Correlation between copy number variation genes (focal events) and molecular subtypes
Pancreatic Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1K9366R
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/C1K9366R
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 43 focal events and 8 molecular subtypes across 91 patients, 45 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_7q22.1 cnv correlated to 'METHLYATION_CNMF'.

  • amp_8q24.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_12p13.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_12p11.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • amp_12q15 cnv correlated to 'CN_CNMF'.

  • amp_18q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_19q13.2 cnv correlated to 'CN_CNMF'.

  • amp_20q13.2 cnv correlated to 'CN_CNMF'.

  • del_1p36.32 cnv correlated to 'CN_CNMF'.

  • del_1p36.11 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_3p24.1 cnv correlated to 'CN_CNMF'.

  • del_5q14.2 cnv correlated to 'CN_CNMF'.

  • del_6p25.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_8p21.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_10q23.2 cnv correlated to 'CN_CNMF'.

  • del_12p12.1 cnv correlated to 'CN_CNMF'.

  • del_12q12 cnv correlated to 'CN_CNMF'.

  • del_12q24.33 cnv correlated to 'CN_CNMF'.

  • del_17q22 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_18q21.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_19p13.3 cnv correlated to 'CN_CNMF'.

  • del_21q21.1 cnv correlated to 'CN_CNMF'.

  • del_22q13.31 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 43 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 45 significant findings detected.

Clinical
Features 		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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
del 9p21 3 58 (64%) 33 1.17e-08
(3.98e-06) 		1.16e-09
(3.98e-07) 		0.000292
(0.0908) 		0.000152
(0.0488) 		1.09e-05
(0.00361) 		0.000183
(0.0579) 		2.56e-05
(0.00837) 		2.54e-05
(0.00834)
amp 18q11 2 30 (33%) 61 2.8e-12
(9.64e-10) 		0.000255
(0.0796) 		0.0216
(1.00) 		0.00219
(0.649) 		0.000407
(0.124) 		0.00517
(1.00) 		0.000418
(0.126) 		2.03e-05
(0.00669)
del 6p25 2 38 (42%) 53 4.43e-07
(0.00015) 		5.97e-06
(0.00199) 		0.0776
(1.00) 		0.000369
(0.113) 		0.0113
(1.00) 		0.0599
(1.00) 		0.0107
(1.00) 		0.00493
(1.00)
del 8p21 3 26 (29%) 65 0.000218
(0.0683) 		0.000425
(0.128) 		0.0225
(1.00) 		0.000415
(0.126) 		0.19
(1.00) 		0.028
(1.00) 		0.0113
(1.00) 		0.0143
(1.00)
amp 8q24 21 36 (40%) 55 2.62e-06
(0.000879) 		2.24e-05
(0.00739) 		0.171
(1.00) 		0.0102
(1.00) 		0.149
(1.00) 		0.0599
(1.00) 		0.0262
(1.00) 		0.0109
(1.00)
amp 12p13 33 15 (16%) 76 2.52e-09
(8.61e-07) 		0.000591
(0.177) 		0.244
(1.00) 		0.0112
(1.00) 		0.821
(1.00) 		0.0629
(1.00) 		0.117
(1.00) 		0.0387
(1.00)
amp 12p11 21 16 (18%) 75 6.1e-09
(2.08e-06) 		0.000146
(0.0471) 		0.483
(1.00) 		0.0112
(1.00) 		0.975
(1.00) 		0.207
(1.00) 		0.089
(1.00) 		0.1
(1.00)
del 1p36 11 30 (33%) 61 0.000164
(0.0522) 		9.12e-06
(0.00303) 		0.0104
(1.00) 		0.00453
(1.00) 		0.239
(1.00) 		0.00306
(0.89) 		0.0191
(1.00) 		0.0105
(1.00)
del 17q22 25 (27%) 66 1.17e-07
(3.95e-05) 		0.000359
(0.11) 		0.0125
(1.00) 		0.00583
(1.00) 		0.05
(1.00) 		0.0544
(1.00) 		0.0169
(1.00) 		0.0197
(1.00)
del 18q21 2 65 (71%) 26 3.56e-06
(0.00119) 		0.000175
(0.0556) 		0.0888
(1.00) 		0.00743
(1.00) 		0.0124
(1.00) 		0.166
(1.00) 		0.00579
(1.00) 		0.0201
(1.00)
amp 7q22 1 26 (29%) 65 0.00201
(0.596) 		0.000359
(0.11) 		0.153
(1.00) 		0.00583
(1.00) 		0.13
(1.00) 		0.0544
(1.00) 		0.0169
(1.00) 		0.0197
(1.00)
amp 12q15 10 (11%) 81 0.000154
(0.0494) 		0.013
(1.00) 		0.122
(1.00) 		0.0257
(1.00) 		0.463
(1.00) 		0.0782
(1.00) 		0.0223
(1.00) 		0.0199
(1.00)
amp 19q13 2 23 (25%) 68 0.0003
(0.0929) 		0.00819
(1.00) 		0.0884
(1.00) 		0.187
(1.00) 		0.11
(1.00) 		0.181
(1.00) 		0.241
(1.00) 		0.143
(1.00)
amp 20q13 2 24 (26%) 67 9.64e-05
(0.0313) 		0.00895
(1.00) 		0.493
(1.00) 		0.187
(1.00) 		0.533
(1.00) 		0.484
(1.00) 		0.325
(1.00) 		0.143
(1.00)
del 1p36 32 21 (23%) 70 0.00022
(0.0689) 		0.00115
(0.344) 		0.02
(1.00) 		0.00788
(1.00) 		0.713
(1.00) 		0.0277
(1.00) 		0.122
(1.00) 		0.131
(1.00)
del 3p24 1 19 (21%) 72 0.000344
(0.106) 		0.0475
(1.00) 		0.698
(1.00) 		0.497
(1.00) 		0.775
(1.00) 		0.606
(1.00) 		0.562
(1.00) 		0.262
(1.00)
del 5q14 2 19 (21%) 72 0.000131
(0.0424) 		0.0475
(1.00) 		0.478
(1.00) 		0.325
(1.00) 		0.633
(1.00) 		0.277
(1.00) 		0.134
(1.00) 		0.262
(1.00)
del 10q23 2 16 (18%) 75 7.66e-05
(0.025) 		0.0158
(1.00) 		0.483
(1.00) 		0.102
(1.00) 		0.804
(1.00) 		0.00817
(1.00) 		0.701
(1.00) 		0.1
(1.00)
del 12p12 1 11 (12%) 80 0.00034
(0.105) 		0.00513
(1.00) 		0.312
(1.00) 		0.191
(1.00) 		0.0945
(1.00) 		0.336
(1.00) 		0.309
(1.00) 		0.0707
(1.00)
del 12q12 11 (12%) 80 0.000179
(0.0566) 		0.00221
(0.651) 		0.312
(1.00) 		0.191
(1.00) 		0.2
(1.00) 		0.0103
(1.00) 		0.309
(1.00) 		0.00883
(1.00)
del 12q24 33 19 (21%) 72 0.000131
(0.0424) 		0.00102
(0.304) 		0.112
(1.00) 		0.00277
(0.811) 		0.651
(1.00) 		0.013
(1.00) 		0.487
(1.00) 		0.213
(1.00)
del 19p13 3 17 (19%) 74 4.19e-06
(0.0014) 		0.00294
(0.859) 		0.108
(1.00) 		0.00496
(1.00) 		0.568
(1.00) 		0.196
(1.00) 		0.125
(1.00) 		0.492
(1.00)
del 21q21 1 35 (38%) 56 1.42e-06
(0.000479) 		0.00381
(1.00) 		0.00731
(1.00) 		0.0022
(0.649) 		0.00785
(1.00) 		0.0438
(1.00) 		0.00703
(1.00) 		0.0462
(1.00)
del 22q13 31 27 (30%) 64 0.000211
(0.0664) 		0.00553
(1.00) 		0.0201
(1.00) 		0.0764
(1.00) 		0.0703
(1.00) 		0.0507
(1.00) 		0.00955
(1.00) 		0.087
(1.00)
amp 1p34 2 7 (8%) 84 0.883
(1.00) 		0.122
(1.00) 		0.755
(1.00) 		1
(1.00) 		1
(1.00) 		0.649
(1.00) 		0.566
(1.00) 		0.656
(1.00)
amp 1p12 15 (16%) 76 0.533
(1.00) 		0.182
(1.00) 		0.922
(1.00) 		0.589
(1.00) 		0.946
(1.00) 		1
(1.00) 		0.721
(1.00) 		0.852
(1.00)
amp 9p13 3 9 (10%) 82 0.138
(1.00) 		0.0786
(1.00) 		0.389
(1.00) 		0.319
(1.00) 		0.155
(1.00) 		0.0381
(1.00) 		0.309
(1.00) 		0.0442
(1.00)
amp 11p11 2 10 (11%) 81 0.0037
(1.00) 		0.0116
(1.00) 		0.385
(1.00) 		0.235
(1.00) 		0.357
(1.00) 		0.424
(1.00) 		0.473
(1.00) 		0.141
(1.00)
amp 17p11 2 4 (4%) 87 0.113
(1.00) 		0.131
(1.00) 		0.806
(1.00) 		1
(1.00) 		0.418
(1.00) 		0.824
(1.00) 		0.345
(1.00) 		0.564
(1.00)
amp 17q21 32 9 (10%) 82 0.0115
(1.00) 		0.0786
(1.00) 		0.385
(1.00) 		0.529
(1.00) 		0.959
(1.00) 		0.424
(1.00) 		1
(1.00) 		0.479
(1.00)
amp xp22 11 5 (5%) 86 0.346
(1.00) 		0.365
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.712
(1.00) 		0.848
(1.00) 		0.597
(1.00)
amp xq27 1 8 (9%) 83 0.12
(1.00) 		0.586
(1.00) 		0.306
(1.00) 		0.515
(1.00) 		0.781
(1.00) 		0.55
(1.00) 		1
(1.00) 		0.353
(1.00)
del 1q42 2 3 (3%) 88 0.796
(1.00) 		0.184
(1.00) 		0.322
(1.00) 		0.315
(1.00) 		0.864
(1.00) 		1
(1.00) 		0.596
(1.00) 		0.324
(1.00)
del 2p23 3 11 (12%) 80 0.00548
(1.00) 		0.0391
(1.00) 		0.191
(1.00) 		0.302
(1.00) 		0.602
(1.00) 		0.0322
(1.00) 		0.418
(1.00) 		0.0438
(1.00)
del 4q35 2 16 (18%) 75 0.211
(1.00) 		0.0349
(1.00) 		0.265
(1.00) 		0.773
(1.00) 		0.898
(1.00) 		1
(1.00) 		0.875
(1.00) 		0.667
(1.00)
del 7q36 1 9 (10%) 82 0.0115
(1.00) 		0.193
(1.00) 		0.563
(1.00) 		0.319
(1.00) 		0.642
(1.00) 		0.624
(1.00) 		0.802
(1.00) 		0.712
(1.00)
del 8q12 1 7 (8%) 84 0.587
(1.00) 		0.0536
(1.00) 		0.594
(1.00) 		0.311
(1.00) 		0.457
(1.00) 		0.882
(1.00) 		0.265
(1.00) 		0.153
(1.00)
del 9q22 33 24 (26%) 67 0.144
(1.00) 		0.0849
(1.00) 		0.952
(1.00) 		1
(1.00) 		0.51
(1.00) 		0.908
(1.00) 		0.423
(1.00) 		0.681
(1.00)
del 9q32 23 (25%) 68 0.0889
(1.00) 		0.4
(1.00) 		1
(1.00) 		1
(1.00) 		0.931
(1.00) 		0.827
(1.00) 		0.905
(1.00) 		0.614
(1.00)
del 11p15 4 15 (16%) 76 0.0147
(1.00) 		0.38
(1.00) 		0.857
(1.00) 		1
(1.00) 		0.624
(1.00) 		0.791
(1.00) 		0.741
(1.00) 		1
(1.00)
del 16q23 1 6 (7%) 85 0.136
(1.00) 		0.118
(1.00) 		0.503
(1.00) 		0.667
(1.00) 		0.924
(1.00) 		0.712
(1.00) 		0.848
(1.00) 		0.852
(1.00)
del 18p11 32 34 (37%) 57 0.827
(1.00) 		0.0613
(1.00) 		0.382
(1.00) 		1
(1.00) 		0.574
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.835
(1.00)
del 19q13 41 10 (11%) 81 0.0141
(1.00) 		0.0325
(1.00) 		0.598
(1.00) 		0.529
(1.00) 		0.583
(1.00) 		0.817
(1.00) 		0.742
(1.00) 		0.817
(1.00)
'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 0.000359 (Fisher's exact test), Q value = 0.11

Table S1.  Gene #3: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 35 24
AMP PEAK 3(7Q22.1) MUTATED 14 2 9
AMP PEAK 3(7Q22.1) WILD-TYPE 17 33 15

Figure S1.  Get High-res Image Gene #3: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 2.62e-06 (Fisher's exact test), Q value = 0.00088

Table S2.  Gene #4: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
AMP PEAK 4(8Q24.21) MUTATED 11 8 17
AMP PEAK 4(8Q24.21) WILD-TYPE 13 38 4

Figure S2.  Get High-res Image Gene #4: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.0074

Table S3.  Gene #4: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 35 24
AMP PEAK 4(8Q24.21) MUTATED 20 4 11
AMP PEAK 4(8Q24.21) WILD-TYPE 11 31 13

Figure S3.  Get High-res Image Gene #4: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'CN_CNMF'

P value = 2.52e-09 (Fisher's exact test), Q value = 8.6e-07

Table S4.  Gene #7: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
AMP PEAK 7(12P13.33) MUTATED 2 0 13
AMP PEAK 7(12P13.33) WILD-TYPE 22 46 8

Figure S4.  Get High-res Image Gene #7: 'amp_12p13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 0.000591 (Fisher's exact test), Q value = 0.18

Table S5.  Gene #7: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 35 24
AMP PEAK 7(12P13.33) MUTATED 9 0 6
AMP PEAK 7(12P13.33) WILD-TYPE 22 35 18

Figure S5.  Get High-res Image Gene #7: 'amp_12p13.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p11.21' versus 'CN_CNMF'

P value = 6.1e-09 (Fisher's exact test), Q value = 2.1e-06

Table S6.  Gene #8: 'amp_12p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
AMP PEAK 8(12P11.21) MUTATED 3 0 13
AMP PEAK 8(12P11.21) WILD-TYPE 21 46 8

Figure S6.  Get High-res Image Gene #8: 'amp_12p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p11.21' versus 'METHLYATION_CNMF'

P value = 0.000146 (Fisher's exact test), Q value = 0.047

Table S7.  Gene #8: 'amp_12p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 35 24
AMP PEAK 8(12P11.21) MUTATED 7 0 9
AMP PEAK 8(12P11.21) WILD-TYPE 24 35 15

Figure S7.  Get High-res Image Gene #8: 'amp_12p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 0.000154 (Fisher's exact test), Q value = 0.049

Table S8.  Gene #9: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
AMP PEAK 9(12Q15) MUTATED 3 0 7
AMP PEAK 9(12Q15) WILD-TYPE 21 46 14

Figure S8.  Get High-res Image Gene #9: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'CN_CNMF'

P value = 2.8e-12 (Fisher's exact test), Q value = 9.6e-10

Table S9.  Gene #12: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
AMP PEAK 12(18Q11.2) MUTATED 22 4 4
AMP PEAK 12(18Q11.2) WILD-TYPE 2 42 17

Figure S9.  Get High-res Image Gene #12: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.08

Table S10.  Gene #12: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 35 24
AMP PEAK 12(18Q11.2) MUTATED 16 3 10
AMP PEAK 12(18Q11.2) WILD-TYPE 15 32 14

Figure S10.  Get High-res Image Gene #12: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.000407 (Fisher's exact test), Q value = 0.12

Table S11.  Gene #12: 'amp_18q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 19 12 22
AMP PEAK 12(18Q11.2) MUTATED 19 5 1 3
AMP PEAK 12(18Q11.2) WILD-TYPE 12 14 11 19

Figure S11.  Get High-res Image Gene #12: 'amp_18q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000418 (Fisher's exact test), Q value = 0.13

Table S12.  Gene #12: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 19 27
AMP PEAK 12(18Q11.2) MUTATED 21 4 3
AMP PEAK 12(18Q11.2) WILD-TYPE 17 15 24

Figure S12.  Get High-res Image Gene #12: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.03e-05 (Fisher's exact test), Q value = 0.0067

Table S13.  Gene #12: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 20 38
AMP PEAK 12(18Q11.2) MUTATED 7 0 21
AMP PEAK 12(18Q11.2) WILD-TYPE 19 20 17

Figure S13.  Get High-res Image Gene #12: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.2' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.093

Table S14.  Gene #13: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
AMP PEAK 13(19Q13.2) MUTATED 8 4 11
AMP PEAK 13(19Q13.2) WILD-TYPE 16 42 10

Figure S14.  Get High-res Image Gene #13: 'amp_19q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'CN_CNMF'

P value = 9.64e-05 (Fisher's exact test), Q value = 0.031

Table S15.  Gene #14: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
AMP PEAK 14(20Q13.2) MUTATED 6 5 13
AMP PEAK 14(20Q13.2) WILD-TYPE 18 41 8

Figure S15.  Get High-res Image Gene #14: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.069

Table S16.  Gene #17: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 1(1P36.32) MUTATED 4 5 12
DEL PEAK 1(1P36.32) WILD-TYPE 20 41 9

Figure S16.  Get High-res Image Gene #17: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 0.000164 (Fisher's exact test), Q value = 0.052

Table S17.  Gene #18: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 2(1P36.11) MUTATED 9 7 14
DEL PEAK 2(1P36.11) WILD-TYPE 15 39 7

Figure S17.  Get High-res Image Gene #18: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 9.12e-06 (Fisher's exact test), Q value = 0.003

Table S18.  Gene #18: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 35 24
DEL PEAK 2(1P36.11) MUTATED 14 2 14
DEL PEAK 2(1P36.11) WILD-TYPE 17 33 10

Figure S18.  Get High-res Image Gene #18: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p24.1' versus 'CN_CNMF'

P value = 0.000344 (Fisher's exact test), Q value = 0.11

Table S19.  Gene #21: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 5(3P24.1) MUTATED 4 4 11
DEL PEAK 5(3P24.1) WILD-TYPE 20 42 10

Figure S19.  Get High-res Image Gene #21: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q14.2' versus 'CN_CNMF'

P value = 0.000131 (Fisher's exact test), Q value = 0.042

Table S20.  Gene #23: 'del_5q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 7(5Q14.2) MUTATED 5 3 11
DEL PEAK 7(5Q14.2) WILD-TYPE 19 43 10

Figure S20.  Get High-res Image Gene #23: 'del_5q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.2' versus 'CN_CNMF'

P value = 4.43e-07 (Fisher's exact test), Q value = 0.00015

Table S21.  Gene #24: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 8(6P25.2) MUTATED 15 7 16
DEL PEAK 8(6P25.2) WILD-TYPE 9 39 5

Figure S21.  Get High-res Image Gene #24: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.2' versus 'METHLYATION_CNMF'

P value = 5.97e-06 (Fisher's exact test), Q value = 0.002

Table S22.  Gene #24: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 35 24
DEL PEAK 8(6P25.2) MUTATED 21 4 12
DEL PEAK 8(6P25.2) WILD-TYPE 10 31 12

Figure S22.  Get High-res Image Gene #24: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000369 (Fisher's exact test), Q value = 0.11

Table S23.  Gene #24: 'del_6p25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 31 52
DEL PEAK 8(6P25.2) MUTATED 0 5 29
DEL PEAK 8(6P25.2) WILD-TYPE 1 26 23

Figure S23.  Get High-res Image Gene #24: 'del_6p25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.3' versus 'CN_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.068

Table S24.  Gene #26: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 10(8P21.3) MUTATED 9 5 12
DEL PEAK 10(8P21.3) WILD-TYPE 15 41 9

Figure S24.  Get High-res Image Gene #26: 'del_8p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p21.3' versus 'METHLYATION_CNMF'

P value = 0.000425 (Fisher's exact test), Q value = 0.13

Table S25.  Gene #26: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 35 24
DEL PEAK 10(8P21.3) MUTATED 13 2 10
DEL PEAK 10(8P21.3) WILD-TYPE 18 33 14

Figure S25.  Get High-res Image Gene #26: 'del_8p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000415 (Fisher's exact test), Q value = 0.13

Table S26.  Gene #26: 'del_8p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 31 52
DEL PEAK 10(8P21.3) MUTATED 0 2 22
DEL PEAK 10(8P21.3) WILD-TYPE 1 29 30

Figure S26.  Get High-res Image Gene #26: 'del_8p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1.17e-08 (Fisher's exact test), Q value = 4e-06

Table S27.  Gene #28: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 12(9P21.3) MUTATED 23 16 19
DEL PEAK 12(9P21.3) WILD-TYPE 1 30 2

Figure S27.  Get High-res Image Gene #28: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1.16e-09 (Fisher's exact test), Q value = 4e-07

Table S28.  Gene #28: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 35 24
DEL PEAK 12(9P21.3) MUTATED 30 9 18
DEL PEAK 12(9P21.3) WILD-TYPE 1 26 6

Figure S28.  Get High-res Image Gene #28: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.000292 (Fisher's exact test), Q value = 0.091

Table S29.  Gene #28: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 24 20
DEL PEAK 12(9P21.3) MUTATED 33 11 7
DEL PEAK 12(9P21.3) WILD-TYPE 7 13 13

Figure S29.  Get High-res Image Gene #28: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000152 (Fisher's exact test), Q value = 0.049

Table S30.  Gene #28: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 31 52
DEL PEAK 12(9P21.3) MUTATED 0 11 40
DEL PEAK 12(9P21.3) WILD-TYPE 1 20 12

Figure S30.  Get High-res Image Gene #28: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0036

Table S31.  Gene #28: 'del_9p21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 19 12 22
DEL PEAK 12(9P21.3) MUTATED 29 9 4 9
DEL PEAK 12(9P21.3) WILD-TYPE 2 10 8 13

Figure S31.  Get High-res Image Gene #28: 'del_9p21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000183 (Fisher's exact test), Q value = 0.058

Table S32.  Gene #28: 'del_9p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 17 30
DEL PEAK 12(9P21.3) MUTATED 31 5 15
DEL PEAK 12(9P21.3) WILD-TYPE 6 12 15

Figure S32.  Get High-res Image Gene #28: 'del_9p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.56e-05 (Fisher's exact test), Q value = 0.0084

Table S33.  Gene #28: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 19 27
DEL PEAK 12(9P21.3) MUTATED 33 8 10
DEL PEAK 12(9P21.3) WILD-TYPE 5 11 17

Figure S33.  Get High-res Image Gene #28: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.54e-05 (Fisher's exact test), Q value = 0.0083

Table S34.  Gene #28: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 20 38
DEL PEAK 12(9P21.3) MUTATED 11 7 33
DEL PEAK 12(9P21.3) WILD-TYPE 15 13 5

Figure S34.  Get High-res Image Gene #28: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.2' versus 'CN_CNMF'

P value = 7.66e-05 (Fisher's exact test), Q value = 0.025

Table S35.  Gene #31: 'del_10q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 15(10Q23.2) MUTATED 7 1 8
DEL PEAK 15(10Q23.2) WILD-TYPE 17 45 13

Figure S35.  Get High-res Image Gene #31: 'del_10q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p12.1' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.11

Table S36.  Gene #33: 'del_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 17(12P12.1) MUTATED 6 0 5
DEL PEAK 17(12P12.1) WILD-TYPE 18 46 16

Figure S36.  Get High-res Image Gene #33: 'del_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q12' versus 'CN_CNMF'

P value = 0.000179 (Fisher's exact test), Q value = 0.057

Table S37.  Gene #34: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 18(12Q12) MUTATED 7 0 4
DEL PEAK 18(12Q12) WILD-TYPE 17 46 17

Figure S37.  Get High-res Image Gene #34: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q24.33' versus 'CN_CNMF'

P value = 0.000131 (Fisher's exact test), Q value = 0.042

Table S38.  Gene #35: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 19(12Q24.33) MUTATED 5 3 11
DEL PEAK 19(12Q24.33) WILD-TYPE 19 43 10

Figure S38.  Get High-res Image Gene #35: 'del_12q24.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q22' versus 'CN_CNMF'

P value = 1.17e-07 (Fisher's exact test), Q value = 3.9e-05

Table S39.  Gene #37: 'del_17q22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 21(17Q22) MUTATED 9 2 14
DEL PEAK 21(17Q22) WILD-TYPE 15 44 7

Figure S39.  Get High-res Image Gene #37: 'del_17q22' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q22' versus 'METHLYATION_CNMF'

P value = 0.000359 (Fisher's exact test), Q value = 0.11

Table S40.  Gene #37: 'del_17q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 35 24
DEL PEAK 21(17Q22) MUTATED 14 2 9
DEL PEAK 21(17Q22) WILD-TYPE 17 33 15

Figure S40.  Get High-res Image Gene #37: 'del_17q22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'CN_CNMF'

P value = 3.56e-06 (Fisher's exact test), Q value = 0.0012

Table S41.  Gene #39: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 23(18Q21.2) MUTATED 24 23 18
DEL PEAK 23(18Q21.2) WILD-TYPE 0 23 3

Figure S41.  Get High-res Image Gene #39: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 0.000175 (Fisher's exact test), Q value = 0.056

Table S42.  Gene #39: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 35 24
DEL PEAK 23(18Q21.2) MUTATED 27 16 21
DEL PEAK 23(18Q21.2) WILD-TYPE 4 19 3

Figure S42.  Get High-res Image Gene #39: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 4.19e-06 (Fisher's exact test), Q value = 0.0014

Table S43.  Gene #40: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 24(19P13.3) MUTATED 5 1 11
DEL PEAK 24(19P13.3) WILD-TYPE 19 45 10

Figure S43.  Get High-res Image Gene #40: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q21.1' versus 'CN_CNMF'

P value = 1.42e-06 (Fisher's exact test), Q value = 0.00048

Table S44.  Gene #42: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 26(21Q21.1) MUTATED 15 6 14
DEL PEAK 26(21Q21.1) WILD-TYPE 9 40 7

Figure S44.  Get High-res Image Gene #42: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 0.000211 (Fisher's exact test), Q value = 0.066

Table S45.  Gene #43: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 46 21
DEL PEAK 27(22Q13.31) MUTATED 11 5 11
DEL PEAK 27(22Q13.31) WILD-TYPE 13 41 10

Figure S45.  Get High-res Image Gene #43: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 91

  • Number of significantly focal cnvs = 43

  • Number of molecular subtypes = 8

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

Fisher's exact test

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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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

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