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 0.00091
(0.00793) 		0.00025
(0.0032) 		0.0287
(0.0795) 		0.00084
(0.00793) 		0.00981
(0.0349) 		0.0163
(0.0497)
8q gain 23 (12%) 168 0.00147
(0.0101) 		0.00039
(0.00452) 		0.0135
(0.0454) 		0.00184
(0.0112) 		0.00711
(0.0268) 		0.0145
(0.0462)
7p loss 17 (9%) 174 4e-05
(0.000698) 		0.00016
(0.00236) 		0.00095
(0.00793) 		1e-05
(0.00024) 		0.00358
(0.0181) 		0.00339
(0.0181)
7q loss 20 (10%) 171 1e-05
(0.00024) 		2e-05
(0.000427) 		0.00585
(0.0252) 		1e-05
(0.00024) 		0.00143
(0.0101) 		0.00084
(0.00793)
22q gain 9 (5%) 182 0.00095
(0.00793) 		0.00425
(0.0204) 		0.137
(0.258) 		0.0168
(0.0504) 		0.0562
(0.132) 		0.0132
(0.0452)
5q loss 6 (3%) 185 1e-05
(0.00024) 		0.00682
(0.0262) 		0.226
(0.364) 		0.633
(0.769) 		0.0312
(0.082) 		0.0327
(0.0848)
17p loss 13 (7%) 178 1e-05
(0.00024) 		0.00187
(0.0112) 		0.157
(0.292) 		0.00138
(0.0101) 		0.161
(0.296) 		0.00385
(0.019)
11q gain 7 (4%) 184 1e-05
(0.00024) 		0.0298
(0.0795) 		0.0667
(0.147) 		0.0736
(0.159) 		0.291
(0.443) 		0.0149
(0.0462)
16q loss 4 (2%) 187 0.00108
(0.00864) 		0.0556
(0.132) 		0.785
(0.923) 		1
(1.00) 		0.0145
(0.0462) 		0.0224
(0.0643)
17q loss 7 (4%) 184 1e-05
(0.00024) 		0.112
(0.218) 		0.0667
(0.147) 		0.234
(0.375) 		0.0375
(0.0959) 		0.0491
(0.119)
xp loss 5 (3%) 186 0.00012
(0.00192) 		0.199
(0.345) 		0.224
(0.364) 		0.631
(0.769) 		0.00353
(0.0181) 		0.00501
(0.0224)
xq loss 5 (3%) 186 4e-05
(0.000698) 		0.201
(0.345) 		0.224
(0.364) 		0.631
(0.769) 		0.0033
(0.0181) 		0.0048
(0.0219)
4p gain 4 (2%) 187 0.0294
(0.0795) 		0.00755
(0.0274) 		0.342
(0.501) 		0.837
(0.962)
4q gain 4 (2%) 187 0.0292
(0.0795) 		0.0074
(0.0273) 		0.342
(0.501) 		0.833
(0.962)
11p gain 4 (2%) 187 0.0007
(0.00747) 		0.43
(0.597) 		0.465
(0.625) 		0.369
(0.533) 		0.523
(0.682) 		0.0221
(0.0643)
13q gain 6 (3%) 185 0.0418
(0.106) 		0.00655
(0.0259) 		0.124
(0.238) 		0.0845
(0.178) 		0.801
(0.932) 		0.0736
(0.159)
xp gain 3 (2%) 188 0.00183
(0.0112) 		0.699
(0.837) 		0.892
(0.978) 		0.0468
(0.115)
xq gain 3 (2%) 188 0.00159
(0.0105) 		0.701
(0.837) 		0.891
(0.978) 		0.0469
(0.115)
15q loss 4 (2%) 187 0.0004
(0.00452) 		0.55
(0.707) 		0.0662
(0.147) 		0.369
(0.533) 		0.0228
(0.0645) 		0.186
(0.326)
18p loss 5 (3%) 186 0.00018
(0.00247) 		0.0207
(0.0613) 		1
(1.00) 		0.864
(0.962) 		0.249
(0.386) 		0.185
(0.326)
1p gain 3 (2%) 188 0.00441
(0.0207) 		0.209
(0.349) 		0.185
(0.326) 		0.592
(0.733) 		0.0911
(0.185) 		0.0927
(0.185)
10q gain 3 (2%) 188 0.0148
(0.0462) 		0.21
(0.349) 		0.184
(0.326) 		0.59
(0.733) 		0.552
(0.707) 		0.0924
(0.185)
17q gain 3 (2%) 188 0.00626
(0.0257) 		0.702
(0.837) 		1
(1.00) 		0.591
(0.733) 		0.482
(0.634) 		0.304
(0.459)
19p gain 5 (3%) 186 0.0141
(0.0462) 		0.249
(0.386) 		1
(1.00) 		0.867
(0.962) 		0.581
(0.733) 		1
(1.00)
19q gain 5 (3%) 186 0.0126
(0.0441) 		0.248
(0.386) 		1
(1.00) 		0.864
(0.962) 		0.578
(0.733) 		1
(1.00)
21q gain 8 (4%) 183 1e-05
(0.00024) 		0.112
(0.218) 		0.125
(0.239) 		0.525
(0.682) 		0.0829
(0.177) 		0.412
(0.582)
3p loss 3 (2%) 188 0.00662
(0.0259) 		0.211
(0.349) 		0.788
(0.923) 		1
(1.00) 		0.0611
(0.141) 		0.0926
(0.185)
3q loss 3 (2%) 188 0.0063
(0.0257) 		0.21
(0.349) 		0.788
(0.923) 		1
(1.00) 		0.0622
(0.142) 		0.0922
(0.185)
12p loss 4 (2%) 187 0.00591
(0.0252) 		0.431
(0.597) 		0.376
(0.538) 		0.39
(0.554) 		0.481
(0.634) 		0.186
(0.326)
18q loss 4 (2%) 187 0.00118
(0.00906) 		0.0566
(0.132) 		0.467
(0.625) 		0.865
(0.962) 		0.101
(0.2) 		0.183
(0.326)
19p loss 4 (2%) 187 0.00318
(0.018) 		0.432
(0.597) 		0.469
(0.625) 		0.864
(0.962) 		0.31
(0.464) 		0.246
(0.386)
19q loss 4 (2%) 187 0.003
(0.0175) 		0.436
(0.598) 		0.468
(0.625) 		0.863
(0.962) 		0.311
(0.464) 		0.252
(0.386)
'1p gain' versus 'CN_CNMF'

P value = 0.00441 (Fisher's exact test), Q value = 0.021

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 = 0.0294 (Fisher's exact test), Q value = 0.08

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 = 0.00755 (Fisher's exact test), Q value = 0.027

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 = 0.08

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 = 0.0074 (Fisher's exact test), Q value = 0.027

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 = 0.00091 (Fisher's exact test), Q value = 0.0079

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 = 0.0287 (Fisher's exact test), Q value = 0.08

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 = 0.00084 (Fisher's exact test), Q value = 0.0079

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 = 0.00981 (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 = 0.0163 (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 = 0.00147 (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 = 0.0045

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 = 0.0135 (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 = 0.00184 (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 = 0.00711 (Fisher's exact test), Q value = 0.027

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 = 0.0145 (Fisher's exact test), Q value = 0.046

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 = 0.0148 (Fisher's exact test), Q value = 0.046

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 = 7e-04 (Fisher's exact test), Q value = 0.0075

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 = 0.0221 (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 = 1e-05 (Fisher's exact test), Q value = 0.00024

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 = 0.0298 (Fisher's exact test), Q value = 0.08

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 = 0.0149 (Fisher's exact test), Q value = 0.046

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 = 0.0418 (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 = 0.00655 (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 = 0.00626 (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 = 0.0141 (Fisher's exact test), Q value = 0.046

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 = 0.0126 (Fisher's exact test), Q value = 0.044

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 = 0.00024

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 = 0.00095 (Fisher's exact test), Q value = 0.0079

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 = 0.00425 (Fisher's exact test), Q value = 0.02

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 = 0.0168 (Fisher's exact test), Q value = 0.05

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 = 0.0132 (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 = 0.00183 (Fisher's exact test), Q value = 0.011

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 = 0.0468 (Fisher's exact test), Q value = 0.12

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 = 0.00159 (Fisher's exact test), Q value = 0.011

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 = 0.0469 (Fisher's exact test), Q value = 0.12

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 = 0.00662 (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 = 0.0063 (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 = 1e-05 (Fisher's exact test), Q value = 0.00024

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 = 0.00682 (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 = 0.0312 (Fisher's exact test), Q value = 0.082

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 = 0.0327 (Fisher's exact test), Q value = 0.085

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 = 7e-04

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 = 0.00016 (Fisher's exact test), Q value = 0.0024

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 = 0.00095 (Fisher's exact test), Q value = 0.0079

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 = 1e-05 (Fisher's exact test), Q value = 0.00024

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 = 0.00358 (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 = 0.00339 (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 = 0.00024

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 = 2e-05 (Fisher's exact test), Q value = 0.00043

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 = 0.00585 (Fisher's exact test), Q value = 0.025

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 = 1e-05 (Fisher's exact test), Q value = 0.00024

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 = 0.00143 (Fisher's exact test), Q value = 0.01

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 = 0.00084 (Fisher's exact test), Q value = 0.0079

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 = 0.00591 (Fisher's exact test), Q value = 0.025

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 = 4e-04 (Fisher's exact test), Q value = 0.0045

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 = 0.0228 (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 = 0.00108 (Fisher's exact test), Q value = 0.0086

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 = 0.0145 (Fisher's exact test), Q value = 0.046

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 = 0.0224 (Fisher's exact test), Q value = 0.064

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 = 0.00024

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 = 0.00187 (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 = 0.00138 (Fisher's exact test), Q value = 0.01

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 = 0.00385 (Fisher's exact test), Q value = 0.019

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 = 1e-05 (Fisher's exact test), Q value = 0.00024

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 = 0.0375 (Fisher's exact test), Q value = 0.096

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 = 0.0491 (Fisher's exact test), Q value = 0.12

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 = 0.00018 (Fisher's exact test), Q value = 0.0025

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 = 0.0207 (Fisher's exact test), Q value = 0.061

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 = 0.00118 (Fisher's exact test), Q value = 0.0091

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 = 0.00318 (Fisher's exact test), Q value = 0.018

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 = 0.003 (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 = 0.00012 (Fisher's exact test), Q value = 0.0019

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 = 0.00353 (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 = 0.00501 (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 = 4e-05 (Fisher's exact test), Q value = 7e-04

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 = 0.0033 (Fisher's exact test), Q value = 0.018

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 = 0.0048 (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/15087096/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/15098833/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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