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 20 focal events and 8 molecular subtypes across 80 patients, 97 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_6p24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_8q24.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q25.3 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • del_1p36.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • del_3p25.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p25.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p22.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3p14.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q24 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_3q29 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q22.31 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q27 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_8p11.22 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_11q24.3 cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.

  • del_16q12.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q23.3 cnv correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q24.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 20 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, 97 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 6p24 3 45 (56%) 35 1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		0.0001
(0.000246) 		2e-05
(5.42e-05)
amp 8q24 22 61 (76%) 19 3e-05
(7.74e-05) 		0.00013
(0.000315) 		0.00387
(0.00784) 		0.00065
(0.00142) 		0.00257
(0.00534) 		0.00056
(0.00126) 		0.00017
(0.000406) 		0.00042
(0.000974)
del 3p25 2 43 (54%) 37 1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05)
del 3p25 1 43 (54%) 37 1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05)
del 3p22 2 43 (54%) 37 1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05)
del 3p14 2 44 (55%) 36 1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05)
del 3q24 44 (55%) 36 1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05)
del 3q29 44 (55%) 36 1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05) 		1e-05
(2.81e-05)
del 8p11 22 19 (24%) 61 1e-05
(2.81e-05) 		7e-05
(0.000175) 		3e-05
(7.74e-05) 		1e-05
(2.81e-05) 		3e-05
(7.74e-05) 		1e-05
(2.81e-05) 		2e-05
(5.42e-05) 		6e-05
(0.000152)
del 16q24 3 17 (21%) 63 0.00111
(0.00237) 		0.0158
(0.0287) 		0.0488
(0.0805) 		0.0046
(0.0092) 		0.357
(0.406) 		0.0387
(0.0652) 		0.0812
(0.119) 		0.00632
(0.012)
del 6q27 24 (30%) 56 0.00102
(0.00221) 		0.0298
(0.0518) 		0.111
(0.157) 		0.00513
(0.01) 		0.176
(0.227) 		0.749
(0.778) 		0.0518
(0.0837) 		0.00381
(0.00782)
del 6q22 31 24 (30%) 56 0.00041
(0.000965) 		0.0639
(0.1) 		0.183
(0.232) 		0.0147
(0.0271) 		0.322
(0.373) 		0.934
(0.946) 		0.171
(0.223) 		0.00117
(0.00246)
del 16q12 1 16 (20%) 64 0.0204
(0.0364) 		0.132
(0.181) 		0.0967
(0.138) 		0.0128
(0.0238) 		0.824
(0.845) 		0.125
(0.172) 		0.144
(0.193) 		0.0463
(0.0771)
del 16q23 3 17 (21%) 63 0.00895
(0.0168) 		0.0797
(0.119) 		0.0502
(0.0819) 		0.00485
(0.00958) 		0.729
(0.763) 		0.0965
(0.138) 		0.0802
(0.119) 		0.0302
(0.052)
amp 17q25 3 14 (18%) 66 0.206
(0.259) 		0.0747
(0.113) 		0.141
(0.191) 		0.112
(0.157) 		0.0059
(0.0114) 		0.00058
(0.00129) 		0.264
(0.32) 		0.33
(0.38)
del 1p36 21 24 (30%) 56 0.00056
(0.00126) 		0.0259
(0.0455) 		0.427
(0.478) 		0.165
(0.219) 		0.518
(0.559) 		0.474
(0.52) 		0.304
(0.358) 		0.491
(0.535)
del 11q24 3 7 (9%) 73 0.0668
(0.103) 		0.0186
(0.0334) 		0.0655
(0.102) 		0.0742
(0.113) 		0.0312
(0.0531) 		0.146
(0.195) 		1
(1.00) 		0.522
(0.56)
del 2q37 2 3 (4%) 77 0.247
(0.302) 		0.0549
(0.087) 		0.297
(0.354) 		0.236
(0.293) 		0.313
(0.365) 		0.443
(0.489) 		0.299
(0.354) 		0.69
(0.727)
del 5q23 1 4 (5%) 76 0.378
(0.426) 		0.117
(0.162) 		0.177
(0.227) 		0.207
(0.259) 		0.338
(0.387) 		0.755
(0.78) 		0.297
(0.354) 		0.893
(0.91)
del 17q12 3 (4%) 77 0.247
(0.302) 		0.0547
(0.087) 		0.0893
(0.13) 		0.169
(0.221) 		0.596
(0.631) 		0.44
(0.489) 		0.593
(0.631) 		0.94
(0.946)
'amp_6p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S1.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
AMP PEAK 1(6P24.3) MUTATED 9 32 4
AMP PEAK 1(6P24.3) WILD-TYPE 13 4 18

Figure S1.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S2.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
AMP PEAK 1(6P24.3) MUTATED 10 8 27
AMP PEAK 1(6P24.3) WILD-TYPE 23 10 2

Figure S2.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S3.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
AMP PEAK 1(6P24.3) MUTATED 8 6 31
AMP PEAK 1(6P24.3) WILD-TYPE 22 9 4

Figure S3.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S4.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
AMP PEAK 1(6P24.3) MUTATED 9 30 6
AMP PEAK 1(6P24.3) WILD-TYPE 20 3 12

Figure S4.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S5.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
AMP PEAK 1(6P24.3) MUTATED 12 5 28
AMP PEAK 1(6P24.3) WILD-TYPE 22 12 1

Figure S5.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S6.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
AMP PEAK 1(6P24.3) MUTATED 4 9 27 5
AMP PEAK 1(6P24.3) WILD-TYPE 13 4 1 17

Figure S6.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00025

Table S7.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
AMP PEAK 1(6P24.3) MUTATED 12 24 5
AMP PEAK 1(6P24.3) WILD-TYPE 20 4 9

Figure S7.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.4e-05

Table S8.  Gene #1: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
AMP PEAK 1(6P24.3) MUTATED 1 6 12 15 1 6
AMP PEAK 1(6P24.3) WILD-TYPE 4 6 4 1 14 4

Figure S8.  Get High-res Image Gene #1: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.22' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.7e-05

Table S9.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
AMP PEAK 2(8Q24.22) MUTATED 22 19 20
AMP PEAK 2(8Q24.22) WILD-TYPE 0 17 2

Figure S9.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.22' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00032

Table S10.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
AMP PEAK 2(8Q24.22) MUTATED 32 13 16
AMP PEAK 2(8Q24.22) WILD-TYPE 1 5 13

Figure S10.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.0078

Table S11.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
AMP PEAK 2(8Q24.22) MUTATED 28 12 21
AMP PEAK 2(8Q24.22) WILD-TYPE 2 3 14

Figure S11.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0014

Table S12.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
AMP PEAK 2(8Q24.22) MUTATED 28 19 14
AMP PEAK 2(8Q24.22) WILD-TYPE 1 14 4

Figure S12.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0053

Table S13.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
AMP PEAK 2(8Q24.22) MUTATED 32 10 19
AMP PEAK 2(8Q24.22) WILD-TYPE 2 7 10

Figure S13.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0013

Table S14.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
AMP PEAK 2(8Q24.22) MUTATED 16 6 18 21
AMP PEAK 2(8Q24.22) WILD-TYPE 1 7 10 1

Figure S14.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00041

Table S15.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
AMP PEAK 2(8Q24.22) MUTATED 31 15 12
AMP PEAK 2(8Q24.22) WILD-TYPE 1 13 2

Figure S15.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.00097

Table S16.  Gene #2: 'amp_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
AMP PEAK 2(8Q24.22) MUTATED 5 11 6 12 14 10
AMP PEAK 2(8Q24.22) WILD-TYPE 0 1 10 4 1 0

Figure S16.  Get High-res Image Gene #2: 'amp_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.3' versus 'MIRSEQ_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 0.011

Table S17.  Gene #3: 'amp_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
AMP PEAK 3(17Q25.3) MUTATED 4 0 10
AMP PEAK 3(17Q25.3) WILD-TYPE 30 17 19

Figure S17.  Get High-res Image Gene #3: 'amp_17q25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0013

Table S18.  Gene #3: 'amp_17q25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
AMP PEAK 3(17Q25.3) MUTATED 3 0 11 0
AMP PEAK 3(17Q25.3) WILD-TYPE 14 13 17 22

Figure S18.  Get High-res Image Gene #3: 'amp_17q25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'CN_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0013

Table S19.  Gene #4: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 1(1P36.21) MUTATED 4 6 14
DEL PEAK 1(1P36.21) WILD-TYPE 18 30 8

Figure S19.  Get High-res Image Gene #4: 'del_1p36.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.21' versus 'METHLYATION_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.046

Table S20.  Gene #4: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
DEL PEAK 1(1P36.21) MUTATED 11 9 4
DEL PEAK 1(1P36.21) WILD-TYPE 22 9 25

Figure S20.  Get High-res Image Gene #4: 'del_1p36.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S21.  Gene #6: 'del_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 3(3P25.2) MUTATED 22 2 19
DEL PEAK 3(3P25.2) WILD-TYPE 0 34 3

Figure S21.  Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p25.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S22.  Gene #6: 'del_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
DEL PEAK 3(3P25.2) MUTATED 33 9 1
DEL PEAK 3(3P25.2) WILD-TYPE 0 9 28

Figure S22.  Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p25.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S23.  Gene #6: 'del_3p25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
DEL PEAK 3(3P25.2) MUTATED 30 10 3
DEL PEAK 3(3P25.2) WILD-TYPE 0 5 32

Figure S23.  Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S24.  Gene #6: 'del_3p25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 3(3P25.2) MUTATED 29 2 12
DEL PEAK 3(3P25.2) WILD-TYPE 0 31 6

Figure S24.  Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S25.  Gene #6: 'del_3p25.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
DEL PEAK 3(3P25.2) MUTATED 29 12 2
DEL PEAK 3(3P25.2) WILD-TYPE 5 5 27

Figure S25.  Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S26.  Gene #6: 'del_3p25.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 3(3P25.2) MUTATED 17 1 3 22
DEL PEAK 3(3P25.2) WILD-TYPE 0 12 25 0

Figure S26.  Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S27.  Gene #6: 'del_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
DEL PEAK 3(3P25.2) MUTATED 29 4 9
DEL PEAK 3(3P25.2) WILD-TYPE 3 24 5

Figure S27.  Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S28.  Gene #6: 'del_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 3(3P25.2) MUTATED 5 7 4 1 15 10
DEL PEAK 3(3P25.2) WILD-TYPE 0 5 12 15 0 0

Figure S28.  Get High-res Image Gene #6: 'del_3p25.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S29.  Gene #7: 'del_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 4(3P25.1) MUTATED 22 2 19
DEL PEAK 4(3P25.1) WILD-TYPE 0 34 3

Figure S29.  Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S30.  Gene #7: 'del_3p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
DEL PEAK 4(3P25.1) MUTATED 33 9 1
DEL PEAK 4(3P25.1) WILD-TYPE 0 9 28

Figure S30.  Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S31.  Gene #7: 'del_3p25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
DEL PEAK 4(3P25.1) MUTATED 30 10 3
DEL PEAK 4(3P25.1) WILD-TYPE 0 5 32

Figure S31.  Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S32.  Gene #7: 'del_3p25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 4(3P25.1) MUTATED 29 2 12
DEL PEAK 4(3P25.1) WILD-TYPE 0 31 6

Figure S32.  Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S33.  Gene #7: 'del_3p25.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
DEL PEAK 4(3P25.1) MUTATED 29 12 2
DEL PEAK 4(3P25.1) WILD-TYPE 5 5 27

Figure S33.  Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S34.  Gene #7: 'del_3p25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 4(3P25.1) MUTATED 17 1 3 22
DEL PEAK 4(3P25.1) WILD-TYPE 0 12 25 0

Figure S34.  Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S35.  Gene #7: 'del_3p25.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
DEL PEAK 4(3P25.1) MUTATED 29 4 9
DEL PEAK 4(3P25.1) WILD-TYPE 3 24 5

Figure S35.  Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S36.  Gene #7: 'del_3p25.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 4(3P25.1) MUTATED 5 7 4 1 15 10
DEL PEAK 4(3P25.1) WILD-TYPE 0 5 12 15 0 0

Figure S36.  Get High-res Image Gene #7: 'del_3p25.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S37.  Gene #8: 'del_3p22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 5(3P22.2) MUTATED 22 2 19
DEL PEAK 5(3P22.2) WILD-TYPE 0 34 3

Figure S37.  Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S38.  Gene #8: 'del_3p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
DEL PEAK 5(3P22.2) MUTATED 33 9 1
DEL PEAK 5(3P22.2) WILD-TYPE 0 9 28

Figure S38.  Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S39.  Gene #8: 'del_3p22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
DEL PEAK 5(3P22.2) MUTATED 30 10 3
DEL PEAK 5(3P22.2) WILD-TYPE 0 5 32

Figure S39.  Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S40.  Gene #8: 'del_3p22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 5(3P22.2) MUTATED 29 2 12
DEL PEAK 5(3P22.2) WILD-TYPE 0 31 6

Figure S40.  Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S41.  Gene #8: 'del_3p22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
DEL PEAK 5(3P22.2) MUTATED 29 12 2
DEL PEAK 5(3P22.2) WILD-TYPE 5 5 27

Figure S41.  Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S42.  Gene #8: 'del_3p22.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 5(3P22.2) MUTATED 17 1 3 22
DEL PEAK 5(3P22.2) WILD-TYPE 0 12 25 0

Figure S42.  Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S43.  Gene #8: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
DEL PEAK 5(3P22.2) MUTATED 29 4 9
DEL PEAK 5(3P22.2) WILD-TYPE 3 24 5

Figure S43.  Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S44.  Gene #8: 'del_3p22.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 5(3P22.2) MUTATED 5 7 4 1 15 10
DEL PEAK 5(3P22.2) WILD-TYPE 0 5 12 15 0 0

Figure S44.  Get High-res Image Gene #8: 'del_3p22.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S45.  Gene #9: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 6(3P14.2) MUTATED 22 2 20
DEL PEAK 6(3P14.2) WILD-TYPE 0 34 2

Figure S45.  Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S46.  Gene #9: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
DEL PEAK 6(3P14.2) MUTATED 33 10 1
DEL PEAK 6(3P14.2) WILD-TYPE 0 8 28

Figure S46.  Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S47.  Gene #9: 'del_3p14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
DEL PEAK 6(3P14.2) MUTATED 30 10 4
DEL PEAK 6(3P14.2) WILD-TYPE 0 5 31

Figure S47.  Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S48.  Gene #9: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 6(3P14.2) MUTATED 29 2 13
DEL PEAK 6(3P14.2) WILD-TYPE 0 31 5

Figure S48.  Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S49.  Gene #9: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
DEL PEAK 6(3P14.2) MUTATED 30 12 2
DEL PEAK 6(3P14.2) WILD-TYPE 4 5 27

Figure S49.  Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S50.  Gene #9: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 6(3P14.2) MUTATED 17 2 3 22
DEL PEAK 6(3P14.2) WILD-TYPE 0 11 25 0

Figure S50.  Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S51.  Gene #9: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
DEL PEAK 6(3P14.2) MUTATED 30 4 9
DEL PEAK 6(3P14.2) WILD-TYPE 2 24 5

Figure S51.  Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S52.  Gene #9: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 6(3P14.2) MUTATED 5 8 4 1 15 10
DEL PEAK 6(3P14.2) WILD-TYPE 0 4 12 15 0 0

Figure S52.  Get High-res Image Gene #9: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q24' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S53.  Gene #10: 'del_3q24' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 7(3Q24) MUTATED 22 2 20
DEL PEAK 7(3Q24) WILD-TYPE 0 34 2

Figure S53.  Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q24' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S54.  Gene #10: 'del_3q24' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
DEL PEAK 7(3Q24) MUTATED 33 10 1
DEL PEAK 7(3Q24) WILD-TYPE 0 8 28

Figure S54.  Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q24' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S55.  Gene #10: 'del_3q24' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
DEL PEAK 7(3Q24) MUTATED 30 10 4
DEL PEAK 7(3Q24) WILD-TYPE 0 5 31

Figure S55.  Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3q24' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S56.  Gene #10: 'del_3q24' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 7(3Q24) MUTATED 29 2 13
DEL PEAK 7(3Q24) WILD-TYPE 0 31 5

Figure S56.  Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3q24' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S57.  Gene #10: 'del_3q24' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
DEL PEAK 7(3Q24) MUTATED 30 12 2
DEL PEAK 7(3Q24) WILD-TYPE 4 5 27

Figure S57.  Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3q24' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S58.  Gene #10: 'del_3q24' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 7(3Q24) MUTATED 17 2 3 22
DEL PEAK 7(3Q24) WILD-TYPE 0 11 25 0

Figure S58.  Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3q24' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S59.  Gene #10: 'del_3q24' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
DEL PEAK 7(3Q24) MUTATED 30 4 9
DEL PEAK 7(3Q24) WILD-TYPE 2 24 5

Figure S59.  Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3q24' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S60.  Gene #10: 'del_3q24' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 7(3Q24) MUTATED 5 8 4 1 15 10
DEL PEAK 7(3Q24) WILD-TYPE 0 4 12 15 0 0

Figure S60.  Get High-res Image Gene #10: 'del_3q24' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q29' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S61.  Gene #11: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 8(3Q29) MUTATED 22 2 20
DEL PEAK 8(3Q29) WILD-TYPE 0 34 2

Figure S61.  Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S62.  Gene #11: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
DEL PEAK 8(3Q29) MUTATED 33 10 1
DEL PEAK 8(3Q29) WILD-TYPE 0 8 28

Figure S62.  Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S63.  Gene #11: 'del_3q29' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
DEL PEAK 8(3Q29) MUTATED 30 10 4
DEL PEAK 8(3Q29) WILD-TYPE 0 5 31

Figure S63.  Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S64.  Gene #11: 'del_3q29' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 8(3Q29) MUTATED 29 2 13
DEL PEAK 8(3Q29) WILD-TYPE 0 31 5

Figure S64.  Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S65.  Gene #11: 'del_3q29' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
DEL PEAK 8(3Q29) MUTATED 30 12 2
DEL PEAK 8(3Q29) WILD-TYPE 4 5 27

Figure S65.  Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S66.  Gene #11: 'del_3q29' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 8(3Q29) MUTATED 17 2 3 22
DEL PEAK 8(3Q29) WILD-TYPE 0 11 25 0

Figure S66.  Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S67.  Gene #11: 'del_3q29' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
DEL PEAK 8(3Q29) MUTATED 30 4 9
DEL PEAK 8(3Q29) WILD-TYPE 2 24 5

Figure S67.  Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3q29' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S68.  Gene #11: 'del_3q29' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 8(3Q29) MUTATED 5 8 4 1 15 10
DEL PEAK 8(3Q29) WILD-TYPE 0 4 12 15 0 0

Figure S68.  Get High-res Image Gene #11: 'del_3q29' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00096

Table S69.  Gene #13: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 10(6Q22.31) MUTATED 13 10 1
DEL PEAK 10(6Q22.31) WILD-TYPE 9 26 21

Figure S69.  Get High-res Image Gene #13: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.027

Table S70.  Gene #13: 'del_6q22.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 10(6Q22.31) MUTATED 13 10 1
DEL PEAK 10(6Q22.31) WILD-TYPE 16 23 17

Figure S70.  Get High-res Image Gene #13: 'del_6q22.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.0025

Table S71.  Gene #13: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 10(6Q22.31) MUTATED 3 2 2 7 2 8
DEL PEAK 10(6Q22.31) WILD-TYPE 2 10 14 9 13 2

Figure S71.  Get High-res Image Gene #13: 'del_6q22.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q27' versus 'CN_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0022

Table S72.  Gene #14: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 11(6Q27) MUTATED 13 9 2
DEL PEAK 11(6Q27) WILD-TYPE 9 27 20

Figure S72.  Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q27' versus 'METHLYATION_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.052

Table S73.  Gene #14: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
DEL PEAK 11(6Q27) MUTATED 15 2 7
DEL PEAK 11(6Q27) WILD-TYPE 18 16 22

Figure S73.  Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q27' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00513 (Fisher's exact test), Q value = 0.01

Table S74.  Gene #14: 'del_6q27' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 11(6Q27) MUTATED 14 9 1
DEL PEAK 11(6Q27) WILD-TYPE 15 24 17

Figure S74.  Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6q27' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.0078

Table S75.  Gene #14: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 11(6Q27) MUTATED 3 2 2 6 3 8
DEL PEAK 11(6Q27) WILD-TYPE 2 10 14 10 12 2

Figure S75.  Get High-res Image Gene #14: 'del_6q27' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S76.  Gene #15: 'del_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 12(8P11.22) MUTATED 16 1 2
DEL PEAK 12(8P11.22) WILD-TYPE 6 35 20

Figure S76.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p11.22' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00017

Table S77.  Gene #15: 'del_8p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
DEL PEAK 12(8P11.22) MUTATED 16 2 1
DEL PEAK 12(8P11.22) WILD-TYPE 17 16 28

Figure S77.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p11.22' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.7e-05

Table S78.  Gene #15: 'del_8p11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
DEL PEAK 12(8P11.22) MUTATED 15 3 1
DEL PEAK 12(8P11.22) WILD-TYPE 15 12 34

Figure S78.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_8p11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S79.  Gene #15: 'del_8p11.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 12(8P11.22) MUTATED 16 1 2
DEL PEAK 12(8P11.22) WILD-TYPE 13 32 16

Figure S79.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.22' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.7e-05

Table S80.  Gene #15: 'del_8p11.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
DEL PEAK 12(8P11.22) MUTATED 15 4 0
DEL PEAK 12(8P11.22) WILD-TYPE 19 13 29

Figure S80.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_8p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S81.  Gene #15: 'del_8p11.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 12(8P11.22) MUTATED 7 1 0 11
DEL PEAK 12(8P11.22) WILD-TYPE 10 12 28 11

Figure S81.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_8p11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.4e-05

Table S82.  Gene #15: 'del_8p11.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
DEL PEAK 12(8P11.22) MUTATED 16 0 3
DEL PEAK 12(8P11.22) WILD-TYPE 16 28 11

Figure S82.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_8p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00015

Table S83.  Gene #15: 'del_8p11.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 12(8P11.22) MUTATED 3 4 0 0 7 5
DEL PEAK 12(8P11.22) WILD-TYPE 2 8 16 16 8 5

Figure S83.  Get High-res Image Gene #15: 'del_8p11.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q24.3' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.033

Table S84.  Gene #16: 'del_11q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
DEL PEAK 15(11Q24.3) MUTATED 1 0 6
DEL PEAK 15(11Q24.3) WILD-TYPE 32 18 23

Figure S84.  Get High-res Image Gene #16: 'del_11q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q24.3' versus 'MIRSEQ_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.053

Table S85.  Gene #16: 'del_11q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
DEL PEAK 15(11Q24.3) MUTATED 1 0 6
DEL PEAK 15(11Q24.3) WILD-TYPE 33 17 23

Figure S85.  Get High-res Image Gene #16: 'del_11q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_16q12.1' versus 'CN_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.036

Table S86.  Gene #17: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 16(16Q12.1) MUTATED 9 5 2
DEL PEAK 16(16Q12.1) WILD-TYPE 13 31 20

Figure S86.  Get High-res Image Gene #17: 'del_16q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.024

Table S87.  Gene #17: 'del_16q12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 16(16Q12.1) MUTATED 11 4 1
DEL PEAK 16(16Q12.1) WILD-TYPE 18 29 17

Figure S87.  Get High-res Image Gene #17: 'del_16q12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0463 (Fisher's exact test), Q value = 0.077

Table S88.  Gene #17: 'del_16q12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 16(16Q12.1) MUTATED 3 2 0 4 4 3
DEL PEAK 16(16Q12.1) WILD-TYPE 2 10 16 12 11 7

Figure S88.  Get High-res Image Gene #17: 'del_16q12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.3' versus 'CN_CNMF'

P value = 0.00895 (Fisher's exact test), Q value = 0.017

Table S89.  Gene #18: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 17(16Q23.3) MUTATED 10 5 2
DEL PEAK 17(16Q23.3) WILD-TYPE 12 31 20

Figure S89.  Get High-res Image Gene #18: 'del_16q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00485 (Fisher's exact test), Q value = 0.0096

Table S90.  Gene #18: 'del_16q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 17(16Q23.3) MUTATED 12 4 1
DEL PEAK 17(16Q23.3) WILD-TYPE 17 29 17

Figure S90.  Get High-res Image Gene #18: 'del_16q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.052

Table S91.  Gene #18: 'del_16q23.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 17(16Q23.3) MUTATED 3 2 0 4 4 4
DEL PEAK 17(16Q23.3) WILD-TYPE 2 10 16 12 11 6

Figure S91.  Get High-res Image Gene #18: 'del_16q23.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.3' versus 'CN_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0024

Table S92.  Gene #19: 'del_16q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
DEL PEAK 18(16Q24.3) MUTATED 11 4 2
DEL PEAK 18(16Q24.3) WILD-TYPE 11 32 20

Figure S92.  Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q24.3' versus 'METHLYATION_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.029

Table S93.  Gene #19: 'del_16q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
DEL PEAK 18(16Q24.3) MUTATED 12 3 2
DEL PEAK 18(16Q24.3) WILD-TYPE 21 15 27

Figure S93.  Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.081

Table S94.  Gene #19: 'del_16q24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
DEL PEAK 18(16Q24.3) MUTATED 11 2 4
DEL PEAK 18(16Q24.3) WILD-TYPE 19 13 31

Figure S94.  Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.0092

Table S95.  Gene #19: 'del_16q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
DEL PEAK 18(16Q24.3) MUTATED 12 4 1
DEL PEAK 18(16Q24.3) WILD-TYPE 17 29 17

Figure S95.  Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0387 (Fisher's exact test), Q value = 0.065

Table S96.  Gene #19: 'del_16q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
DEL PEAK 18(16Q24.3) MUTATED 6 0 4 7
DEL PEAK 18(16Q24.3) WILD-TYPE 11 13 24 15

Figure S96.  Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00632 (Fisher's exact test), Q value = 0.012

Table S97.  Gene #19: 'del_16q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
DEL PEAK 18(16Q24.3) MUTATED 3 1 0 4 4 5
DEL PEAK 18(16Q24.3) WILD-TYPE 2 11 16 12 11 5

Figure S97.  Get High-res Image Gene #19: 'del_16q24.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/19783311/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/19785804/UVM-TP.transferedmergedcluster.txt

  • Number of patients = 80

  • Number of significantly focal cnvs = 20

  • 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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