Correlation between copy number variation genes (focal events) and molecular subtypes
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 28 focal events and 8 molecular subtypes across 162 patients, 33 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_17q21.31 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

  • del_1p12 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_3p24.1 cnv correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q26.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_11p15.4 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q22.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • del_17p13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_17q11.2 cnv correlated to 'CN_CNMF'.

  • del_22q13.31 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_xp21.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 28 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, 33 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 11p15 4 58 (36%) 104 1e-05
(0.00224) 		2e-05
(0.00422) 		0.00057
(0.112) 		1e-05
(0.00224) 		0.00013
(0.0266) 		1e-05
(0.00224) 		1e-05
(0.00224) 		0.00038
(0.0768)
del 3p24 1 64 (40%) 98 0.00156
(0.298) 		0.00744
(1.00) 		5e-05
(0.0103) 		3e-05
(0.00621) 		1e-05
(0.00224) 		0.00022
(0.0447) 		1e-05
(0.00224) 		2e-05
(0.00422)
del 1p12 113 (70%) 49 1e-05
(0.00224) 		2e-05
(0.00422) 		1e-05
(0.00224) 		1e-05
(0.00224) 		0.00066
(0.129) 		0.0167
(1.00) 		0.0074
(1.00) 		0.0153
(1.00)
del 11q22 1 48 (30%) 114 1e-05
(0.00224) 		0.209
(1.00) 		0.00066
(0.129) 		0.0101
(1.00) 		0.00346
(0.65) 		0.0007
(0.136) 		0.00038
(0.0768) 		0.0311
(1.00)
del 3q26 1 93 (57%) 69 2e-05
(0.00422) 		0.517
(1.00) 		0.0238
(1.00) 		1e-05
(0.00224) 		0.0192
(1.00) 		0.00951
(1.00) 		0.0115
(1.00) 		0.0108
(1.00)
del 17p13 2 64 (40%) 98 0.00017
(0.0347) 		0.00042
(0.084) 		0.016
(1.00) 		0.00619
(1.00) 		0.0272
(1.00) 		0.00788
(1.00) 		0.171
(1.00) 		0.0169
(1.00)
del 22q13 31 65 (40%) 97 1e-05
(0.00224) 		0.0203
(1.00) 		0.0203
(1.00) 		0.00047
(0.0935) 		0.011
(1.00) 		0.0267
(1.00) 		0.0162
(1.00) 		0.0192
(1.00)
del xp21 1 46 (28%) 116 0.00099
(0.19) 		0.00593
(1.00) 		0.0336
(1.00) 		0.00388
(0.722) 		0.00072
(0.139) 		0.0451
(1.00) 		0.185
(1.00) 		0.0335
(1.00)
amp 17q21 31 16 (10%) 146 0.628
(1.00) 		0.89
(1.00) 		0.536
(1.00) 		0.00053
(0.105) 		0.753
(1.00) 		0.143
(1.00) 		0.0663
(1.00) 		0.455
(1.00)
del 17q11 2 42 (26%) 120 1e-05
(0.00224) 		0.00371
(0.694) 		0.0242
(1.00) 		0.00289
(0.546) 		0.103
(1.00) 		0.0713
(1.00) 		0.368
(1.00) 		0.14
(1.00)
amp 1q21 3 30 (19%) 132 0.00488
(0.903) 		0.609
(1.00) 		0.637
(1.00) 		0.941
(1.00) 		0.902
(1.00) 		0.447
(1.00) 		0.693
(1.00) 		0.825
(1.00)
amp 4q25 6 (4%) 156 0.882
(1.00) 		0.761
(1.00) 		0.13
(1.00) 		0.388
(1.00) 		0.766
(1.00) 		0.624
(1.00) 		0.293
(1.00) 		0.504
(1.00)
amp 4q31 1 13 (8%) 149 0.00548
(1.00) 		0.0661
(1.00) 		0.613
(1.00) 		0.00781
(1.00) 		0.405
(1.00) 		0.228
(1.00) 		0.115
(1.00) 		0.323
(1.00)
amp 11p15 2 8 (5%) 154 0.0936
(1.00) 		0.0782
(1.00) 		0.332
(1.00) 		0.104
(1.00) 		0.41
(1.00) 		0.399
(1.00) 		0.458
(1.00) 		0.81
(1.00)
amp 12q13 3 16 (10%) 146 0.0449
(1.00) 		0.139
(1.00) 		0.61
(1.00) 		0.62
(1.00) 		0.0466
(1.00) 		0.274
(1.00) 		0.129
(1.00) 		0.323
(1.00)
amp 14q24 3 10 (6%) 152 0.0298
(1.00) 		0.199
(1.00) 		0.852
(1.00) 		0.173
(1.00) 		0.457
(1.00) 		0.711
(1.00) 		0.443
(1.00) 		0.858
(1.00)
del 1q42 13 18 (11%) 144 0.0219
(1.00) 		0.136
(1.00) 		0.025
(1.00) 		0.178
(1.00) 		0.333
(1.00) 		0.536
(1.00) 		0.0729
(1.00) 		0.247
(1.00)
del 4q28 3 10 (6%) 152 0.0734
(1.00) 		0.242
(1.00) 		0.0182
(1.00) 		0.338
(1.00) 		0.457
(1.00) 		0.715
(1.00) 		0.325
(1.00) 		0.321
(1.00)
del 5q15 12 (7%) 150 0.596
(1.00) 		1
(1.00) 		0.975
(1.00) 		1
(1.00) 		0.928
(1.00) 		0.187
(1.00) 		0.244
(1.00) 		0.294
(1.00)
del 6p12 3 10 (6%) 152 0.0113
(1.00) 		0.266
(1.00) 		0.0205
(1.00) 		0.0864
(1.00) 		0.197
(1.00) 		0.163
(1.00) 		0.929
(1.00) 		0.0513
(1.00)
del 6q16 1 24 (15%) 138 0.136
(1.00) 		0.0765
(1.00) 		0.0263
(1.00) 		0.00747
(1.00) 		0.0152
(1.00) 		0.0057
(1.00) 		0.0829
(1.00) 		0.0959
(1.00)
del 8p22 25 (15%) 137 0.00167
(0.317) 		0.0833
(1.00) 		0.00636
(1.00) 		0.00903
(1.00) 		0.209
(1.00) 		0.239
(1.00) 		0.027
(1.00) 		0.243
(1.00)
del 8q23 3 13 (8%) 149 0.0326
(1.00) 		0.868
(1.00) 		0.275
(1.00) 		0.518
(1.00) 		0.0718
(1.00) 		0.465
(1.00) 		0.929
(1.00) 		0.297
(1.00)
del 9p24 2 15 (9%) 147 0.288
(1.00) 		0.34
(1.00) 		0.0914
(1.00) 		0.177
(1.00) 		0.481
(1.00) 		0.0779
(1.00) 		0.482
(1.00) 		0.305
(1.00)
del 9q21 12 14 (9%) 148 0.00968
(1.00) 		0.549
(1.00) 		0.369
(1.00) 		0.389
(1.00) 		0.726
(1.00) 		0.111
(1.00) 		0.585
(1.00) 		0.343
(1.00)
del 12q21 33 8 (5%) 154 0.0599
(1.00) 		0.892
(1.00) 		0.913
(1.00) 		0.877
(1.00) 		0.592
(1.00) 		0.697
(1.00) 		0.835
(1.00) 		1
(1.00)
del 13q22 3 8 (5%) 154 0.249
(1.00) 		0.893
(1.00) 		0.272
(1.00) 		0.429
(1.00) 		1
(1.00) 		0.611
(1.00) 		0.719
(1.00) 		0.856
(1.00)
del 16q21 5 (3%) 157 0.0662
(1.00) 		0.115
(1.00) 		0.551
(1.00) 		0.0261
(1.00) 		0.212
(1.00) 		0.59
(1.00) 		0.0901
(1.00) 		0.828
(1.00)
'amp_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.1

Table S1.  Gene #7: 'amp_17q21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
AMP PEAK 7(17Q21.31) MUTATED 10 5 1 0
AMP PEAK 7(17Q21.31) WILD-TYPE 24 59 42 21

Figure S1.  Get High-res Image Gene #7: 'amp_17q21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S2.  Gene #8: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 1(1P12) MUTATED 54 27 32
DEL PEAK 1(1P12) WILD-TYPE 6 36 7

Figure S2.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p12' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0042

Table S3.  Gene #8: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
DEL PEAK 1(1P12) MUTATED 24 68 21
DEL PEAK 1(1P12) WILD-TYPE 16 10 23

Figure S3.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S4.  Gene #8: 'del_1p12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 1(1P12) MUTATED 24 58 21 10
DEL PEAK 1(1P12) WILD-TYPE 9 6 23 11

Figure S4.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S5.  Gene #8: 'del_1p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 1(1P12) MUTATED 19 58 27 9
DEL PEAK 1(1P12) WILD-TYPE 15 6 16 12

Figure S5.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p12' versus 'MIRSEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.13

Table S6.  Gene #8: 'del_1p12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 1(1P12) MUTATED 39 51 23
DEL PEAK 1(1P12) WILD-TYPE 26 7 16

Figure S6.  Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p24.1' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.01

Table S7.  Gene #10: 'del_3p24.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 3(3P24.1) MUTATED 18 15 27 4
DEL PEAK 3(3P24.1) WILD-TYPE 15 49 17 17

Figure S7.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0062

Table S8.  Gene #10: 'del_3p24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 3(3P24.1) MUTATED 12 17 31 4
DEL PEAK 3(3P24.1) WILD-TYPE 22 47 12 17

Figure S8.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S9.  Gene #10: 'del_3p24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 3(3P24.1) MUTATED 39 19 6
DEL PEAK 3(3P24.1) WILD-TYPE 26 39 33

Figure S9.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.045

Table S10.  Gene #10: 'del_3p24.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 3(3P24.1) MUTATED 39 15 6 4
DEL PEAK 3(3P24.1) WILD-TYPE 27 39 12 20

Figure S10.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S11.  Gene #10: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
DEL PEAK 3(3P24.1) MUTATED 12 15 2 29 6
DEL PEAK 3(3P24.1) WILD-TYPE 22 43 9 6 17

Figure S11.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0042

Table S12.  Gene #10: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
DEL PEAK 3(3P24.1) MUTATED 18 36 6 4
DEL PEAK 3(3P24.1) WILD-TYPE 53 17 12 15

Figure S12.  Get High-res Image Gene #10: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0042

Table S13.  Gene #11: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 4(3Q26.1) MUTATED 40 22 31
DEL PEAK 4(3Q26.1) WILD-TYPE 20 41 8

Figure S13.  Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S14.  Gene #11: 'del_3q26.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 4(3Q26.1) MUTATED 6 47 33 7
DEL PEAK 4(3Q26.1) WILD-TYPE 28 17 10 14

Figure S14.  Get High-res Image Gene #11: 'del_3q26.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S15.  Gene #20: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 13(11P15.4) MUTATED 2 39 17
DEL PEAK 13(11P15.4) WILD-TYPE 58 24 22

Figure S15.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0042

Table S16.  Gene #20: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
DEL PEAK 13(11P15.4) MUTATED 23 14 21
DEL PEAK 13(11P15.4) WILD-TYPE 17 64 23

Figure S16.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.4' versus 'MRNASEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.11

Table S17.  Gene #20: 'del_11p15.4' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 13(11P15.4) MUTATED 13 13 26 6
DEL PEAK 13(11P15.4) WILD-TYPE 20 51 18 15

Figure S17.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11p15.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S18.  Gene #20: 'del_11p15.4' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 13(11P15.4) MUTATED 11 10 31 6
DEL PEAK 13(11P15.4) WILD-TYPE 23 54 12 15

Figure S18.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.027

Table S19.  Gene #20: 'del_11p15.4' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 13(11P15.4) MUTATED 36 12 10
DEL PEAK 13(11P15.4) WILD-TYPE 29 46 29

Figure S19.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_11p15.4' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S20.  Gene #20: 'del_11p15.4' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 13(11P15.4) MUTATED 39 8 5 6
DEL PEAK 13(11P15.4) WILD-TYPE 27 46 13 18

Figure S20.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S21.  Gene #20: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
DEL PEAK 13(11P15.4) MUTATED 12 8 2 24 11
DEL PEAK 13(11P15.4) WILD-TYPE 22 50 9 11 12

Figure S21.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11p15.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.077

Table S22.  Gene #20: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 71 53 18 19
DEL PEAK 13(11P15.4) MUTATED 16 31 5 5
DEL PEAK 13(11P15.4) WILD-TYPE 55 22 13 14

Figure S22.  Get High-res Image Gene #20: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S23.  Gene #21: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 14(11Q22.1) MUTATED 4 26 18
DEL PEAK 14(11Q22.1) WILD-TYPE 56 37 21

Figure S23.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.13

Table S24.  Gene #21: 'del_11q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 64 44 21
DEL PEAK 14(11Q22.1) MUTATED 9 10 23 6
DEL PEAK 14(11Q22.1) WILD-TYPE 24 54 21 15

Figure S24.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.14

Table S25.  Gene #21: 'del_11q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 54 18 24
DEL PEAK 14(11Q22.1) MUTATED 30 8 2 8
DEL PEAK 14(11Q22.1) WILD-TYPE 36 46 16 16

Figure S25.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.077

Table S26.  Gene #21: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 58 11 35 23
DEL PEAK 14(11Q22.1) MUTATED 10 8 2 20 8
DEL PEAK 14(11Q22.1) WILD-TYPE 24 50 9 15 15

Figure S26.  Get High-res Image Gene #21: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_17p13.2' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.035

Table S27.  Gene #25: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 18(17P13.2) MUTATED 22 16 26
DEL PEAK 18(17P13.2) WILD-TYPE 38 47 13

Figure S27.  Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.084

Table S28.  Gene #25: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 40 78 44
DEL PEAK 18(17P13.2) MUTATED 9 43 12
DEL PEAK 18(17P13.2) WILD-TYPE 31 35 32

Figure S28.  Get High-res Image Gene #25: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S29.  Gene #26: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 19(17Q11.2) MUTATED 13 4 25
DEL PEAK 19(17Q11.2) WILD-TYPE 47 59 14

Figure S29.  Get High-res Image Gene #26: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0022

Table S30.  Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 20(22Q13.31) MUTATED 40 9 16
DEL PEAK 20(22Q13.31) WILD-TYPE 20 54 23

Figure S30.  Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.094

Table S31.  Gene #27: 'del_22q13.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 64 43 21
DEL PEAK 20(22Q13.31) MUTATED 13 37 8 7
DEL PEAK 20(22Q13.31) WILD-TYPE 21 27 35 14

Figure S31.  Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.19

Table S32.  Gene #28: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 63 39
DEL PEAK 21(XP21.1) MUTATED 21 8 17
DEL PEAK 21(XP21.1) WILD-TYPE 39 55 22

Figure S32.  Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.14

Table S33.  Gene #28: 'del_xp21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 58 39
DEL PEAK 21(XP21.1) MUTATED 13 27 6
DEL PEAK 21(XP21.1) WILD-TYPE 52 31 33

Figure S33.  Get High-res Image Gene #28: 'del_xp21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 162

  • Number of significantly focal cnvs = 28

  • 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.

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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