Correlation between copy number variation genes (focal events) and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1K93602
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 variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1K93602
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 30 focal events and 6 molecular subtypes across 191 patients, 31 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 3p cnv correlated to 'CN_CNMF'.

  • 3q cnv correlated to 'CN_CNMF'.

  • 4p cnv correlated to 'CN_CNMF'.

  • 4q cnv correlated to 'CN_CNMF'.

  • 5q cnv correlated to 'CN_CNMF'.

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

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

  • 8p cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

  • 11p cnv correlated to 'CN_CNMF'.

  • 11q cnv correlated to 'CN_CNMF'.

  • 15q cnv correlated to 'CN_CNMF'.

  • 16q cnv correlated to 'CN_CNMF'.

  • 17p cnv correlated to 'CN_CNMF'.

  • 17q cnv correlated to 'CN_CNMF'.

  • 18p cnv correlated to 'CN_CNMF'.

  • 18q cnv correlated to 'CN_CNMF'.

  • 19p cnv correlated to 'CN_CNMF'.

  • 19q cnv correlated to 'CN_CNMF'.

  • 21q cnv correlated to 'CN_CNMF'.

  • 22q cnv correlated to 'CN_CNMF'.

  • xq 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 focal 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, 31 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
7p 18 (9%) 173 1.01e-05
(0.00173) 		9.23e-05
(0.0153) 		0.000852
(0.136) 		0.00141
(0.219) 		0.00123
(0.194) 		5.37e-05
(0.00902)
7q 20 (10%) 171 3.95e-06
(0.000687) 		1.14e-05
(0.00195) 		0.00641
(0.885) 		0.0125
(1.00) 		0.00168
(0.25) 		7.26e-05
(0.0121)
8p 23 (12%) 168 0.000433
(0.0702) 		0.000115
(0.0189) 		0.0138
(1.00) 		0.00397
(0.583) 		0.00452
(0.651) 		0.043
(1.00)
8q 23 (12%) 168 0.00162
(0.243) 		0.000904
(0.144) 		0.0138
(1.00) 		0.00397
(0.583) 		0.00745
(1.00) 		0.114
(1.00)
3p 4 (2%) 187 0.00151
(0.232) 		0.185
(1.00) 		0.467
(1.00) 		0.604
(1.00) 		0.0147
(1.00) 		0.0116
(1.00)
3q 4 (2%) 187 0.00151
(0.232) 		0.185
(1.00) 		0.467
(1.00) 		0.604
(1.00) 		0.0147
(1.00) 		0.0116
(1.00)
4p 6 (3%) 185 0.00126
(0.197) 		0.284
(1.00) 		1
(1.00) 		1
(1.00) 		0.895
(1.00) 		0.863
(1.00)
4q 6 (3%) 185 0.00126
(0.197) 		0.284
(1.00) 		1
(1.00) 		1
(1.00) 		0.895
(1.00) 		0.863
(1.00)
5q 6 (3%) 185 3.23e-05
(0.00549) 		0.0134
(1.00) 		0.224
(1.00) 		0.664
(1.00) 		0.0318
(1.00) 		0.0205
(1.00)
11p 6 (3%) 185 0.000101
(0.0167) 		0.0134
(1.00) 		0.124
(1.00) 		0.665
(1.00) 		0.206
(1.00) 		0.139
(1.00)
11q 7 (4%) 184 8.12e-06
(0.00141) 		0.00516
(0.733) 		0.0668
(1.00) 		0.425
(1.00) 		0.291
(1.00) 		0.271
(1.00)
15q 4 (2%) 187 0.000504
(0.0811) 		0.654
(1.00) 		0.066
(1.00) 		0.301
(1.00) 		0.0228
(1.00) 		0.0116
(1.00)
16q 4 (2%) 187 0.00151
(0.232) 		0.0808
(1.00) 		0.786
(1.00) 		1
(1.00) 		0.0147
(1.00) 		0.0116
(1.00)
17p 13 (7%) 178 1.97e-12
(3.54e-10) 		0.00581
(0.808) 		0.151
(1.00) 		0.0624
(1.00) 		0.16
(1.00) 		0.00532
(0.745)
17q 10 (5%) 181 4.1e-09
(7.35e-07) 		0.0499
(1.00) 		0.218
(1.00) 		0.167
(1.00) 		0.192
(1.00) 		0.00208
(0.308)
18p 5 (3%) 186 0.000142
(0.0231) 		0.0335
(1.00) 		1
(1.00) 		1
(1.00) 		0.248
(1.00) 		0.329
(1.00)
18q 4 (2%) 187 0.00151
(0.232) 		0.0808
(1.00) 		0.467
(1.00) 		1
(1.00) 		0.101
(1.00) 		0.0704
(1.00)
19p 9 (5%) 182 1.05e-06
(0.000186) 		0.584
(1.00) 		0.597
(1.00) 		0.718
(1.00) 		1
(1.00) 		0.362
(1.00)
19q 9 (5%) 182 1.05e-06
(0.000186) 		0.584
(1.00) 		0.597
(1.00) 		0.718
(1.00) 		1
(1.00) 		0.362
(1.00)
21q 10 (5%) 181 4.52e-07
(8.05e-05) 		0.0509
(1.00) 		0.0349
(1.00) 		0.718
(1.00) 		0.023
(1.00) 		0.0731
(1.00)
22q 11 (6%) 180 4.56e-05
(0.00771) 		0.00841
(1.00) 		0.0367
(1.00) 		0.101
(1.00) 		0.018
(1.00) 		0.0548
(1.00)
xq 8 (4%) 183 6.53e-07
(0.000116) 		0.106
(1.00) 		0.0668
(1.00) 		0.425
(1.00) 		0.0482
(1.00) 		0.0113
(1.00)
1p 3 (2%) 188 0.00511
(0.731) 		0.185
(1.00) 		0.186
(1.00) 		0.552
(1.00) 		0.0923
(1.00) 		0.0481
(1.00)
5p 3 (2%) 188 0.113
(1.00) 		0.658
(1.00) 		0.786
(1.00) 		1
(1.00) 		0.0618
(1.00) 		0.145
(1.00)
9p 3 (2%) 188 0.113
(1.00) 		0.185
(1.00) 		0.186
(1.00) 		0.552
(1.00) 		0.0618
(1.00) 		0.0481
(1.00)
9q 3 (2%) 188 0.113
(1.00) 		0.185
(1.00) 		0.186
(1.00) 		0.552
(1.00) 		0.0618
(1.00) 		0.0481
(1.00)
10p 3 (2%) 188 0.012
(1.00) 		0.185
(1.00) 		0.186
(1.00) 		0.552
(1.00) 		0.552
(1.00) 		0.222
(1.00)
10q 4 (2%) 187 0.00421
(0.611) 		0.0808
(1.00) 		0.066
(1.00) 		0.301
(1.00) 		0.248
(1.00) 		0.0704
(1.00)
12p 4 (2%) 187 0.00809
(1.00) 		0.0759
(1.00) 		0.374
(1.00) 		0.301
(1.00) 		0.483
(1.00) 		0.0704
(1.00)
13q 7 (4%) 184 0.00982
(1.00) 		0.00516
(0.733) 		0.0668
(1.00) 		0.0965
(1.00) 		0.735
(1.00) 		0.198
(1.00)
'3p' versus 'CN_CNMF'

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

Table S1.  Gene #2: '3p' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S1.  Get High-res Image Gene #2: '3p' versus Molecular Subtype #1: 'CN_CNMF'

'3q' versus 'CN_CNMF'

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

Table S2.  Gene #3: '3q' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S2.  Get High-res Image Gene #3: '3q' versus Molecular Subtype #1: 'CN_CNMF'

'4p' versus 'CN_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.2

Table S3.  Gene #4: '4p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
4P MUTATED 1 0 5 0
4P WILD-TYPE 146 14 22 3

Figure S3.  Get High-res Image Gene #4: '4p' versus Molecular Subtype #1: 'CN_CNMF'

'4q' versus 'CN_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.2

Table S4.  Gene #5: '4q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
4Q MUTATED 1 0 5 0
4Q WILD-TYPE 146 14 22 3

Figure S4.  Get High-res Image Gene #5: '4q' versus Molecular Subtype #1: 'CN_CNMF'

'5q' versus 'CN_CNMF'

P value = 3.23e-05 (Fisher's exact test), Q value = 0.0055

Table S5.  Gene #7: '5q' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S5.  Get High-res Image Gene #7: '5q' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'CN_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0017

Table S6.  Gene #8: '7p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
7P MUTATED 7 0 9 2
7P WILD-TYPE 140 14 18 1

Figure S6.  Get High-res Image Gene #8: '7p' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 9.23e-05 (Chi-square test), Q value = 0.015

Table S7.  Gene #8: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
7P MUTATED 1 0 15 1 1
7P WILD-TYPE 45 44 46 13 19

Figure S7.  Get High-res Image Gene #8: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 0.000852 (Fisher's exact test), Q value = 0.14

Table S8.  Gene #8: '7p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

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

Figure S8.  Get High-res Image Gene #8: '7p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.22

Table S9.  Gene #8: '7p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 56 110
7P MUTATED 0 16
7P WILD-TYPE 56 94

Figure S9.  Get High-res Image Gene #8: '7p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p' versus 'MIRSEQ_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.19

Table S10.  Gene #8: '7p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 37 41 43
7P MUTATED 1 10 3 4
7P WILD-TYPE 57 27 38 39

Figure S10.  Get High-res Image Gene #8: '7p' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.37e-05 (Fisher's exact test), Q value = 0.009

Table S11.  Gene #8: '7p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 79 65
7P MUTATED 11 2 5
7P WILD-TYPE 24 77 60

Figure S11.  Get High-res Image Gene #8: '7p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q' versus 'CN_CNMF'

P value = 3.95e-06 (Fisher's exact test), Q value = 0.00069

Table S12.  Gene #9: '7q' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S12.  Get High-res Image Gene #9: '7q' versus Molecular Subtype #1: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 1.14e-05 (Chi-square test), Q value = 0.0019

Table S13.  Gene #9: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S13.  Get High-res Image Gene #9: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.26e-05 (Fisher's exact test), Q value = 0.012

Table S14.  Gene #9: '7q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 79 65
7Q MUTATED 11 2 6
7Q WILD-TYPE 24 77 59

Figure S14.  Get High-res Image Gene #9: '7q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8p' versus 'CN_CNMF'

P value = 0.000433 (Fisher's exact test), Q value = 0.07

Table S15.  Gene #10: '8p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
8P MUTATED 11 1 10 1
8P WILD-TYPE 136 13 17 2

Figure S15.  Get High-res Image Gene #10: '8p' versus Molecular Subtype #1: 'CN_CNMF'

'8p' versus 'METHLYATION_CNMF'

P value = 0.000115 (Chi-square test), Q value = 0.019

Table S16.  Gene #10: '8p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 61 14 20
8P MUTATED 2 1 17 0 2
8P WILD-TYPE 44 43 44 14 18

Figure S16.  Get High-res Image Gene #10: '8p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q' versus 'CN_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.24

Table S17.  Gene #11: '8q' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S17.  Get High-res Image Gene #11: '8q' versus Molecular Subtype #1: 'CN_CNMF'

'8q' versus 'METHLYATION_CNMF'

P value = 0.000904 (Chi-square test), Q value = 0.14

Table S18.  Gene #11: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S18.  Get High-res Image Gene #11: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p' versus 'CN_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.017

Table S19.  Gene #16: '11p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
11P MUTATED 0 3 3 0
11P WILD-TYPE 147 11 24 3

Figure S19.  Get High-res Image Gene #16: '11p' versus Molecular Subtype #1: 'CN_CNMF'

'11q' versus 'CN_CNMF'

P value = 8.12e-06 (Fisher's exact test), Q value = 0.0014

Table S20.  Gene #17: '11q' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S20.  Get High-res Image Gene #17: '11q' versus Molecular Subtype #1: 'CN_CNMF'

'15q' versus 'CN_CNMF'

P value = 0.000504 (Fisher's exact test), Q value = 0.081

Table S21.  Gene #20: '15q' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S21.  Get High-res Image Gene #20: '15q' versus Molecular Subtype #1: 'CN_CNMF'

'16q' versus 'CN_CNMF'

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

Table S22.  Gene #21: '16q' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S22.  Get High-res Image Gene #21: '16q' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'CN_CNMF'

P value = 1.97e-12 (Fisher's exact test), Q value = 3.5e-10

Table S23.  Gene #22: '17p' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S23.  Get High-res Image Gene #22: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'17q' versus 'CN_CNMF'

P value = 4.1e-09 (Fisher's exact test), Q value = 7.3e-07

Table S24.  Gene #23: '17q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
17Q MUTATED 0 0 10 0
17Q WILD-TYPE 147 14 17 3

Figure S24.  Get High-res Image Gene #23: '17q' versus Molecular Subtype #1: 'CN_CNMF'

'18p' versus 'CN_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.023

Table S25.  Gene #24: '18p' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S25.  Get High-res Image Gene #24: '18p' versus Molecular Subtype #1: 'CN_CNMF'

'18q' versus 'CN_CNMF'

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

Table S26.  Gene #25: '18q' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S26.  Get High-res Image Gene #25: '18q' versus Molecular Subtype #1: 'CN_CNMF'

'19p' versus 'CN_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00019

Table S27.  Gene #26: '19p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
19P MUTATED 0 2 7 0
19P WILD-TYPE 147 12 20 3

Figure S27.  Get High-res Image Gene #26: '19p' versus Molecular Subtype #1: 'CN_CNMF'

'19q' versus 'CN_CNMF'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00019

Table S28.  Gene #27: '19q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
19Q MUTATED 0 2 7 0
19Q WILD-TYPE 147 12 20 3

Figure S28.  Get High-res Image Gene #27: '19q' versus Molecular Subtype #1: 'CN_CNMF'

'21q' versus 'CN_CNMF'

P value = 4.52e-07 (Fisher's exact test), Q value = 8e-05

Table S29.  Gene #28: '21q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
21Q MUTATED 1 0 9 0
21Q WILD-TYPE 146 14 18 3

Figure S29.  Get High-res Image Gene #28: '21q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'CN_CNMF'

P value = 4.56e-05 (Fisher's exact test), Q value = 0.0077

Table S30.  Gene #29: '22q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
22Q MUTATED 2 2 7 0
22Q WILD-TYPE 145 12 20 3

Figure S30.  Get High-res Image Gene #29: '22q' versus Molecular Subtype #1: 'CN_CNMF'

'xq' versus 'CN_CNMF'

P value = 6.53e-07 (Fisher's exact test), Q value = 0.00012

Table S31.  Gene #30: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 14 27 3
XQ MUTATED 0 1 5 2
XQ WILD-TYPE 147 13 22 1

Figure S31.  Get High-res Image Gene #30: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

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

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

  • Number of patients = 191

  • Number of significantly focal cnvs = 30

  • Number of molecular subtypes = 6

  • Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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