Correlation between gene mutation status and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C12N50HV
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C12N50HV
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 18 genes and 12 molecular subtypes across 220 patients, 38 significant findings detected with P value < 0.05 and Q value < 0.25.

- ATRX mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- IDH1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- CIC mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- FUBP1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- NOTCH1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- PIK3CA mutation correlated to 'METHLYATION_CNMF'.

- PTEN mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 18 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 38 significant findings detected.

|  | Clinical Features | MRNA CNMF | MRNA CHIERARCHICAL | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nMutated (%) | 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 | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test
PTEN | 13 (6%) | 207 |  |  | 2.24e-07 (3.96e-05) | 6.77e-11 (1.25e-08) | 0.000979 (0.156) | 0.00248 (0.392) | 4.11e-07 (7.19e-05) | 0.000474 (0.0768) | 0.000594 (0.0957) | 0.000142 (0.0236) | 1.01e-08 (1.82e-06) | 1.18e-06 (0.000204)
IDH1 | 167 (76%) | 53 | 0.225 (1.00) | 0.478 (1.00) | 1.38e-11 (2.57e-09) | 2.38e-32 (4.63e-30) | 4.02e-06 (0.000691) | 0.0871 (1.00) | 4.54e-09 (8.27e-07) | 0.027 (1.00) | 0.0194 (1.00) | 2.96e-05 (0.00503) | 5.92e-13 (1.11e-10) | 1.55e-15 (2.95e-13)
CIC | 39 (18%) | 181 | 0.0502 (1.00) | 0.00351 (0.547) | 2.56e-08 (4.57e-06) | 7.83e-22 (1.51e-19) | 0.000206 (0.0339) | 0.528 (1.00) | 2.46e-05 (0.00421) | 4.54e-17 (8.68e-15) | 4.53e-05 (0.00756) | 0.362 (1.00) | 1.51e-07 (2.69e-05) | 0.0456 (1.00)
TP53 | 116 (53%) | 104 | 0.113 (1.00) | 0.0133 (1.00) | 3.84e-17 (7.36e-15) | 2.06e-41 (4.03e-39) | 0.0543 (1.00) | 0.838 (1.00) | 0.159 (1.00) | 8.69e-14 (1.64e-11) | 0.0268 (1.00) | 0.00444 (0.684) | 1.43e-10 (2.64e-08) | 4.42e-05 (0.00742)
ATRX | 97 (44%) | 123 | 0.0256 (1.00) | 0.0671 (1.00) | 2.79e-11 (5.19e-09) | 8.28e-29 (1.61e-26) | 0.16 (1.00) | 0.932 (1.00) | 0.373 (1.00) | 5.86e-09 (1.06e-06) | 0.0411 (1.00) | 0.0356 (1.00) | 1.04e-06 (0.000181) | 0.00378 (0.586)
FUBP1 | 21 (10%) | 199 | 0.0231 (1.00) | 0.00587 (0.898) | 0.000249 (0.0406) | 1.41e-09 (2.59e-07) | 0.0696 (1.00) | 0.666 (1.00) | 0.0176 (1.00) | 3.86e-07 (6.79e-05) | 0.0893 (1.00) | 0.932 (1.00) | 0.0592 (1.00) | 0.505 (1.00)
NOTCH1 | 19 (9%) | 201 | 0.615 (1.00) | 0.237 (1.00) | 0.0423 (1.00) | 3.74e-05 (0.00631) | 0.104 (1.00) | 0.893 (1.00) | 0.0559 (1.00) | 0.000698 (0.112) | 0.0835 (1.00) | 0.0803 (1.00) | 0.0397 (1.00) | 0.0987 (1.00)
PIK3CA | 19 (9%) | 201 |  |  | 0.301 (1.00) | 0.00017 (0.028) | 0.769 (1.00) | 0.079 (1.00) | 1 (1.00) | 0.326 (1.00) | 0.214 (1.00) | 0.854 (1.00) | 0.0482 (1.00) | 0.285 (1.00)
IL32 | 9 (4%) | 211 |  |  | 0.128 (1.00) | 0.135 (1.00) | 0.551 (1.00) | 0.619 (1.00) | 0.636 (1.00) | 0.805 (1.00) | 0.425 (1.00) | 0.856 (1.00) | 0.791 (1.00) | 0.434 (1.00)
IDH2 | 8 (4%) | 212 |  |  | 0.0805 (1.00) | 0.115 (1.00) | 1 (1.00) | 1 (1.00) | 0.0791 (1.00) | 0.00342 (0.536) | 0.145 (1.00) | 0.485 (1.00) | 0.216 (1.00) | 0.501 (1.00)
PIK3R1 | 13 (6%) | 207 | 0.615 (1.00) | 0.856 (1.00) | 0.187 (1.00) | 0.065 (1.00) | 0.495 (1.00) | 1 (1.00) | 0.722 (1.00) | 0.311 (1.00) | 0.927 (1.00) | 1 (1.00) | 0.373 (1.00) | 0.927 (1.00)
CREBZF | 4 (2%) | 216 |  |  | 0.384 (1.00) | 0.0499 (1.00) | 0.197 (1.00) | 0.154 (1.00) | 0.036 (1.00) | 0.065 (1.00) | 0.385 (1.00) | 0.061 (1.00) | 0.514 (1.00) | 0.128 (1.00)
PCDHAC2 | 14 (6%) | 206 | 1 (1.00) | 1 (1.00) | 0.0167 (1.00) | 0.0287 (1.00) | 0.661 (1.00) | 0.302 (1.00) | 0.835 (1.00) | 0.865 (1.00) | 0.188 (1.00) | 0.0866 (1.00) | 0.883 (1.00) | 0.0577 (1.00)
NOX4 | 5 (2%) | 215 |  |  | 0.215 (1.00) | 0.922 (1.00) | 0.309 (1.00) | 0.715 (1.00) | 0.379 (1.00) | 0.355 (1.00) | 0.598 (1.00) | 0.165 (1.00) | 0.749 (1.00) | 0.587 (1.00)
ZNF57 | 6 (3%) | 214 |  |  | 0.103 (1.00) | 0.242 (1.00) | 0.449 (1.00) | 0.104 (1.00) | 0.0212 (1.00) | 0.0673 (1.00) | 0.321 (1.00) | 0.0735 (1.00) | 0.491 (1.00) | 0.0377 (1.00)
EIF1AX | 3 (1%) | 217 |  |  | 1 (1.00) | 0.439 (1.00) | 0.704 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.433 (1.00) | 0.397 (1.00) | 0.245 (1.00) | 0.765 (1.00)
DCP1B | 4 (2%) | 216 |  |  | 0.196 (1.00) | 0.403 (1.00) | 0.0144 (1.00) | 0.154 (1.00) | 1 (1.00) | 1 (1.00) | 0.394 (1.00) | 0.474 (1.00) | 0.205 (1.00) | 0.661 (1.00)
NAB2 | 4 (2%) | 216 |  |  | 0.919 (1.00) | 0.233 (1.00) | 0.598 (1.00) | 0.11 (1.00) | 0.689 (1.00) | 0.146 (1.00) | 0.612 (1.00) | 0.723 (1.00) | 0.475 (1.00) | 1 (1.00)

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 2.79e-11 (Fisher's exact test), Q value = 5.2e-09

Table S1. Gene #2: 'ATRX MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 45 | 45 | 85
ATRX MUTATED | 36 | 17 | 26 | 18
ATRX WILD-TYPE | 7 | 28 | 19 | 67

Figure S1. Get High-res Image Gene #2: 'ATRX MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 8.28e-29 (Fisher's exact test), Q value = 1.6e-26

Table S2. Gene #2: 'ATRX MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 97 | 34 | 57 | 27
ATRX MUTATED | 81 | 4 | 2 | 9
ATRX WILD-TYPE | 16 | 30 | 55 | 18

Figure S2. Get High-res Image Gene #2: 'ATRX MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.86e-09 (Fisher's exact test), Q value = 1.1e-06

Table S3. Gene #2: 'ATRX MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 111 | 76
ATRX MUTATED | 1 | 65 | 31
ATRX WILD-TYPE | 32 | 46 | 45

Figure S3. Get High-res Image Gene #2: 'ATRX MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.04e-06 (Chi-square test), Q value = 0.00018

Table S4. Gene #2: 'ATRX MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 38 | 34 | 17 | 61 | 27 | 31 | 4 | 7
ATRX MUTATED | 31 | 7 | 11 | 21 | 7 | 14 | 3 | 2
ATRX WILD-TYPE | 7 | 27 | 6 | 40 | 20 | 17 | 1 | 5

Figure S4. Get High-res Image Gene #2: 'ATRX MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.38e-11 (Fisher's exact test), Q value = 2.6e-09

Table S5. Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 45 | 45 | 85
IDH1 MUTATED | 42 | 16 | 36 | 72
IDH1 WILD-TYPE | 1 | 29 | 9 | 13

Figure S5. Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.38e-32 (Fisher's exact test), Q value = 4.6e-30

Table S6. Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 97 | 34 | 57 | 27
IDH1 MUTATED | 95 | 0 | 52 | 16
IDH1 WILD-TYPE | 2 | 34 | 5 | 11

Figure S6. Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 4.02e-06 (Fisher's exact test), Q value = 0.00069

Table S7. Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 49 | 61 | 63
IDH1 MUTATED | 29 | 25 | 57 | 50
IDH1 WILD-TYPE | 8 | 24 | 4 | 13

Figure S7. Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.54e-09 (Fisher's exact test), Q value = 8.3e-07

Table S8. Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 67 | 79
IDH1 MUTATED | 39 | 64 | 64
IDH1 WILD-TYPE | 35 | 3 | 15

Figure S8. Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.96e-05 (Fisher's exact test), Q value = 0.005

Table S9. Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 118 | 87
IDH1 MUTATED | 3 | 92 | 71
IDH1 WILD-TYPE | 11 | 26 | 16

Figure S9. Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.92e-13 (Chi-square test), Q value = 1.1e-10

Table S10. Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 38 | 34 | 17 | 61 | 27 | 31 | 4 | 7
IDH1 MUTATED | 38 | 8 | 16 | 46 | 24 | 23 | 4 | 7
IDH1 WILD-TYPE | 0 | 26 | 1 | 15 | 3 | 8 | 0 | 0

Figure S10. Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.55e-15 (Fisher's exact test), Q value = 3e-13

Table S11. Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 35 | 87 | 97
IDH1 MUTATED | 6 | 76 | 84
IDH1 WILD-TYPE | 29 | 11 | 13

Figure S11. Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 3.84e-17 (Fisher's exact test), Q value = 7.4e-15

Table S12. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 45 | 45 | 85
TP53 MUTATED | 42 | 19 | 33 | 22
TP53 WILD-TYPE | 1 | 26 | 12 | 63

Figure S12. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.06e-41 (Fisher's exact test), Q value = 4e-39

Table S13. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 97 | 34 | 57 | 27
TP53 MUTATED | 95 | 7 | 2 | 11
TP53 WILD-TYPE | 2 | 27 | 55 | 16

Figure S13. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.69e-14 (Fisher's exact test), Q value = 1.6e-11

Table S14. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 111 | 76
TP53 MUTATED | 1 | 81 | 34
TP53 WILD-TYPE | 32 | 30 | 42

Figure S14. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.43e-10 (Chi-square test), Q value = 2.6e-08

Table S15. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 38 | 34 | 17 | 61 | 27 | 31 | 4 | 7
TP53 MUTATED | 37 | 9 | 14 | 26 | 7 | 15 | 4 | 3
TP53 WILD-TYPE | 1 | 25 | 3 | 35 | 20 | 16 | 0 | 4

Figure S15. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.42e-05 (Fisher's exact test), Q value = 0.0074

Table S16. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 35 | 87 | 97
TP53 MUTATED | 11 | 61 | 43
TP53 WILD-TYPE | 24 | 26 | 54

Figure S16. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'CN_CNMF'

P value = 2.56e-08 (Fisher's exact test), Q value = 4.6e-06

Table S17. Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 45 | 45 | 85
CIC MUTATED | 0 | 1 | 9 | 29
CIC WILD-TYPE | 43 | 44 | 36 | 56

Figure S17. Get High-res Image Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'CIC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 7.83e-22 (Fisher's exact test), Q value = 1.5e-19

Table S18. Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 97 | 34 | 57 | 27
CIC MUTATED | 0 | 1 | 35 | 2
CIC WILD-TYPE | 97 | 33 | 22 | 25

Figure S18. Get High-res Image Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'CIC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.000206 (Fisher's exact test), Q value = 0.034

Table S19. Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 49 | 61 | 63
CIC MUTATED | 1 | 4 | 20 | 14
CIC WILD-TYPE | 36 | 45 | 41 | 49

Figure S19. Get High-res Image Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'CIC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.46e-05 (Fisher's exact test), Q value = 0.0042

Table S20. Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 67 | 79
CIC MUTATED | 2 | 18 | 19
CIC WILD-TYPE | 72 | 49 | 60

Figure S20. Get High-res Image Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'CIC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.54e-17 (Fisher's exact test), Q value = 8.7e-15

Table S21. Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 111 | 76
CIC MUTATED | 22 | 1 | 16
CIC WILD-TYPE | 11 | 110 | 60

Figure S21. Get High-res Image Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 4.53e-05 (Chi-square test), Q value = 0.0076

Table S22. Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 51 | 34 | 71 | 15 | 48
CIC MUTATED | 6 | 1 | 15 | 9 | 8
CIC WILD-TYPE | 45 | 33 | 56 | 6 | 40

Figure S22. Get High-res Image Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.51e-07 (Chi-square test), Q value = 2.7e-05

Table S23. Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 38 | 34 | 17 | 61 | 27 | 31 | 4 | 7
CIC MUTATED | 0 | 2 | 2 | 12 | 16 | 6 | 0 | 1
CIC WILD-TYPE | 38 | 32 | 15 | 49 | 11 | 25 | 4 | 6

Figure S23. Get High-res Image Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'FUBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.041

Table S24. Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 45 | 45 | 85
FUBP1 MUTATED | 0 | 1 | 3 | 17
FUBP1 WILD-TYPE | 43 | 44 | 42 | 68

Figure S24. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'FUBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.41e-09 (Fisher's exact test), Q value = 2.6e-07

Table S25. Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 97 | 34 | 57 | 27
FUBP1 MUTATED | 0 | 1 | 17 | 0
FUBP1 WILD-TYPE | 97 | 33 | 40 | 27

Figure S25. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.86e-07 (Fisher's exact test), Q value = 6.8e-05

Table S26. Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 111 | 76
FUBP1 MUTATED | 12 | 2 | 7
FUBP1 WILD-TYPE | 21 | 109 | 69

Figure S26. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.74e-05 (Fisher's exact test), Q value = 0.0063

Table S27. Gene #8: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 97 | 34 | 57 | 27
NOTCH1 MUTATED | 3 | 1 | 14 | 0
NOTCH1 WILD-TYPE | 94 | 33 | 43 | 27

Figure S27. Get High-res Image Gene #8: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000698 (Fisher's exact test), Q value = 0.11

Table S28. Gene #8: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 111 | 76
NOTCH1 MUTATED | 8 | 3 | 8
NOTCH1 WILD-TYPE | 25 | 108 | 68

Figure S28. Get High-res Image Gene #8: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.028

Table S29. Gene #9: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 97 | 34 | 57 | 27
PIK3CA MUTATED | 1 | 5 | 11 | 2
PIK3CA WILD-TYPE | 96 | 29 | 46 | 25

Figure S29. Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 2.24e-07 (Fisher's exact test), Q value = 4e-05

Table S30. Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 43 | 45 | 45 | 85
PTEN MUTATED | 0 | 11 | 2 | 0
PTEN WILD-TYPE | 43 | 34 | 43 | 85

Figure S30. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.77e-11 (Fisher's exact test), Q value = 1.3e-08

Table S31. Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 97 | 34 | 57 | 27
PTEN MUTATED | 0 | 12 | 0 | 0
PTEN WILD-TYPE | 97 | 22 | 57 | 27

Figure S31. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.000979 (Fisher's exact test), Q value = 0.16

Table S32. Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 37 | 49 | 61 | 63
PTEN MUTATED | 1 | 8 | 2 | 0
PTEN WILD-TYPE | 36 | 41 | 59 | 63

Figure S32. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.11e-07 (Fisher's exact test), Q value = 7.2e-05

Table S33. Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 67 | 79
PTEN MUTATED | 13 | 0 | 0
PTEN WILD-TYPE | 61 | 67 | 79

Figure S33. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000474 (Fisher's exact test), Q value = 0.077

Table S34. Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 111 | 76
PTEN MUTATED | 0 | 13 | 0
PTEN WILD-TYPE | 33 | 98 | 76

Figure S34. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000594 (Chi-square test), Q value = 0.096

Table S35. Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 51 | 34 | 71 | 15 | 48
PTEN MUTATED | 9 | 3 | 1 | 0 | 0
PTEN WILD-TYPE | 42 | 31 | 70 | 15 | 48

Figure S35. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S36. Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 14 | 118 | 87
PTEN MUTATED | 4 | 9 | 0
PTEN WILD-TYPE | 10 | 109 | 87

Figure S36. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.01e-08 (Chi-square test), Q value = 1.8e-06

Table S37. Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 38 | 34 | 17 | 61 | 27 | 31 | 4 | 7
PTEN MUTATED | 0 | 11 | 0 | 1 | 0 | 1 | 0 | 0
PTEN WILD-TYPE | 38 | 23 | 17 | 60 | 27 | 30 | 4 | 7

Figure S37. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.18e-06 (Fisher's exact test), Q value = 2e-04

Table S38. Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 35 | 87 | 97
PTEN MUTATED | 9 | 4 | 0
PTEN WILD-TYPE | 26 | 83 | 97

Figure S38. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

- Mutation data file = LGG-TP.mutsig.cluster.txt

- Molecular subtypes file = LGG-TP.transferedmergedcluster.txt

- Number of patients = 220

- Number of significantly mutated genes = 18

- Number of Molecular subtypes = 12

- 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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