Correlation between copy number variations of arm-level result and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1BR8QXK
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1BR8QXK
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 30 arm-level events and 6 molecular subtypes across 191 patients, 28 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • 8q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q 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'.

  • 5q loss cnv correlated to 'CN_CNMF'.

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

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

  • 15q loss cnv correlated to 'CN_CNMF'.

  • 16q loss cnv correlated to 'CN_CNMF'.

  • 17p loss cnv correlated to 'CN_CNMF'.

  • 17q loss cnv correlated to 'CN_CNMF'.

  • 18p loss cnv correlated to 'CN_CNMF'.

  • 18q loss cnv correlated to 'CN_CNMF'.

  • xq loss cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 30 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, 28 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
7q loss 20 (10%) 171 1e-05
(0.00174) 		3e-05
(0.00504) 		0.00601
(0.805) 		1e-05
(0.00174) 		0.00142
(0.214) 		0.00088
(0.136)
7p loss 17 (9%) 174 0.00013
(0.0214) 		0.00029
(0.047) 		0.00097
(0.149) 		1e-05
(0.00174) 		0.00382
(0.535) 		0.00295
(0.425)
8p gain 22 (12%) 169 0.001
(0.153) 		0.00047
(0.0757) 		0.0287
(1.00) 		0.00082
(0.128) 		0.01
(1.00) 		0.016
(1.00)
8q gain 23 (12%) 168 0.0017
(0.25) 		0.0016
(0.237) 		0.0134
(1.00) 		0.00173
(0.253) 		0.00721
(0.956) 		0.0146
(1.00)
11p gain 4 (2%) 187 0.00066
(0.105) 		0.147
(1.00) 		0.467
(1.00) 		0.365
(1.00) 		0.519
(1.00) 		0.022
(1.00)
11q gain 7 (4%) 184 2e-05
(0.00338) 		0.0121
(1.00) 		0.0655
(1.00) 		0.0737
(1.00) 		0.291
(1.00) 		0.0154
(1.00)
19p gain 5 (3%) 186 0.00078
(0.122) 		0.645
(1.00) 		1
(1.00) 		0.864
(1.00) 		0.579
(1.00) 		1
(1.00)
19q gain 5 (3%) 186 0.00071
(0.112) 		0.646
(1.00) 		1
(1.00) 		0.865
(1.00) 		0.578
(1.00) 		1
(1.00)
21q gain 8 (4%) 183 1e-05
(0.00174) 		0.23
(1.00) 		0.126
(1.00) 		0.524
(1.00) 		0.0813
(1.00) 		0.409
(1.00)
22q gain 9 (5%) 182 0.00124
(0.188) 		0.0178
(1.00) 		0.136
(1.00) 		0.0162
(1.00) 		0.0567
(1.00) 		0.0132
(1.00)
5q loss 6 (3%) 185 6e-05
(0.00996) 		0.0302
(1.00) 		0.224
(1.00) 		0.632
(1.00) 		0.0314
(1.00) 		0.0329
(1.00)
15q loss 4 (2%) 187 0.00052
(0.0832) 		0.57
(1.00) 		0.0657
(1.00) 		0.366
(1.00) 		0.0236
(1.00) 		0.186
(1.00)
16q loss 4 (2%) 187 0.00159
(0.237) 		0.149
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.0147
(1.00) 		0.0217
(1.00)
17p loss 13 (7%) 178 1e-05
(0.00174) 		0.00418
(0.574) 		0.156
(1.00) 		0.00192
(0.278) 		0.162
(1.00) 		0.00345
(0.49)
17q loss 7 (4%) 184 3e-05
(0.00504) 		0.216
(1.00) 		0.0685
(1.00) 		0.233
(1.00) 		0.04
(1.00) 		0.0475
(1.00)
18p loss 5 (3%) 186 0.00021
(0.0342) 		0.0687
(1.00) 		1
(1.00) 		0.865
(1.00) 		0.248
(1.00) 		0.185
(1.00)
18q loss 4 (2%) 187 0.00157
(0.235) 		0.148
(1.00) 		0.468
(1.00) 		0.864
(1.00) 		0.101
(1.00) 		0.186
(1.00)
xq loss 5 (3%) 186 0.00013
(0.0214) 		0.145
(1.00) 		0.224
(1.00) 		0.632
(1.00) 		0.00347
(0.49) 		0.00482
(0.656)
1p gain 3 (2%) 188 0.00552
(0.745) 		0.266
(1.00) 		0.185
(1.00) 		0.588
(1.00) 		0.0906
(1.00) 		0.0936
(1.00)
4p gain 4 (2%) 187 0.0266
(1.00) 		0.0483
(1.00) 		0.341
(1.00) 		0.835
(1.00)
4q gain 4 (2%) 187 0.0256
(1.00) 		0.05
(1.00) 		0.342
(1.00) 		0.833
(1.00)
10q gain 3 (2%) 188 0.0119
(1.00) 		0.27
(1.00) 		0.187
(1.00) 		0.588
(1.00) 		0.554
(1.00) 		0.0949
(1.00)
13q gain 6 (3%) 185 0.033
(1.00) 		0.0303
(1.00) 		0.125
(1.00) 		0.0837
(1.00) 		0.799
(1.00) 		0.0729
(1.00)
17q gain 3 (2%) 188 0.00856
(1.00) 		0.302
(1.00) 		1
(1.00) 		0.589
(1.00) 		0.484
(1.00) 		0.305
(1.00)
xq gain 3 (2%) 188 0.00296
(0.425) 		0.88
(1.00) 		0.893
(1.00) 		0.0459
(1.00)
3p loss 3 (2%) 188 0.00719
(0.956) 		0.268
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.0607
(1.00) 		0.0926
(1.00)
3q loss 3 (2%) 188 0.0075
(0.982) 		0.264
(1.00) 		0.786
(1.00) 		1
(1.00) 		0.062
(1.00) 		0.092
(1.00)
12p loss 4 (2%) 187 0.0084
(1.00) 		0.0949
(1.00) 		0.373
(1.00) 		0.393
(1.00) 		0.484
(1.00) 		0.185
(1.00)
19p loss 4 (2%) 187 0.00416
(0.574) 		0.536
(1.00) 		0.468
(1.00) 		0.866
(1.00) 		0.312
(1.00) 		0.247
(1.00)
19q loss 4 (2%) 187 0.00406
(0.564) 		0.534
(1.00) 		0.465
(1.00) 		0.865
(1.00) 		0.311
(1.00) 		0.248
(1.00)
'8p gain' versus 'CN_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.15

Table S1.  Gene #4: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
8P GAIN MUTATED 11 1 10 0
8P GAIN WILD-TYPE 136 13 17 3

Figure S1.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.076

Table S2.  Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
8P GAIN MUTATED 2 1 16 0 2
8P GAIN WILD-TYPE 44 43 45 14 18

Figure S2.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.13

Table S3.  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 S3.  Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.25

Table S4.  Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
8Q GAIN MUTATED 12 1 10 0
8Q GAIN WILD-TYPE 135 13 17 3

Figure S4.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.24

Table S5.  Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
8Q GAIN MUTATED 2 2 16 0 2
8Q GAIN WILD-TYPE 44 42 45 14 18

Figure S5.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.1

Table S6.  Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
11P GAIN MUTATED 0 3 1 0
11P GAIN WILD-TYPE 147 11 26 3

Figure S6.  Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0034

Table S7.  Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
11Q GAIN MUTATED 0 4 3 0
11Q GAIN WILD-TYPE 147 10 24 3

Figure S7.  Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.12

Table S8.  Gene #11: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
19P GAIN MUTATED 0 1 4 0
19P GAIN WILD-TYPE 147 13 23 3

Figure S8.  Get High-res Image Gene #11: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.11

Table S9.  Gene #12: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
19Q GAIN MUTATED 0 1 4 0
19Q GAIN WILD-TYPE 147 13 23 3

Figure S9.  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 = 0.0017

Table S10.  Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
21Q GAIN MUTATED 0 0 8 0
21Q GAIN WILD-TYPE 147 14 19 3

Figure S10.  Get High-res Image Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.19

Table S11.  Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
22Q GAIN MUTATED 2 2 5 0
22Q GAIN WILD-TYPE 145 12 22 3

Figure S11.  Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.01

Table S12.  Gene #18: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
5Q LOSS MUTATED 0 0 6 0
5Q LOSS WILD-TYPE 147 14 21 3

Figure S12.  Get High-res Image Gene #18: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.021

Table S13.  Gene #19: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
7P LOSS MUTATED 7 0 8 2
7P LOSS WILD-TYPE 140 14 19 1

Figure S13.  Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.047

Table S14.  Gene #19: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
7P LOSS MUTATED 1 0 14 1 1
7P LOSS WILD-TYPE 45 44 47 13 19

Figure S14.  Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.15

Table S15.  Gene #19: '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 S15.  Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0017

Table S16.  Gene #19: '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 S16.  Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0017

Table S17.  Gene #20: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
7Q LOSS MUTATED 8 0 10 2
7Q LOSS WILD-TYPE 139 14 17 1

Figure S17.  Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.005

Table S18.  Gene #20: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
7Q LOSS MUTATED 1 0 17 1 1
7Q LOSS WILD-TYPE 45 44 44 13 19

Figure S18.  Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0017

Table S19.  Gene #20: '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 S19.  Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.21

Table S20.  Gene #20: '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 S20.  Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.14

Table S21.  Gene #20: '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 S21.  Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.083

Table S22.  Gene #22: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
15Q LOSS MUTATED 0 0 3 1
15Q LOSS WILD-TYPE 147 14 24 2

Figure S22.  Get High-res Image Gene #22: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.24

Table S23.  Gene #23: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
16Q LOSS MUTATED 0 0 4 0
16Q LOSS WILD-TYPE 147 14 23 3

Figure S23.  Get High-res Image Gene #23: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0017

Table S24.  Gene #24: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
17P LOSS MUTATED 0 0 13 0
17P LOSS WILD-TYPE 147 14 14 3

Figure S24.  Get High-res Image Gene #24: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.005

Table S25.  Gene #25: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
17Q LOSS MUTATED 0 0 7 0
17Q LOSS WILD-TYPE 147 14 20 3

Figure S25.  Get High-res Image Gene #25: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.034

Table S26.  Gene #26: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
18P LOSS MUTATED 0 0 5 0
18P LOSS WILD-TYPE 147 14 22 3

Figure S26.  Get High-res Image Gene #26: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00157 (Fisher's exact test), Q value = 0.24

Table S27.  Gene #27: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
18Q LOSS MUTATED 0 0 4 0
18Q LOSS WILD-TYPE 147 14 23 3

Figure S27.  Get High-res Image Gene #27: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.021

Table S28.  Gene #30: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
XQ LOSS MUTATED 0 0 4 1
XQ LOSS WILD-TYPE 147 14 23 2

Figure S28.  Get High-res Image Gene #30: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtypes file = LAML-TB.transferedmergedcluster.txt

  • Number of patients = 191

  • Number of significantly arm-level cnvs = 30

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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