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 18 focal events and 10 molecular subtypes across 123 patients, 94 significant findings detected with P value < 0.05 and Q value < 0.25.

  • amp_1q41 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_12p12.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • amp_17q11.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • amp_xq23 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_2q37.1 cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

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

  • del_6p25.2 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_6q21 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_7q36.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_9p22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_10q26.3 cnv correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_19p13.11 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_22q12.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • del_22q13.32 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 18 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 94 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
amp 1q41 28 (23%) 95 0.00028
(0.0012) 		1e-05
(9.47e-05) 		0.00027
(0.0012) 		1e-05
(9.47e-05) 		1e-05
(9.47e-05) 		1e-05
(9.47e-05) 		1e-05
(9.47e-05) 		1e-05
(9.47e-05) 		1e-05
(9.47e-05) 		1e-05
(9.47e-05)
del 6p25 2 26 (21%) 97 6e-05
(0.00036) 		1e-05
(9.47e-05) 		2e-05
(0.000164) 		0.00022
(0.00107) 		0.00213
(0.0071) 		6e-05
(0.00036) 		0.00136
(0.0048) 		0.00651
(0.018) 		1e-05
(9.47e-05) 		0.00632
(0.0178)
del 6q21 20 (16%) 103 3e-05
(0.000225) 		1e-05
(9.47e-05) 		0.0003
(0.00126) 		4e-05
(0.000277) 		1e-05
(9.47e-05) 		2e-05
(0.000164) 		1e-05
(9.47e-05) 		0.0002
(0.001) 		1e-05
(9.47e-05) 		6e-05
(0.00036)
amp 12p12 3 6 (5%) 117 0.0249
(0.0547) 		0.00054
(0.00211) 		0.193
(0.272) 		0.0291
(0.0608) 		0.0001
(0.000545) 		0.00032
(0.00128) 		0.0611
(0.112) 		0.00261
(0.00831) 		0.00873
(0.0221) 		0.0159
(0.0381)
amp xq23 7 (6%) 116 0.00238
(0.00779) 		5e-05
(0.000333) 		0.369
(0.459) 		0.157
(0.237) 		0.00839
(0.0216) 		0.0139
(0.0342) 		0.00399
(0.0116) 		0.0452
(0.0875) 		0.00263
(0.00831) 		0.0264
(0.056)
del 3p22 2 14 (11%) 109 0.00104
(0.0039) 		1e-05
(9.47e-05) 		0.052
(0.0985) 		4e-05
(0.000277) 		0.0322
(0.0659) 		0.0154
(0.0376) 		0.0161
(0.0381) 		0.0646
(0.117) 		0.00028
(0.0012) 		0.0399
(0.079)
del 9p21 3 11 (9%) 112 0.00025
(0.00118) 		0.00017
(9e-04) 		0.198
(0.276) 		0.00129
(0.00464) 		8e-05
(0.000465) 		1e-05
(9.47e-05) 		0.634
(0.692) 		0.00031
(0.00127) 		0.114
(0.179) 		0.0352
(0.0709)
amp 17q11 2 10 (8%) 113 1e-05
(9.47e-05) 		0.00319
(0.00973) 		0.0564
(0.105) 		0.0483
(0.0924) 		0.00139
(0.00481) 		2e-05
(0.000164) 		0.713
(0.751) 		0.0008
(0.00306) 		0.0796
(0.133) 		0.113
(0.179)
del 9p22 1 6 (5%) 117 3e-05
(0.000225) 		0.00831
(0.0216) 		0.0653
(0.117) 		0.131
(0.199) 		0.00286
(0.00888) 		9e-05
(0.000506) 		1
(1.00) 		0.00174
(0.00591) 		0.522
(0.599) 		0.12
(0.184)
del 19p13 11 5 (4%) 118 0.00018
(0.000926) 		0.0114
(0.0286) 		0.187
(0.269) 		0.203
(0.279) 		0.00387
(0.0114) 		0.00028
(0.0012) 		0.744
(0.775) 		0.00483
(0.0138) 		0.392
(0.473) 		0.242
(0.32)
del 22q12 1 19 (15%) 104 1e-05
(9.47e-05) 		0.0265
(0.056) 		0.0074
(0.0199) 		0.0536
(0.101) 		0.0189
(0.0435) 		0.073
(0.126) 		0.732
(0.766) 		0.457
(0.54) 		0.0247
(0.0547) 		0.459
(0.54)
del 22q13 32 15 (12%) 108 1e-05
(9.47e-05) 		0.0246
(0.0547) 		0.0438
(0.0857) 		0.0806
(0.133) 		0.0743
(0.127) 		0.0258
(0.056) 		0.595
(0.677) 		0.3
(0.391) 		0.0195
(0.0445) 		0.9
(0.931)
del 7q36 3 3 (2%) 120 0.00679
(0.0185) 		0.00755
(0.02) 		0.375
(0.46) 		0.202
(0.279) 		0.00125
(0.00459) 		0.00373
(0.0112) 		0.662
(0.707) 		0.117
(0.182) 		0.0756
(0.128) 		0.619
(0.683)
del 10q26 3 6 (5%) 117 0.37
(0.459) 		0.113
(0.179) 		0.184
(0.269) 		0.0318
(0.0658) 		0.0696
(0.122) 		0.219
(0.294) 		0.16
(0.24) 		0.0654
(0.117) 		0.52
(0.599) 		0.0354
(0.0709)
del 2q37 1 5 (4%) 118 0.598
(0.677) 		0.425
(0.51) 		0.191
(0.271) 		0.111
(0.179) 		0.672
(0.711) 		0.309
(0.4) 		1
(1.00) 		0.0188
(0.0435) 		0.64
(0.694) 		0.213
(0.289)
amp 10q11 21 3 (2%) 120 0.168
(0.248) 		0.0866
(0.142) 		0.0677
(0.119) 		0.188
(0.269) 		0.663
(0.707) 		0.105
(0.17) 		0.0761
(0.128) 		0.62
(0.683)
amp 21q22 2 3 (2%) 120 0.167
(0.248) 		0.381
(0.463) 		0.373
(0.46) 		0.205
(0.28) 		0.495
(0.578) 		0.188
(0.269) 		0.661
(0.707) 		0.344
(0.438) 		0.615
(0.683) 		0.622
(0.683)
amp xp11 22 3 (2%) 120 0.256
(0.336) 		0.522
(0.599) 		0.356
(0.448) 		0.328
(0.422) 		0.23
(0.307) 		0.615
(0.683) 		0.345
(0.438) 		0.44
(0.525)
'amp_1q41' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0012

Table S1.  Gene #1: 'amp_1q41' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
AMP PEAK 1(1Q41) MUTATED 14 0 7 4 3
AMP PEAK 1(1Q41) WILD-TYPE 22 27 12 27 7

Figure S1.  Get High-res Image Gene #1: 'amp_1q41' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q41' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S2.  Gene #1: 'amp_1q41' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
AMP PEAK 1(1Q41) MUTATED 4 0 14 9 0 0 0 1
AMP PEAK 1(1Q41) WILD-TYPE 33 23 5 1 18 8 2 5

Figure S2.  Get High-res Image Gene #1: 'amp_1q41' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q41' versus 'RPPA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0012

Table S3.  Gene #1: 'amp_1q41' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
AMP PEAK 1(1Q41) MUTATED 14 1 4
AMP PEAK 1(1Q41) WILD-TYPE 17 24 30

Figure S3.  Get High-res Image Gene #1: 'amp_1q41' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_1q41' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S4.  Gene #1: 'amp_1q41' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
AMP PEAK 1(1Q41) MUTATED 0 0 5 14
AMP PEAK 1(1Q41) WILD-TYPE 16 23 26 6

Figure S4.  Get High-res Image Gene #1: 'amp_1q41' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q41' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S5.  Gene #1: 'amp_1q41' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
AMP PEAK 1(1Q41) MUTATED 18 0 0 10
AMP PEAK 1(1Q41) WILD-TYPE 27 30 30 4

Figure S5.  Get High-res Image Gene #1: 'amp_1q41' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q41' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S6.  Gene #1: 'amp_1q41' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
AMP PEAK 1(1Q41) MUTATED 20 0 0 8
AMP PEAK 1(1Q41) WILD-TYPE 27 42 20 2

Figure S6.  Get High-res Image Gene #1: 'amp_1q41' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q41' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S7.  Gene #1: 'amp_1q41' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
AMP PEAK 1(1Q41) MUTATED 24 0 4 0
AMP PEAK 1(1Q41) WILD-TYPE 32 61 1 1

Figure S7.  Get High-res Image Gene #1: 'amp_1q41' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q41' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S8.  Gene #1: 'amp_1q41' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
AMP PEAK 1(1Q41) MUTATED 10 0 12 6 0 0
AMP PEAK 1(1Q41) WILD-TYPE 17 18 16 1 16 27

Figure S8.  Get High-res Image Gene #1: 'amp_1q41' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q41' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S9.  Gene #1: 'amp_1q41' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
AMP PEAK 1(1Q41) MUTATED 1 0 26 1
AMP PEAK 1(1Q41) WILD-TYPE 27 51 17 0

Figure S9.  Get High-res Image Gene #1: 'amp_1q41' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q41' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S10.  Gene #1: 'amp_1q41' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
AMP PEAK 1(1Q41) MUTATED 9 0 19 0
AMP PEAK 1(1Q41) WILD-TYPE 18 33 16 28

Figure S10.  Get High-res Image Gene #1: 'amp_1q41' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.3' versus 'CN_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.055

Table S11.  Gene #3: 'amp_12p12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
AMP PEAK 3(12P12.3) MUTATED 1 0 4 1 0
AMP PEAK 3(12P12.3) WILD-TYPE 35 27 15 30 10

Figure S11.  Get High-res Image Gene #3: 'amp_12p12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.3' versus 'METHLYATION_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0021

Table S12.  Gene #3: 'amp_12p12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
AMP PEAK 3(12P12.3) MUTATED 0 0 1 4 0 0 0 1
AMP PEAK 3(12P12.3) WILD-TYPE 37 23 18 6 18 8 2 5

Figure S12.  Get High-res Image Gene #3: 'amp_12p12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p12.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.061

Table S13.  Gene #3: 'amp_12p12.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
AMP PEAK 3(12P12.3) MUTATED 1 0 0 3
AMP PEAK 3(12P12.3) WILD-TYPE 15 23 31 17

Figure S13.  Get High-res Image Gene #3: 'amp_12p12.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_12p12.3' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00055

Table S14.  Gene #3: 'amp_12p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
AMP PEAK 3(12P12.3) MUTATED 1 0 0 5
AMP PEAK 3(12P12.3) WILD-TYPE 44 30 30 9

Figure S14.  Get High-res Image Gene #3: 'amp_12p12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0013

Table S15.  Gene #3: 'amp_12p12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
AMP PEAK 3(12P12.3) MUTATED 1 0 1 4
AMP PEAK 3(12P12.3) WILD-TYPE 46 42 19 6

Figure S15.  Get High-res Image Gene #3: 'amp_12p12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00261 (Fisher's exact test), Q value = 0.0083

Table S16.  Gene #3: 'amp_12p12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
AMP PEAK 3(12P12.3) MUTATED 1 0 2 3 0 0
AMP PEAK 3(12P12.3) WILD-TYPE 26 18 26 4 16 27

Figure S16.  Get High-res Image Gene #3: 'amp_12p12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00873 (Fisher's exact test), Q value = 0.022

Table S17.  Gene #3: 'amp_12p12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
AMP PEAK 3(12P12.3) MUTATED 0 0 6 0
AMP PEAK 3(12P12.3) WILD-TYPE 28 51 37 1

Figure S17.  Get High-res Image Gene #3: 'amp_12p12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.038

Table S18.  Gene #3: 'amp_12p12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
AMP PEAK 3(12P12.3) MUTATED 1 0 5 0
AMP PEAK 3(12P12.3) WILD-TYPE 26 33 30 28

Figure S18.  Get High-res Image Gene #3: 'amp_12p12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S19.  Gene #4: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
AMP PEAK 4(17Q11.2) MUTATED 0 2 8 0 0
AMP PEAK 4(17Q11.2) WILD-TYPE 36 25 11 31 10

Figure S19.  Get High-res Image Gene #4: 'amp_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00319 (Fisher's exact test), Q value = 0.0097

Table S20.  Gene #4: 'amp_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
AMP PEAK 4(17Q11.2) MUTATED 1 3 1 5 0 0 0 0
AMP PEAK 4(17Q11.2) WILD-TYPE 36 20 18 5 18 8 2 6

Figure S20.  Get High-res Image Gene #4: 'amp_17q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.092

Table S21.  Gene #4: 'amp_17q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
AMP PEAK 4(17Q11.2) MUTATED 1 2 0 4
AMP PEAK 4(17Q11.2) WILD-TYPE 15 21 31 16

Figure S21.  Get High-res Image Gene #4: 'amp_17q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0048

Table S22.  Gene #4: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
AMP PEAK 4(17Q11.2) MUTATED 2 0 3 5
AMP PEAK 4(17Q11.2) WILD-TYPE 43 30 27 9

Figure S22.  Get High-res Image Gene #4: 'amp_17q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S23.  Gene #4: 'amp_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
AMP PEAK 4(17Q11.2) MUTATED 2 0 3 5
AMP PEAK 4(17Q11.2) WILD-TYPE 45 42 17 5

Figure S23.  Get High-res Image Gene #4: 'amp_17q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.0031

Table S24.  Gene #4: 'amp_17q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
AMP PEAK 4(17Q11.2) MUTATED 1 0 2 3 4 0
AMP PEAK 4(17Q11.2) WILD-TYPE 26 18 26 4 12 27

Figure S24.  Get High-res Image Gene #4: 'amp_17q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq23' versus 'CN_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.0078

Table S25.  Gene #7: 'amp_xq23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
AMP PEAK 7(XQ23) MUTATED 7 0 0 0 0
AMP PEAK 7(XQ23) WILD-TYPE 29 27 19 31 10

Figure S25.  Get High-res Image Gene #7: 'amp_xq23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq23' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

Table S26.  Gene #7: 'amp_xq23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
AMP PEAK 7(XQ23) MUTATED 0 0 7 0 0 0 0 0
AMP PEAK 7(XQ23) WILD-TYPE 37 23 12 10 18 8 2 6

Figure S26.  Get High-res Image Gene #7: 'amp_xq23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq23' versus 'MRNASEQ_CNMF'

P value = 0.00839 (Fisher's exact test), Q value = 0.022

Table S27.  Gene #7: 'amp_xq23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
AMP PEAK 7(XQ23) MUTATED 7 0 0 0
AMP PEAK 7(XQ23) WILD-TYPE 38 30 30 14

Figure S27.  Get High-res Image Gene #7: 'amp_xq23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.034

Table S28.  Gene #7: 'amp_xq23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
AMP PEAK 7(XQ23) MUTATED 7 0 0 0
AMP PEAK 7(XQ23) WILD-TYPE 40 42 20 10

Figure S28.  Get High-res Image Gene #7: 'amp_xq23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq23' versus 'MIRSEQ_CNMF'

P value = 0.00399 (Fisher's exact test), Q value = 0.012

Table S29.  Gene #7: 'amp_xq23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
AMP PEAK 7(XQ23) MUTATED 5 0 2 0
AMP PEAK 7(XQ23) WILD-TYPE 51 61 3 1

Figure S29.  Get High-res Image Gene #7: 'amp_xq23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 0.087

Table S30.  Gene #7: 'amp_xq23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
AMP PEAK 7(XQ23) MUTATED 5 0 2 0 0 0
AMP PEAK 7(XQ23) WILD-TYPE 22 18 26 7 16 27

Figure S30.  Get High-res Image Gene #7: 'amp_xq23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00263 (Fisher's exact test), Q value = 0.0083

Table S31.  Gene #7: 'amp_xq23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
AMP PEAK 7(XQ23) MUTATED 0 0 7 0
AMP PEAK 7(XQ23) WILD-TYPE 28 51 36 1

Figure S31.  Get High-res Image Gene #7: 'amp_xq23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xq23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 0.056

Table S32.  Gene #7: 'amp_xq23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
AMP PEAK 7(XQ23) MUTATED 4 0 3 0
AMP PEAK 7(XQ23) WILD-TYPE 23 33 32 28

Figure S32.  Get High-res Image Gene #7: 'amp_xq23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.044

Table S33.  Gene #8: 'del_2q37.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
DEL PEAK 1(2Q37.1) MUTATED 0 3 1 1 0 0
DEL PEAK 1(2Q37.1) WILD-TYPE 27 15 27 6 16 27

Figure S33.  Get High-res Image Gene #8: 'del_2q37.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.2' versus 'CN_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0039

Table S34.  Gene #9: 'del_3p22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
DEL PEAK 2(3P22.2) MUTATED 7 0 5 0 2
DEL PEAK 2(3P22.2) WILD-TYPE 29 27 14 31 8

Figure S34.  Get High-res Image Gene #9: '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 = 9.5e-05

Table S35.  Gene #9: 'del_3p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
DEL PEAK 2(3P22.2) MUTATED 0 1 9 3 1 0 0 0
DEL PEAK 2(3P22.2) WILD-TYPE 37 22 10 7 17 8 2 6

Figure S35.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p22.2' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00028

Table S36.  Gene #9: 'del_3p22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
DEL PEAK 2(3P22.2) MUTATED 3 0 0 8
DEL PEAK 2(3P22.2) WILD-TYPE 13 23 31 12

Figure S36.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p22.2' versus 'MRNASEQ_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.066

Table S37.  Gene #9: 'del_3p22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
DEL PEAK 2(3P22.2) MUTATED 9 1 1 3
DEL PEAK 2(3P22.2) WILD-TYPE 36 29 29 11

Figure S37.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.038

Table S38.  Gene #9: 'del_3p22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
DEL PEAK 2(3P22.2) MUTATED 10 1 1 2
DEL PEAK 2(3P22.2) WILD-TYPE 37 41 19 8

Figure S38.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.038

Table S39.  Gene #9: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
DEL PEAK 2(3P22.2) MUTATED 11 2 1 0
DEL PEAK 2(3P22.2) WILD-TYPE 45 59 4 1

Figure S39.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0012

Table S40.  Gene #9: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
DEL PEAK 2(3P22.2) MUTATED 0 2 12 0
DEL PEAK 2(3P22.2) WILD-TYPE 28 49 31 1

Figure S40.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0399 (Fisher's exact test), Q value = 0.079

Table S41.  Gene #9: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
DEL PEAK 2(3P22.2) MUTATED 6 1 6 1
DEL PEAK 2(3P22.2) WILD-TYPE 21 32 29 27

Figure S41.  Get High-res Image Gene #9: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.2' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00036

Table S42.  Gene #10: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
DEL PEAK 3(6P25.2) MUTATED 14 0 8 3 1
DEL PEAK 3(6P25.2) WILD-TYPE 22 27 11 28 9

Figure S42.  Get High-res Image Gene #10: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S43.  Gene #10: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
DEL PEAK 3(6P25.2) MUTATED 1 2 13 7 3 0 0 0
DEL PEAK 3(6P25.2) WILD-TYPE 36 21 6 3 15 8 2 6

Figure S43.  Get High-res Image Gene #10: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.2' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S44.  Gene #10: 'del_6p25.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
DEL PEAK 3(6P25.2) MUTATED 15 5 1
DEL PEAK 3(6P25.2) WILD-TYPE 16 20 33

Figure S44.  Get High-res Image Gene #10: 'del_6p25.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p25.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S45.  Gene #10: 'del_6p25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
DEL PEAK 3(6P25.2) MUTATED 3 4 2 12
DEL PEAK 3(6P25.2) WILD-TYPE 13 19 29 8

Figure S45.  Get High-res Image Gene #10: 'del_6p25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6p25.2' versus 'MRNASEQ_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.0071

Table S46.  Gene #10: 'del_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
DEL PEAK 3(6P25.2) MUTATED 14 1 4 6
DEL PEAK 3(6P25.2) WILD-TYPE 31 29 26 8

Figure S46.  Get High-res Image Gene #10: 'del_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00036

Table S47.  Gene #10: 'del_6p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
DEL PEAK 3(6P25.2) MUTATED 15 4 0 6
DEL PEAK 3(6P25.2) WILD-TYPE 32 38 20 4

Figure S47.  Get High-res Image Gene #10: 'del_6p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.2' versus 'MIRSEQ_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.0048

Table S48.  Gene #10: 'del_6p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
DEL PEAK 3(6P25.2) MUTATED 19 5 2 0
DEL PEAK 3(6P25.2) WILD-TYPE 37 56 3 1

Figure S48.  Get High-res Image Gene #10: 'del_6p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00651 (Fisher's exact test), Q value = 0.018

Table S49.  Gene #10: 'del_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
DEL PEAK 3(6P25.2) MUTATED 10 3 8 3 0 2
DEL PEAK 3(6P25.2) WILD-TYPE 17 15 20 4 16 25

Figure S49.  Get High-res Image Gene #10: 'del_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S50.  Gene #10: 'del_6p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
DEL PEAK 3(6P25.2) MUTATED 0 5 21 0
DEL PEAK 3(6P25.2) WILD-TYPE 28 46 22 1

Figure S50.  Get High-res Image Gene #10: 'del_6p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00632 (Fisher's exact test), Q value = 0.018

Table S51.  Gene #10: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
DEL PEAK 3(6P25.2) MUTATED 9 3 12 2
DEL PEAK 3(6P25.2) WILD-TYPE 18 30 23 26

Figure S51.  Get High-res Image Gene #10: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q21' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S52.  Gene #11: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
DEL PEAK 4(6Q21) MUTATED 11 0 8 1 0
DEL PEAK 4(6Q21) WILD-TYPE 25 27 11 30 10

Figure S52.  Get High-res Image Gene #11: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S53.  Gene #11: 'del_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
DEL PEAK 4(6Q21) MUTATED 1 0 12 6 0 0 0 1
DEL PEAK 4(6Q21) WILD-TYPE 36 23 7 4 18 8 2 5

Figure S53.  Get High-res Image Gene #11: 'del_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q21' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0013

Table S54.  Gene #11: 'del_6q21' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
DEL PEAK 4(6Q21) MUTATED 12 2 1
DEL PEAK 4(6Q21) WILD-TYPE 19 23 33

Figure S54.  Get High-res Image Gene #11: 'del_6q21' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q21' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00028

Table S55.  Gene #11: 'del_6q21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
DEL PEAK 4(6Q21) MUTATED 2 1 1 11
DEL PEAK 4(6Q21) WILD-TYPE 14 22 30 9

Figure S55.  Get High-res Image Gene #11: 'del_6q21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S56.  Gene #11: 'del_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
DEL PEAK 4(6Q21) MUTATED 13 0 0 7
DEL PEAK 4(6Q21) WILD-TYPE 32 30 30 7

Figure S56.  Get High-res Image Gene #11: 'del_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00016

Table S57.  Gene #11: 'del_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
DEL PEAK 4(6Q21) MUTATED 14 0 1 5
DEL PEAK 4(6Q21) WILD-TYPE 33 42 19 5

Figure S57.  Get High-res Image Gene #11: 'del_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S58.  Gene #11: 'del_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 61 5 1
DEL PEAK 4(6Q21) MUTATED 17 1 2 0
DEL PEAK 4(6Q21) WILD-TYPE 39 60 3 1

Figure S58.  Get High-res Image Gene #11: 'del_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.001

Table S59.  Gene #11: 'del_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
DEL PEAK 4(6Q21) MUTATED 9 0 7 3 1 0
DEL PEAK 4(6Q21) WILD-TYPE 18 18 21 4 15 27

Figure S59.  Get High-res Image Gene #11: 'del_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S60.  Gene #11: 'del_6q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
DEL PEAK 4(6Q21) MUTATED 0 0 20 0
DEL PEAK 4(6Q21) WILD-TYPE 28 51 23 1

Figure S60.  Get High-res Image Gene #11: 'del_6q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00036

Table S61.  Gene #11: 'del_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
DEL PEAK 4(6Q21) MUTATED 8 1 11 0
DEL PEAK 4(6Q21) WILD-TYPE 19 32 24 28

Figure S61.  Get High-res Image Gene #11: 'del_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

P value = 0.00679 (Fisher's exact test), Q value = 0.019

Table S62.  Gene #12: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
DEL PEAK 5(7Q36.3) MUTATED 0 0 3 0 0
DEL PEAK 5(7Q36.3) WILD-TYPE 36 27 16 31 10

Figure S62.  Get High-res Image Gene #12: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 0.02

Table S63.  Gene #12: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
DEL PEAK 5(7Q36.3) MUTATED 0 0 0 2 0 0 0 1
DEL PEAK 5(7Q36.3) WILD-TYPE 37 23 19 8 18 8 2 5

Figure S63.  Get High-res Image Gene #12: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0046

Table S64.  Gene #12: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
DEL PEAK 5(7Q36.3) MUTATED 0 0 0 3
DEL PEAK 5(7Q36.3) WILD-TYPE 45 30 30 11

Figure S64.  Get High-res Image Gene #12: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00373 (Fisher's exact test), Q value = 0.011

Table S65.  Gene #12: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
DEL PEAK 5(7Q36.3) MUTATED 0 0 1 2
DEL PEAK 5(7Q36.3) WILD-TYPE 47 42 19 8

Figure S65.  Get High-res Image Gene #12: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p22.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S66.  Gene #13: 'del_9p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
DEL PEAK 6(9P22.1) MUTATED 0 0 6 0 0
DEL PEAK 6(9P22.1) WILD-TYPE 36 27 13 31 10

Figure S66.  Get High-res Image Gene #13: 'del_9p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p22.1' versus 'METHLYATION_CNMF'

P value = 0.00831 (Fisher's exact test), Q value = 0.022

Table S67.  Gene #13: 'del_9p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
DEL PEAK 6(9P22.1) MUTATED 0 3 0 3 0 0 0 0
DEL PEAK 6(9P22.1) WILD-TYPE 37 20 19 7 18 8 2 6

Figure S67.  Get High-res Image Gene #13: 'del_9p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00286 (Fisher's exact test), Q value = 0.0089

Table S68.  Gene #13: 'del_9p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
DEL PEAK 6(9P22.1) MUTATED 0 0 3 3
DEL PEAK 6(9P22.1) WILD-TYPE 45 30 27 11

Figure S68.  Get High-res Image Gene #13: 'del_9p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00051

Table S69.  Gene #13: 'del_9p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
DEL PEAK 6(9P22.1) MUTATED 0 0 3 3
DEL PEAK 6(9P22.1) WILD-TYPE 47 42 17 7

Figure S69.  Get High-res Image Gene #13: 'del_9p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.0059

Table S70.  Gene #13: 'del_9p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
DEL PEAK 6(9P22.1) MUTATED 0 0 1 2 3 0
DEL PEAK 6(9P22.1) WILD-TYPE 27 18 27 5 13 27

Figure S70.  Get High-res Image Gene #13: 'del_9p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0012

Table S71.  Gene #14: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
DEL PEAK 7(9P21.3) MUTATED 1 0 7 2 1
DEL PEAK 7(9P21.3) WILD-TYPE 35 27 12 29 9

Figure S71.  Get High-res Image Gene #14: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 9e-04

Table S72.  Gene #14: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
DEL PEAK 7(9P21.3) MUTATED 0 3 1 6 1 0 0 0
DEL PEAK 7(9P21.3) WILD-TYPE 37 20 18 4 17 8 2 6

Figure S72.  Get High-res Image Gene #14: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.0046

Table S73.  Gene #14: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
DEL PEAK 7(9P21.3) MUTATED 0 3 0 6
DEL PEAK 7(9P21.3) WILD-TYPE 16 20 31 14

Figure S73.  Get High-res Image Gene #14: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00046

Table S74.  Gene #14: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
DEL PEAK 7(9P21.3) MUTATED 1 0 3 6
DEL PEAK 7(9P21.3) WILD-TYPE 44 30 27 8

Figure S74.  Get High-res Image Gene #14: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S75.  Gene #14: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
DEL PEAK 7(9P21.3) MUTATED 1 0 3 6
DEL PEAK 7(9P21.3) WILD-TYPE 46 42 17 4

Figure S75.  Get High-res Image Gene #14: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0013

Table S76.  Gene #14: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
DEL PEAK 7(9P21.3) MUTATED 0 0 3 4 3 1
DEL PEAK 7(9P21.3) WILD-TYPE 27 18 25 3 13 26

Figure S76.  Get High-res Image Gene #14: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.071

Table S77.  Gene #14: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
DEL PEAK 7(9P21.3) MUTATED 0 3 7 1
DEL PEAK 7(9P21.3) WILD-TYPE 27 30 28 27

Figure S77.  Get High-res Image Gene #14: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.066

Table S78.  Gene #15: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
DEL PEAK 8(10Q26.3) MUTATED 0 4 0 1
DEL PEAK 8(10Q26.3) WILD-TYPE 16 19 31 19

Figure S78.  Get High-res Image Gene #15: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.071

Table S79.  Gene #15: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 33 35 28
DEL PEAK 8(10Q26.3) MUTATED 2 4 0 0
DEL PEAK 8(10Q26.3) WILD-TYPE 25 29 35 28

Figure S79.  Get High-res Image Gene #15: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.11' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00093

Table S80.  Gene #16: 'del_19p13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
DEL PEAK 9(19P13.11) MUTATED 0 0 5 0 0
DEL PEAK 9(19P13.11) WILD-TYPE 36 27 14 31 10

Figure S80.  Get High-res Image Gene #16: 'del_19p13.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.11' versus 'METHLYATION_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.029

Table S81.  Gene #16: 'del_19p13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
DEL PEAK 9(19P13.11) MUTATED 0 2 0 3 0 0 0 0
DEL PEAK 9(19P13.11) WILD-TYPE 37 21 19 7 18 8 2 6

Figure S81.  Get High-res Image Gene #16: 'del_19p13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.11' versus 'MRNASEQ_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.011

Table S82.  Gene #16: 'del_19p13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
DEL PEAK 9(19P13.11) MUTATED 0 0 2 3
DEL PEAK 9(19P13.11) WILD-TYPE 45 30 28 11

Figure S82.  Get High-res Image Gene #16: 'del_19p13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.0012

Table S83.  Gene #16: 'del_19p13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
DEL PEAK 9(19P13.11) MUTATED 0 0 2 3
DEL PEAK 9(19P13.11) WILD-TYPE 47 42 18 7

Figure S83.  Get High-res Image Gene #16: 'del_19p13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.014

Table S84.  Gene #16: 'del_19p13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 27 18 28 7 16 27
DEL PEAK 9(19P13.11) MUTATED 0 0 1 2 2 0
DEL PEAK 9(19P13.11) WILD-TYPE 27 18 27 5 14 27

Figure S84.  Get High-res Image Gene #16: 'del_19p13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S85.  Gene #17: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
DEL PEAK 10(22Q12.1) MUTATED 4 5 10 0 0
DEL PEAK 10(22Q12.1) WILD-TYPE 32 22 9 31 10

Figure S85.  Get High-res Image Gene #17: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.1' versus 'METHLYATION_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.056

Table S86.  Gene #17: 'del_22q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
DEL PEAK 10(22Q12.1) MUTATED 1 5 2 3 5 2 1 0
DEL PEAK 10(22Q12.1) WILD-TYPE 36 18 17 7 13 6 1 6

Figure S86.  Get High-res Image Gene #17: 'del_22q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.1' versus 'RPPA_CNMF'

P value = 0.0074 (Fisher's exact test), Q value = 0.02

Table S87.  Gene #17: 'del_22q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
DEL PEAK 10(22Q12.1) MUTATED 5 8 1
DEL PEAK 10(22Q12.1) WILD-TYPE 26 17 33

Figure S87.  Get High-res Image Gene #17: 'del_22q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q12.1' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.044

Table S88.  Gene #17: 'del_22q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 30 30 14
DEL PEAK 10(22Q12.1) MUTATED 2 5 8 4
DEL PEAK 10(22Q12.1) WILD-TYPE 43 25 22 10

Figure S88.  Get High-res Image Gene #17: 'del_22q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.055

Table S89.  Gene #17: 'del_22q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
DEL PEAK 10(22Q12.1) MUTATED 0 10 9 0
DEL PEAK 10(22Q12.1) WILD-TYPE 28 41 34 1

Figure S89.  Get High-res Image Gene #17: 'del_22q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.5e-05

Table S90.  Gene #18: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 27 19 31 10
DEL PEAK 11(22Q13.32) MUTATED 2 2 11 0 0
DEL PEAK 11(22Q13.32) WILD-TYPE 34 25 8 31 10

Figure S90.  Get High-res Image Gene #18: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.055

Table S91.  Gene #18: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 37 23 19 10 18 8 2 6
DEL PEAK 11(22Q13.32) MUTATED 1 3 2 4 2 2 1 0
DEL PEAK 11(22Q13.32) WILD-TYPE 36 20 17 6 16 6 1 6

Figure S91.  Get High-res Image Gene #18: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.0438 (Fisher's exact test), Q value = 0.086

Table S92.  Gene #18: 'del_22q13.32' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
DEL PEAK 11(22Q13.32) MUTATED 4 6 1
DEL PEAK 11(22Q13.32) WILD-TYPE 27 19 33

Figure S92.  Get High-res Image Gene #18: 'del_22q13.32' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.056

Table S93.  Gene #18: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
DEL PEAK 11(22Q13.32) MUTATED 3 4 4 4
DEL PEAK 11(22Q13.32) WILD-TYPE 44 38 16 6

Figure S93.  Get High-res Image Gene #18: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.044

Table S94.  Gene #18: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 51 43 1
DEL PEAK 11(22Q13.32) MUTATED 0 5 10 0
DEL PEAK 11(22Q13.32) WILD-TYPE 28 46 33 1

Figure S94.  Get High-res Image Gene #18: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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/THYM-TP/22516313/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/22541006/THYM-TP.transferedmergedcluster.txt

  • Number of patients = 123

  • Number of significantly focal cnvs = 18

  • Number of molecular subtypes = 10

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

Fisher's exact test

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

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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