Correlation between copy number variations of arm-level result and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C14747WS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C14747WS
Overview
Introduction

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

Summary

Testing the association between copy number variation 51 arm-level results and 10 molecular subtypes across 220 patients, 66 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'MRNASEQ_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • 10p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 1p loss cnv correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 1q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 4p loss cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 4q loss cnv correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • 14q loss cnv correlated to 'METHLYATION_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 22q loss 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 51 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 66 significant findings detected.

Molecular
subtypes 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test
1p loss 0 (0%) 153 0.00361
(1.00) 		8.75e-06
(0.0036) 		4.56e-47
(2.03e-44) 		6.37e-49
(2.84e-46) 		1.61e-24
(7.07e-22) 		1.37e-30
(6.07e-28) 		3.3e-14
(1.42e-11) 		5.67e-07
(0.000238) 		9.54e-07
(0.000398) 		9.66e-09
(4.1e-06)
19q loss 0 (0%) 144 0.247
(1.00) 		0.0112
(1.00) 		1.4e-45
(6.22e-43) 		7.86e-38
(3.48e-35) 		9.57e-22
(4.19e-19) 		4.5e-27
(1.99e-24) 		4.75e-13
(2.04e-10) 		7.33e-07
(0.000306) 		2.87e-07
(0.000121) 		9.09e-09
(3.86e-06)
7p gain 0 (0%) 183 0.175
(1.00) 		0.653
(1.00) 		1.86e-17
(8.06e-15) 		5.3e-11
(2.26e-08) 		8.17e-12
(3.49e-09) 		0.000204
(0.0793) 		1.93e-05
(0.00783) 		0.00221
(0.796) 		0.000435
(0.167) 		0.000263
(0.102)
4p loss 0 (0%) 205 0.415
(1.00) 		0.0907
(1.00) 		0.000882
(0.333) 		6.87e-05
(0.0275) 		0.000108
(0.0425) 		0.000418
(0.161) 		1.41e-05
(0.00579) 		0.397
(1.00) 		8.05e-05
(0.0321) 		0.0697
(1.00)
10p loss 0 (0%) 189 0.271
(1.00) 		0.561
(1.00) 		2.3e-17
(9.96e-15) 		1.19e-22
(5.24e-20) 		4.79e-19
(2.08e-16) 		0.0016
(0.587) 		0.0111
(1.00) 		0.00172
(0.627) 		9.88e-07
(0.000411) 		0.000409
(0.157)
7q gain 0 (0%) 169 0.282
(1.00) 		0.382
(1.00) 		6.78e-15
(2.92e-12) 		1.22e-09
(5.2e-07) 		6.56e-08
(2.78e-05) 		0.00139
(0.511) 		0.000112
(0.0442) 		0.0586
(1.00) 		0.00116
(0.431) 		0.0113
(1.00)
10q loss 0 (0%) 188 0.271
(1.00) 		0.561
(1.00) 		3.46e-16
(1.5e-13) 		1.78e-21
(7.77e-19) 		3.81e-20
(1.66e-17) 		0.00109
(0.41) 		0.00793
(1.00) 		0.00468
(1.00) 		1.86e-06
(0.000768) 		0.00111
(0.416)
19q gain 0 (0%) 211 0.00034
(0.131) 		0.000539
(0.206) 		0.000336
(0.13) 		0.0217
(1.00) 		0.0422
(1.00) 		0.104
(1.00) 		0.278
(1.00) 		0.0546
(1.00)
20p gain 0 (0%) 203 1.66e-05
(0.00681) 		0.000127
(0.0498) 		1.7e-05
(0.00694) 		0.259
(1.00) 		0.0123
(1.00) 		0.162
(1.00) 		0.554
(1.00) 		0.0378
(1.00)
20q gain 0 (0%) 204 8.04e-05
(0.0321) 		4.28e-05
(0.0172) 		7.35e-08
(3.1e-05) 		0.0252
(1.00) 		0.000833
(0.316) 		0.0198
(1.00) 		0.314
(1.00) 		0.00493
(1.00)
1q loss 0 (0%) 211 0.0889
(1.00) 		0.0202
(1.00) 		8.38e-05
(0.0333) 		1.9e-05
(0.00775) 		0.00603
(1.00) 		0.00013
(0.0511) 		0.00694
(1.00) 		0.506
(1.00) 		0.00175
(0.635) 		0.123
(1.00)
4q loss 0 (0%) 196 0.839
(1.00) 		0.404
(1.00) 		0.0049
(1.00) 		0.000168
(0.0657) 		0.002
(0.721) 		0.00355
(1.00) 		1.16e-06
(0.000481) 		0.0589
(1.00) 		0.000136
(0.0532) 		0.0311
(1.00)
22q loss 0 (0%) 205 1
(1.00) 		0.0879
(1.00) 		7.15e-06
(0.00295) 		9.74e-05
(0.0386) 		1.92e-05
(0.00779) 		0.0451
(1.00) 		0.293
(1.00) 		0.29
(1.00) 		0.0556
(1.00) 		0.227
(1.00)
10p gain 0 (0%) 199 6.41e-07
(0.000269) 		1.13e-05
(0.00466) 		0.0175
(1.00) 		0.094
(1.00) 		0.873
(1.00) 		0.921
(1.00) 		0.265
(1.00) 		1
(1.00)
19p gain 0 (0%) 209 2.25e-05
(0.00911) 		4.84e-05
(0.0194) 		0.00122
(0.453) 		0.0102
(1.00) 		0.0218
(1.00) 		0.0177
(1.00) 		0.264
(1.00) 		0.00704
(1.00)
1p gain 0 (0%) 214 0.0272
(1.00) 		0.0878
(1.00) 		3.39e-05
(0.0136) 		0.103
(1.00) 		0.391
(1.00) 		0.114
(1.00) 		0.155
(1.00) 		0.747
(1.00)
14q loss 0 (0%) 196 0.00111
(0.416) 		0.000494
(0.189) 		0.00126
(0.467) 		0.452
(1.00) 		0.0696
(1.00) 		0.112
(1.00) 		0.008
(1.00) 		0.44
(1.00)
1q gain 0 (0%) 212 0.00126
(0.467) 		0.0896
(1.00) 		0.0312
(1.00) 		0.618
(1.00) 		0.918
(1.00) 		0.368
(1.00) 		0.563
(1.00) 		1
(1.00)
6p gain 0 (0%) 216 0.213
(1.00) 		0.31
(1.00) 		0.0517
(1.00) 		0.279
(1.00) 		0.157
(1.00) 		0.681
(1.00) 		0.232
(1.00) 		0.674
(1.00)
8p gain 0 (0%) 206 0.0337
(1.00) 		0.229
(1.00) 		0.606
(1.00) 		0.464
(1.00) 		0.0461
(1.00) 		0.372
(1.00) 		0.453
(1.00) 		0.411
(1.00)
8q gain 0 (0%) 203 0.00467
(1.00) 		0.0611
(1.00) 		0.377
(1.00) 		0.203
(1.00) 		0.0606
(1.00) 		0.339
(1.00) 		0.537
(1.00) 		0.315
(1.00)
9p gain 0 (0%) 216 0.213
(1.00) 		0.635
(1.00) 		0.0715
(1.00) 		1
(1.00) 		1
(1.00) 		0.119
(1.00) 		0.791
(1.00) 		0.413
(1.00)
9q gain 0 (0%) 214 0.0272
(1.00) 		0.244
(1.00) 		0.00231
(0.826) 		0.519
(1.00) 		0.794
(1.00) 		0.276
(1.00) 		0.437
(1.00) 		0.15
(1.00)
11p gain 0 (0%) 211 0.5
(1.00) 		0.147
(1.00) 		0.00395
(1.00) 		0.00261
(0.922) 		0.179
(1.00) 		0.424
(1.00) 		0.772
(1.00) 		0.641
(1.00)
11q gain 0 (0%) 206 0.353
(1.00) 		0.299
(1.00) 		0.172
(1.00) 		0.107
(1.00) 		0.759
(1.00) 		0.372
(1.00) 		0.71
(1.00) 		0.739
(1.00)
12p gain 0 (0%) 209 0.0368
(1.00) 		0.112
(1.00) 		0.286
(1.00) 		0.17
(1.00) 		0.0994
(1.00) 		0.042
(1.00) 		0.405
(1.00) 		0.0363
(1.00)
12q gain 0 (0%) 215 0.848
(1.00) 		0.662
(1.00) 		0.934
(1.00) 		0.346
(1.00) 		0.0533
(1.00) 		0.118
(1.00) 		0.346
(1.00) 		0.111
(1.00)
18p gain 0 (0%) 216 0.213
(1.00) 		0.635
(1.00) 		0.569
(1.00) 		0.279
(1.00) 		0.469
(1.00) 		0.173
(1.00) 		0.479
(1.00) 		1
(1.00)
21q gain 0 (0%) 217 0.328
(1.00) 		0.443
(1.00) 		0.158
(1.00) 		0.0879
(1.00) 		1
(1.00) 		1
(1.00) 		0.0864
(1.00) 		1
(1.00)
2p loss 0 (0%) 216 0.825
(1.00) 		1
(1.00) 		0.464
(1.00) 		0.37
(1.00) 		0.339
(1.00) 		0.0404
(1.00) 		0.285
(1.00) 		0.674
(1.00)
2q loss 0 (0%) 217 0.796
(1.00) 		1
(1.00) 		0.513
(1.00) 		0.259
(1.00) 		0.0258
(1.00) 		1
(1.00) 		0.0649
(1.00) 		1
(1.00)
3p loss 0 (0%) 216 0.553
(1.00) 		0.635
(1.00) 		0.356
(1.00) 		0.279
(1.00) 		0.2
(1.00) 		0.681
(1.00) 		0.232
(1.00) 		0.674
(1.00)
3q loss 0 (0%) 211 0.175
(1.00) 		0.561
(1.00) 		0.128
(1.00) 		0.164
(1.00) 		0.547
(1.00) 		0.453
(1.00) 		0.869
(1.00) 		1
(1.00) 		0.698
(1.00) 		1
(1.00)
5p loss 0 (0%) 209 1
(1.00) 		0.0138
(1.00) 		0.0162
(1.00) 		0.0197
(1.00) 		0.847
(1.00) 		0.36
(1.00) 		0.0379
(1.00) 		0.349
(1.00) 		0.596
(1.00) 		0.688
(1.00)
5q loss 0 (0%) 211 0.615
(1.00) 		0.00137
(0.503) 		0.0453
(1.00) 		0.0671
(1.00) 		0.0439
(1.00) 		0.0217
(1.00) 		0.00244
(0.867) 		0.171
(1.00) 		0.0128
(1.00) 		0.641
(1.00)
6p loss 0 (0%) 213 0.12
(1.00) 		0.0264
(1.00) 		0.139
(1.00) 		1
(1.00) 		0.501
(1.00) 		0.106
(1.00) 		0.886
(1.00) 		0.0111
(1.00)
6q loss 0 (0%) 199 0.00431
(1.00) 		0.0232
(1.00) 		0.362
(1.00) 		0.332
(1.00) 		0.206
(1.00) 		0.337
(1.00) 		0.048
(1.00) 		0.0797
(1.00)
8p loss 0 (0%) 217 0.17
(1.00) 		0.216
(1.00) 		0.571
(1.00) 		1
(1.00) 		0.0258
(1.00) 		1
(1.00) 		0.753
(1.00) 		1
(1.00)
9p loss 0 (0%) 182 0.384
(1.00) 		0.27
(1.00) 		0.00289
(1.00) 		0.125
(1.00) 		0.692
(1.00) 		0.245
(1.00) 		0.672
(1.00) 		0.947
(1.00) 		0.492
(1.00) 		0.609
(1.00)
9q loss 0 (0%) 214 0.0702
(1.00) 		0.0342
(1.00) 		0.0111
(1.00) 		0.000882
(0.333) 		0.00498
(1.00) 		0.531
(1.00) 		0.298
(1.00) 		0.199
(1.00)
11p loss 0 (0%) 200 0.815
(1.00) 		0.106
(1.00) 		0.00199
(0.721) 		0.000876
(0.332) 		0.0162
(1.00) 		0.00897
(1.00) 		0.00579
(1.00) 		0.359
(1.00) 		0.0445
(1.00) 		0.539
(1.00)
11q loss 0 (0%) 216 0.00243
(0.863) 		0.233
(1.00) 		0.00187
(0.678) 		0.279
(1.00) 		0.633
(1.00) 		0.0404
(1.00) 		0.507
(1.00) 		0.674
(1.00)
12q loss 0 (0%) 212 0.0444
(1.00) 		0.192
(1.00) 		0.686
(1.00) 		0.618
(1.00) 		0.116
(1.00) 		1
(1.00) 		0.0932
(1.00) 		0.595
(1.00)
13q loss 0 (0%) 192 1
(1.00) 		0.0138
(1.00) 		0.635
(1.00) 		0.0922
(1.00) 		0.86
(1.00) 		0.537
(1.00) 		0.722
(1.00) 		0.617
(1.00) 		0.36
(1.00) 		0.592
(1.00)
15q loss 0 (0%) 208 0.00582
(1.00) 		0.00224
(0.805) 		0.000977
(0.367) 		0.00504
(1.00) 		0.497
(1.00) 		1
(1.00) 		0.913
(1.00) 		0.848
(1.00)
16q loss 0 (0%) 214 0.662
(1.00) 		0.0878
(1.00) 		0.302
(1.00) 		0.519
(1.00) 		0.713
(1.00) 		0.755
(1.00) 		0.367
(1.00) 		0.747
(1.00)
18p loss 0 (0%) 205 0.344
(1.00) 		0.212
(1.00) 		0.144
(1.00) 		0.0405
(1.00) 		0.119
(1.00) 		0.117
(1.00) 		0.0756
(1.00) 		0.125
(1.00) 		0.0489
(1.00) 		0.27
(1.00)
18q loss 0 (0%) 204 0.0889
(1.00) 		0.0468
(1.00) 		0.00296
(1.00) 		0.00295
(1.00) 		0.0024
(0.856) 		0.0264
(1.00) 		0.109
(1.00) 		0.236
(1.00) 		0.0243
(1.00) 		0.458
(1.00)
19p loss 0 (0%) 210 0.302
(1.00) 		0.0636
(1.00) 		0.0618
(1.00) 		0.0892
(1.00) 		0.0747
(1.00) 		0.0204
(1.00) 		0.0278
(1.00) 		0.834
(1.00) 		0.00532
(1.00) 		0.826
(1.00)
21q loss 0 (0%) 212 0.588
(1.00) 		0.577
(1.00) 		0.46
(1.00) 		0.618
(1.00) 		0.0647
(1.00) 		0.00928
(1.00) 		0.628
(1.00) 		0.461
(1.00)
Xq loss 0 (0%) 214 0.132
(1.00) 		0.28
(1.00) 		0.698
(1.00) 		0.103
(1.00) 		0.0468
(1.00) 		0.383
(1.00) 		0.521
(1.00) 		0.363
(1.00)
'1p gain' versus 'MRNASEQ_CNMF'

P value = 3.39e-05 (Chi-square test), Q value = 0.014

Table S1.  Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
1P GAIN CNV 0 6 0 0 0
1P GAIN WILD-TYPE 60 36 35 70 11

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1.86e-17 (Fisher's exact test), Q value = 8.1e-15

Table S2.  Gene #4: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
7P GAIN CNV 5 30 2
7P GAIN WILD-TYPE 89 20 74

Figure S2.  Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 5.3e-11 (Fisher's exact test), Q value = 2.3e-08

Table S3.  Gene #4: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
7P GAIN CNV 12 21 1 2
7P GAIN WILD-TYPE 86 13 27 53

Figure S3.  Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 8.17e-12 (Chi-square test), Q value = 3.5e-09

Table S4.  Gene #4: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
7P GAIN CNV 10 23 2 2 0
7P GAIN WILD-TYPE 50 19 33 68 11

Figure S4.  Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.079

Table S5.  Gene #4: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 117 69
7P GAIN CNV 2 31 4
7P GAIN WILD-TYPE 30 86 65

Figure S5.  Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0078

Table S6.  Gene #4: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 32 82 47
7P GAIN CNV 17 1 5 14
7P GAIN WILD-TYPE 41 31 77 33

Figure S6.  Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000435 (Chi-square test), Q value = 0.17

Table S7.  Gene #4: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 27 70 33 30 20
7P GAIN CNV 13 2 4 8 9 1
7P GAIN WILD-TYPE 26 25 66 25 21 19

Figure S7.  Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000263 (Fisher's exact test), Q value = 0.1

Table S8.  Gene #4: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 116 96
7P GAIN CNV 4 26 7
7P GAIN WILD-TYPE 3 90 89

Figure S8.  Get High-res Image Gene #4: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 6.78e-15 (Fisher's exact test), Q value = 2.9e-12

Table S9.  Gene #5: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
7Q GAIN CNV 10 34 7
7Q GAIN WILD-TYPE 84 16 69

Figure S9.  Get High-res Image Gene #5: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1.22e-09 (Fisher's exact test), Q value = 5.2e-07

Table S10.  Gene #5: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
7Q GAIN CNV 20 23 1 6
7Q GAIN WILD-TYPE 78 11 27 49

Figure S10.  Get High-res Image Gene #5: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 6.56e-08 (Chi-square test), Q value = 2.8e-05

Table S11.  Gene #5: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
7Q GAIN CNV 17 23 4 6 0
7Q GAIN WILD-TYPE 43 19 31 64 11

Figure S11.  Get High-res Image Gene #5: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.000112 (Fisher's exact test), Q value = 0.044

Table S12.  Gene #5: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 32 82 47
7Q GAIN CNV 19 2 11 19
7Q GAIN WILD-TYPE 39 30 71 28

Figure S12.  Get High-res Image Gene #5: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 6.41e-07 (Fisher's exact test), Q value = 0.00027

Table S13.  Gene #10: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
10P GAIN CNV 20 0 1
10P GAIN WILD-TYPE 74 50 75

Figure S13.  Get High-res Image Gene #10: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0047

Table S14.  Gene #10: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
10P GAIN CNV 20 0 1 0
10P GAIN WILD-TYPE 78 34 27 55

Figure S14.  Get High-res Image Gene #10: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.0091

Table S15.  Gene #16: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
19P GAIN CNV 2 9 0
19P GAIN WILD-TYPE 92 41 76

Figure S15.  Get High-res Image Gene #16: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 4.84e-05 (Fisher's exact test), Q value = 0.019

Table S16.  Gene #16: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
19P GAIN CNV 3 8 0 0
19P GAIN WILD-TYPE 95 26 28 55

Figure S16.  Get High-res Image Gene #16: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.13

Table S17.  Gene #17: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
19Q GAIN CNV 2 7 0
19Q GAIN WILD-TYPE 92 43 76

Figure S17.  Get High-res Image Gene #17: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.000539 (Fisher's exact test), Q value = 0.21

Table S18.  Gene #17: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
19Q GAIN CNV 2 6 0 0
19Q GAIN WILD-TYPE 96 28 28 55

Figure S18.  Get High-res Image Gene #17: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.000336 (Chi-square test), Q value = 0.13

Table S19.  Gene #17: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
19Q GAIN CNV 1 7 0 1 0
19Q GAIN WILD-TYPE 59 35 35 69 11

Figure S19.  Get High-res Image Gene #17: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.0068

Table S20.  Gene #18: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
20P GAIN CNV 4 12 1
20P GAIN WILD-TYPE 90 38 75

Figure S20.  Get High-res Image Gene #18: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.05

Table S21.  Gene #18: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
20P GAIN CNV 5 10 1 1
20P GAIN WILD-TYPE 93 24 27 54

Figure S21.  Get High-res Image Gene #18: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1.7e-05 (Chi-square test), Q value = 0.0069

Table S22.  Gene #18: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
20P GAIN CNV 2 11 1 2 0
20P GAIN WILD-TYPE 58 31 34 68 11

Figure S22.  Get High-res Image Gene #18: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 8.04e-05 (Fisher's exact test), Q value = 0.032

Table S23.  Gene #19: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
20Q GAIN CNV 4 11 1
20Q GAIN WILD-TYPE 90 39 75

Figure S23.  Get High-res Image Gene #19: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 4.28e-05 (Fisher's exact test), Q value = 0.017

Table S24.  Gene #19: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
20Q GAIN CNV 5 10 0 1
20Q GAIN WILD-TYPE 93 24 28 54

Figure S24.  Get High-res Image Gene #19: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 7.35e-08 (Chi-square test), Q value = 3.1e-05

Table S25.  Gene #19: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
20Q GAIN CNV 2 12 1 0 0
20Q GAIN WILD-TYPE 58 30 34 70 11

Figure S25.  Get High-res Image Gene #19: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 8.75e-06 (Fisher's exact test), Q value = 0.0036

Table S26.  Gene #21: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 6 10 4
1P LOSS CNV 7 2 0 0
1P LOSS WILD-TYPE 0 4 10 4

Figure S26.  Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 4.56e-47 (Fisher's exact test), Q value = 2e-44

Table S27.  Gene #21: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
1P LOSS CNV 0 0 67
1P LOSS WILD-TYPE 94 50 9

Figure S27.  Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 6.37e-49 (Fisher's exact test), Q value = 2.8e-46

Table S28.  Gene #21: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
1P LOSS CNV 0 0 9 55
1P LOSS WILD-TYPE 98 34 19 0

Figure S28.  Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1.61e-24 (Chi-square test), Q value = 7.1e-22

Table S29.  Gene #21: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
1P LOSS CNV 0 0 33 31 3
1P LOSS WILD-TYPE 60 42 2 39 8

Figure S29.  Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-30 (Fisher's exact test), Q value = 6.1e-28

Table S30.  Gene #21: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 117 69
1P LOSS CNV 32 4 31
1P LOSS WILD-TYPE 0 113 38

Figure S30.  Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 3.3e-14 (Fisher's exact test), Q value = 1.4e-11

Table S31.  Gene #21: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 32 82 47
1P LOSS CNV 6 21 39 1
1P LOSS WILD-TYPE 52 11 43 46

Figure S31.  Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.67e-07 (Fisher's exact test), Q value = 0.00024

Table S32.  Gene #21: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 95 116
1P LOSS CNV 3 46 18
1P LOSS WILD-TYPE 5 49 98

Figure S32.  Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.54e-07 (Chi-square test), Q value = 4e-04

Table S33.  Gene #21: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 27 70 33 30 20
1P LOSS CNV 3 14 31 13 0 6
1P LOSS WILD-TYPE 36 13 39 20 30 14

Figure S33.  Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.66e-09 (Fisher's exact test), Q value = 4.1e-06

Table S34.  Gene #21: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 116 96
1P LOSS CNV 2 16 49
1P LOSS WILD-TYPE 5 100 47

Figure S34.  Get High-res Image Gene #21: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 8.38e-05 (Fisher's exact test), Q value = 0.033

Table S35.  Gene #22: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
1Q LOSS CNV 0 0 9
1Q LOSS WILD-TYPE 94 50 67

Figure S35.  Get High-res Image Gene #22: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 1.9e-05 (Fisher's exact test), Q value = 0.0077

Table S36.  Gene #22: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
1Q LOSS CNV 0 0 0 9
1Q LOSS WILD-TYPE 98 34 28 46

Figure S36.  Get High-res Image Gene #22: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.051

Table S37.  Gene #22: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 117 69
1Q LOSS CNV 5 0 4
1Q LOSS WILD-TYPE 27 117 65

Figure S37.  Get High-res Image Gene #22: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'METHLYATION_CNMF'

P value = 6.87e-05 (Fisher's exact test), Q value = 0.027

Table S38.  Gene #27: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
4P LOSS CNV 3 0 0 12
4P LOSS WILD-TYPE 95 34 28 43

Figure S38.  Get High-res Image Gene #27: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.000108 (Chi-square test), Q value = 0.042

Table S39.  Gene #27: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
4P LOSS CNV 0 0 8 7 0
4P LOSS WILD-TYPE 60 42 27 63 11

Figure S39.  Get High-res Image Gene #27: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000418 (Fisher's exact test), Q value = 0.16

Table S40.  Gene #27: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 117 69
4P LOSS CNV 7 2 6
4P LOSS WILD-TYPE 25 115 63

Figure S40.  Get High-res Image Gene #27: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0058

Table S41.  Gene #27: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 32 82 47
4P LOSS CNV 0 9 5 1
4P LOSS WILD-TYPE 58 23 77 46

Figure S41.  Get High-res Image Gene #27: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.05e-05 (Chi-square test), Q value = 0.032

Table S42.  Gene #27: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 27 70 33 30 20
4P LOSS CNV 0 7 3 5 0 0
4P LOSS WILD-TYPE 39 20 67 28 30 20

Figure S42.  Get High-res Image Gene #27: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.066

Table S43.  Gene #28: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
4Q LOSS CNV 8 0 1 15
4Q LOSS WILD-TYPE 90 34 27 40

Figure S43.  Get High-res Image Gene #28: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00048

Table S44.  Gene #28: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 32 82 47
4Q LOSS CNV 1 13 8 2
4Q LOSS WILD-TYPE 57 19 74 45

Figure S44.  Get High-res Image Gene #28: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000136 (Chi-square test), Q value = 0.053

Table S45.  Gene #28: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 27 70 33 30 20
4Q LOSS CNV 1 9 6 7 0 1
4Q LOSS WILD-TYPE 38 18 64 26 30 19

Figure S45.  Get High-res Image Gene #28: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 2.3e-17 (Fisher's exact test), Q value = 1e-14

Table S46.  Gene #36: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
10P LOSS CNV 1 27 3
10P LOSS WILD-TYPE 93 23 73

Figure S46.  Get High-res Image Gene #36: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1.19e-22 (Fisher's exact test), Q value = 5.2e-20

Table S47.  Gene #36: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
10P LOSS CNV 1 26 0 3
10P LOSS WILD-TYPE 97 8 28 52

Figure S47.  Get High-res Image Gene #36: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 4.79e-19 (Chi-square test), Q value = 2.1e-16

Table S48.  Gene #36: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
10P LOSS CNV 1 25 1 3 0
10P LOSS WILD-TYPE 59 17 34 67 11

Figure S48.  Get High-res Image Gene #36: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.88e-07 (Chi-square test), Q value = 0.00041

Table S49.  Gene #36: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 27 70 33 30 20
10P LOSS CNV 15 0 4 9 3 0
10P LOSS WILD-TYPE 24 27 66 24 27 20

Figure S49.  Get High-res Image Gene #36: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000409 (Fisher's exact test), Q value = 0.16

Table S50.  Gene #36: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 116 96
10P LOSS CNV 4 21 6
10P LOSS WILD-TYPE 3 95 90

Figure S50.  Get High-res Image Gene #36: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 3.46e-16 (Fisher's exact test), Q value = 1.5e-13

Table S51.  Gene #37: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
10Q LOSS CNV 2 27 3
10Q LOSS WILD-TYPE 92 23 73

Figure S51.  Get High-res Image Gene #37: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1.78e-21 (Fisher's exact test), Q value = 7.8e-19

Table S52.  Gene #37: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
10Q LOSS CNV 2 26 0 3
10Q LOSS WILD-TYPE 96 8 28 52

Figure S52.  Get High-res Image Gene #37: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 3.81e-20 (Chi-square test), Q value = 1.7e-17

Table S53.  Gene #37: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
10Q LOSS CNV 1 26 1 3 0
10Q LOSS WILD-TYPE 59 16 34 67 11

Figure S53.  Get High-res Image Gene #37: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.86e-06 (Chi-square test), Q value = 0.00077

Table S54.  Gene #37: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 27 70 33 30 20
10Q LOSS CNV 15 0 4 9 4 0
10Q LOSS WILD-TYPE 24 27 66 24 26 20

Figure S54.  Get High-res Image Gene #37: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 0.000494 (Fisher's exact test), Q value = 0.19

Table S55.  Gene #42: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
14Q LOSS CNV 8 11 0 5
14Q LOSS WILD-TYPE 90 23 28 50

Figure S55.  Get High-res Image Gene #42: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 1.4e-45 (Fisher's exact test), Q value = 6.2e-43

Table S56.  Gene #48: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
19Q LOSS CNV 2 3 71
19Q LOSS WILD-TYPE 92 47 5

Figure S56.  Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 7.86e-38 (Fisher's exact test), Q value = 3.5e-35

Table S57.  Gene #48: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
19Q LOSS CNV 7 2 9 55
19Q LOSS WILD-TYPE 91 32 19 0

Figure S57.  Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 9.57e-22 (Chi-square test), Q value = 4.2e-19

Table S58.  Gene #48: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
19Q LOSS CNV 4 1 33 36 2
19Q LOSS WILD-TYPE 56 41 2 34 9

Figure S58.  Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.5e-27 (Fisher's exact test), Q value = 2e-24

Table S59.  Gene #48: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 117 69
19Q LOSS CNV 32 9 35
19Q LOSS WILD-TYPE 0 108 34

Figure S59.  Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 4.75e-13 (Fisher's exact test), Q value = 2e-10

Table S60.  Gene #48: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 32 82 47
19Q LOSS CNV 7 23 42 4
19Q LOSS WILD-TYPE 51 9 40 43

Figure S60.  Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.33e-07 (Fisher's exact test), Q value = 0.00031

Table S61.  Gene #48: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 95 116
19Q LOSS CNV 2 51 23
19Q LOSS WILD-TYPE 6 44 93

Figure S61.  Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.87e-07 (Chi-square test), Q value = 0.00012

Table S62.  Gene #48: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 27 70 33 30 20
19Q LOSS CNV 4 17 35 13 2 5
19Q LOSS WILD-TYPE 35 10 35 20 28 15

Figure S62.  Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.09e-09 (Fisher's exact test), Q value = 3.9e-06

Table S63.  Gene #48: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 116 96
19Q LOSS CNV 1 21 54
19Q LOSS WILD-TYPE 6 95 42

Figure S63.  Get High-res Image Gene #48: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 7.15e-06 (Fisher's exact test), Q value = 0.003

Table S64.  Gene #50: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 50 76
22Q LOSS CNV 4 11 0
22Q LOSS WILD-TYPE 90 39 76

Figure S64.  Get High-res Image Gene #50: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 9.74e-05 (Fisher's exact test), Q value = 0.039

Table S65.  Gene #50: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 34 28 55
22Q LOSS CNV 5 9 1 0
22Q LOSS WILD-TYPE 93 25 27 55

Figure S65.  Get High-res Image Gene #50: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1.92e-05 (Chi-square test), Q value = 0.0078

Table S66.  Gene #50: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 60 42 35 70 11
22Q LOSS CNV 1 10 0 3 0
22Q LOSS WILD-TYPE 59 32 35 67 11

Figure S66.  Get High-res Image Gene #50: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Molecular subtypes file = LGG-TP.transferedmergedcluster.txt

  • Number of patients = 220

  • Number of significantly arm-level cnvs = 51

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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