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 21 focal events and 10 molecular subtypes across 87 patients, 61 significant findings detected with P value < 0.05 and Q value < 0.25.

  • del_1p36.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_1p21.3 cnv correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • del_2q35 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_3p21.1 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_4q26 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • del_5q23.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • del_6q22.1 cnv correlated to 'CN_CNMF'.

  • del_6q26 cnv correlated to 'CN_CNMF'.

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

  • del_10p15.3 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • del_10q25.2 cnv correlated to 'MIRSEQ_CNMF'.

  • del_11q23.2 cnv correlated to 'CN_CNMF'.

  • del_12p13.31 cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

  • del_13q14.11 cnv correlated to 'CN_CNMF'.

  • del_14q32.31 cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • del_15q15.1 cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • del_16q24.1 cnv correlated to 'CN_CNMF'.

  • del_22q12.2 cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 21 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, 61 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 3p21 1 48 (55%) 39 0.00034
(0.0042) 		8e-05
(0.00153) 		0.517
(0.696) 		0.597
(0.751) 		0.00023
(0.00345) 		2e-05
(7e-04) 		0.0352
(0.142) 		0.0152
(0.0888) 		0.961
(0.989) 		0.00284
(0.0259)
del 9p21 3 51 (59%) 36 1e-05
(0.00042) 		0.00588
(0.0457) 		0.0248
(0.116) 		0.0605
(0.188) 		0.025
(0.116) 		0.00011
(0.00192) 		0.0562
(0.183) 		0.13
(0.296) 		0.375
(0.55) 		0.0063
(0.0472)
del 1p36 31 33 (38%) 54 3e-05
(0.000787) 		0.0101
(0.0683) 		0.0882
(0.235) 		0.236
(0.403) 		0.319
(0.5) 		0.0305
(0.128) 		0.18
(0.34) 		0.00881
(0.0631) 		0.882
(0.941) 		0.0462
(0.167)
del 4q26 38 (44%) 49 1e-05
(0.00042) 		0.11
(0.271) 		0.2
(0.36) 		0.0946
(0.242) 		0.00234
(0.0234) 		0.0003
(0.0042) 		0.0141
(0.0872) 		0.05
(0.172) 		0.61
(0.758) 		0.0883
(0.235)
del 4q34 3 41 (47%) 46 1e-05
(0.00042) 		0.00284
(0.0259) 		0.159
(0.328) 		0.576
(0.735) 		0.0426
(0.157) 		0.00067
(0.00703) 		0.0696
(0.208) 		0.239
(0.405) 		0.961
(0.989) 		0.0267
(0.117)
del 10p15 3 28 (32%) 59 0.00021
(0.00339) 		0.0299
(0.128) 		0.165
(0.328) 		0.697
(0.822) 		0.0344
(0.142) 		0.0389
(0.149) 		0.0369
(0.146) 		0.443
(0.634) 		0.335
(0.503) 		0.111
(0.271)
del 14q32 31 39 (45%) 48 1e-05
(0.00042) 		0.00065
(0.00703) 		0.57
(0.734) 		0.326
(0.502) 		0.00048
(0.0056) 		4e-05
(0.000933) 		0.0751
(0.211) 		0.00901
(0.0631) 		0.0703
(0.208) 		0.0565
(0.183)
del 1p21 3 37 (43%) 50 0.0422
(0.157) 		0.128
(0.296) 		0.0174
(0.0936) 		0.0926
(0.24) 		0.00032
(0.0042) 		0.00497
(0.0401) 		0.169
(0.329) 		0.31
(0.493) 		0.591
(0.748) 		0.224
(0.395)
del 22q12 2 68 (78%) 19 0.0522
(0.177) 		0.0188
(0.0989) 		0.189
(0.352) 		0.816
(0.916) 		0.0391
(0.149) 		0.0151
(0.0888) 		0.0474
(0.169) 		0.628
(0.776) 		0.182
(0.341) 		0.322
(0.501)
del 15q15 1 28 (32%) 59 0.00462
(0.0388) 		0.0742
(0.211) 		0.331
(0.502) 		0.454
(0.64) 		0.0207
(0.106) 		0.0713
(0.208) 		0.491
(0.675) 		0.526
(0.699) 		0.603
(0.753) 		0.022
(0.11)
del 2q35 17 (20%) 70 0.00323
(0.0283) 		0.0758
(0.211) 		0.802
(0.905) 		0.201
(0.36) 		0.556
(0.725) 		0.0159
(0.0892) 		0.291
(0.477) 		0.0849
(0.232) 		1
(1.00) 		0.296
(0.479)
del 5q23 2 17 (20%) 70 0.0104
(0.0683) 		0.786
(0.892) 		0.636
(0.776) 		0.255
(0.428) 		0.725
(0.85) 		0.0253
(0.116) 		0.23
(0.398) 		0.435
(0.626) 		1
(1.00) 		0.873
(0.935)
del 12p13 31 11 (13%) 76 0.309
(0.493) 		0.059
(0.188) 		0.0628
(0.191) 		0.562
(0.729) 		0.0263
(0.117) 		0.152
(0.328) 		0.0161
(0.0892) 		0.105
(0.262) 		1
(1.00) 		0.194
(0.354)
del 6q22 1 41 (47%) 46 8e-05
(0.00153) 		0.577
(0.735) 		0.831
(0.925) 		0.663
(0.795) 		0.162
(0.328) 		0.475
(0.665) 		0.175
(0.338) 		0.203
(0.361) 		0.289
(0.477) 		0.0542
(0.181)
del 6q26 36 (41%) 51 1e-05
(0.00042) 		0.853
(0.928) 		0.328
(0.502) 		0.167
(0.328) 		0.744
(0.863) 		0.663
(0.795) 		0.0763
(0.211) 		0.497
(0.678) 		0.332
(0.502) 		0.114
(0.275)
del 10q25 2 31 (36%) 56 0.316
(0.5) 		0.153
(0.328) 		0.164
(0.328) 		0.779
(0.889) 		0.355
(0.529) 		0.516
(0.696) 		0.0255
(0.116) 		0.193
(0.354) 		0.156
(0.328) 		0.226
(0.395)
del 11q23 2 18 (21%) 69 0.0135
(0.086) 		0.861
(0.928) 		0.523
(0.699) 		0.41
(0.594) 		0.137
(0.31) 		0.258
(0.43) 		0.18
(0.34) 		0.13
(0.296) 		0.544
(0.719) 		0.061
(0.188)
del 13q14 11 44 (51%) 43 3e-05
(0.000787) 		0.837
(0.925) 		0.403
(0.588) 		0.103
(0.26) 		0.485
(0.674) 		0.293
(0.477) 		0.923
(0.969) 		0.634
(0.776) 		0.116
(0.275) 		0.844
(0.928)
del 16q24 1 22 (25%) 65 0.0491
(0.172) 		0.158
(0.328) 		0.853
(0.928) 		0.666
(0.795) 		0.231
(0.398) 		0.373
(0.55) 		0.946
(0.983) 		0.167
(0.328) 		1
(1.00) 		0.14
(0.312)
del 8p23 2 18 (21%) 69 0.492
(0.675) 		0.161
(0.328) 		0.971
(0.994) 		0.899
(0.953) 		0.859
(0.928) 		0.915
(0.966) 		0.159
(0.328) 		0.834
(0.925) 		0.941
(0.983) 		0.73
(0.852)
del 16p13 3 6 (7%) 81 0.448
(0.635) 		0.116
(0.275) 		0.55
(0.721) 		0.671
(0.796) 		0.166
(0.328) 		0.0897
(0.236) 		1
(1.00) 		0.662
(0.795) 		0.758
(0.87) 		0.748
(0.863)
'del_1p36.31' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00079

Table S1.  Gene #1: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 1(1P36.31) MUTATED 1 14 10 8
DEL PEAK 1(1P36.31) WILD-TYPE 26 7 6 15

Figure S1.  Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.068

Table S2.  Gene #1: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 19 18 25 9
DEL PEAK 1(1P36.31) MUTATED 1 9 11 8 4
DEL PEAK 1(1P36.31) WILD-TYPE 15 10 7 17 5

Figure S2.  Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.13

Table S3.  Gene #1: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 12 21 15 16
DEL PEAK 1(1P36.31) MUTATED 4 8 11 5 5
DEL PEAK 1(1P36.31) WILD-TYPE 19 4 10 10 11

Figure S3.  Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00881 (Fisher's exact test), Q value = 0.063

Table S4.  Gene #1: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 25 6 13 14
DEL PEAK 1(1P36.31) MUTATED 9 12 5 6 1
DEL PEAK 1(1P36.31) WILD-TYPE 20 13 1 7 13

Figure S4.  Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.17

Table S5.  Gene #1: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 18 16 34
DEL PEAK 1(1P36.31) MUTATED 2 10 7 14
DEL PEAK 1(1P36.31) WILD-TYPE 15 8 9 20

Figure S5.  Get High-res Image Gene #1: 'del_1p36.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p21.3' versus 'CN_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.16

Table S6.  Gene #2: 'del_1p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 2(1P21.3) MUTATED 6 11 10 10
DEL PEAK 2(1P21.3) WILD-TYPE 21 10 6 13

Figure S6.  Get High-res Image Gene #2: 'del_1p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p21.3' versus 'RPPA_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.094

Table S7.  Gene #2: 'del_1p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 24 24 7
DEL PEAK 2(1P21.3) MUTATED 1 14 15 1
DEL PEAK 2(1P21.3) WILD-TYPE 7 10 9 6

Figure S7.  Get High-res Image Gene #2: 'del_1p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0042

Table S8.  Gene #2: 'del_1p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 21 19 21
DEL PEAK 2(1P21.3) MUTATED 5 11 5 16
DEL PEAK 2(1P21.3) WILD-TYPE 21 10 14 5

Figure S8.  Get High-res Image Gene #2: 'del_1p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00497 (Fisher's exact test), Q value = 0.04

Table S9.  Gene #2: 'del_1p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 12 21 15 16
DEL PEAK 2(1P21.3) MUTATED 5 8 10 3 11
DEL PEAK 2(1P21.3) WILD-TYPE 18 4 11 12 5

Figure S9.  Get High-res Image Gene #2: 'del_1p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q35' versus 'CN_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.028

Table S10.  Gene #3: 'del_2q35' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 3(2Q35) MUTATED 0 7 5 5
DEL PEAK 3(2Q35) WILD-TYPE 27 14 11 18

Figure S10.  Get High-res Image Gene #3: 'del_2q35' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q35' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.089

Table S11.  Gene #3: 'del_2q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 12 21 15 16
DEL PEAK 3(2Q35) MUTATED 1 6 6 2 2
DEL PEAK 3(2Q35) WILD-TYPE 22 6 15 13 14

Figure S11.  Get High-res Image Gene #3: 'del_2q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.1' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0042

Table S12.  Gene #4: 'del_3p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 4(3P21.1) MUTATED 19 15 10 4
DEL PEAK 4(3P21.1) WILD-TYPE 8 6 6 19

Figure S12.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S13.  Gene #4: 'del_3p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 19 18 25 9
DEL PEAK 4(3P21.1) MUTATED 13 5 16 12 2
DEL PEAK 4(3P21.1) WILD-TYPE 3 14 2 13 7

Figure S13.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0034

Table S14.  Gene #4: 'del_3p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 21 19 21
DEL PEAK 4(3P21.1) MUTATED 21 4 10 13
DEL PEAK 4(3P21.1) WILD-TYPE 5 17 9 8

Figure S14.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7e-04

Table S15.  Gene #4: 'del_3p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 12 21 15 16
DEL PEAK 4(3P21.1) MUTATED 17 12 3 8 8
DEL PEAK 4(3P21.1) WILD-TYPE 6 0 18 7 8

Figure S15.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.1' versus 'MIRSEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.14

Table S16.  Gene #4: 'del_3p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 25 16 25
DEL PEAK 4(3P21.1) MUTATED 10 19 5 14
DEL PEAK 4(3P21.1) WILD-TYPE 11 6 11 11

Figure S16.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.089

Table S17.  Gene #4: 'del_3p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 25 6 13 14
DEL PEAK 4(3P21.1) MUTATED 16 8 3 9 12
DEL PEAK 4(3P21.1) WILD-TYPE 13 17 3 4 2

Figure S17.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00284 (Fisher's exact test), Q value = 0.026

Table S18.  Gene #4: 'del_3p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 18 16 34
DEL PEAK 4(3P21.1) MUTATED 14 4 8 21
DEL PEAK 4(3P21.1) WILD-TYPE 3 14 8 13

Figure S18.  Get High-res Image Gene #4: 'del_3p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S19.  Gene #5: 'del_4q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 5(4Q26) MUTATED 1 19 8 10
DEL PEAK 5(4Q26) WILD-TYPE 26 2 8 13

Figure S19.  Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q26' versus 'MRNASEQ_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.023

Table S20.  Gene #5: 'del_4q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 21 19 21
DEL PEAK 5(4Q26) MUTATED 4 11 9 14
DEL PEAK 5(4Q26) WILD-TYPE 22 10 10 7

Figure S20.  Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0042

Table S21.  Gene #5: 'del_4q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 12 21 15 16
DEL PEAK 5(4Q26) MUTATED 2 9 11 6 10
DEL PEAK 5(4Q26) WILD-TYPE 21 3 10 9 6

Figure S21.  Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q26' versus 'MIRSEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.087

Table S22.  Gene #5: 'del_4q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 25 16 25
DEL PEAK 5(4Q26) MUTATED 14 12 7 5
DEL PEAK 5(4Q26) WILD-TYPE 7 13 9 20

Figure S22.  Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.17

Table S23.  Gene #5: 'del_4q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 25 6 13 14
DEL PEAK 5(4Q26) MUTATED 14 12 5 5 2
DEL PEAK 5(4Q26) WILD-TYPE 15 13 1 8 12

Figure S23.  Get High-res Image Gene #5: 'del_4q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S24.  Gene #6: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 6(4Q34.3) MUTATED 0 19 10 12
DEL PEAK 6(4Q34.3) WILD-TYPE 27 2 6 11

Figure S24.  Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.026

Table S25.  Gene #6: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 19 18 25 9
DEL PEAK 6(4Q34.3) MUTATED 3 14 12 8 4
DEL PEAK 6(4Q34.3) WILD-TYPE 13 5 6 17 5

Figure S25.  Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.16

Table S26.  Gene #6: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 21 19 21
DEL PEAK 6(4Q34.3) MUTATED 7 13 8 13
DEL PEAK 6(4Q34.3) WILD-TYPE 19 8 11 8

Figure S26.  Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.007

Table S27.  Gene #6: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 12 21 15 16
DEL PEAK 6(4Q34.3) MUTATED 3 9 13 6 10
DEL PEAK 6(4Q34.3) WILD-TYPE 20 3 8 9 6

Figure S27.  Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 0.12

Table S28.  Gene #6: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 18 16 34
DEL PEAK 6(4Q34.3) MUTATED 4 12 5 19
DEL PEAK 6(4Q34.3) WILD-TYPE 13 6 11 15

Figure S28.  Get High-res Image Gene #6: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q23.2' versus 'CN_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.068

Table S29.  Gene #7: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 7(5Q23.2) MUTATED 2 6 7 2
DEL PEAK 7(5Q23.2) WILD-TYPE 25 15 9 21

Figure S29.  Get High-res Image Gene #7: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0253 (Fisher's exact test), Q value = 0.12

Table S30.  Gene #7: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 12 21 15 16
DEL PEAK 7(5Q23.2) MUTATED 3 7 3 2 2
DEL PEAK 7(5Q23.2) WILD-TYPE 20 5 18 13 14

Figure S30.  Get High-res Image Gene #7: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.1' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S31.  Gene #8: 'del_6q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 8(6Q22.1) MUTATED 14 17 7 3
DEL PEAK 8(6Q22.1) WILD-TYPE 13 4 9 20

Figure S31.  Get High-res Image Gene #8: 'del_6q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S32.  Gene #9: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 9(6Q26) MUTATED 10 19 5 2
DEL PEAK 9(6Q26) WILD-TYPE 17 2 11 21

Figure S32.  Get High-res Image Gene #9: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S33.  Gene #11: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 11(9P21.3) MUTATED 5 20 15 11
DEL PEAK 11(9P21.3) WILD-TYPE 22 1 1 12

Figure S33.  Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 0.00588 (Fisher's exact test), Q value = 0.046

Table S34.  Gene #11: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 19 18 25 9
DEL PEAK 11(9P21.3) MUTATED 5 13 16 13 4
DEL PEAK 11(9P21.3) WILD-TYPE 11 6 2 12 5

Figure S34.  Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.12

Table S35.  Gene #11: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 24 24 7
DEL PEAK 11(9P21.3) MUTATED 3 19 11 6
DEL PEAK 11(9P21.3) WILD-TYPE 5 5 13 1

Figure S35.  Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 0.12

Table S36.  Gene #11: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 21 19 21
DEL PEAK 11(9P21.3) MUTATED 9 14 12 16
DEL PEAK 11(9P21.3) WILD-TYPE 17 7 7 5

Figure S36.  Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0019

Table S37.  Gene #11: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 12 21 15 16
DEL PEAK 11(9P21.3) MUTATED 5 12 14 9 11
DEL PEAK 11(9P21.3) WILD-TYPE 18 0 7 6 5

Figure S37.  Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0063 (Fisher's exact test), Q value = 0.047

Table S38.  Gene #11: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 18 16 34
DEL PEAK 11(9P21.3) MUTATED 4 12 9 25
DEL PEAK 11(9P21.3) WILD-TYPE 13 6 7 9

Figure S38.  Get High-res Image Gene #11: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0034

Table S39.  Gene #12: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 12(10P15.3) MUTATED 2 12 9 5
DEL PEAK 12(10P15.3) WILD-TYPE 25 9 7 18

Figure S39.  Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.13

Table S40.  Gene #12: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 19 18 25 9
DEL PEAK 12(10P15.3) MUTATED 1 9 9 7 2
DEL PEAK 12(10P15.3) WILD-TYPE 15 10 9 18 7

Figure S40.  Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.14

Table S41.  Gene #12: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 21 19 21
DEL PEAK 12(10P15.3) MUTATED 3 8 7 10
DEL PEAK 12(10P15.3) WILD-TYPE 23 13 12 11

Figure S41.  Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.15

Table S42.  Gene #12: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 12 21 15 16
DEL PEAK 12(10P15.3) MUTATED 2 6 7 6 7
DEL PEAK 12(10P15.3) WILD-TYPE 21 6 14 9 9

Figure S42.  Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.15

Table S43.  Gene #12: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 25 16 25
DEL PEAK 12(10P15.3) MUTATED 9 12 2 5
DEL PEAK 12(10P15.3) WILD-TYPE 12 13 14 20

Figure S43.  Get High-res Image Gene #12: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q25.2' versus 'MIRSEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.12

Table S44.  Gene #13: 'del_10q25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 25 16 25
DEL PEAK 13(10Q25.2) MUTATED 13 9 3 6
DEL PEAK 13(10Q25.2) WILD-TYPE 8 16 13 19

Figure S44.  Get High-res Image Gene #13: 'del_10q25.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q23.2' versus 'CN_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.086

Table S45.  Gene #14: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 14(11Q23.2) MUTATED 3 1 5 9
DEL PEAK 14(11Q23.2) WILD-TYPE 24 20 11 14

Figure S45.  Get High-res Image Gene #14: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.31' versus 'MRNASEQ_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.12

Table S46.  Gene #15: 'del_12p13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 21 19 21
DEL PEAK 15(12P13.31) MUTATED 0 5 4 2
DEL PEAK 15(12P13.31) WILD-TYPE 26 16 15 19

Figure S46.  Get High-res Image Gene #15: 'del_12p13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.31' versus 'MIRSEQ_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.089

Table S47.  Gene #15: 'del_12p13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 25 16 25
DEL PEAK 15(12P13.31) MUTATED 6 4 1 0
DEL PEAK 15(12P13.31) WILD-TYPE 15 21 15 25

Figure S47.  Get High-res Image Gene #15: 'del_12p13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q14.11' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00079

Table S48.  Gene #16: 'del_13q14.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 16(13Q14.11) MUTATED 10 20 8 6
DEL PEAK 16(13Q14.11) WILD-TYPE 17 1 8 17

Figure S48.  Get High-res Image Gene #16: 'del_13q14.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00042

Table S49.  Gene #17: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 17(14Q32.31) MUTATED 1 16 9 13
DEL PEAK 17(14Q32.31) WILD-TYPE 26 5 7 10

Figure S49.  Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.31' versus 'METHLYATION_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.007

Table S50.  Gene #17: 'del_14q32.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 19 18 25 9
DEL PEAK 17(14Q32.31) MUTATED 3 16 7 8 5
DEL PEAK 17(14Q32.31) WILD-TYPE 13 3 11 17 4

Figure S50.  Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.31' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0056

Table S51.  Gene #17: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 21 19 21
DEL PEAK 17(14Q32.31) MUTATED 7 17 5 10
DEL PEAK 17(14Q32.31) WILD-TYPE 19 4 14 11

Figure S51.  Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00093

Table S52.  Gene #17: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 12 21 15 16
DEL PEAK 17(14Q32.31) MUTATED 5 8 17 2 7
DEL PEAK 17(14Q32.31) WILD-TYPE 18 4 4 13 9

Figure S52.  Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00901 (Fisher's exact test), Q value = 0.063

Table S53.  Gene #17: 'del_14q32.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 29 25 6 13 14
DEL PEAK 17(14Q32.31) MUTATED 8 15 4 9 3
DEL PEAK 17(14Q32.31) WILD-TYPE 21 10 2 4 11

Figure S53.  Get High-res Image Gene #17: 'del_14q32.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 0.00462 (Fisher's exact test), Q value = 0.039

Table S54.  Gene #18: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 18(15Q15.1) MUTATED 4 6 11 7
DEL PEAK 18(15Q15.1) WILD-TYPE 23 15 5 16

Figure S54.  Get High-res Image Gene #18: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.11

Table S55.  Gene #18: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 21 19 21
DEL PEAK 18(15Q15.1) MUTATED 3 11 6 8
DEL PEAK 18(15Q15.1) WILD-TYPE 23 10 13 13

Figure S55.  Get High-res Image Gene #18: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.11

Table S56.  Gene #18: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 18 16 34
DEL PEAK 18(15Q15.1) MUTATED 3 8 1 14
DEL PEAK 18(15Q15.1) WILD-TYPE 14 10 15 20

Figure S56.  Get High-res Image Gene #18: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.1' versus 'CN_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.17

Table S57.  Gene #20: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 21 16 23
DEL PEAK 20(16Q24.1) MUTATED 2 8 5 7
DEL PEAK 20(16Q24.1) WILD-TYPE 25 13 11 16

Figure S57.  Get High-res Image Gene #20: 'del_16q24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q12.2' versus 'METHLYATION_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.099

Table S58.  Gene #21: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 19 18 25 9
DEL PEAK 21(22Q12.2) MUTATED 12 15 18 15 8
DEL PEAK 21(22Q12.2) WILD-TYPE 4 4 0 10 1

Figure S58.  Get High-res Image Gene #21: 'del_22q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q12.2' versus 'MRNASEQ_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.15

Table S59.  Gene #21: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 21 19 21
DEL PEAK 21(22Q12.2) MUTATED 20 17 11 20
DEL PEAK 21(22Q12.2) WILD-TYPE 6 4 8 1

Figure S59.  Get High-res Image Gene #21: 'del_22q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.089

Table S60.  Gene #21: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 12 21 15 16
DEL PEAK 21(22Q12.2) MUTATED 16 12 17 8 15
DEL PEAK 21(22Q12.2) WILD-TYPE 7 0 4 7 1

Figure S60.  Get High-res Image Gene #21: 'del_22q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q12.2' versus 'MIRSEQ_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.17

Table S61.  Gene #21: 'del_22q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 25 16 25
DEL PEAK 21(22Q12.2) MUTATED 19 22 9 18
DEL PEAK 21(22Q12.2) WILD-TYPE 2 3 7 7

Figure S61.  Get High-res Image Gene #21: 'del_22q12.2' versus Molecular Subtype #7: 'MIRSEQ_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/MESO-TP/22533663/transformed.cor.cli.txt

  • Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/MESO-TP/22541489/MESO-TP.transferedmergedcluster.txt

  • Number of patients = 87

  • Number of significantly focal cnvs = 21

  • 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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