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S16.  Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
AMP PEAK 5(7Q31.2) MUTATED 23 41 67 46
AMP PEAK 5(7Q31.2) WILD-TYPE 32 25 14 40

Figure S16.  Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S17.  Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
AMP PEAK 5(7Q31.2) MUTATED 33 64 35
AMP PEAK 5(7Q31.2) WILD-TYPE 36 17 36

Figure S17.  Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S18.  Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
AMP PEAK 5(7Q31.2) MUTATED 67 35 4 26
AMP PEAK 5(7Q31.2) WILD-TYPE 31 42 12 4

Figure S18.  Get High-res Image Gene #5: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S19.  Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
AMP PEAK 6(17Q25.2) MUTATED 43 76 45 37
AMP PEAK 6(17Q25.2) WILD-TYPE 71 0 1 15

Figure S19.  Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S20.  Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
AMP PEAK 6(17Q25.2) MUTATED 38 34 89
AMP PEAK 6(17Q25.2) WILD-TYPE 25 24 14

Figure S20.  Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.026

Table S21.  Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 17 22 29 22 27 39 25 25
AMP PEAK 6(17Q25.2) MUTATED 15 20 26 11 13 23 21 17
AMP PEAK 6(17Q25.2) WILD-TYPE 2 2 3 11 14 16 4 8

Figure S21.  Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S22.  Gene #6: 'amp_17q25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
AMP PEAK 6(17Q25.2) MUTATED 54 101 45
AMP PEAK 6(17Q25.2) WILD-TYPE 24 13 50

Figure S22.  Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S23.  Gene #6: 'amp_17q25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
AMP PEAK 6(17Q25.2) MUTATED 79 68 35 18
AMP PEAK 6(17Q25.2) WILD-TYPE 46 4 9 28

Figure S23.  Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.22

Table S24.  Gene #6: 'amp_17q25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 66 81 86
AMP PEAK 6(17Q25.2) MUTATED 30 46 69 56
AMP PEAK 6(17Q25.2) WILD-TYPE 25 20 12 30

Figure S24.  Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00105 (Fisher's exact test), Q value = 0.22

Table S25.  Gene #6: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
AMP PEAK 6(17Q25.2) MUTATED 72 45 7 27
AMP PEAK 6(17Q25.2) WILD-TYPE 26 32 9 3

Figure S25.  Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S26.  Gene #7: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
AMP PEAK 7(19P13.2) MUTATED 1 22 0 8
AMP PEAK 7(19P13.2) WILD-TYPE 113 54 46 44

Figure S26.  Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.19

Table S27.  Gene #7: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
AMP PEAK 7(19P13.2) MUTATED 3 22 6
AMP PEAK 7(19P13.2) WILD-TYPE 75 92 89

Figure S27.  Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.2

Table S28.  Gene #7: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
AMP PEAK 7(19P13.2) MUTATED 4 11 9 7
AMP PEAK 7(19P13.2) WILD-TYPE 121 61 35 39

Figure S28.  Get High-res Image Gene #7: 'amp_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S29.  Gene #8: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 1(1P36.31) MUTATED 21 0 2 32
DEL PEAK 1(1P36.31) WILD-TYPE 93 76 44 20

Figure S29.  Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S30.  Gene #8: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 1(1P36.31) MUTATED 11 22 9
DEL PEAK 1(1P36.31) WILD-TYPE 52 36 94

Figure S30.  Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S31.  Gene #8: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 1(1P36.31) MUTATED 11 6 38
DEL PEAK 1(1P36.31) WILD-TYPE 67 108 57

Figure S31.  Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S32.  Gene #8: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 1(1P36.31) MUTATED 29 6 1 19
DEL PEAK 1(1P36.31) WILD-TYPE 96 66 43 27

Figure S32.  Get High-res Image Gene #8: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.069

Table S33.  Gene #10: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 3(2Q22.1) MUTATED 1 0 9
DEL PEAK 3(2Q22.1) WILD-TYPE 77 114 86

Figure S33.  Get High-res Image Gene #10: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S34.  Gene #12: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 5(3P22.1) MUTATED 6 0 0 19
DEL PEAK 5(3P22.1) WILD-TYPE 108 76 46 33

Figure S34.  Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S35.  Gene #12: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 5(3P22.1) MUTATED 3 14 1
DEL PEAK 5(3P22.1) WILD-TYPE 60 44 102

Figure S35.  Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S36.  Gene #12: 'del_3p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 5(3P22.1) MUTATED 5 0 20
DEL PEAK 5(3P22.1) WILD-TYPE 73 114 75

Figure S36.  Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S37.  Gene #12: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 5(3P22.1) MUTATED 21 0 0 4
DEL PEAK 5(3P22.1) WILD-TYPE 104 72 44 42

Figure S37.  Get High-res Image Gene #12: 'del_3p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S38.  Gene #13: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 6(4Q34.3) MUTATED 8 1 1 22
DEL PEAK 6(4Q34.3) WILD-TYPE 106 75 45 30

Figure S38.  Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S39.  Gene #13: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 6(4Q34.3) MUTATED 4 20 2
DEL PEAK 6(4Q34.3) WILD-TYPE 59 38 101

Figure S39.  Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S40.  Gene #13: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 6(4Q34.3) MUTATED 4 2 26
DEL PEAK 6(4Q34.3) WILD-TYPE 74 112 69

Figure S40.  Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S41.  Gene #13: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 6(4Q34.3) MUTATED 18 1 1 12
DEL PEAK 6(4Q34.3) WILD-TYPE 107 71 43 34

Figure S41.  Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S42.  Gene #13: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
DEL PEAK 6(4Q34.3) MUTATED 7 11 8 0
DEL PEAK 6(4Q34.3) WILD-TYPE 91 66 8 30

Figure S42.  Get High-res Image Gene #13: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q35.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0098

Table S43.  Gene #15: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 8(5Q35.2) MUTATED 1 9 0
DEL PEAK 8(5Q35.2) WILD-TYPE 62 49 103

Figure S43.  Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.2' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S44.  Gene #15: 'del_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 8(5Q35.2) MUTATED 1 0 10
DEL PEAK 8(5Q35.2) WILD-TYPE 77 114 85

Figure S44.  Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S45.  Gene #15: 'del_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 8(5Q35.2) MUTATED 3 0 0 8
DEL PEAK 8(5Q35.2) WILD-TYPE 122 72 44 38

Figure S45.  Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S46.  Gene #15: 'del_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
DEL PEAK 8(5Q35.2) MUTATED 1 1 8 0
DEL PEAK 8(5Q35.2) WILD-TYPE 97 76 8 30

Figure S46.  Get High-res Image Gene #15: 'del_5q35.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S47.  Gene #16: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 9(6P12.3) MUTATED 8 0 1 17
DEL PEAK 9(6P12.3) WILD-TYPE 106 76 45 35

Figure S47.  Get High-res Image Gene #16: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S48.  Gene #17: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 10(6Q22.31) MUTATED 8 0 1 20
DEL PEAK 10(6Q22.31) WILD-TYPE 106 76 45 32

Figure S48.  Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S49.  Gene #17: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 10(6Q22.31) MUTATED 5 3 21
DEL PEAK 10(6Q22.31) WILD-TYPE 73 111 74

Figure S49.  Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S50.  Gene #17: 'del_6q22.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 10(6Q22.31) MUTATED 14 2 0 13
DEL PEAK 10(6Q22.31) WILD-TYPE 111 70 44 33

Figure S50.  Get High-res Image Gene #17: 'del_6q22.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S51.  Gene #18: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 11(6Q25.3) MUTATED 7 0 1 24
DEL PEAK 11(6Q25.3) WILD-TYPE 107 76 45 28

Figure S51.  Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q25.3' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.097

Table S52.  Gene #18: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 11(6Q25.3) MUTATED 5 14 4
DEL PEAK 11(6Q25.3) WILD-TYPE 58 44 99

Figure S52.  Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S53.  Gene #18: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 11(6Q25.3) MUTATED 6 3 23
DEL PEAK 11(6Q25.3) WILD-TYPE 72 111 72

Figure S53.  Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S54.  Gene #18: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 11(6Q25.3) MUTATED 18 2 0 12
DEL PEAK 11(6Q25.3) WILD-TYPE 107 70 44 34

Figure S54.  Get High-res Image Gene #18: 'del_6q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S55.  Gene #19: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 12(9P21.3) MUTATED 11 2 1 26
DEL PEAK 12(9P21.3) WILD-TYPE 103 74 45 26

Figure S55.  Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S56.  Gene #19: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 12(9P21.3) MUTATED 9 20 2
DEL PEAK 12(9P21.3) WILD-TYPE 54 38 101

Figure S56.  Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.16

Table S57.  Gene #19: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 17 22 29 22 27 39 25 25
DEL PEAK 12(9P21.3) MUTATED 0 3 0 5 9 3 2 7
DEL PEAK 12(9P21.3) WILD-TYPE 17 19 29 17 18 36 23 18

Figure S57.  Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S58.  Gene #19: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 12(9P21.3) MUTATED 6 2 32
DEL PEAK 12(9P21.3) WILD-TYPE 72 112 63

Figure S58.  Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S59.  Gene #19: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 12(9P21.3) MUTATED 20 0 0 20
DEL PEAK 12(9P21.3) WILD-TYPE 105 72 44 26

Figure S59.  Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.084

Table S60.  Gene #19: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 89 103 96
DEL PEAK 12(9P21.3) MUTATED 3 16 21
DEL PEAK 12(9P21.3) WILD-TYPE 86 87 75

Figure S60.  Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.023

Table S61.  Gene #19: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 81 71
DEL PEAK 12(9P21.3) MUTATED 8 4 21
DEL PEAK 12(9P21.3) WILD-TYPE 61 77 50

Figure S61.  Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S62.  Gene #19: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
DEL PEAK 12(9P21.3) MUTATED 7 19 7 0
DEL PEAK 12(9P21.3) WILD-TYPE 91 58 9 30

Figure S62.  Get High-res Image Gene #19: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S63.  Gene #20: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 13(10Q21.1) MUTATED 5 0 0 14
DEL PEAK 13(10Q21.1) WILD-TYPE 109 76 46 38

Figure S63.  Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0098

Table S64.  Gene #20: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 13(10Q21.1) MUTATED 1 12 2
DEL PEAK 13(10Q21.1) WILD-TYPE 62 46 101

Figure S64.  Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S65.  Gene #20: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 13(10Q21.1) MUTATED 3 1 15
DEL PEAK 13(10Q21.1) WILD-TYPE 75 113 80

Figure S65.  Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.17

Table S66.  Gene #20: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 13(10Q21.1) MUTATED 14 0 0 5
DEL PEAK 13(10Q21.1) WILD-TYPE 111 72 44 41

Figure S66.  Get High-res Image Gene #20: 'del_10q21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S67.  Gene #21: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 14(11Q22.3) MUTATED 8 4 1 18
DEL PEAK 14(11Q22.3) WILD-TYPE 106 72 45 34

Figure S67.  Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.034

Table S68.  Gene #21: 'del_11q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 14(11Q22.3) MUTATED 4 6 21
DEL PEAK 14(11Q22.3) WILD-TYPE 74 108 74

Figure S68.  Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.045

Table S69.  Gene #21: 'del_11q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 14(11Q22.3) MUTATED 18 0 4 9
DEL PEAK 14(11Q22.3) WILD-TYPE 107 72 40 37

Figure S69.  Get High-res Image Gene #21: 'del_11q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S70.  Gene #22: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 15(11Q23.3) MUTATED 6 4 0 19
DEL PEAK 15(11Q23.3) WILD-TYPE 108 72 46 33

Figure S70.  Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.034

Table S71.  Gene #22: 'del_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 15(11Q23.3) MUTATED 6 14 3
DEL PEAK 15(11Q23.3) WILD-TYPE 57 44 100

Figure S71.  Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.3' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S72.  Gene #22: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 15(11Q23.3) MUTATED 3 5 21
DEL PEAK 15(11Q23.3) WILD-TYPE 75 109 74

Figure S72.  Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.063

Table S73.  Gene #22: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 15(11Q23.3) MUTATED 18 0 3 8
DEL PEAK 15(11Q23.3) WILD-TYPE 107 72 41 38

Figure S73.  Get High-res Image Gene #22: 'del_11q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S74.  Gene #23: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 16(14Q11.2) MUTATED 20 1 2 28
DEL PEAK 16(14Q11.2) WILD-TYPE 94 75 44 24

Figure S74.  Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S75.  Gene #23: 'del_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 16(14Q11.2) MUTATED 13 6 32
DEL PEAK 16(14Q11.2) WILD-TYPE 65 108 63

Figure S75.  Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S76.  Gene #23: 'del_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 16(14Q11.2) MUTATED 26 2 4 19
DEL PEAK 16(14Q11.2) WILD-TYPE 99 70 40 27

Figure S76.  Get High-res Image Gene #23: 'del_14q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S77.  Gene #24: 'del_14q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 17(14Q24.2) MUTATED 21 0 1 28
DEL PEAK 17(14Q24.2) WILD-TYPE 93 76 45 24

Figure S77.  Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S78.  Gene #24: 'del_14q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 17(14Q24.2) MUTATED 11 5 34
DEL PEAK 17(14Q24.2) WILD-TYPE 67 109 61

Figure S78.  Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S79.  Gene #24: 'del_14q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 17(14Q24.2) MUTATED 26 2 3 19
DEL PEAK 17(14Q24.2) WILD-TYPE 99 70 41 27

Figure S79.  Get High-res Image Gene #24: 'del_14q24.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S80.  Gene #25: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 18(15Q13.3) MUTATED 12 0 3 20
DEL PEAK 18(15Q13.3) WILD-TYPE 102 76 43 32

Figure S80.  Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0098

Table S81.  Gene #25: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 18(15Q13.3) MUTATED 10 15 3
DEL PEAK 18(15Q13.3) WILD-TYPE 53 43 100

Figure S81.  Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S82.  Gene #25: 'del_15q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 18(15Q13.3) MUTATED 7 3 25
DEL PEAK 18(15Q13.3) WILD-TYPE 71 111 70

Figure S82.  Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S83.  Gene #25: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 18(15Q13.3) MUTATED 17 2 1 15
DEL PEAK 18(15Q13.3) WILD-TYPE 108 70 43 31

Figure S83.  Get High-res Image Gene #25: 'del_15q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.1' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.058

Table S84.  Gene #26: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 19(16Q24.1) MUTATED 4 0 0 8
DEL PEAK 19(16Q24.1) WILD-TYPE 110 76 46 44

Figure S84.  Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0098

Table S85.  Gene #26: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 19(16Q24.1) MUTATED 1 9 0
DEL PEAK 19(16Q24.1) WILD-TYPE 62 49 103

Figure S85.  Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q24.1' versus 'MRNASEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.19

Table S86.  Gene #26: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 19(16Q24.1) MUTATED 3 0 9
DEL PEAK 19(16Q24.1) WILD-TYPE 75 114 86

Figure S86.  Get High-res Image Gene #26: 'del_16q24.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S87.  Gene #27: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 20(19P13.3) MUTATED 4 4 1 14
DEL PEAK 20(19P13.3) WILD-TYPE 110 72 45 38

Figure S87.  Get High-res Image Gene #27: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.42' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S88.  Gene #28: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 21(19Q13.42) MUTATED 2 3 2 12
DEL PEAK 21(19Q13.42) WILD-TYPE 112 73 44 40

Figure S88.  Get High-res Image Gene #28: 'del_19q13.42' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S89.  Gene #29: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 22(22Q12.2) MUTATED 23 6 2 32
DEL PEAK 22(22Q12.2) WILD-TYPE 91 70 44 20

Figure S89.  Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S90.  Gene #29: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 22(22Q12.2) MUTATED 9 32 11
DEL PEAK 22(22Q12.2) WILD-TYPE 54 26 92

Figure S90.  Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S91.  Gene #29: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 22(22Q12.2) MUTATED 15 8 40
DEL PEAK 22(22Q12.2) WILD-TYPE 63 106 55

Figure S91.  Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S92.  Gene #29: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 22(22Q12.2) MUTATED 37 6 2 18
DEL PEAK 22(22Q12.2) WILD-TYPE 88 66 42 28

Figure S92.  Get High-res Image Gene #29: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S93.  Gene #30: 'del_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 23(XP11.4) MUTATED 12 1 1 20
DEL PEAK 23(XP11.4) WILD-TYPE 102 75 45 32

Figure S93.  Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.4' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S94.  Gene #30: 'del_xp11.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 23(XP11.4) MUTATED 4 18 2
DEL PEAK 23(XP11.4) WILD-TYPE 59 40 101

Figure S94.  Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.4' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S95.  Gene #30: 'del_xp11.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 23(XP11.4) MUTATED 5 3 26
DEL PEAK 23(XP11.4) WILD-TYPE 73 111 69

Figure S95.  Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp11.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0051

Table S96.  Gene #30: 'del_xp11.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 125 72 44 46
DEL PEAK 23(XP11.4) MUTATED 19 1 2 12
DEL PEAK 23(XP11.4) WILD-TYPE 106 71 42 34

Figure S96.  Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.088

Table S97.  Gene #30: 'del_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 77 16 30
DEL PEAK 23(XP11.4) MUTATED 5 16 4 0
DEL PEAK 23(XP11.4) WILD-TYPE 93 61 12 30

Figure S97.  Get High-res Image Gene #30: 'del_xp11.4' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S98.  Gene #31: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 114 76 46 52
DEL PEAK 24(XQ28) MUTATED 10 0 1 17
DEL PEAK 24(XQ28) WILD-TYPE 104 76 45 35

Figure S98.  Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq28' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.028

Table S99.  Gene #31: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 58 103
DEL PEAK 24(XQ28) MUTATED 3 13 3
DEL PEAK 24(XQ28) WILD-TYPE 60 45 100

Figure S99.  Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq28' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0031

Table S100.  Gene #31: 'del_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 114 95
DEL PEAK 24(XQ28) MUTATED 4 3 21
DEL PEAK 24(XQ28) WILD-TYPE 74 111 74

Figure S100.  Get High-res Image Gene #31: 'del_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = KIRP-TP.transferedmergedcluster.txt

  • Number of patients = 288

  • Number of significantly focal cnvs = 31

  • 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)