Correlation between copy number variations of arm-level result and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1GT5M1G
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/C1GT5M1G
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, 27 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',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 11p gain cnv correlated to 'CN_CNMF'.

  • 11q 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, 27 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) 		4e-05
(0.00664) 		0.00618
(0.834) 		1e-05
(0.00174) 		0.00151
(0.226) 		0.00076
(0.119)
7p loss 17 (9%) 174 4e-05
(0.00664) 		0.00012
(0.0196) 		0.00096
(0.149) 		1e-05
(0.00174) 		0.00351
(0.495) 		0.00357
(0.5)
8p gain 22 (12%) 169 0.00084
(0.131) 		0.00049
(0.0784) 		0.0283
(1.00) 		0.00074
(0.117) 		0.0103
(1.00) 		0.0162
(1.00)
8q gain 23 (12%) 168 0.00145
(0.219) 		0.00152
(0.226) 		0.0131
(1.00) 		0.00157
(0.232) 		0.00719
(0.942) 		0.015
(1.00)
11p gain 4 (2%) 187 0.00071
(0.113) 		0.147
(1.00) 		0.467
(1.00) 		0.366
(1.00) 		0.527
(1.00) 		0.0226
(1.00)
11q gain 7 (4%) 184 2e-05
(0.00338) 		0.0126
(1.00) 		0.0664
(1.00) 		0.0744
(1.00) 		0.293
(1.00) 		0.016
(1.00)
21q gain 8 (4%) 183 1e-05
(0.00174) 		0.231
(1.00) 		0.126
(1.00) 		0.525
(1.00) 		0.0818
(1.00) 		0.411
(1.00)
22q gain 9 (5%) 182 0.00104
(0.16) 		0.0179
(1.00) 		0.134
(1.00) 		0.0163
(1.00) 		0.055
(1.00) 		0.0127
(1.00)
5q loss 6 (3%) 185 2e-05
(0.00338) 		0.0304
(1.00) 		0.225
(1.00) 		0.631
(1.00) 		0.0316
(1.00) 		0.0327
(1.00)
15q loss 4 (2%) 187 0.00045
(0.0724) 		0.571
(1.00) 		0.0665
(1.00) 		0.368
(1.00) 		0.023
(1.00) 		0.184
(1.00)
16q loss 4 (2%) 187 0.00126
(0.193) 		0.147
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.0144
(1.00) 		0.0221
(1.00)
17p loss 13 (7%) 178 1e-05
(0.00174) 		0.00449
(0.62) 		0.157
(1.00) 		0.00191
(0.279) 		0.16
(1.00) 		0.00343
(0.487)
17q loss 7 (4%) 184 2e-05
(0.00338) 		0.214
(1.00) 		0.065
(1.00) 		0.233
(1.00) 		0.0391
(1.00) 		0.0485
(1.00)
18p loss 5 (3%) 186 0.00033
(0.0535) 		0.0685
(1.00) 		1
(1.00) 		0.866
(1.00) 		0.247
(1.00) 		0.186
(1.00)
18q loss 4 (2%) 187 0.00134
(0.204) 		0.145
(1.00) 		0.467
(1.00) 		0.865
(1.00) 		0.101
(1.00) 		0.184
(1.00)
xq loss 5 (3%) 186 6e-05
(0.00984) 		0.145
(1.00) 		0.221
(1.00) 		0.631
(1.00) 		0.00331
(0.473) 		0.00462
(0.633)
1p gain 3 (2%) 188 0.00412
(0.573) 		0.265
(1.00) 		0.187
(1.00) 		0.587
(1.00) 		0.0925
(1.00) 		0.0919
(1.00)
4p gain 4 (2%) 187 0.0286
(1.00) 		0.0485
(1.00) 		0.341
(1.00) 		0.835
(1.00)
4q gain 4 (2%) 187 0.028
(1.00) 		0.0495
(1.00) 		0.345
(1.00) 		0.834
(1.00)
10q gain 3 (2%) 188 0.0148
(1.00) 		0.266
(1.00) 		0.185
(1.00) 		0.589
(1.00) 		0.554
(1.00) 		0.0913
(1.00)
13q gain 6 (3%) 185 0.0418
(1.00) 		0.0293
(1.00) 		0.124
(1.00) 		0.0832
(1.00) 		0.802
(1.00) 		0.074
(1.00)
17q gain 3 (2%) 188 0.00621
(0.834) 		0.302
(1.00) 		1
(1.00) 		0.59
(1.00) 		0.482
(1.00) 		0.307
(1.00)
19p gain 5 (3%) 186 0.0127
(1.00) 		0.643
(1.00) 		1
(1.00) 		0.864
(1.00) 		0.578
(1.00) 		1
(1.00)
19q gain 5 (3%) 186 0.0127
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.865
(1.00) 		0.581
(1.00) 		1
(1.00)
xq gain 3 (2%) 188 0.00174
(0.256) 		0.882
(1.00) 		0.891
(1.00) 		0.0452
(1.00)
3p loss 3 (2%) 188 0.00707
(0.933) 		0.264
(1.00) 		0.787
(1.00) 		1
(1.00) 		0.0615
(1.00) 		0.0918
(1.00)
3q loss 3 (2%) 188 0.0067
(0.891) 		0.266
(1.00) 		0.786
(1.00) 		1
(1.00) 		0.0617
(1.00) 		0.0938
(1.00)
12p loss 4 (2%) 187 0.00599
(0.815) 		0.0952
(1.00) 		0.375
(1.00) 		0.39
(1.00) 		0.484
(1.00) 		0.185
(1.00)
19p loss 4 (2%) 187 0.00307
(0.442) 		0.536
(1.00) 		0.465
(1.00) 		0.865
(1.00) 		0.312
(1.00) 		0.248
(1.00)
19q loss 4 (2%) 187 0.00298
(0.432) 		0.536
(1.00) 		0.468
(1.00) 		0.864
(1.00) 		0.314
(1.00) 		0.251
(1.00)
'8p gain' versus 'CN_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.13

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

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.078

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 = 0.00074 (Fisher's exact test), Q value = 0.12

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 = 0.00145 (Fisher's exact test), Q value = 0.22

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

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.23

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'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.23

Table S6.  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 S6.  Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

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

Table S7.  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 S7.  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 S8.  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 S8.  Get High-res Image Gene #8: '11q 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 S9.  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 S9.  Get High-res Image Gene #13: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.16

Table S10.  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 S10.  Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'CN_CNMF'

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

Table S11.  Gene #18: '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 S11.  Get High-res Image Gene #18: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0066

Table S12.  Gene #19: '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 S12.  Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.02

Table S13.  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 S13.  Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.15

Table S14.  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 S14.  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 S15.  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 S15.  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 S16.  Gene #20: '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 S16.  Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0066

Table S17.  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 S17.  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 S18.  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 S18.  Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.23

Table S19.  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 S19.  Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.12

Table S20.  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 S20.  Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.072

Table S21.  Gene #22: '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 S21.  Get High-res Image Gene #22: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.19

Table S22.  Gene #23: '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 S22.  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 S23.  Gene #24: '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 S23.  Get High-res Image Gene #24: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'CN_CNMF'

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

Table S24.  Gene #25: '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 S24.  Get High-res Image Gene #25: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.053

Table S25.  Gene #26: '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 S25.  Get High-res Image Gene #26: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.2

Table S26.  Gene #27: '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 S26.  Get High-res Image Gene #27: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0098

Table S27.  Gene #30: '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 S27.  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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