Correlation between copy number variations of arm-level result and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 32 arm-level events and 6 molecular subtypes across 191 patients, 79 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p gain cnv correlated to 'CN_CNMF'.

  • 4p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 4q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 8q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'CN_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 11q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 13q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 17q gain cnv correlated to 'CN_CNMF'.

  • 19p gain cnv correlated to 'CN_CNMF'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 21q gain cnv correlated to 'CN_CNMF'.

  • 22q gain cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • xp gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • xq gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 3p loss cnv correlated to 'CN_CNMF'.

  • 3q loss cnv correlated to 'CN_CNMF'.

  • 5q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 7p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 7q loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 12p loss cnv correlated to 'CN_CNMF'.

  • 15q loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 17q loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 18p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • 19p loss cnv correlated to 'CN_CNMF'.

  • 19q loss cnv correlated to 'CN_CNMF'.

  • xp loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • xq loss cnv correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 32 arm-level events and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 79 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
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
8p gain 22 (12%) 169 0.00081
(0.00778) 		0.00025
(0.0032) 		0.0285
(0.0783) 		0.00088
(0.00805) 		0.00985
(0.035) 		0.0167
(0.05)
8q gain 23 (12%) 168 0.00138
(0.0102) 		0.00039
(0.0044) 		0.014
(0.0453) 		0.00174
(0.0111) 		0.0069
(0.026) 		0.0138
(0.0453)
7p loss 17 (9%) 174 4e-05
(0.000853) 		0.00019
(0.00261) 		0.00096
(0.00826) 		2e-05
(0.00048) 		0.00373
(0.0184) 		0.00346
(0.0184)
7q loss 20 (10%) 171 1e-05
(0.00048) 		1e-05
(0.00048) 		0.00609
(0.0257) 		2e-05
(0.00048) 		0.00148
(0.0105) 		0.00078
(0.00778)
22q gain 9 (5%) 182 0.00099
(0.00826) 		0.00384
(0.0184) 		0.137
(0.257) 		0.0161
(0.049) 		0.0555
(0.132) 		0.0131
(0.0448)
5q loss 6 (3%) 185 5e-05
(0.00096) 		0.00641
(0.0257) 		0.226
(0.365) 		0.63
(0.768) 		0.0314
(0.0826) 		0.0322
(0.0835)
17p loss 13 (7%) 178 1e-05
(0.00048) 		0.00169
(0.0111) 		0.154
(0.287) 		0.00164
(0.0111) 		0.161
(0.298) 		0.00359
(0.0184)
11q gain 7 (4%) 184 2e-05
(0.00048) 		0.0308
(0.0822) 		0.0676
(0.149) 		0.0751
(0.162) 		0.291
(0.444) 		0.0155
(0.0482)
16q loss 4 (2%) 187 0.0011
(0.0088) 		0.0565
(0.132) 		0.787
(0.922) 		1
(1.00) 		0.0152
(0.0477) 		0.0216
(0.0629)
17q loss 7 (4%) 184 2e-05
(0.00048) 		0.113
(0.219) 		0.0669
(0.149) 		0.237
(0.38) 		0.0369
(0.0944) 		0.0472
(0.115)
xp loss 5 (3%) 186 0.0001
(0.00175) 		0.199
(0.345) 		0.224
(0.365) 		0.632
(0.768) 		0.00369
(0.0184) 		0.00483
(0.0216)
xq loss 5 (3%) 186 0.00011
(0.00176) 		0.202
(0.346) 		0.225
(0.365) 		0.631
(0.768) 		0.00313
(0.0172) 		0.00476
(0.0216)
4p gain 4 (2%) 187 0.0276
(0.0769) 		0.0075
(0.0277) 		0.341
(0.5) 		0.834
(0.961)
4q gain 4 (2%) 187 0.0292
(0.079) 		0.00795
(0.0288) 		0.341
(0.5) 		0.836
(0.961)
11p gain 4 (2%) 187 0.00065
(0.00693) 		0.432
(0.596) 		0.467
(0.626) 		0.367
(0.53) 		0.523
(0.68) 		0.0222
(0.0636)
13q gain 6 (3%) 185 0.042
(0.106) 		0.00667
(0.0257) 		0.123
(0.236) 		0.0832
(0.176) 		0.802
(0.933) 		0.0736
(0.161)
xp gain 3 (2%) 188 0.00196
(0.0121) 		0.704
(0.839) 		0.892
(0.978) 		0.047
(0.115)
xq gain 3 (2%) 188 0.00201
(0.0121) 		0.7
(0.839) 		0.89
(0.978) 		0.0455
(0.113)
15q loss 4 (2%) 187 0.00027
(0.00324) 		0.549
(0.707) 		0.0666
(0.149) 		0.367
(0.53) 		0.0227
(0.064) 		0.183
(0.328)
18p loss 5 (3%) 186 0.00012
(0.00177) 		0.0213
(0.0629) 		1
(1.00) 		0.865
(0.961) 		0.252
(0.387) 		0.185
(0.328)
1p gain 3 (2%) 188 0.00394
(0.0185) 		0.209
(0.35) 		0.187
(0.328) 		0.589
(0.731) 		0.0927
(0.187) 		0.0937
(0.187)
10q gain 3 (2%) 188 0.0142
(0.0453) 		0.209
(0.35) 		0.185
(0.328) 		0.59
(0.731) 		0.553
(0.708) 		0.0909
(0.187)
17q gain 3 (2%) 188 0.00657
(0.0257) 		0.704
(0.839) 		1
(1.00) 		0.587
(0.731) 		0.483
(0.637) 		0.305
(0.461)
19p gain 5 (3%) 186 0.0134
(0.0452) 		0.246
(0.385) 		1
(1.00) 		0.863
(0.961) 		0.58
(0.731) 		1
(1.00)
19q gain 5 (3%) 186 0.0128
(0.0445) 		0.246
(0.385) 		1
(1.00) 		0.864
(0.961) 		0.579
(0.731) 		1
(1.00)
21q gain 8 (4%) 183 1e-05
(0.00048) 		0.113
(0.219) 		0.125
(0.238) 		0.524
(0.68) 		0.0811
(0.173) 		0.412
(0.581)
3p loss 3 (2%) 188 0.00668
(0.0257) 		0.21
(0.35) 		0.784
(0.922) 		1
(1.00) 		0.0633
(0.145) 		0.092
(0.187)
3q loss 3 (2%) 188 0.00658
(0.0257) 		0.212
(0.351) 		0.785
(0.922) 		1
(1.00) 		0.0627
(0.145) 		0.0913
(0.187)
12p loss 4 (2%) 187 0.00613
(0.0257) 		0.431
(0.596) 		0.374
(0.536) 		0.389
(0.553) 		0.484
(0.637) 		0.186
(0.328)
18q loss 4 (2%) 187 0.00132
(0.0101) 		0.0557
(0.132) 		0.469
(0.626) 		0.862
(0.961) 		0.102
(0.203) 		0.188
(0.328)
19p loss 4 (2%) 187 0.00295
(0.0172) 		0.435
(0.596) 		0.467
(0.626) 		0.863
(0.961) 		0.31
(0.461) 		0.248
(0.385)
19q loss 4 (2%) 187 0.00309
(0.0172) 		0.431
(0.596) 		0.467
(0.626) 		0.866
(0.961) 		0.309
(0.461) 		0.249
(0.385)
'1p gain' versus 'CN_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
1P GAIN MUTATED 0 2 1 0
1P GAIN WILD-TYPE 148 12 26 2

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

'4p gain' versus 'CN_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.077

Table S2.  Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
4P GAIN MUTATED 1 0 3 0
4P GAIN WILD-TYPE 147 14 24 2

Figure S2.  Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.0075 (Fisher's exact test), Q value = 0.028

Table S3.  Gene #2: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
4P GAIN MUTATED 0 0 4 0
4P GAIN WILD-TYPE 33 61 43 44

Figure S3.  Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.079

Table S4.  Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
4Q GAIN MUTATED 1 0 3 0
4Q GAIN WILD-TYPE 147 14 24 2

Figure S4.  Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.00795 (Fisher's exact test), Q value = 0.029

Table S5.  Gene #3: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
4Q GAIN MUTATED 0 0 4 0
4Q GAIN WILD-TYPE 33 61 43 44

Figure S5.  Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0078

Table S6.  Gene #4: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
8P GAIN MUTATED 11 1 10 0
8P GAIN WILD-TYPE 137 13 17 2

Figure S6.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0032

Table S7.  Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
8P GAIN MUTATED 1 16 3 1
8P GAIN WILD-TYPE 32 45 44 43

Figure S7.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.078

Table S8.  Gene #4: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 52 44
8P GAIN MUTATED 13 2 3
8P GAIN WILD-TYPE 57 50 41

Figure S8.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.008

Table S9.  Gene #4: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
8P GAIN MUTATED 1 0 0 15 1 1
8P GAIN WILD-TYPE 15 13 14 40 25 41

Figure S9.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.00985 (Fisher's exact test), Q value = 0.035

Table S10.  Gene #4: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
8P GAIN MUTATED 2 9 3 7
8P GAIN WILD-TYPE 56 28 38 36

Figure S10.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.05

Table S11.  Gene #4: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
8P GAIN MUTATED 3 8 10
8P GAIN WILD-TYPE 64 26 68

Figure S11.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.01

Table S12.  Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
8Q GAIN MUTATED 12 1 10 0
8Q GAIN WILD-TYPE 136 13 17 2

Figure S12.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0044

Table S13.  Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
8Q GAIN MUTATED 1 16 4 1
8Q GAIN WILD-TYPE 32 45 43 43

Figure S13.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.045

Table S14.  Gene #5: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 52 44
8Q GAIN MUTATED 14 2 3
8Q GAIN WILD-TYPE 56 50 41

Figure S14.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.011

Table S15.  Gene #5: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
8Q GAIN MUTATED 1 0 1 15 1 1
8Q GAIN WILD-TYPE 15 13 13 40 25 41

Figure S15.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.0069 (Fisher's exact test), Q value = 0.026

Table S16.  Gene #5: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
8Q GAIN MUTATED 2 9 3 8
8Q GAIN WILD-TYPE 56 28 38 35

Figure S16.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.045

Table S17.  Gene #5: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
8Q GAIN MUTATED 3 8 11
8Q GAIN WILD-TYPE 64 26 67

Figure S17.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.045

Table S18.  Gene #6: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
10Q GAIN MUTATED 0 1 2 0
10Q GAIN WILD-TYPE 148 13 25 2

Figure S18.  Get High-res Image Gene #6: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0069

Table S19.  Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
11P GAIN MUTATED 0 3 1 0
11P GAIN WILD-TYPE 148 11 26 2

Figure S19.  Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.064

Table S20.  Gene #7: '11p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
11P GAIN MUTATED 0 3 1
11P GAIN WILD-TYPE 67 31 77

Figure S20.  Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00048

Table S21.  Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
11Q GAIN MUTATED 0 4 3 0
11Q GAIN WILD-TYPE 148 10 24 2

Figure S21.  Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.082

Table S22.  Gene #8: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
11Q GAIN MUTATED 0 6 1 0
11Q GAIN WILD-TYPE 33 55 46 44

Figure S22.  Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.048

Table S23.  Gene #8: '11q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
11Q GAIN MUTATED 0 4 3
11Q GAIN WILD-TYPE 67 30 75

Figure S23.  Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.11

Table S24.  Gene #9: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
13Q GAIN MUTATED 2 1 3 0
13Q GAIN WILD-TYPE 146 13 24 2

Figure S24.  Get High-res Image Gene #9: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00667 (Fisher's exact test), Q value = 0.026

Table S25.  Gene #9: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
13Q GAIN MUTATED 0 6 0 0
13Q GAIN WILD-TYPE 33 55 47 44

Figure S25.  Get High-res Image Gene #9: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.00657 (Fisher's exact test), Q value = 0.026

Table S26.  Gene #10: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
17Q GAIN MUTATED 0 0 3 0
17Q GAIN WILD-TYPE 148 14 24 2

Figure S26.  Get High-res Image Gene #10: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.045

Table S27.  Gene #11: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
19P GAIN MUTATED 1 1 3 0
19P GAIN WILD-TYPE 147 13 24 2

Figure S27.  Get High-res Image Gene #11: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.045

Table S28.  Gene #12: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
19Q GAIN MUTATED 1 1 3 0
19Q GAIN WILD-TYPE 147 13 24 2

Figure S28.  Get High-res Image Gene #12: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S29.  Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
21Q GAIN MUTATED 0 0 8 0
21Q GAIN WILD-TYPE 148 14 19 2

Figure S29.  Get High-res Image Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0083

Table S30.  Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
22Q GAIN MUTATED 2 2 5 0
22Q GAIN WILD-TYPE 146 12 22 2

Figure S30.  Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.018

Table S31.  Gene #14: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
22Q GAIN MUTATED 0 8 1 0
22Q GAIN WILD-TYPE 33 53 46 44

Figure S31.  Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.049

Table S32.  Gene #14: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
22Q GAIN MUTATED 0 1 0 8 0 0
22Q GAIN WILD-TYPE 16 12 14 47 26 42

Figure S32.  Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.045

Table S33.  Gene #14: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
22Q GAIN MUTATED 0 4 5
22Q GAIN WILD-TYPE 67 30 73

Figure S33.  Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.012

Table S34.  Gene #15: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
XP GAIN MUTATED 0 1 1 1
XP GAIN WILD-TYPE 148 13 26 1

Figure S34.  Get High-res Image Gene #15: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.11

Table S35.  Gene #15: 'xp gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
XP GAIN MUTATED 1 2 0
XP GAIN WILD-TYPE 66 32 78

Figure S35.  Get High-res Image Gene #15: 'xp gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.012

Table S36.  Gene #16: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
XQ GAIN MUTATED 0 1 1 1
XQ GAIN WILD-TYPE 148 13 26 1

Figure S36.  Get High-res Image Gene #16: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.11

Table S37.  Gene #16: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
XQ GAIN MUTATED 1 2 0
XQ GAIN WILD-TYPE 66 32 78

Figure S37.  Get High-res Image Gene #16: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.00668 (Fisher's exact test), Q value = 0.026

Table S38.  Gene #17: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
3P LOSS MUTATED 0 0 3 0
3P LOSS WILD-TYPE 148 14 24 2

Figure S38.  Get High-res Image Gene #17: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.00658 (Fisher's exact test), Q value = 0.026

Table S39.  Gene #18: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
3Q LOSS MUTATED 0 0 3 0
3Q LOSS WILD-TYPE 148 14 24 2

Figure S39.  Get High-res Image Gene #18: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00096

Table S40.  Gene #19: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
5Q LOSS MUTATED 0 0 6 0
5Q LOSS WILD-TYPE 148 14 21 2

Figure S40.  Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.00641 (Fisher's exact test), Q value = 0.026

Table S41.  Gene #19: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
5Q LOSS MUTATED 0 6 0 0
5Q LOSS WILD-TYPE 33 55 47 44

Figure S41.  Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.083

Table S42.  Gene #19: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
5Q LOSS MUTATED 0 3 2 0
5Q LOSS WILD-TYPE 58 34 39 43

Figure S42.  Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.083

Table S43.  Gene #19: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
5Q LOSS MUTATED 0 3 2
5Q LOSS WILD-TYPE 67 31 76

Figure S43.  Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00085

Table S44.  Gene #20: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
7P LOSS MUTATED 7 0 9 1
7P LOSS WILD-TYPE 141 14 18 1

Figure S44.  Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0026

Table S45.  Gene #20: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
7P LOSS MUTATED 0 14 1 2
7P LOSS WILD-TYPE 33 47 46 42

Figure S45.  Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0083

Table S46.  Gene #20: '7p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 52 44
7P LOSS MUTATED 13 0 3
7P LOSS WILD-TYPE 57 52 41

Figure S46.  Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00048

Table S47.  Gene #20: '7p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
7P LOSS MUTATED 0 0 0 16 0 0
7P LOSS WILD-TYPE 16 13 14 39 26 42

Figure S47.  Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 0.00373 (Fisher's exact test), Q value = 0.018

Table S48.  Gene #20: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
7P LOSS MUTATED 1 9 3 4
7P LOSS WILD-TYPE 57 28 38 39

Figure S48.  Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00346 (Fisher's exact test), Q value = 0.018

Table S49.  Gene #20: '7p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
7P LOSS MUTATED 1 7 9
7P LOSS WILD-TYPE 66 27 69

Figure S49.  Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S50.  Gene #21: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
7Q LOSS MUTATED 8 0 11 1
7Q LOSS WILD-TYPE 140 14 16 1

Figure S50.  Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S51.  Gene #21: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
7Q LOSS MUTATED 0 17 1 2
7Q LOSS WILD-TYPE 33 44 46 42

Figure S51.  Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.00609 (Fisher's exact test), Q value = 0.026

Table S52.  Gene #21: '7q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 52 44
7Q LOSS MUTATED 13 1 3
7Q LOSS WILD-TYPE 57 51 41

Figure S52.  Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00048

Table S53.  Gene #21: '7q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
7Q LOSS MUTATED 0 0 0 17 0 0
7Q LOSS WILD-TYPE 16 13 14 38 26 42

Figure S53.  Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.011

Table S54.  Gene #21: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
7Q LOSS MUTATED 1 10 4 4
7Q LOSS WILD-TYPE 57 27 37 39

Figure S54.  Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0078

Table S55.  Gene #21: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
7Q LOSS MUTATED 1 8 10
7Q LOSS WILD-TYPE 66 26 68

Figure S55.  Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 0.00613 (Fisher's exact test), Q value = 0.026

Table S56.  Gene #22: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
12P LOSS MUTATED 1 0 2 1
12P LOSS WILD-TYPE 147 14 25 1

Figure S56.  Get High-res Image Gene #22: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0032

Table S57.  Gene #23: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
15Q LOSS MUTATED 0 0 3 1
15Q LOSS WILD-TYPE 148 14 24 1

Figure S57.  Get High-res Image Gene #23: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.064

Table S58.  Gene #23: '15q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
15Q LOSS MUTATED 0 3 0 1
15Q LOSS WILD-TYPE 58 34 41 42

Figure S58.  Get High-res Image Gene #23: '15q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0088

Table S59.  Gene #24: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
16Q LOSS MUTATED 0 0 4 0
16Q LOSS WILD-TYPE 148 14 23 2

Figure S59.  Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.048

Table S60.  Gene #24: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
16Q LOSS MUTATED 0 3 1 0
16Q LOSS WILD-TYPE 58 34 40 43

Figure S60.  Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.063

Table S61.  Gene #24: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
16Q LOSS MUTATED 0 3 1
16Q LOSS WILD-TYPE 67 31 77

Figure S61.  Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00048

Table S62.  Gene #25: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
17P LOSS MUTATED 0 0 13 0
17P LOSS WILD-TYPE 148 14 14 2

Figure S62.  Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.011

Table S63.  Gene #25: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
17P LOSS MUTATED 0 10 3 0
17P LOSS WILD-TYPE 33 51 44 44

Figure S63.  Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00164 (Fisher's exact test), Q value = 0.011

Table S64.  Gene #25: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 14 55 26 42
17P LOSS MUTATED 0 0 0 12 0 1
17P LOSS WILD-TYPE 16 13 14 43 26 41

Figure S64.  Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00359 (Fisher's exact test), Q value = 0.018

Table S65.  Gene #25: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
17P LOSS MUTATED 0 4 9
17P LOSS WILD-TYPE 67 30 69

Figure S65.  Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00048

Table S66.  Gene #26: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
17Q LOSS MUTATED 0 0 7 0
17Q LOSS WILD-TYPE 148 14 20 2

Figure S66.  Get High-res Image Gene #26: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.094

Table S67.  Gene #26: '17q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
17Q LOSS MUTATED 0 4 1 2
17Q LOSS WILD-TYPE 58 33 40 41

Figure S67.  Get High-res Image Gene #26: '17q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.11

Table S68.  Gene #26: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
17Q LOSS MUTATED 0 3 4
17Q LOSS WILD-TYPE 67 31 74

Figure S68.  Get High-res Image Gene #26: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0018

Table S69.  Gene #27: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
18P LOSS MUTATED 0 0 5 0
18P LOSS WILD-TYPE 148 14 22 2

Figure S69.  Get High-res Image Gene #27: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.063

Table S70.  Gene #27: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 61 47 44
18P LOSS MUTATED 0 5 0 0
18P LOSS WILD-TYPE 33 56 47 44

Figure S70.  Get High-res Image Gene #27: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.01

Table S71.  Gene #28: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
18Q LOSS MUTATED 0 0 4 0
18Q LOSS WILD-TYPE 148 14 23 2

Figure S71.  Get High-res Image Gene #28: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 0.00295 (Fisher's exact test), Q value = 0.017

Table S72.  Gene #29: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
19P LOSS MUTATED 0 1 3 0
19P LOSS WILD-TYPE 148 13 24 2

Figure S72.  Get High-res Image Gene #29: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 0.00309 (Fisher's exact test), Q value = 0.017

Table S73.  Gene #30: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
19Q LOSS MUTATED 0 1 3 0
19Q LOSS WILD-TYPE 148 13 24 2

Figure S73.  Get High-res Image Gene #30: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0017

Table S74.  Gene #31: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
XP LOSS MUTATED 0 0 4 1
XP LOSS WILD-TYPE 148 14 23 1

Figure S74.  Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.00369 (Fisher's exact test), Q value = 0.018

Table S75.  Gene #31: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
XP LOSS MUTATED 0 4 1 0
XP LOSS WILD-TYPE 58 33 40 43

Figure S75.  Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.022

Table S76.  Gene #31: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
XP LOSS MUTATED 0 4 1
XP LOSS WILD-TYPE 67 30 77

Figure S76.  Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0018

Table S77.  Gene #32: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 14 27 2
XQ LOSS MUTATED 0 0 4 1
XQ LOSS WILD-TYPE 148 14 23 1

Figure S77.  Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.017

Table S78.  Gene #32: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
XQ LOSS MUTATED 0 4 1 0
XQ LOSS WILD-TYPE 58 33 40 43

Figure S78.  Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.022

Table S79.  Gene #32: 'xq loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 34 78
XQ LOSS MUTATED 0 4 1
XQ LOSS WILD-TYPE 67 30 77

Figure S79.  Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/19782154/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/19785823/LAML-TB.transferedmergedcluster.txt

  • Number of patients = 191

  • Number of significantly arm-level cnvs = 32

  • Number of molecular subtypes = 6

  • Exclude genes that fewer than K tumors have mutations, 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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