Correlation between copy number variation genes (focal events) and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C10C4T7F
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/C10C4T7F
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 40 focal events and 10 molecular subtypes across 278 patients, 38 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 3p cnv correlated to 'CN_CNMF'.

  • 3q cnv correlated to 'CN_CNMF'.

  • 5p cnv correlated to 'CN_CNMF'.

  • 5q cnv correlated to 'CN_CNMF'.

  • 6p cnv correlated to 'CN_CNMF'.

  • 6q cnv correlated to 'CN_CNMF'.

  • 7p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

  • 8p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • 8q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9p cnv correlated to 'CN_CNMF'.

  • 9q cnv correlated to 'CN_CNMF'.

  • 10p cnv correlated to 'CN_CNMF'.

  • 10q cnv correlated to 'CN_CNMF'.

  • 12q cnv correlated to 'CN_CNMF'.

  • 13q cnv correlated to 'CN_CNMF'.

  • 15q cnv correlated to 'CN_CNMF'.

  • 16p cnv correlated to 'CN_CNMF'.

  • 16q cnv correlated to 'CN_CNMF'.

  • 17p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 17q cnv correlated to 'CN_CNMF'.

  • 18p cnv correlated to 'CN_CNMF'.

  • 18q cnv correlated to 'CN_CNMF'.

  • 19q cnv correlated to 'CN_CNMF'.

  • 21q cnv correlated to 'CN_CNMF'.

  • 22q cnv correlated to 'CN_CNMF'.

  • xq cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 40 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, 38 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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
8p 119 (43%) 159 1.79e-17
(7.15e-15) 		5.46e-11
(2.16e-08) 		0.0642
(1.00) 		0.0714
(1.00) 		2.13e-06
(0.000818) 		2.55e-06
(0.000976) 		0.000109
(0.04) 		0.95
(1.00) 		0.669
(1.00) 		0.89
(1.00)
7p 46 (17%) 232 5.53e-07
(0.000214) 		1.05e-06
(0.000405) 		0.413
(1.00) 		0.561
(1.00) 		6.61e-05
(0.0245) 		0.0219
(1.00) 		0.418
(1.00) 		0.962
(1.00) 		0.73
(1.00) 		0.902
(1.00)
7q 43 (15%) 235 4.36e-06
(0.00166) 		1.73e-06
(0.000666) 		0.586
(1.00) 		0.551
(1.00) 		8.81e-05
(0.0324) 		0.0572
(1.00) 		0.415
(1.00) 		0.829
(1.00) 		0.728
(1.00) 		0.87
(1.00)
8q 70 (25%) 208 1.08e-22
(4.3e-20) 		3.46e-05
(0.0129) 		0.0138
(1.00) 		0.0186
(1.00) 		0.0106
(1.00) 		1.68e-05
(0.00633) 		0.0585
(1.00) 		0.218
(1.00) 		0.488
(1.00) 		0.553
(1.00)
17p 40 (14%) 238 4.19e-15
(1.67e-12) 		0.0162
(1.00) 		0.0153
(1.00) 		0.0173
(1.00) 		0.00349
(1.00) 		0.000105
(0.0384) 		0.858
(1.00) 		0.823
(1.00) 		0.832
(1.00) 		0.716
(1.00)
3p 23 (8%) 255 0.000395
(0.144) 		0.12
(1.00) 		0.182
(1.00) 		0.696
(1.00) 		0.536
(1.00) 		0.0169
(1.00) 		0.129
(1.00) 		1
(1.00) 		0.752
(1.00) 		0.423
(1.00)
3q 27 (10%) 251 1.08e-05
(0.00407) 		0.0792
(1.00) 		0.0633
(1.00) 		0.256
(1.00) 		0.205
(1.00) 		0.00725
(1.00) 		0.345
(1.00) 		0.947
(1.00) 		0.938
(1.00) 		0.61
(1.00)
5p 10 (4%) 268 7.55e-06
(0.00286) 		0.0353
(1.00) 		0.228
(1.00) 		0.635
(1.00) 		0.175
(1.00) 		0.0931
(1.00) 		0.356
(1.00) 		0.141
(1.00) 		0.257
(1.00) 		0.277
(1.00)
5q 11 (4%) 267 4.27e-06
(0.00163) 		0.192
(1.00) 		0.228
(1.00) 		0.264
(1.00) 		0.302
(1.00) 		0.173
(1.00) 		0.519
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.76
(1.00)
6p 11 (4%) 267 4.27e-06
(0.00163) 		0.0145
(1.00) 		0.15
(1.00) 		0.118
(1.00) 		0.0696
(1.00) 		0.00179
(0.632) 		0.64
(1.00) 		0.74
(1.00) 		0.862
(1.00) 		0.929
(1.00)
6q 18 (6%) 260 2.2e-07
(8.52e-05) 		0.00128
(0.455) 		0.138
(1.00) 		0.359
(1.00) 		0.0256
(1.00) 		0.00203
(0.713) 		0.423
(1.00) 		0.518
(1.00) 		0.543
(1.00) 		0.653
(1.00)
9p 22 (8%) 256 1.23e-07
(4.78e-05) 		0.544
(1.00) 		0.0715
(1.00) 		0.183
(1.00) 		0.457
(1.00) 		0.701
(1.00) 		0.677
(1.00) 		0.527
(1.00) 		0.628
(1.00) 		0.597
(1.00)
9q 25 (9%) 253 5.19e-08
(2.02e-05) 		0.302
(1.00) 		0.0377
(1.00) 		0.0779
(1.00) 		0.757
(1.00) 		0.318
(1.00) 		0.783
(1.00) 		0.309
(1.00) 		0.529
(1.00) 		0.652
(1.00)
10p 25 (9%) 253 2.36e-08
(9.25e-06) 		0.00126
(0.448) 		0.00345
(1.00) 		0.01
(1.00) 		0.0284
(1.00) 		0.00104
(0.372) 		0.0676
(1.00) 		0.0479
(1.00) 		0.0168
(1.00) 		0.0916
(1.00)
10q 30 (11%) 248 2.11e-10
(8.31e-08) 		0.0071
(1.00) 		0.00158
(0.561) 		0.00573
(1.00) 		0.132
(1.00) 		0.00293
(1.00) 		0.188
(1.00) 		0.188
(1.00) 		0.024
(1.00) 		0.116
(1.00)
12q 16 (6%) 262 7.16e-05
(0.0265) 		0.667
(1.00) 		0.267
(1.00) 		0.487
(1.00) 		0.509
(1.00) 		0.266
(1.00) 		0.837
(1.00) 		1
(1.00) 		0.888
(1.00) 		0.943
(1.00)
13q 41 (15%) 237 2.06e-08
(8.09e-06) 		0.225
(1.00) 		0.272
(1.00) 		0.342
(1.00) 		0.809
(1.00) 		0.244
(1.00) 		0.89
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.879
(1.00)
15q 19 (7%) 259 4.01e-05
(0.0149) 		0.0639
(1.00) 		0.00876
(1.00) 		0.0212
(1.00) 		0.487
(1.00) 		0.0895
(1.00) 		0.38
(1.00) 		0.352
(1.00) 		0.176
(1.00) 		0.321
(1.00)
16p 30 (11%) 248 1.11e-05
(0.0042) 		0.0647
(1.00) 		0.23
(1.00) 		0.275
(1.00) 		0.71
(1.00) 		0.406
(1.00) 		0.244
(1.00) 		0.33
(1.00) 		0.0863
(1.00) 		0.206
(1.00)
16q 58 (21%) 220 3.15e-12
(1.25e-09) 		0.0031
(1.00) 		0.313
(1.00) 		0.163
(1.00) 		0.0553
(1.00) 		0.0325
(1.00) 		0.529
(1.00) 		1
(1.00) 		0.211
(1.00) 		0.51
(1.00)
17q 11 (4%) 267 2.57e-05
(0.0096) 		0.245
(1.00) 		0.228
(1.00) 		0.118
(1.00) 		0.0696
(1.00) 		0.312
(1.00) 		0.906
(1.00) 		1
(1.00) 		0.612
(1.00) 		0.666
(1.00)
18p 43 (15%) 235 4.25e-10
(1.67e-07) 		0.1
(1.00) 		0.0954
(1.00) 		0.0711
(1.00) 		0.0874
(1.00) 		0.0763
(1.00) 		0.662
(1.00) 		0.728
(1.00) 		0.295
(1.00) 		0.414
(1.00)
18q 54 (19%) 224 7.32e-11
(2.89e-08) 		0.0652
(1.00) 		0.0283
(1.00) 		0.0162
(1.00) 		0.00886
(1.00) 		0.0293
(1.00) 		0.847
(1.00) 		0.829
(1.00) 		0.833
(1.00) 		0.868
(1.00)
19q 13 (5%) 265 0.000349
(0.127) 		0.366
(1.00) 		0.297
(1.00) 		0.495
(1.00) 		0.232
(1.00) 		0.399
(1.00) 		0.342
(1.00) 		0.386
(1.00) 		0.279
(1.00) 		0.31
(1.00)
21q 15 (5%) 263 0.000166
(0.0606) 		0.045
(1.00) 		0.209
(1.00) 		0.126
(1.00) 		0.384
(1.00) 		0.128
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.773
(1.00) 		0.349
(1.00)
22q 20 (7%) 258 7.22e-05
(0.0266) 		0.169
(1.00) 		0.264
(1.00) 		0.619
(1.00) 		0.467
(1.00) 		0.107
(1.00) 		0.597
(1.00) 		0.644
(1.00) 		0.385
(1.00) 		0.479
(1.00)
xq 19 (7%) 259 1.74e-05
(0.00651) 		0.00095
(0.342) 		0.193
(1.00) 		0.235
(1.00) 		0.00262
(0.913) 		0.0191
(1.00) 		0.182
(1.00) 		0.173
(1.00) 		0.0906
(1.00) 		0.113
(1.00)
1p 15 (5%) 263 0.000749
(0.271) 		0.00487
(1.00) 		0.00255
(0.892) 		0.085
(1.00) 		0.0614
(1.00) 		0.0108
(1.00) 		0.351
(1.00) 		0.588
(1.00) 		0.351
(1.00) 		0.777
(1.00)
1q 12 (4%) 266 0.0379
(1.00) 		0.0186
(1.00) 		0.00859
(1.00) 		0.126
(1.00) 		0.163
(1.00) 		0.0329
(1.00) 		0.619
(1.00) 		0.923
(1.00) 		0.862
(1.00) 		0.74
(1.00)
2p 7 (3%) 271 0.0351
(1.00) 		0.122
(1.00) 		0.784
(1.00) 		0.635
(1.00) 		0.484
(1.00) 		0.124
(1.00) 		0.218
(1.00) 		0.559
(1.00) 		0.11
(1.00) 		0.639
(1.00)
2q 7 (3%) 271 0.00305
(1.00) 		0.504
(1.00) 		0.784
(1.00) 		0.635
(1.00) 		0.915
(1.00) 		0.454
(1.00) 		0.309
(1.00) 		0.559
(1.00) 		0.11
(1.00) 		0.639
(1.00)
4p 13 (5%) 265 0.0104
(1.00) 		0.105
(1.00) 		0.658
(1.00) 		0.585
(1.00) 		0.0496
(1.00) 		0.186
(1.00) 		0.401
(1.00) 		0.064
(1.00) 		0.397
(1.00) 		0.491
(1.00)
4q 9 (3%) 269 0.155
(1.00) 		0.295
(1.00) 		1
(1.00) 		0.145
(1.00) 		0.189
(1.00) 		0.489
(1.00) 		0.756
(1.00) 		0.277
(1.00) 		0.637
(1.00) 		0.362
(1.00)
11p 10 (4%) 268 0.00346
(1.00) 		0.609
(1.00) 		0.768
(1.00) 		0.585
(1.00) 		0.495
(1.00) 		0.457
(1.00) 		0.93
(1.00) 		0.914
(1.00) 		1
(1.00) 		0.836
(1.00)
11q 10 (4%) 268 0.00346
(1.00) 		0.609
(1.00) 		0.896
(1.00) 		0.564
(1.00) 		0.495
(1.00) 		0.457
(1.00) 		0.93
(1.00) 		0.914
(1.00) 		1
(1.00) 		0.836
(1.00)
12p 28 (10%) 250 0.00119
(0.425) 		0.116
(1.00) 		0.0718
(1.00) 		0.507
(1.00) 		0.195
(1.00) 		0.176
(1.00) 		0.889
(1.00) 		0.202
(1.00) 		0.457
(1.00) 		0.776
(1.00)
14q 15 (5%) 263 0.0118
(1.00) 		0.045
(1.00) 		0.209
(1.00) 		0.126
(1.00) 		0.11
(1.00) 		0.0722
(1.00) 		0.0085
(1.00) 		0.0945
(1.00) 		0.0378
(1.00) 		0.174
(1.00)
19p 12 (4%) 266 0.00093
(0.336) 		0.428
(1.00) 		0.24
(1.00) 		0.445
(1.00) 		0.286
(1.00) 		0.603
(1.00) 		0.426
(1.00) 		0.347
(1.00) 		0.33
(1.00) 		0.362
(1.00)
20p 16 (6%) 262 0.0847
(1.00) 		0.00176
(0.622) 		0.356
(1.00) 		0.415
(1.00) 		0.221
(1.00) 		0.0569
(1.00) 		0.496
(1.00) 		0.127
(1.00) 		0.638
(1.00) 		1
(1.00)
20q 14 (5%) 264 0.00196
(0.689) 		0.00985
(1.00) 		0.602
(1.00) 		0.696
(1.00) 		0.158
(1.00) 		0.202
(1.00) 		0.945
(1.00) 		0.501
(1.00) 		0.836
(1.00) 		0.58
(1.00)
'3p' versus 'CN_CNMF'

P value = 0.000395 (Fisher's exact test), Q value = 0.14

Table S1.  Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
3P MUTATED 4 4 15
3P WILD-TYPE 44 141 70

Figure S1.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

'3q' versus 'CN_CNMF'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0041

Table S2.  Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
3Q MUTATED 4 4 19
3Q WILD-TYPE 44 141 66

Figure S2.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

'5p' versus 'CN_CNMF'

P value = 7.55e-06 (Fisher's exact test), Q value = 0.0029

Table S3.  Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
5P MUTATED 0 0 10
5P WILD-TYPE 48 145 75

Figure S3.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

'5q' versus 'CN_CNMF'

P value = 4.27e-06 (Fisher's exact test), Q value = 0.0016

Table S4.  Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
5Q MUTATED 0 0 11
5Q WILD-TYPE 48 145 74

Figure S4.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

'6p' versus 'CN_CNMF'

P value = 4.27e-06 (Fisher's exact test), Q value = 0.0016

Table S5.  Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
6P MUTATED 0 0 11
6P WILD-TYPE 48 145 74

Figure S5.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

'6q' versus 'CN_CNMF'

P value = 2.2e-07 (Fisher's exact test), Q value = 8.5e-05

Table S6.  Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
6Q MUTATED 3 0 15
6Q WILD-TYPE 45 145 70

Figure S6.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'CN_CNMF'

P value = 5.53e-07 (Fisher's exact test), Q value = 0.00021

Table S7.  Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
7P MUTATED 14 8 24
7P WILD-TYPE 34 137 61

Figure S7.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 4e-04

Table S8.  Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 93 105
7P MUTATED 27 4 15
7P WILD-TYPE 53 89 90

Figure S8.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 6.61e-05 (Fisher's exact test), Q value = 0.025

Table S9.  Gene #13: '7p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 65 80 56
7P MUTATED 25 9 10 2
7P WILD-TYPE 51 56 70 54

Figure S9.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q' versus 'CN_CNMF'

P value = 4.36e-06 (Fisher's exact test), Q value = 0.0017

Table S10.  Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
7Q MUTATED 13 8 22
7Q WILD-TYPE 35 137 63

Figure S10.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 1.73e-06 (Fisher's exact test), Q value = 0.00067

Table S11.  Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 93 105
7Q MUTATED 26 4 13
7Q WILD-TYPE 54 89 92

Figure S11.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q' versus 'MRNASEQ_CNMF'

P value = 8.81e-05 (Fisher's exact test), Q value = 0.032

Table S12.  Gene #14: '7q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 65 80 56
7Q MUTATED 24 8 9 2
7Q WILD-TYPE 52 57 71 54

Figure S12.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p' versus 'CN_CNMF'

P value = 1.79e-17 (Fisher's exact test), Q value = 7.2e-15

Table S13.  Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
8P MUTATED 10 40 69
8P WILD-TYPE 38 105 16

Figure S13.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

'8p' versus 'METHLYATION_CNMF'

P value = 5.46e-11 (Fisher's exact test), Q value = 2.2e-08

Table S14.  Gene #15: '8p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 93 105
8P MUTATED 45 14 60
8P WILD-TYPE 35 79 45

Figure S14.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p' versus 'MRNASEQ_CNMF'

P value = 2.13e-06 (Fisher's exact test), Q value = 0.00082

Table S15.  Gene #15: '8p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 65 80 56
8P MUTATED 35 24 50 10
8P WILD-TYPE 41 41 30 46

Figure S15.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.55e-06 (Fisher's exact test), Q value = 0.00098

Table S16.  Gene #15: '8p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 86 70 40
8P MUTATED 17 52 34 16
8P WILD-TYPE 64 34 36 24

Figure S16.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p' versus 'MIRSEQ_CNMF'

P value = 0.000109 (Chi-square test), Q value = 0.04

Table S17.  Gene #15: '8p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 65 27 15 69 80
8P MUTATED 34 3 1 31 40
8P WILD-TYPE 31 24 14 38 40

Figure S17.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q' versus 'CN_CNMF'

P value = 1.08e-22 (Fisher's exact test), Q value = 4.3e-20

Table S18.  Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
8Q MUTATED 7 8 55
8Q WILD-TYPE 41 137 30

Figure S18.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

'8q' versus 'METHLYATION_CNMF'

P value = 3.46e-05 (Fisher's exact test), Q value = 0.013

Table S19.  Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 93 105
8Q MUTATED 32 10 28
8Q WILD-TYPE 48 83 77

Figure S19.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.0063

Table S20.  Gene #16: '8q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 86 70 40
8Q MUTATED 6 31 24 9
8Q WILD-TYPE 75 55 46 31

Figure S20.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p' versus 'CN_CNMF'

P value = 1.23e-07 (Fisher's exact test), Q value = 4.8e-05

Table S21.  Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
9P MUTATED 1 2 19
9P WILD-TYPE 47 143 66

Figure S21.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

'9q' versus 'CN_CNMF'

P value = 5.19e-08 (Fisher's exact test), Q value = 2e-05

Table S22.  Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
9Q MUTATED 1 3 21
9Q WILD-TYPE 47 142 64

Figure S22.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'CN_CNMF'

P value = 2.36e-08 (Fisher's exact test), Q value = 9.2e-06

Table S23.  Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
10P MUTATED 2 2 21
10P WILD-TYPE 46 143 64

Figure S23.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'CN_CNMF'

P value = 2.11e-10 (Fisher's exact test), Q value = 8.3e-08

Table S24.  Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
10Q MUTATED 5 1 24
10Q WILD-TYPE 43 144 61

Figure S24.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'12q' versus 'CN_CNMF'

P value = 7.16e-05 (Fisher's exact test), Q value = 0.026

Table S25.  Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
12Q MUTATED 1 2 13
12Q WILD-TYPE 47 143 72

Figure S25.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'CN_CNMF'

P value = 2.06e-08 (Fisher's exact test), Q value = 8.1e-06

Table S26.  Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
13Q MUTATED 10 5 26
13Q WILD-TYPE 38 140 59

Figure S26.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

'15q' versus 'CN_CNMF'

P value = 4.01e-05 (Fisher's exact test), Q value = 0.015

Table S27.  Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
15Q MUTATED 1 3 15
15Q WILD-TYPE 47 142 70

Figure S27.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

'16p' versus 'CN_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0042

Table S28.  Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
16P MUTATED 3 6 21
16P WILD-TYPE 45 139 64

Figure S28.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

'16q' versus 'CN_CNMF'

P value = 3.15e-12 (Fisher's exact test), Q value = 1.3e-09

Table S29.  Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
16Q MUTATED 6 11 41
16Q WILD-TYPE 42 134 44

Figure S29.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'CN_CNMF'

P value = 4.19e-15 (Fisher's exact test), Q value = 1.7e-12

Table S30.  Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
17P MUTATED 1 4 35
17P WILD-TYPE 47 141 50

Figure S30.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000105 (Fisher's exact test), Q value = 0.038

Table S31.  Gene #30: '17p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 81 86 70 40
17P MUTATED 5 25 8 2
17P WILD-TYPE 76 61 62 38

Figure S31.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 2.57e-05 (Fisher's exact test), Q value = 0.0096

Table S32.  Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
17Q MUTATED 1 0 10
17Q WILD-TYPE 47 145 75

Figure S32.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

'18p' versus 'CN_CNMF'

P value = 4.25e-10 (Fisher's exact test), Q value = 1.7e-07

Table S33.  Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
18P MUTATED 4 7 32
18P WILD-TYPE 44 138 53

Figure S33.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #1: 'CN_CNMF'

'18q' versus 'CN_CNMF'

P value = 7.32e-11 (Fisher's exact test), Q value = 2.9e-08

Table S34.  Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
18Q MUTATED 8 9 37
18Q WILD-TYPE 40 136 48

Figure S34.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

'19q' versus 'CN_CNMF'

P value = 0.000349 (Fisher's exact test), Q value = 0.13

Table S35.  Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
19Q MUTATED 2 1 10
19Q WILD-TYPE 46 144 75

Figure S35.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

'21q' versus 'CN_CNMF'

P value = 0.000166 (Fisher's exact test), Q value = 0.061

Table S36.  Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
21Q MUTATED 1 2 12
21Q WILD-TYPE 47 143 73

Figure S36.  Get High-res Image Gene #38: '21q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'CN_CNMF'

P value = 7.22e-05 (Fisher's exact test), Q value = 0.027

Table S37.  Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
22Q MUTATED 2 3 15
22Q WILD-TYPE 46 142 70

Figure S37.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

'xq' versus 'CN_CNMF'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.0065

Table S38.  Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 145 85
XQ MUTATED 2 2 15
XQ WILD-TYPE 46 143 70

Figure S38.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 278

  • Number of significantly focal cnvs = 40

  • 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

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

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] 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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