Correlation between copy number variations of arm-level result and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1Q81BPT
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/C1Q81BPT
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, 26 significant findings detected with P value < 0.05 and Q value < 0.25.

- 8p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 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', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 7q loss cnv correlated to 'CN_CNMF', 'METHLYATION_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, 26 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 loss | 17 (9%) | 174 | 4.46e-05 (0.00758) | 0.000252 (0.0416) | 0.000852 (0.135) | 0.00141 (0.219) | 0.00382 (0.561) | 0.000194 (0.0322)
7q loss | 20 (10%) | 171 | 3.95e-06 (0.000691) | 1.14e-05 (0.00196) | 0.00641 (0.885) | 0.0125 (1.00) | 0.00168 (0.254) | 7.26e-05 (0.0123)
8p gain | 22 (12%) | 169 | 0.000968 (0.152) | 0.000303 (0.0498) | 0.0274 (1.00) | 0.00695 (0.953) | 0.0109 (1.00) | 0.0972 (1.00)
8q gain | 23 (12%) | 168 | 0.00162 (0.247) | 0.000904 (0.143) | 0.0138 (1.00) | 0.00397 (0.579) | 0.00745 (1.00) | 0.114 (1.00)
11p gain | 4 (2%) | 187 | 0.000687 (0.111) | 0.0808 (1.00) | 0.467 (1.00) | 1 (1.00) | 0.523 (1.00) | 0.0704 (1.00)
11q gain | 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)
19p gain | 5 (3%) | 186 | 0.000749 (0.121) | 0.633 (1.00) | 1 (1.00) | 1 (1.00) | 0.578 (1.00) | 1 (1.00)
19q gain | 5 (3%) | 186 | 0.000749 (0.121) | 0.633 (1.00) | 1 (1.00) | 1 (1.00) | 0.578 (1.00) | 1 (1.00)
21q gain | 8 (4%) | 183 | 3.41e-07 (6e-05) | 0.203 (1.00) | 0.124 (1.00) | 1 (1.00) | 0.0814 (1.00) | 0.198 (1.00)
22q gain | 9 (5%) | 182 | 0.00109 (0.17) | 0.00832 (1.00) | 0.136 (1.00) | 0.275 (1.00) | 0.0556 (1.00) | 0.147 (1.00)
5q loss | 6 (3%) | 185 | 3.23e-05 (0.00552) | 0.0134 (1.00) | 0.224 (1.00) | 0.664 (1.00) | 0.0318 (1.00) | 0.0205 (1.00)
15q loss | 4 (2%) | 187 | 0.000504 (0.0821) | 0.654 (1.00) | 0.066 (1.00) | 0.301 (1.00) | 0.0228 (1.00) | 0.0116 (1.00)
16q loss | 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 loss | 13 (7%) | 178 | 1.97e-12 (3.48e-10) | 0.00581 (0.813) | 0.151 (1.00) | 0.0624 (1.00) | 0.16 (1.00) | 0.00532 (0.751)
17q loss | 7 (4%) | 184 | 5.11e-06 (0.00089) | 0.201 (1.00) | 0.0668 (1.00) | 0.425 (1.00) | 0.0385 (1.00) | 0.00633 (0.88)
18p loss | 5 (3%) | 186 | 0.000142 (0.0237) | 0.0335 (1.00) | 1 (1.00) | 1 (1.00) | 0.248 (1.00) | 0.329 (1.00)
18q loss | 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)
xq loss | 5 (3%) | 186 | 0.000101 (0.017) | 0.15 (1.00) | 0.224 (1.00) | 0.664 (1.00) | 0.00335 (0.496) | 0.00258 (0.386)
1p gain | 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)
4p gain | 4 (2%) | 187 | 0.0259 (1.00) | 0.0502 (1.00) |  | 0.55 (1.00) | 0.343 (1.00) | 0.831 (1.00)
4q gain | 4 (2%) | 187 | 0.0259 (1.00) | 0.0502 (1.00) |  | 0.55 (1.00) | 0.343 (1.00) | 0.831 (1.00)
10q gain | 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)
13q gain | 6 (3%) | 185 | 0.0333 (1.00) | 0.0134 (1.00) | 0.124 (1.00) | 0.0978 (1.00) | 0.8 (1.00) | 0.25 (1.00)
17q gain | 3 (2%) | 188 | 0.00767 (1.00) | 0.38 (1.00) | 1 (1.00) | 0.552 (1.00) | 0.482 (1.00) | 0.222 (1.00)
xq gain | 3 (2%) | 188 | 0.00296 (0.442) | 0.658 (1.00) |  | 0.55 (1.00) | 0.891 (1.00) | 0.787 (1.00)
3p loss | 3 (2%) | 188 | 0.00767 (1.00) | 0.185 (1.00) | 0.786 (1.00) | 1 (1.00) | 0.0618 (1.00) | 0.0481 (1.00)
3q loss | 3 (2%) | 188 | 0.00767 (1.00) | 0.185 (1.00) | 0.786 (1.00) | 1 (1.00) | 0.0618 (1.00) | 0.0481 (1.00)
12p loss | 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)
19p loss | 4 (2%) | 187 | 0.00421 (0.611) | 0.411 (1.00) | 0.467 (1.00) | 1 (1.00) | 0.311 (1.00) | 0.144 (1.00)
19q loss | 4 (2%) | 187 | 0.00421 (0.611) | 0.411 (1.00) | 0.467 (1.00) | 1 (1.00) | 0.311 (1.00) | 0.144 (1.00)

'8p gain' versus 'CN_CNMF'

P value = 0.000968 (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 = 0.000303 (Chi-square test), Q value = 0.05

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'

'8q gain' versus 'CN_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.25

Table S3. 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 S3. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

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

Table S4. 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 S4. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.000687 (Fisher's exact test), Q value = 0.11

Table S5. 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 S5. Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

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

Table S6. 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 S6. Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.000749 (Fisher's exact test), Q value = 0.12

Table S7. 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 S7. Get High-res Image Gene #11: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 0.000749 (Fisher's exact test), Q value = 0.12

Table S8. 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 S8. Get High-res Image Gene #12: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 3.41e-07 (Fisher's exact test), Q value = 6e-05

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

'22q gain' versus 'CN_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.17

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

'5q loss' versus 'CN_CNMF'

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

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

'7p loss' versus 'CN_CNMF'

P value = 4.46e-05 (Fisher's exact test), Q value = 0.0076

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

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.000252 (Chi-square test), Q value = 0.042

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

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

Table S15. Gene #19: '7p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

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

Figure S15. Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000194 (Fisher's exact test), Q value = 0.032

Table S16. Gene #19: '7p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 35 | 79 | 65
7P LOSS MUTATED | 10 | 2 | 5
7P LOSS WILD-TYPE | 25 | 77 | 60

Figure S16. Get High-res Image Gene #19: '7p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

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

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 = 1.14e-05 (Chi-square test), Q value = 0.002

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 'MIRSEQ_CHIERARCHICAL'

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

Table S19. Gene #20: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

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

Figure S19. Get High-res Image Gene #20: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 0.000504 (Fisher's exact test), Q value = 0.082

Table S20. 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 S20. Get High-res Image Gene #22: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'CN_CNMF'

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

Table S21. 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 S21. Get High-res Image Gene #23: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'CN_CNMF'

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

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

'17q loss' versus 'CN_CNMF'

P value = 5.11e-06 (Fisher's exact test), Q value = 0.00089

Table S23. 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 S23. Get High-res Image Gene #25: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'CN_CNMF'

P value = 0.000142 (Fisher's exact test), Q value = 0.024

Table S24. 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 S24. Get High-res Image Gene #26: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

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

Table S25. 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 S25. Get High-res Image Gene #27: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'CN_CNMF'

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

Table S26. 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 S26. 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

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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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