Correlation between copy number variations of arm-level result and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
28 January 2016 | analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1X066F1
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1X066F1
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, 58 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1p gain cnv correlated to 'MIRSEQ_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 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 8q gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 11p gain cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- 11q gain cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

- 13q gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.

- 21q gain cnv correlated to 'MIRSEQ_CNMF'.

- 22q gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- xp gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

- xq gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

- 3p loss cnv correlated to 'CN_CNMF'.

- 3q loss cnv correlated to 'CN_CNMF'.

- 5q loss cnv correlated to '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'.

- 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 'MIRSEQ_CHIERARCHICAL'.

- 18p 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, 58 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
7p loss | 17 (9%) | 174 | 1e-05 (0.000384) | 0.00042 (0.0134) | 0.00111 (0.0194) | 1e-05 (0.000384) | 0.00658 (0.0486) | 0.00293 (0.0316)
7q loss | 20 (10%) | 171 | 1e-05 (0.000384) | 1e-05 (0.000384) | 0.00978 (0.0626) | 1e-05 (0.000384) | 0.00296 (0.0316) | 0.0008 (0.0171)
8p gain | 22 (12%) | 169 | 0.959 (1.00) | 0.00223 (0.0268) | 0.0273 (0.109) | 0.00076 (0.0171) | 0.0683 (0.212) | 0.0165 (0.0835)
8q gain | 23 (12%) | 168 | 0.886 (0.989) | 0.00558 (0.045) | 0.0141 (0.08) | 0.00182 (0.0233) | 0.0618 (0.198) | 0.0142 (0.08)
22q gain | 9 (5%) | 182 | 0.239 (0.455) | 0.0121 (0.0749) | 0.148 (0.345) | 0.0163 (0.0835) | 0.00067 (0.0171) | 0.0136 (0.08)
17p loss | 13 (7%) | 178 | 0.0171 (0.0843) | 0.00356 (0.0344) | 0.171 (0.377) | 0.00157 (0.0233) | 0.195 (0.407) | 0.00358 (0.0344)
5q loss | 6 (3%) | 185 | 0.302 (0.523) | 0.0223 (0.101) | 0.228 (0.452) | 0.632 (0.795) | 0.0325 (0.122) | 0.032 (0.122)
16q loss | 4 (2%) | 187 | 0.0357 (0.128) | 0.161 (0.361) | 0.789 (0.925) | 1 (1.00) | 0.0237 (0.101) | 0.023 (0.101)
xp loss | 5 (3%) | 186 | 0.00926 (0.0626) | 0.308 (0.523) | 0.23 (0.452) | 0.633 (0.795) | 0.00563 (0.045) | 0.00504 (0.044)
xq loss | 5 (3%) | 186 | 0.00945 (0.0626) | 0.307 (0.523) | 0.228 (0.452) | 0.631 (0.795) | 0.00598 (0.0459) | 0.00495 (0.044)
4p gain | 4 (2%) | 187 | 0.0359 (0.128) | 0.0259 (0.108) |  |  | 0.592 (0.758) | 0.835 (0.96)
4q gain | 4 (2%) | 187 | 0.0354 (0.128) | 0.0265 (0.108) |  |  | 0.593 (0.758) | 0.833 (0.96)
11p gain | 5 (3%) | 186 | 0.443 (0.645) | 0.306 (0.523) | 0.231 (0.452) | 0.235 (0.452) | 0.0151 (0.0807) | 0.0321 (0.122)
11q gain | 7 (4%) | 184 | 0.233 (0.452) | 0.0728 (0.221) | 0.0767 (0.223) | 0.0747 (0.221) | 0.00177 (0.0233) | 0.015 (0.0807)
13q gain | 6 (3%) | 185 | 0.423 (0.629) | 0.0238 (0.101) | 0.149 (0.345) | 0.0832 (0.235) | 0.00182 (0.0233) | 0.0736 (0.221)
1p gain | 3 (2%) | 188 | 0.56 (0.742) | 0.336 (0.555) | 0.261 (0.486) | 0.588 (0.758) | 0.00105 (0.0194) | 0.0919 (0.245)
21q gain | 8 (4%) | 183 | 0.126 (0.31) | 0.215 (0.445) | 0.149 (0.345) | 0.525 (0.725) | 0.0498 (0.165) | 0.409 (0.62)
xp gain | 3 (2%) | 188 | 0.794 (0.925) | 0.479 (0.672) |  |  | 0.443 (0.645) | 0.046 (0.159)
xq gain | 3 (2%) | 188 | 0.795 (0.925) | 0.478 (0.672) |  |  | 0.442 (0.645) | 0.047 (0.159)
3p loss | 3 (2%) | 188 | 0.0227 (0.101) | 0.338 (0.555) | 0.787 (0.925) | 1 (1.00) | 0.101 (0.255) | 0.0921 (0.245)
3q loss | 3 (2%) | 188 | 0.0217 (0.101) | 0.336 (0.555) | 0.785 (0.925) | 1 (1.00) | 0.101 (0.255) | 0.0932 (0.245)
17q loss | 7 (4%) | 184 | 0.0858 (0.239) | 0.149 (0.345) | 0.0782 (0.224) | 0.236 (0.452) | 0.119 (0.297) | 0.0471 (0.159)
18p loss | 5 (3%) | 186 | 0.00909 (0.0626) | 0.0647 (0.204) | 1 (1.00) | 0.865 (0.972) | 0.269 (0.486) | 0.185 (0.392)
10q gain | 3 (2%) | 188 | 0.447 (0.645) | 0.337 (0.555) | 0.262 (0.486) | 0.587 (0.758) | 0.159 (0.361) | 0.093 (0.245)
17q gain | 3 (2%) | 188 | 0.795 (0.925) | 0.783 (0.925) | 1 (1.00) | 0.589 (0.758) | 0.664 (0.827) | 0.303 (0.523)
19p gain | 5 (3%) | 186 | 0.399 (0.62) | 0.265 (0.486) | 1 (1.00) | 0.865 (0.972) | 0.409 (0.62) | 1 (1.00)
19q gain | 5 (3%) | 186 | 0.397 (0.62) | 0.267 (0.486) | 1 (1.00) | 0.866 (0.972) | 0.41 (0.62) | 1 (1.00)
12p loss | 4 (2%) | 187 | 0.538 (0.728) | 0.502 (0.698) | 0.381 (0.614) | 0.389 (0.62) | 0.398 (0.62) | 0.184 (0.392)
15q loss | 4 (2%) | 187 | 0.539 (0.728) | 0.45 (0.645) | 0.0968 (0.251) | 0.369 (0.601) | 0.143 (0.345) | 0.185 (0.392)
18q loss | 4 (2%) | 187 | 0.538 (0.728) | 0.162 (0.361) | 0.475 (0.672) | 0.864 (0.972) | 0.0617 (0.198) | 0.186 (0.392)
19p loss | 3 (2%) | 188 | 0.56 (0.742) | 0.783 (0.925) | 0.787 (0.925) | 1 (1.00) | 0.283 (0.503) | 0.413 (0.62)
19q loss | 3 (2%) | 188 | 0.559 (0.742) | 0.783 (0.925) | 0.787 (0.925) | 1 (1.00) | 0.283 (0.503) | 0.413 (0.62)

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.019

Table S1. Gene #1: '1p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
1P GAIN MUTATED | 0 | 0 | 0 | 0 | 3
1P GAIN WILD-TYPE | 57 | 31 | 39 | 33 | 16

Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.13

Table S2. Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
4P GAIN MUTATED | 0 | 3 | 0 | 1
4P GAIN WILD-TYPE | 49 | 41 | 55 | 42

Figure S2. Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.11

Table S3. Gene #2: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
4P GAIN MUTATED | 2 | 0 | 0 | 2 | 0
4P GAIN WILD-TYPE | 21 | 25 | 60 | 33 | 42

Figure S3. Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.13

Table S4. Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
4Q GAIN MUTATED | 0 | 3 | 0 | 1
4Q GAIN WILD-TYPE | 49 | 41 | 55 | 42

Figure S4. Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.11

Table S5. Gene #3: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
4Q GAIN MUTATED | 2 | 0 | 0 | 2 | 0
4Q GAIN WILD-TYPE | 21 | 25 | 60 | 33 | 42

Figure S5. Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.027

Table S6. Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
8P GAIN MUTATED | 2 | 2 | 15 | 1 | 1
8P GAIN WILD-TYPE | 21 | 23 | 45 | 34 | 41

Figure S6. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.11

Table S7. Gene #4: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 71 | 50 | 45
8P GAIN MUTATED | 13 | 2 | 3
8P GAIN WILD-TYPE | 58 | 48 | 42

Figure S7. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.017

Table S8. 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 S8. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.083

Table S9. 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 S9. Get High-res Image Gene #4: '8p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00558 (Fisher's exact test), Q value = 0.045

Table S10. Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
8Q GAIN MUTATED | 2 | 2 | 15 | 2 | 1
8Q GAIN WILD-TYPE | 21 | 23 | 45 | 33 | 41

Figure S10. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.08

Table S11. Gene #5: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 71 | 50 | 45
8Q GAIN MUTATED | 14 | 2 | 3
8Q GAIN WILD-TYPE | 57 | 48 | 42

Figure S11. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00182 (Fisher's exact test), Q value = 0.023

Table S12. 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 S12. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.08

Table S13. 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 S13. Get High-res Image Gene #5: '8q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.081

Table S14. Gene #7: '11p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
11P GAIN MUTATED | 1 | 1 | 0 | 0 | 3
11P GAIN WILD-TYPE | 56 | 30 | 39 | 33 | 16

Figure S14. Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0321 (Fisher's exact test), Q value = 0.12

Table S15. 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 | 2
11P GAIN WILD-TYPE | 67 | 31 | 76

Figure S15. Get High-res Image Gene #7: '11p gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.023

Table S16. Gene #8: '11q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
11Q GAIN MUTATED | 1 | 2 | 0 | 0 | 4
11Q GAIN WILD-TYPE | 56 | 29 | 39 | 33 | 15

Figure S16. Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.081

Table S17. 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 S17. Get High-res Image Gene #8: '11q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.1

Table S18. Gene #9: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
13Q GAIN MUTATED | 0 | 0 | 6 | 0 | 0
13Q GAIN WILD-TYPE | 23 | 25 | 54 | 35 | 42

Figure S18. Get High-res Image Gene #9: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.023

Table S19. Gene #9: '13q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
13Q GAIN MUTATED | 1 | 1 | 0 | 0 | 4
13Q GAIN WILD-TYPE | 56 | 30 | 39 | 33 | 15

Figure S19. Get High-res Image Gene #9: '13q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.16

Table S20. Gene #13: '21q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
21Q GAIN MUTATED | 1 | 2 | 0 | 4 | 0
21Q GAIN WILD-TYPE | 56 | 29 | 39 | 29 | 19

Figure S20. Get High-res Image Gene #13: '21q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.075

Table S21. Gene #14: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
22Q GAIN MUTATED | 0 | 0 | 8 | 1 | 0
22Q GAIN WILD-TYPE | 23 | 25 | 52 | 34 | 42

Figure S21. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.083

Table S22. 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 S22. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.017

Table S23. Gene #14: '22q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
22Q GAIN MUTATED | 0 | 2 | 1 | 1 | 5
22Q GAIN WILD-TYPE | 57 | 29 | 38 | 32 | 14

Figure S23. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.08

Table S24. 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 S24. Get High-res Image Gene #14: '22q gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.16

Table S25. 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 S25. Get High-res Image Gene #15: 'xp gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.16

Table S26. 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 S26. Get High-res Image Gene #16: 'xq gain' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.1

Table S27. Gene #17: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
3P LOSS MUTATED | 0 | 3 | 0 | 0
3P LOSS WILD-TYPE | 49 | 41 | 55 | 43

Figure S27. Get High-res Image Gene #17: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.1

Table S28. Gene #18: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
3Q LOSS MUTATED | 0 | 3 | 0 | 0
3Q LOSS WILD-TYPE | 49 | 41 | 55 | 43

Figure S28. Get High-res Image Gene #18: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.1

Table S29. Gene #19: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
5Q LOSS MUTATED | 0 | 0 | 6 | 0 | 0
5Q LOSS WILD-TYPE | 23 | 25 | 54 | 35 | 42

Figure S29. Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.12

Table S30. Gene #19: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
5Q LOSS MUTATED | 0 | 3 | 0 | 1 | 1
5Q LOSS WILD-TYPE | 57 | 28 | 39 | 32 | 18

Figure S30. Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.12

Table S31. 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 S31. Get High-res Image Gene #19: '5q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S32. Gene #20: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
7P LOSS MUTATED | 0 | 5 | 0 | 12
7P LOSS WILD-TYPE | 49 | 39 | 55 | 31

Figure S32. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.013

Table S33. Gene #20: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
7P LOSS MUTATED | 1 | 1 | 14 | 0 | 1
7P LOSS WILD-TYPE | 22 | 24 | 46 | 35 | 41

Figure S33. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.019

Table S34. Gene #20: '7p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 71 | 50 | 45
7P LOSS MUTATED | 13 | 0 | 3
7P LOSS WILD-TYPE | 58 | 50 | 42

Figure S34. 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 = 0.00038

Table S35. 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 S35. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 0.00658 (Fisher's exact test), Q value = 0.049

Table S36. Gene #20: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
7P LOSS MUTATED | 1 | 8 | 4 | 2 | 2
7P LOSS WILD-TYPE | 56 | 23 | 35 | 31 | 17

Figure S36. Get High-res Image Gene #20: '7p loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00293 (Fisher's exact test), Q value = 0.032

Table S37. 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 S37. 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 = 0.00038

Table S38. Gene #21: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
7Q LOSS MUTATED | 1 | 6 | 0 | 13
7Q LOSS WILD-TYPE | 48 | 38 | 55 | 30

Figure S38. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

Table S39. Gene #21: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
7Q LOSS MUTATED | 1 | 1 | 17 | 0 | 1
7Q LOSS WILD-TYPE | 22 | 24 | 43 | 35 | 41

Figure S39. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.00978 (Fisher's exact test), Q value = 0.063

Table S40. Gene #21: '7q loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 71 | 50 | 45
7Q LOSS MUTATED | 13 | 1 | 3
7Q LOSS WILD-TYPE | 58 | 49 | 42

Figure S40. 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 = 0.00038

Table S41. 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 S41. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.032

Table S42. Gene #21: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
7Q LOSS MUTATED | 1 | 9 | 4 | 3 | 2
7Q LOSS WILD-TYPE | 56 | 22 | 35 | 30 | 17

Figure S42. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.017

Table S43. 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 S43. Get High-res Image Gene #21: '7q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.13

Table S44. Gene #24: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
16Q LOSS MUTATED | 0 | 3 | 0 | 1
16Q LOSS WILD-TYPE | 49 | 41 | 55 | 42

Figure S44. Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.1

Table S45. Gene #24: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
16Q LOSS MUTATED | 0 | 3 | 0 | 1 | 0
16Q LOSS WILD-TYPE | 57 | 28 | 39 | 32 | 19

Figure S45. Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.1

Table S46. 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 S46. Get High-res Image Gene #24: '16q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.084

Table S47. Gene #25: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
17P LOSS MUTATED | 0 | 7 | 3 | 3
17P LOSS WILD-TYPE | 49 | 37 | 52 | 40

Figure S47. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00356 (Fisher's exact test), Q value = 0.034

Table S48. Gene #25: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 23 | 25 | 60 | 35 | 42
17P LOSS MUTATED | 0 | 0 | 10 | 3 | 0
17P LOSS WILD-TYPE | 23 | 25 | 50 | 32 | 42

Figure S48. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.023

Table S49. 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 S49. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.034

Table S50. 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 S50. Get High-res Image Gene #25: '17p loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0471 (Fisher's exact test), Q value = 0.16

Table S51. 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 S51. Get High-res Image Gene #26: '17q loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.00909 (Fisher's exact test), Q value = 0.063

Table S52. Gene #27: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
18P LOSS MUTATED | 0 | 4 | 0 | 1
18P LOSS WILD-TYPE | 49 | 40 | 55 | 42

Figure S52. Get High-res Image Gene #27: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.063

Table S53. Gene #31: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
XP LOSS MUTATED | 0 | 4 | 0 | 1
XP LOSS WILD-TYPE | 49 | 40 | 55 | 42

Figure S53. Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 0.00563 (Fisher's exact test), Q value = 0.045

Table S54. Gene #31: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
XP LOSS MUTATED | 0 | 4 | 0 | 1 | 0
XP LOSS WILD-TYPE | 57 | 27 | 39 | 32 | 19

Figure S54. Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00504 (Fisher's exact test), Q value = 0.044

Table S55. 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 S55. Get High-res Image Gene #31: 'xp loss' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00945 (Fisher's exact test), Q value = 0.063

Table S56. Gene #32: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 49 | 44 | 55 | 43
XQ LOSS MUTATED | 0 | 4 | 0 | 1
XQ LOSS WILD-TYPE | 49 | 40 | 55 | 42

Figure S56. Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 0.00598 (Fisher's exact test), Q value = 0.046

Table S57. Gene #32: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 57 | 31 | 39 | 33 | 19
XQ LOSS MUTATED | 0 | 4 | 0 | 1 | 0
XQ LOSS WILD-TYPE | 57 | 27 | 39 | 32 | 19

Figure S57. Get High-res Image Gene #32: 'xq loss' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00495 (Fisher's exact test), Q value = 0.044

Table S58. 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 S58. 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/22529564/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/22541002/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.

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] 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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