Correlation between copy number variation genes (focal events) and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
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/C1GM8621
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 29 focal events and 8 molecular subtypes across 224 patients, 69 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_3p12.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_3q26.31 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_7q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • del_1p36.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

  • del_6q27 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

  • del_10p11.21 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

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

  • del_11q24.2 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

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

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

  • del_16q24.1 cnv correlated to 'METHLYATION_CNMF'.

  • del_21q22.3 cnv correlated to 'CN_CNMF'.

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

  • del_xp11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 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 29 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, 69 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
amp 7q22 1 135 (60%) 89 1e-05
(0.00232)
1e-05
(0.00232)
1e-05
(0.00232)
1e-05
(0.00232)
0.116
(1.00)
0.00779
(1.00)
0.023
(1.00)
2e-05
(0.0041)
del 9p21 3 33 (15%) 191 1e-05
(0.00232)
1e-05
(0.00232)
1e-05
(0.00232)
2e-05
(0.0041)
0.00626
(0.945)
0.0102
(1.00)
0.0822
(1.00)
8e-05
(0.015)
amp 3p12 1 64 (29%) 160 1e-05
(0.00232)
0.00445
(0.681)
3e-05
(0.00603)
0.00038
(0.0669)
0.212
(1.00)
0.00674
(1.00)
0.315
(1.00)
5e-05
(0.0098)
amp 17q25 2 160 (71%) 64 1e-05
(0.00232)
0.0001
(0.0185)
6e-05
(0.0115)
2e-05
(0.0041)
0.228
(1.00)
0.12
(1.00)
0.215
(1.00)
0.0201
(1.00)
del 3p22 1 19 (8%) 205 0.00019
(0.034)
2e-05
(0.0041)
1e-05
(0.00232)
0.00209
(0.334)
0.0859
(1.00)
0.113
(1.00)
0.0707
(1.00)
1e-05
(0.00232)
del 4q34 3 26 (12%) 198 0.00013
(0.0237)
1e-05
(0.00232)
1e-05
(0.00232)
0.0109
(1.00)
0.445
(1.00)
0.214
(1.00)
0.932
(1.00)
3e-05
(0.00603)
del 5q35 2 11 (5%) 213 0.0107
(1.00)
3e-05
(0.00603)
0.00045
(0.0783)
0.00146
(0.239)
0.0441
(1.00)
0.0017
(0.277)
0.208
(1.00)
1e-05
(0.00232)
del 22q12 2 53 (24%) 171 5e-05
(0.0098)
1e-05
(0.00232)
1e-05
(0.00232)
0.0493
(1.00)
0.904
(1.00)
0.938
(1.00)
0.509
(1.00)
1e-05
(0.00232)
amp 3q26 31 80 (36%) 144 1e-05
(0.00232)
0.056
(1.00)
7e-05
(0.0133)
0.00312
(0.487)
0.068
(1.00)
0.0144
(1.00)
0.333
(1.00)
1e-05
(0.00232)
del 1p36 32 44 (20%) 180 1e-05
(0.00232)
7e-05
(0.0133)
1e-05
(0.00232)
0.0556
(1.00)
0.891
(1.00)
0.951
(1.00)
0.467
(1.00)
0.00391
(0.602)
del 6q27 24 (11%) 200 0.00016
(0.0288)
0.00053
(0.0906)
7e-05
(0.0133)
0.0645
(1.00)
0.545
(1.00)
0.636
(1.00)
0.636
(1.00)
0.00807
(1.00)
del 11q22 3 23 (10%) 201 0.0004
(0.07)
0.00056
(0.0952)
0.00046
(0.0796)
0.028
(1.00)
0.203
(1.00)
0.238
(1.00)
0.258
(1.00)
0.229
(1.00)
del 14q11 2 44 (20%) 180 1e-05
(0.00232)
0.0341
(1.00)
0.00058
(0.098)
0.00134
(0.222)
0.575
(1.00)
0.498
(1.00)
0.619
(1.00)
0.0868
(1.00)
del 15q13 3 29 (13%) 195 5e-05
(0.0098)
0.0001
(0.0185)
3e-05
(0.00603)
0.00184
(0.296)
0.11
(1.00)
0.145
(1.00)
0.203
(1.00)
0.0032
(0.496)
del xp11 22 21 (9%) 203 9e-05
(0.0167)
1e-05
(0.00232)
1e-05
(0.00232)
0.0123
(1.00)
0.198
(1.00)
0.223
(1.00)
0.39
(1.00)
0.0251
(1.00)
del xq28 20 (9%) 204 0.00012
(0.022)
0.00071
(0.119)
0.00024
(0.0427)
0.266
(1.00)
0.36
(1.00)
0.685
(1.00)
0.466
(1.00)
0.0537
(1.00)
del 6q22 31 21 (9%) 203 0.00049
(0.0843)
0.0211
(1.00)
0.00031
(0.0549)
0.146
(1.00)
0.655
(1.00)
0.421
(1.00)
0.651
(1.00)
0.00225
(0.358)
del 10p11 21 13 (6%) 211 0.00447
(0.681)
0.00136
(0.224)
5e-05
(0.0098)
0.12
(1.00)
0.147
(1.00)
0.872
(1.00)
0.456
(1.00)
0.0694
(1.00)
del 11q24 2 23 (10%) 201 0.00293
(0.46)
5e-05
(0.0098)
0.00014
(0.0253)
0.0279
(1.00)
0.203
(1.00)
0.216
(1.00)
0.259
(1.00)
0.0154
(1.00)
amp 2p23 2 41 (18%) 183 1e-05
(0.00232)
0.00712
(1.00)
0.0446
(1.00)
0.165
(1.00)
0.0163
(1.00)
0.854
(1.00)
0.0587
(1.00)
0.121
(1.00)
amp 2q32 1 48 (21%) 176 1e-05
(0.00232)
0.057
(1.00)
0.0629
(1.00)
0.14
(1.00)
0.255
(1.00)
0.674
(1.00)
0.0824
(1.00)
0.658
(1.00)
del 6p12 3 19 (8%) 205 0.00079
(0.132)
0.0307
(1.00)
0.00629
(0.945)
0.429
(1.00)
0.321
(1.00)
0.448
(1.00)
0.123
(1.00)
0.142
(1.00)
del 16q24 1 9 (4%) 215 0.0196
(1.00)
1e-05
(0.00232)
0.0108
(1.00)
0.111
(1.00)
0.842
(1.00)
0.153
(1.00)
0.912
(1.00)
0.00227
(0.359)
del 21q22 3 36 (16%) 188 4e-05
(0.00788)
0.387
(1.00)
0.267
(1.00)
0.866
(1.00)
0.218
(1.00)
0.34
(1.00)
0.32
(1.00)
0.093
(1.00)
amp 19p13 2 24 (11%) 200 0.0845
(1.00)
0.028
(1.00)
0.0181
(1.00)
0.0371
(1.00)
0.36
(1.00)
1
(1.00)
0.224
(1.00)
0.00943
(1.00)
del 2q37 3 11 (5%) 213 0.00966
(1.00)
0.00183
(0.296)
0.173
(1.00)
0.0141
(1.00)
0.0713
(1.00)
0.186
(1.00)
0.0294
(1.00)
0.0101
(1.00)
del 5p14 2 10 (4%) 214 0.416
(1.00)
0.0108
(1.00)
0.126
(1.00)
0.163
(1.00)
0.166
(1.00)
0.191
(1.00)
0.257
(1.00)
0.0683
(1.00)
del 19p13 3 17 (8%) 207 0.0571
(1.00)
0.0343
(1.00)
0.0255
(1.00)
0.485
(1.00)
0.157
(1.00)
0.576
(1.00)
0.195
(1.00)
0.33
(1.00)
del 19q13 42 16 (7%) 208 0.158
(1.00)
0.0333
(1.00)
0.00791
(1.00)
0.465
(1.00)
0.19
(1.00)
0.746
(1.00)
0.0608
(1.00)
0.0549
(1.00)
'amp_2p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
AMP PEAK 1(2P23.2) MUTATED 1 16 24
AMP PEAK 1(2P23.2) WILD-TYPE 83 91 9

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 = 0.0023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
AMP PEAK 2(2Q32.1) MUTATED 1 22 25
AMP PEAK 2(2Q32.1) WILD-TYPE 83 85 8

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

'amp_3p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S3.  Gene #3: 'amp_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
AMP PEAK 3(3P12.1) MUTATED 29 9 26
AMP PEAK 3(3P12.1) WILD-TYPE 55 98 7

Figure S3.  Get High-res Image Gene #3: 'amp_3p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3p12.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.006

Table S4.  Gene #3: 'amp_3p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
AMP PEAK 3(3P12.1) MUTATED 23 8 24 7
AMP PEAK 3(3P12.1) WILD-TYPE 24 62 38 25

Figure S4.  Get High-res Image Gene #3: 'amp_3p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.067

Table S5.  Gene #3: 'amp_3p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
AMP PEAK 3(3P12.1) MUTATED 23 10 29
AMP PEAK 3(3P12.1) WILD-TYPE 50 62 37

Figure S5.  Get High-res Image Gene #3: 'amp_3p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0098

Table S6.  Gene #3: 'amp_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
AMP PEAK 3(3P12.1) MUTATED 13 2 11 7 6 21 4
AMP PEAK 3(3P12.1) WILD-TYPE 14 32 25 25 29 19 16

Figure S6.  Get High-res Image Gene #3: 'amp_3p12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S7.  Gene #4: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
AMP PEAK 4(3Q26.31) MUTATED 35 16 29
AMP PEAK 4(3Q26.31) WILD-TYPE 49 91 4

Figure S7.  Get High-res Image Gene #4: 'amp_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.31' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.013

Table S8.  Gene #4: 'amp_3q26.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
AMP PEAK 4(3Q26.31) MUTATED 26 11 26 14
AMP PEAK 4(3Q26.31) WILD-TYPE 21 59 36 18

Figure S8.  Get High-res Image Gene #4: 'amp_3q26.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S9.  Gene #4: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
AMP PEAK 4(3Q26.31) MUTATED 16 4 13 9 7 26 5
AMP PEAK 4(3Q26.31) WILD-TYPE 11 30 23 23 28 14 15

Figure S9.  Get High-res Image Gene #4: 'amp_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S10.  Gene #5: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
AMP PEAK 5(7Q22.1) MUTATED 79 29 27
AMP PEAK 5(7Q22.1) WILD-TYPE 5 78 6

Figure S10.  Get High-res Image Gene #5: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S11.  Gene #5: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
AMP PEAK 5(7Q22.1) MUTATED 28 18 78
AMP PEAK 5(7Q22.1) WILD-TYPE 28 38 18

Figure S11.  Get High-res Image Gene #5: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S12.  Gene #5: 'amp_7q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
AMP PEAK 5(7Q22.1) MUTATED 27 22 55 25
AMP PEAK 5(7Q22.1) WILD-TYPE 20 48 7 7

Figure S12.  Get High-res Image Gene #5: 'amp_7q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S13.  Gene #5: 'amp_7q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
AMP PEAK 5(7Q22.1) MUTATED 32 37 60
AMP PEAK 5(7Q22.1) WILD-TYPE 41 35 6

Figure S13.  Get High-res Image Gene #5: 'amp_7q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0041

Table S14.  Gene #5: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
AMP PEAK 5(7Q22.1) MUTATED 15 10 28 24 20 32 6
AMP PEAK 5(7Q22.1) WILD-TYPE 12 24 8 8 15 8 14

Figure S14.  Get High-res Image Gene #5: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S15.  Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
AMP PEAK 6(17Q25.2) MUTATED 83 47 30
AMP PEAK 6(17Q25.2) WILD-TYPE 1 60 3

Figure S15.  Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.2' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.018

Table S16.  Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
AMP PEAK 6(17Q25.2) MUTATED 33 33 82
AMP PEAK 6(17Q25.2) WILD-TYPE 23 23 14

Figure S16.  Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.011

Table S17.  Gene #6: 'amp_17q25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
AMP PEAK 6(17Q25.2) MUTATED 37 38 56 23
AMP PEAK 6(17Q25.2) WILD-TYPE 10 32 6 9

Figure S17.  Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_17q25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0041

Table S18.  Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
AMP PEAK 6(17Q25.2) MUTATED 49 44 61
AMP PEAK 6(17Q25.2) WILD-TYPE 24 28 5

Figure S18.  Get High-res Image Gene #6: 'amp_17q25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S19.  Gene #8: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 1(1P36.32) MUTATED 1 34 9
DEL PEAK 1(1P36.32) WILD-TYPE 83 73 24

Figure S19.  Get High-res Image Gene #8: 'del_1p36.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.013

Table S20.  Gene #8: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 1(1P36.32) MUTATED 10 22 9
DEL PEAK 1(1P36.32) WILD-TYPE 46 34 87

Figure S20.  Get High-res Image Gene #8: 'del_1p36.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S21.  Gene #8: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 1(1P36.32) MUTATED 5 31 5 0
DEL PEAK 1(1P36.32) WILD-TYPE 42 39 57 32

Figure S21.  Get High-res Image Gene #8: 'del_1p36.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.034

Table S22.  Gene #10: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 3(3P22.1) MUTATED 0 16 3
DEL PEAK 3(3P22.1) WILD-TYPE 84 91 30

Figure S22.  Get High-res Image Gene #10: 'del_3p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p22.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0041

Table S23.  Gene #10: 'del_3p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 3(3P22.1) MUTATED 3 14 1
DEL PEAK 3(3P22.1) WILD-TYPE 53 42 95

Figure S23.  Get High-res Image Gene #10: '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 = 0.0023

Table S24.  Gene #10: 'del_3p22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 3(3P22.1) MUTATED 1 16 0 0
DEL PEAK 3(3P22.1) WILD-TYPE 46 54 62 32

Figure S24.  Get High-res Image Gene #10: 'del_3p22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S25.  Gene #10: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
DEL PEAK 3(3P22.1) MUTATED 0 10 1 0 5 0 3
DEL PEAK 3(3P22.1) WILD-TYPE 27 24 35 32 30 40 17

Figure S25.  Get High-res Image Gene #10: 'del_3p22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.024

Table S26.  Gene #11: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 4(4Q34.3) MUTATED 1 20 5
DEL PEAK 4(4Q34.3) WILD-TYPE 83 87 28

Figure S26.  Get High-res Image Gene #11: '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 = 0.0023

Table S27.  Gene #11: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 4(4Q34.3) MUTATED 3 19 2
DEL PEAK 4(4Q34.3) WILD-TYPE 53 37 94

Figure S27.  Get High-res Image Gene #11: '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 = 0.0023

Table S28.  Gene #11: 'del_4q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 4(4Q34.3) MUTATED 2 22 1 0
DEL PEAK 4(4Q34.3) WILD-TYPE 45 48 61 32

Figure S28.  Get High-res Image Gene #11: 'del_4q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.006

Table S29.  Gene #11: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
DEL PEAK 4(4Q34.3) MUTATED 2 8 3 0 2 2 9
DEL PEAK 4(4Q34.3) WILD-TYPE 25 26 33 32 33 38 11

Figure S29.  Get High-res Image Gene #11: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q35.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.006

Table S30.  Gene #13: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 6(5Q35.2) MUTATED 1 9 0
DEL PEAK 6(5Q35.2) WILD-TYPE 55 47 96

Figure S30.  Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q35.2' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.078

Table S31.  Gene #13: 'del_5q35.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 6(5Q35.2) MUTATED 1 10 0 0
DEL PEAK 6(5Q35.2) WILD-TYPE 46 60 62 32

Figure S31.  Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_5q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.24

Table S32.  Gene #13: 'del_5q35.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
DEL PEAK 6(5Q35.2) MUTATED 2 9 0
DEL PEAK 6(5Q35.2) WILD-TYPE 71 63 66

Figure S32.  Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S33.  Gene #13: 'del_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
DEL PEAK 6(5Q35.2) MUTATED 0 2 0 0 0 1 8
DEL PEAK 6(5Q35.2) WILD-TYPE 27 32 36 32 35 39 12

Figure S33.  Get High-res Image Gene #13: 'del_5q35.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p12.3' versus 'CN_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.13

Table S34.  Gene #14: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 7(6P12.3) MUTATED 1 11 7
DEL PEAK 7(6P12.3) WILD-TYPE 83 96 26

Figure S34.  Get High-res Image Gene #14: 'del_6p12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.084

Table S35.  Gene #15: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 8(6Q22.31) MUTATED 1 13 7
DEL PEAK 8(6Q22.31) WILD-TYPE 83 94 26

Figure S35.  Get High-res Image Gene #15: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.055

Table S36.  Gene #15: 'del_6q22.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 8(6Q22.31) MUTATED 2 16 3 0
DEL PEAK 8(6Q22.31) WILD-TYPE 45 54 59 32

Figure S36.  Get High-res Image Gene #15: 'del_6q22.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.029

Table S37.  Gene #16: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 9(6Q27) MUTATED 1 15 8
DEL PEAK 9(6Q27) WILD-TYPE 83 92 25

Figure S37.  Get High-res Image Gene #16: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.091

Table S38.  Gene #16: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 9(6Q27) MUTATED 5 14 4
DEL PEAK 9(6Q27) WILD-TYPE 51 42 92

Figure S38.  Get High-res Image Gene #16: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.013

Table S39.  Gene #16: 'del_6q27' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 9(6Q27) MUTATED 3 18 3 0
DEL PEAK 9(6Q27) WILD-TYPE 44 52 59 32

Figure S39.  Get High-res Image Gene #16: 'del_6q27' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S40.  Gene #17: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 10(9P21.3) MUTATED 1 25 7
DEL PEAK 10(9P21.3) WILD-TYPE 83 82 26

Figure S40.  Get High-res Image Gene #17: '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 = 0.0023

Table S41.  Gene #17: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 10(9P21.3) MUTATED 9 19 2
DEL PEAK 10(9P21.3) WILD-TYPE 47 37 94

Figure S41.  Get High-res Image Gene #17: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S42.  Gene #17: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 10(9P21.3) MUTATED 3 28 0 1
DEL PEAK 10(9P21.3) WILD-TYPE 44 42 62 31

Figure S42.  Get High-res Image Gene #17: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0041

Table S43.  Gene #17: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
DEL PEAK 10(9P21.3) MUTATED 10 21 1
DEL PEAK 10(9P21.3) WILD-TYPE 63 51 65

Figure S43.  Get High-res Image Gene #17: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.015

Table S44.  Gene #17: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
DEL PEAK 10(9P21.3) MUTATED 0 7 5 0 10 3 8
DEL PEAK 10(9P21.3) WILD-TYPE 27 27 31 32 25 37 12

Figure S44.  Get High-res Image Gene #17: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.22

Table S45.  Gene #18: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 11(10P11.21) MUTATED 1 9 2
DEL PEAK 11(10P11.21) WILD-TYPE 55 47 94

Figure S45.  Get High-res Image Gene #18: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0098

Table S46.  Gene #18: 'del_10p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 11(10P11.21) MUTATED 0 12 1 0
DEL PEAK 11(10P11.21) WILD-TYPE 47 58 61 32

Figure S46.  Get High-res Image Gene #18: 'del_10p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11q22.3' versus 'CN_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.07

Table S47.  Gene #19: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 12(11Q22.3) MUTATED 1 16 6
DEL PEAK 12(11Q22.3) WILD-TYPE 83 91 27

Figure S47.  Get High-res Image Gene #19: 'del_11q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.3' versus 'METHLYATION_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.095

Table S48.  Gene #19: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 12(11Q22.3) MUTATED 6 13 3
DEL PEAK 12(11Q22.3) WILD-TYPE 50 43 93

Figure S48.  Get High-res Image Gene #19: 'del_11q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.08

Table S49.  Gene #19: 'del_11q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 12(11Q22.3) MUTATED 2 16 2 1
DEL PEAK 12(11Q22.3) WILD-TYPE 45 54 60 31

Figure S49.  Get High-res Image Gene #19: 'del_11q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11q24.2' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0098

Table S50.  Gene #20: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 13(11Q24.2) MUTATED 6 14 2
DEL PEAK 13(11Q24.2) WILD-TYPE 50 42 94

Figure S50.  Get High-res Image Gene #20: 'del_11q24.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q24.2' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.025

Table S51.  Gene #20: 'del_11q24.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 13(11Q24.2) MUTATED 2 16 1 2
DEL PEAK 13(11Q24.2) WILD-TYPE 45 54 61 30

Figure S51.  Get High-res Image Gene #20: 'del_11q24.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S52.  Gene #21: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 14(14Q11.2) MUTATED 3 32 9
DEL PEAK 14(14Q11.2) WILD-TYPE 81 75 24

Figure S52.  Get High-res Image Gene #21: 'del_14q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.098

Table S53.  Gene #21: 'del_14q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 14(14Q11.2) MUTATED 10 24 5 3
DEL PEAK 14(14Q11.2) WILD-TYPE 37 46 57 29

Figure S53.  Get High-res Image Gene #21: 'del_14q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.22

Table S54.  Gene #21: 'del_14q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 72 66
DEL PEAK 14(14Q11.2) MUTATED 14 23 5
DEL PEAK 14(14Q11.2) WILD-TYPE 59 49 61

Figure S54.  Get High-res Image Gene #21: 'del_14q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.3' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0098

Table S55.  Gene #22: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 15(15Q13.3) MUTATED 1 21 7
DEL PEAK 15(15Q13.3) WILD-TYPE 83 86 26

Figure S55.  Get High-res Image Gene #22: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.3' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.018

Table S56.  Gene #22: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 15(15Q13.3) MUTATED 10 14 3
DEL PEAK 15(15Q13.3) WILD-TYPE 46 42 93

Figure S56.  Get High-res Image Gene #22: 'del_15q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q13.3' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.006

Table S57.  Gene #22: 'del_15q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 15(15Q13.3) MUTATED 4 20 2 0
DEL PEAK 15(15Q13.3) WILD-TYPE 43 50 60 32

Figure S57.  Get High-res Image Gene #22: 'del_15q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S58.  Gene #23: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 16(16Q24.1) MUTATED 0 9 0
DEL PEAK 16(16Q24.1) WILD-TYPE 56 47 96

Figure S58.  Get High-res Image Gene #23: 'del_16q24.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0079

Table S59.  Gene #26: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 19(21Q22.3) MUTATED 8 13 15
DEL PEAK 19(21Q22.3) WILD-TYPE 76 94 18

Figure S59.  Get High-res Image Gene #26: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.2' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0098

Table S60.  Gene #27: 'del_22q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 20(22Q12.2) MUTATED 7 38 8
DEL PEAK 20(22Q12.2) WILD-TYPE 77 69 25

Figure S60.  Get High-res Image Gene #27: '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 = 0.0023

Table S61.  Gene #27: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 20(22Q12.2) MUTATED 8 31 11
DEL PEAK 20(22Q12.2) WILD-TYPE 48 25 85

Figure S61.  Get High-res Image Gene #27: '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 = 0.0023

Table S62.  Gene #27: 'del_22q12.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 20(22Q12.2) MUTATED 8 36 5 2
DEL PEAK 20(22Q12.2) WILD-TYPE 39 34 57 30

Figure S62.  Get High-res Image Gene #27: 'del_22q12.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_22q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S63.  Gene #27: 'del_22q12.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 27 34 36 32 35 40 20
DEL PEAK 20(22Q12.2) MUTATED 2 20 9 1 8 5 8
DEL PEAK 20(22Q12.2) WILD-TYPE 25 14 27 31 27 35 12

Figure S63.  Get High-res Image Gene #27: 'del_22q12.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp11.22' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.017

Table S64.  Gene #28: 'del_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 21(XP11.22) MUTATED 0 15 6
DEL PEAK 21(XP11.22) WILD-TYPE 84 92 27

Figure S64.  Get High-res Image Gene #28: 'del_xp11.22' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S65.  Gene #28: 'del_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 21(XP11.22) MUTATED 3 15 1
DEL PEAK 21(XP11.22) WILD-TYPE 53 41 95

Figure S65.  Get High-res Image Gene #28: 'del_xp11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S66.  Gene #28: 'del_xp11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 21(XP11.22) MUTATED 2 18 0 0
DEL PEAK 21(XP11.22) WILD-TYPE 45 52 62 32

Figure S66.  Get High-res Image Gene #28: 'del_xp11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xq28' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.022

Table S67.  Gene #29: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 84 107 33
DEL PEAK 22(XQ28) MUTATED 0 15 5
DEL PEAK 22(XQ28) WILD-TYPE 84 92 28

Figure S67.  Get High-res Image Gene #29: 'del_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq28' versus 'METHLYATION_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.12

Table S68.  Gene #29: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 56 96
DEL PEAK 22(XQ28) MUTATED 3 12 3
DEL PEAK 22(XQ28) WILD-TYPE 53 44 93

Figure S68.  Get High-res Image Gene #29: 'del_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq28' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.043

Table S69.  Gene #29: 'del_xq28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 70 62 32
DEL PEAK 22(XQ28) MUTATED 2 15 2 0
DEL PEAK 22(XQ28) WILD-TYPE 45 55 60 32

Figure S69.  Get High-res Image Gene #29: 'del_xq28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

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

  • Number of patients = 224

  • Number of significantly focal cnvs = 29

  • 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)