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 12 focal events and 10 molecular subtypes across 123 patients, 65 significant findings detected with P value < 0.05 and Q value < 0.25.

  • del_2q37.1 cnv correlated to 'METHLYATION_CNMF' and '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 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_9q22.33 cnv correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

  • del_11q22.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 12 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, 65 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
del 6p25 2 26 (21%) 97 1e-05
(9.23e-05) 		1e-05
(9.23e-05) 		5e-05
(0.000316) 		0.00019
(0.00095) 		0.00201
(0.00709) 		0.00011
(6e-04) 		0.00109
(0.00451) 		0.00628
(0.0188) 		3e-05
(0.00024) 		0.00515
(0.0167)
del 6q21 20 (16%) 103 1e-05
(9.23e-05) 		1e-05
(9.23e-05) 		0.00023
(0.0011) 		1e-05
(9.23e-05) 		1e-05
(9.23e-05) 		1e-05
(9.23e-05) 		2e-05
(0.000171) 		0.00014
(0.00073) 		1e-05
(9.23e-05) 		5e-05
(0.000316)
del 11q22 1 7 (6%) 116 7e-05
(0.00042) 		1e-05
(9.23e-05) 		0.0478
(0.0899) 		0.00627
(0.0188) 		0.0313
(0.0668) 		0.0142
(0.0387) 		0.0332
(0.0686) 		0.114
(0.169) 		0.00195
(0.00709) 		0.00874
(0.025)
del 3p22 2 14 (11%) 109 8e-05
(0.000457) 		1e-05
(9.23e-05) 		0.0528
(0.096) 		4e-05
(3e-04) 		0.0317
(0.0668) 		0.0152
(0.0396) 		0.025
(0.0576) 		0.0659
(0.107) 		0.00046
(0.00197) 		0.0296
(0.0658)
del 9p21 3 11 (9%) 112 0.0166
(0.0406) 		0.00399
(0.0133) 		0.197
(0.256) 		0.0012
(0.0048) 		5e-05
(0.000316) 		1e-05
(9.23e-05) 		0.559
(0.621) 		0.00025
(0.00115) 		0.144
(0.208) 		0.0163
(0.0406)
del 19p13 11 5 (4%) 118 0.258
(0.31) 		0.0445
(0.0861) 		0.189
(0.255) 		0.201
(0.257) 		0.00187
(0.00701) 		0.00032
(0.00142) 		0.723
(0.755) 		0.00543
(0.0171) 		0.574
(0.632) 		0.169
(0.241)
del 22q12 1 19 (15%) 104 1e-05
(9.23e-05) 		0.0127
(0.0353) 		0.00797
(0.0233) 		0.0548
(0.0981) 		0.0159
(0.0406) 		0.0731
(0.117) 		0.244
(0.298) 		0.455
(0.515) 		0.52
(0.583) 		0.429
(0.49)
del 9q22 33 3 (2%) 120 0.604
(0.658) 		0.177
(0.244) 		0.373
(0.431) 		0.0145
(0.0388) 		0.048
(0.0899) 		0.0292
(0.0658) 		0.198
(0.256) 		0.066
(0.107) 		0.106
(0.161) 		0.0592
(0.105)
del 10q26 3 6 (5%) 117 0.626
(0.665) 		0.0379
(0.0772) 		0.183
(0.249) 		0.0315
(0.0668) 		0.065
(0.107) 		0.222
(0.274) 		0.74
(0.765) 		0.0655
(0.107) 		0.858
(0.88) 		0.049
(0.0904)
del 22q13 32 15 (12%) 108 1e-05
(9.23e-05) 		0.0863
(0.134) 		0.0441
(0.0861) 		0.0812
(0.128) 		0.0659
(0.107) 		0.0249
(0.0576) 		0.209
(0.262) 		0.299
(0.355) 		0.197
(0.256) 		0.901
(0.916)
del 2q37 1 5 (4%) 118 0.258
(0.31) 		0.0442
(0.0861) 		0.193
(0.256) 		0.113
(0.169) 		0.626
(0.665) 		0.305
(0.358) 		1
(1.00) 		0.0195
(0.0467) 		1
(1.00) 		0.171
(0.241)
del 7q36 3 3 (2%) 120 0.0606
(0.105) 		0.176
(0.244) 		0.373
(0.431) 		0.206
(0.26) 		0.00126
(0.00488) 		0.00348
(0.0119) 		0.649
(0.684) 		0.116
(0.169) 		0.106
(0.161) 		0.616
(0.665)
'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.086

Table S1.  Gene #1: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
DEL PEAK 1(2Q37.1) MUTATED 0 4 1 0
DEL PEAK 1(2Q37.1) WILD-TYPE 39 32 23 24

Figure S1.  Get High-res Image Gene #1: 'del_2q37.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.047

Table S2.  Gene #1: '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 S2.  Get High-res Image Gene #1: 'del_2q37.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p22.2' versus 'CN_CNMF'

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

Table S3.  Gene #2: 'del_3p22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
DEL PEAK 2(3P22.2) MUTATED 1 10 3
DEL PEAK 2(3P22.2) WILD-TYPE 64 21 24

Figure S3.  Get High-res Image Gene #2: '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 = 9.2e-05

Table S4.  Gene #2: 'del_3p22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
DEL PEAK 2(3P22.2) MUTATED 0 3 10 1
DEL PEAK 2(3P22.2) WILD-TYPE 39 33 14 23

Figure S4.  Get High-res Image Gene #2: '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 = 3e-04

Table S5.  Gene #2: '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 S5.  Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p22.2' versus 'MRNASEQ_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.067

Table S6.  Gene #2: 'del_3p22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
DEL PEAK 2(3P22.2) MUTATED 9 1 1 3
DEL PEAK 2(3P22.2) WILD-TYPE 36 30 28 11

Figure S6.  Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.04

Table S7.  Gene #2: '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 S7.  Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p22.2' versus 'MIRSEQ_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.058

Table S8.  Gene #2: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
DEL PEAK 2(3P22.2) MUTATED 12 2 0 0 0
DEL PEAK 2(3P22.2) WILD-TYPE 46 59 1 2 1

Figure S8.  Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.002

Table S9.  Gene #2: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
DEL PEAK 2(3P22.2) MUTATED 0 2 12
DEL PEAK 2(3P22.2) WILD-TYPE 18 57 34

Figure S9.  Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.066

Table S10.  Gene #2: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
DEL PEAK 2(3P22.2) MUTATED 7 1 5 1
DEL PEAK 2(3P22.2) WILD-TYPE 22 32 28 27

Figure S10.  Get High-res Image Gene #2: 'del_3p22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S11.  Gene #3: 'del_6p25.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
DEL PEAK 3(6P25.2) MUTATED 1 20 5
DEL PEAK 3(6P25.2) WILD-TYPE 64 11 22

Figure S11.  Get High-res Image Gene #3: '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 = 9.2e-05

Table S12.  Gene #3: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
DEL PEAK 3(6P25.2) MUTATED 2 6 15 3
DEL PEAK 3(6P25.2) WILD-TYPE 37 30 9 21

Figure S12.  Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.2' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00032

Table S13.  Gene #3: '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 S13.  Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6p25.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00095

Table S14.  Gene #3: '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 S14.  Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6p25.2' versus 'MRNASEQ_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.0071

Table S15.  Gene #3: 'del_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
DEL PEAK 3(6P25.2) MUTATED 14 1 4 6
DEL PEAK 3(6P25.2) WILD-TYPE 31 30 25 8

Figure S15.  Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 6e-04

Table S16.  Gene #3: '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 S16.  Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.2' versus 'MIRSEQ_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0045

Table S17.  Gene #3: 'del_6p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
DEL PEAK 3(6P25.2) MUTATED 20 5 0 1 0
DEL PEAK 3(6P25.2) WILD-TYPE 38 56 1 1 1

Figure S17.  Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00628 (Fisher's exact test), Q value = 0.019

Table S18.  Gene #3: '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 S18.  Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00024

Table S19.  Gene #3: 'del_6p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
DEL PEAK 3(6P25.2) MUTATED 1 5 20
DEL PEAK 3(6P25.2) WILD-TYPE 17 54 26

Figure S19.  Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p25.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00515 (Fisher's exact test), Q value = 0.017

Table S20.  Gene #3: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
DEL PEAK 3(6P25.2) MUTATED 11 3 10 2
DEL PEAK 3(6P25.2) WILD-TYPE 18 30 23 26

Figure S20.  Get High-res Image Gene #3: 'del_6p25.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S21.  Gene #4: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
DEL PEAK 4(6Q21) MUTATED 0 18 2
DEL PEAK 4(6Q21) WILD-TYPE 65 13 25

Figure S21.  Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S22.  Gene #4: 'del_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
DEL PEAK 4(6Q21) MUTATED 1 3 16 0
DEL PEAK 4(6Q21) WILD-TYPE 38 33 8 24

Figure S22.  Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q21' versus 'RPPA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S23.  Gene #4: '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 S23.  Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_6q21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S24.  Gene #4: '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 S24.  Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_6q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S25.  Gene #4: 'del_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
DEL PEAK 4(6Q21) MUTATED 13 0 0 7
DEL PEAK 4(6Q21) WILD-TYPE 32 31 29 7

Figure S25.  Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S26.  Gene #4: '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 S26.  Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q21' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00017

Table S27.  Gene #4: 'del_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
DEL PEAK 4(6Q21) MUTATED 18 1 0 1 0
DEL PEAK 4(6Q21) WILD-TYPE 40 60 1 1 1

Figure S27.  Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00073

Table S28.  Gene #4: '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 S28.  Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S29.  Gene #4: 'del_6q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
DEL PEAK 4(6Q21) MUTATED 0 0 20
DEL PEAK 4(6Q21) WILD-TYPE 18 59 26

Figure S29.  Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00032

Table S30.  Gene #4: 'del_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
DEL PEAK 4(6Q21) MUTATED 10 1 9 0
DEL PEAK 4(6Q21) WILD-TYPE 19 32 24 28

Figure S30.  Get High-res Image Gene #4: 'del_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0049

Table S31.  Gene #5: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
DEL PEAK 5(7Q36.3) MUTATED 0 0 0 3
DEL PEAK 5(7Q36.3) WILD-TYPE 45 31 29 11

Figure S31.  Get High-res Image Gene #5: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00348 (Fisher's exact test), Q value = 0.012

Table S32.  Gene #5: '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 S32.  Get High-res Image Gene #5: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.041

Table S33.  Gene #6: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
DEL PEAK 6(9P21.3) MUTATED 2 6 3
DEL PEAK 6(9P21.3) WILD-TYPE 63 25 24

Figure S33.  Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00399 (Fisher's exact test), Q value = 0.013

Table S34.  Gene #6: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
DEL PEAK 6(9P21.3) MUTATED 0 8 2 1
DEL PEAK 6(9P21.3) WILD-TYPE 39 28 22 23

Figure S34.  Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0048

Table S35.  Gene #6: '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 6(9P21.3) MUTATED 0 3 0 6
DEL PEAK 6(9P21.3) WILD-TYPE 16 20 31 14

Figure S35.  Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00032

Table S36.  Gene #6: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
DEL PEAK 6(9P21.3) MUTATED 1 0 3 6
DEL PEAK 6(9P21.3) WILD-TYPE 44 31 26 8

Figure S36.  Get High-res Image Gene #6: '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 = 9.2e-05

Table S37.  Gene #6: '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 6(9P21.3) MUTATED 1 0 3 6
DEL PEAK 6(9P21.3) WILD-TYPE 46 42 17 4

Figure S37.  Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S38.  Gene #6: '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 6(9P21.3) MUTATED 0 0 3 4 3 1
DEL PEAK 6(9P21.3) WILD-TYPE 27 18 25 3 13 26

Figure S38.  Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.041

Table S39.  Gene #6: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
DEL PEAK 6(9P21.3) MUTATED 0 3 7 1
DEL PEAK 6(9P21.3) WILD-TYPE 29 30 26 27

Figure S39.  Get High-res Image Gene #6: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q22.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.039

Table S40.  Gene #7: 'del_9q22.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
DEL PEAK 7(9Q22.33) MUTATED 0 0 0 3
DEL PEAK 7(9Q22.33) WILD-TYPE 16 23 31 17

Figure S40.  Get High-res Image Gene #7: 'del_9q22.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9q22.33' versus 'MRNASEQ_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.09

Table S41.  Gene #7: 'del_9q22.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
DEL PEAK 7(9Q22.33) MUTATED 1 0 0 2
DEL PEAK 7(9Q22.33) WILD-TYPE 44 31 29 12

Figure S41.  Get High-res Image Gene #7: 'del_9q22.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q22.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.066

Table S42.  Gene #7: 'del_9q22.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
DEL PEAK 7(9Q22.33) MUTATED 1 0 0 2
DEL PEAK 7(9Q22.33) WILD-TYPE 46 42 20 8

Figure S42.  Get High-res Image Gene #7: 'del_9q22.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 0.0379 (Fisher's exact test), Q value = 0.077

Table S43.  Gene #8: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
DEL PEAK 8(10Q26.3) MUTATED 0 3 3 0
DEL PEAK 8(10Q26.3) WILD-TYPE 39 33 21 24

Figure S43.  Get High-res Image Gene #8: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0315 (Fisher's exact test), Q value = 0.067

Table S44.  Gene #8: '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 S44.  Get High-res Image Gene #8: 'del_10q26.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.09

Table S45.  Gene #8: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Figure S45.  Get High-res Image Gene #8: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.1' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00042

Table S46.  Gene #9: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
DEL PEAK 9(11Q22.1) MUTATED 0 7 0
DEL PEAK 9(11Q22.1) WILD-TYPE 65 24 27

Figure S46.  Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S47.  Gene #9: 'del_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
DEL PEAK 9(11Q22.1) MUTATED 0 0 7 0
DEL PEAK 9(11Q22.1) WILD-TYPE 39 36 17 24

Figure S47.  Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q22.1' versus 'RPPA_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.09

Table S48.  Gene #9: 'del_11q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
DEL PEAK 9(11Q22.1) MUTATED 4 1 0
DEL PEAK 9(11Q22.1) WILD-TYPE 27 24 34

Figure S48.  Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00627 (Fisher's exact test), Q value = 0.019

Table S49.  Gene #9: 'del_11q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 31 20
DEL PEAK 9(11Q22.1) MUTATED 1 0 0 4
DEL PEAK 9(11Q22.1) WILD-TYPE 15 23 31 16

Figure S49.  Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.067

Table S50.  Gene #9: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
DEL PEAK 9(11Q22.1) MUTATED 6 0 0 1
DEL PEAK 9(11Q22.1) WILD-TYPE 39 31 29 13

Figure S50.  Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.039

Table S51.  Gene #9: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 42 20 10
DEL PEAK 9(11Q22.1) MUTATED 7 0 0 0
DEL PEAK 9(11Q22.1) WILD-TYPE 40 42 20 10

Figure S51.  Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.069

Table S52.  Gene #9: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 61 1 2 1
DEL PEAK 9(11Q22.1) MUTATED 7 0 0 0 0
DEL PEAK 9(11Q22.1) WILD-TYPE 51 61 1 2 1

Figure S52.  Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.0071

Table S53.  Gene #9: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 59 46
DEL PEAK 9(11Q22.1) MUTATED 0 0 7
DEL PEAK 9(11Q22.1) WILD-TYPE 18 59 39

Figure S53.  Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00874 (Fisher's exact test), Q value = 0.025

Table S54.  Gene #9: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 33 33 28
DEL PEAK 9(11Q22.1) MUTATED 5 0 2 0
DEL PEAK 9(11Q22.1) WILD-TYPE 24 33 31 28

Figure S54.  Get High-res Image Gene #9: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.11' versus 'METHLYATION_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.086

Table S55.  Gene #10: 'del_19p13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
DEL PEAK 10(19P13.11) MUTATED 0 4 1 0
DEL PEAK 10(19P13.11) WILD-TYPE 39 32 23 24

Figure S55.  Get High-res Image Gene #10: 'del_19p13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.11' versus 'MRNASEQ_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.007

Table S56.  Gene #10: 'del_19p13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
DEL PEAK 10(19P13.11) MUTATED 0 0 2 3
DEL PEAK 10(19P13.11) WILD-TYPE 45 31 27 11

Figure S56.  Get High-res Image Gene #10: 'del_19p13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0014

Table S57.  Gene #10: '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 10(19P13.11) MUTATED 0 0 2 3
DEL PEAK 10(19P13.11) WILD-TYPE 47 42 18 7

Figure S57.  Get High-res Image Gene #10: 'del_19p13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00543 (Fisher's exact test), Q value = 0.017

Table S58.  Gene #10: '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 10(19P13.11) MUTATED 0 0 1 2 2 0
DEL PEAK 10(19P13.11) WILD-TYPE 27 18 27 5 14 27

Figure S58.  Get High-res Image Gene #10: '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 = 9.2e-05

Table S59.  Gene #11: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
DEL PEAK 11(22Q12.1) MUTATED 0 4 15
DEL PEAK 11(22Q12.1) WILD-TYPE 65 27 12

Figure S59.  Get High-res Image Gene #11: 'del_22q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.1' versus 'METHLYATION_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.035

Table S60.  Gene #11: 'del_22q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 36 24 24
DEL PEAK 11(22Q12.1) MUTATED 1 9 3 6
DEL PEAK 11(22Q12.1) WILD-TYPE 38 27 21 18

Figure S60.  Get High-res Image Gene #11: 'del_22q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.1' versus 'RPPA_CNMF'

P value = 0.00797 (Fisher's exact test), Q value = 0.023

Table S61.  Gene #11: 'del_22q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
DEL PEAK 11(22Q12.1) MUTATED 5 8 1
DEL PEAK 11(22Q12.1) WILD-TYPE 26 17 33

Figure S61.  Get High-res Image Gene #11: 'del_22q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q12.1' versus 'MRNASEQ_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.041

Table S62.  Gene #11: 'del_22q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 45 31 29 14
DEL PEAK 11(22Q12.1) MUTATED 2 5 8 4
DEL PEAK 11(22Q12.1) WILD-TYPE 43 26 21 10

Figure S62.  Get High-res Image Gene #11: 'del_22q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 9.2e-05

Table S63.  Gene #12: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 31 27
DEL PEAK 12(22Q13.32) MUTATED 1 4 10
DEL PEAK 12(22Q13.32) WILD-TYPE 64 27 17

Figure S63.  Get High-res Image Gene #12: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.086

Table S64.  Gene #12: 'del_22q13.32' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 34
DEL PEAK 12(22Q13.32) MUTATED 4 6 1
DEL PEAK 12(22Q13.32) WILD-TYPE 27 19 33

Figure S64.  Get High-res Image Gene #12: 'del_22q13.32' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.058

Table S65.  Gene #12: '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 12(22Q13.32) MUTATED 3 4 4 4
DEL PEAK 12(22Q13.32) WILD-TYPE 44 38 16 6

Figure S65.  Get High-res Image Gene #12: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_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/THYM-TP/19781936/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/20140903/THYM-TP.transferedmergedcluster.txt

  • Number of patients = 123

  • Number of significantly focal cnvs = 12

  • 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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