Brain Lower Grade Glioma: Correlation between gene mutation status and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

Testing the association between mutation status of 33 genes and 8 molecular subtypes across 170 patients, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

- IDH1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

- PIK3CA mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

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

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

- PTEN mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- NF1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- EGFR mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 33 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 36 significant findings detected.

|  | Clinical Features | MRNA CNMF | MRNA CHIERARCHICAL | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL
| nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test
TP53 | 88 (52%) | 82 | 0.136 (1.00) | 0.188 (1.00) | 8.29e-19 (1.72e-16) | 4.16e-34 (8.74e-32) | 5.91e-12 (1.19e-09) | 1.65e-10 (3.26e-08) | 2.46e-05 (0.00456) | 0.377 (1.00)
ATRX | 73 (43%) | 97 | 0.0421 (1.00) | 0.0271 (1.00) | 1.44e-10 (2.86e-08) | 4.03e-23 (8.38e-21) | 1.76e-12 (3.58e-10) | 5.04e-07 (9.68e-05) | 1.32e-05 (0.00248) | 0.465 (1.00)
CIC | 35 (21%) | 135 | 0.0764 (1.00) | 0.118 (1.00) | 6.08e-15 (1.24e-12) | 6.46e-18 (1.33e-15) | 4.68e-10 (9.23e-08) | 5.81e-12 (1.17e-09) | 2.72e-07 (5.28e-05) | 0.15 (1.00)
FUBP1 | 19 (11%) | 151 | 0.0862 (1.00) | 0.0919 (1.00) | 3.3e-08 (6.47e-06) | 1.6e-07 (3.13e-05) | 3.36e-05 (0.00618) | 1.6e-05 (0.00297) | 0.000268 (0.0487) | 0.922 (1.00)
IDH1 | 131 (77%) | 39 | 0.179 (1.00) | 0.272 (1.00) | 4.15e-11 (8.31e-09) | 1.3e-25 (2.72e-23) | 1.16e-16 (2.38e-14) | 0.064 (1.00) | 0.148 (1.00) | 0.0741 (1.00)
NOTCH1 | 16 (9%) | 154 | 0.502 (1.00) | 0.463 (1.00) | 0.000671 (0.119) | 0.00056 (0.101) | 0.0188 (1.00) | 0.00063 (0.113) | 0.00675 (1.00) | 0.043 (1.00)
PTEN | 8 (5%) | 162 |  |  | 5.51e-06 (0.00104) | 1.42e-06 (0.000271) | 3.34e-07 (6.44e-05) | 0.0227 (1.00) | 0.00448 (0.78) | 0.235 (1.00)
EGFR | 8 (5%) | 162 |  |  | 5.51e-06 (0.00104) | 1.63e-06 (0.00031) | 0.00121 (0.213) | 0.382 (1.00) | 0.0688 (1.00) | 1 (1.00)
PIK3CA | 15 (9%) | 155 |  |  | 0.000481 (0.087) | 8.12e-05 (0.0149) | 0.0362 (1.00) | 0.215 (1.00) | 0.573 (1.00) | 0.305 (1.00)
NF1 | 11 (6%) | 159 |  |  | 0.0489 (1.00) | 0.000742 (0.131) | 0.00123 (0.216) | 0.306 (1.00) | 0.29 (1.00) | 0.763 (1.00)
IDH2 | 6 (4%) | 164 |  |  | 0.24 (1.00) | 0.331 (1.00) | 0.133 (1.00) | 0.00734 (1.00) | 0.0436 (1.00) | 0.787 (1.00)
PIK3R1 | 12 (7%) | 158 |  |  | 0.0331 (1.00) | 0.454 (1.00) | 0.78 (1.00) | 0.915 (1.00) | 0.867 (1.00) | 0.79 (1.00)
ZNF844 | 5 (3%) | 165 |  |  | 0.451 (1.00) | 1 (1.00) | 0.376 (1.00) | 0.711 (1.00) | 0.414 (1.00) | 0.382 (1.00)
IL32 | 4 (2%) | 166 |  |  | 0.128 (1.00) | 0.0922 (1.00) | 0.233 (1.00) | 1 (1.00) | 0.826 (1.00) | 0.239 (1.00)
TIMD4 | 6 (4%) | 164 |  |  | 0.447 (1.00) | 0.653 (1.00) | 0.699 (1.00) | 0.737 (1.00) | 0.558 (1.00) | 1 (1.00)
CREBZF | 4 (2%) | 166 |  |  | 0.177 (1.00) | 0.416 (1.00) | 0.347 (1.00) | 0.0594 (1.00) | 0.313 (1.00) | 0.0527 (1.00)
ZNF57 | 6 (4%) | 164 |  |  | 0.134 (1.00) | 0.21 (1.00) | 0.0959 (1.00) | 0.0725 (1.00) | 0.0297 (1.00) | 0.272 (1.00)
ARID1A | 11 (6%) | 159 |  |  | 0.646 (1.00) | 0.714 (1.00) | 0.304 (1.00) | 0.25 (1.00) | 0.307 (1.00) | 0.265 (1.00)
TCF12 | 6 (4%) | 164 |  |  | 1 (1.00) | 0.564 (1.00) | 0.871 (1.00) | 0.322 (1.00) | 0.34 (1.00) | 0.366 (1.00)
NOX4 | 5 (3%) | 165 |  |  | 0.141 (1.00) | 0.802 (1.00) | 0.589 (1.00) | 0.248 (1.00) | 0.623 (1.00) | 0.219 (1.00)
ZBTB20 | 7 (4%) | 163 |  |  | 0.386 (1.00) | 0.227 (1.00) | 0.626 (1.00) | 1 (1.00) | 0.951 (1.00) | 0.416 (1.00)
MUC7 | 5 (3%) | 165 |  |  | 0.174 (1.00) | 0.246 (1.00) | 0.323 (1.00) | 0.577 (1.00) | 0.923 (1.00) | 0.382 (1.00)
ZNF845 | 6 (4%) | 164 |  |  | 0.285 (1.00) | 0.909 (1.00) | 0.699 (1.00) | 0.552 (1.00) | 0.836 (1.00) | 0.0872 (1.00)
ANKRD30A | 7 (4%) | 163 |  |  | 0.615 (1.00) | 0.243 (1.00) | 0.473 (1.00) | 0.869 (1.00) | 0.19 (1.00) | 0.151 (1.00)
SPDYE5 | 4 (2%) | 166 |  |  | 0.0598 (1.00) | 0.0283 (1.00) | 0.0616 (1.00) | 0.295 (1.00) | 0.0693 (1.00) | 0.329 (1.00)
SCAF1 | 4 (2%) | 166 |  |  | 1 (1.00) | 0.87 (1.00) | 0.456 (1.00) | 0.394 (1.00) | 0.118 (1.00) | 1 (1.00)
PRDM9 | 5 (3%) | 165 |  |  | 0.845 (1.00) | 0.343 (1.00) | 0.64 (1.00) | 0.711 (1.00) | 0.196 (1.00) | 0.562 (1.00)
PRAMEF11 | 5 (3%) | 165 |  |  | 0.845 (1.00) | 0.521 (1.00) | 0.293 (1.00) | 0.464 (1.00) | 0.414 (1.00) | 0.0231 (1.00)
ZCCHC12 | 3 (2%) | 167 |  |  | 0.0628 (1.00) | 0.108 (1.00) | 0.556 (1.00) | 0.152 (1.00) | 0.505 (1.00) | 0.147 (1.00)
ZNF91 | 5 (3%) | 165 |  |  | 0.369 (1.00) | 0.00702 (1.00) | 0.369 (1.00) | 0.388 (1.00) | 1 (1.00) | 1 (1.00)
C3ORF35 | 3 (2%) | 167 |  |  | 1 (1.00) | 0.794 (1.00) | 0.566 (1.00) | 0.581 (1.00) | 0.774 (1.00) | 0.147 (1.00)
RPTN | 5 (3%) | 165 |  |  | 0.248 (1.00) | 0.106 (1.00) | 0.549 (1.00) | 0.823 (1.00) | 0.809 (1.00) | 0.562 (1.00)
DDX5 | 5 (3%) | 165 |  |  | 1 (1.00) | 0.802 (1.00) | 0.437 (1.00) | 0.108 (1.00) | 0.414 (1.00) | 0.219 (1.00)

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 4.15e-11 (Fisher's exact test), Q value = 8.3e-09

Table S1. Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 40 | 63
IDH1 MUTATED | 58 | 14 | 58
IDH1 WILD-TYPE | 8 | 26 | 5

Figure S1. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.3e-25 (Fisher's exact test), Q value = 2.7e-23

Table S2. Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 79 | 25 | 50 | 12
IDH1 MUTATED | 77 | 0 | 46 | 5
IDH1 WILD-TYPE | 2 | 25 | 4 | 7

Figure S2. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.16e-16 (Chi-square test), Q value = 2.4e-14

Table S3. Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 44 | 32 | 31 | 54 | 7
IDH1 MUTATED | 44 | 6 | 28 | 46 | 6
IDH1 WILD-TYPE | 0 | 26 | 3 | 8 | 1

Figure S3. Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 8.29e-19 (Fisher's exact test), Q value = 1.7e-16

Table S4. Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 40 | 63
TP53 MUTATED | 60 | 18 | 10
TP53 WILD-TYPE | 6 | 22 | 53

Figure S4. Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.16e-34 (Fisher's exact test), Q value = 8.7e-32

Table S5. Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 79 | 25 | 50 | 12
TP53 MUTATED | 77 | 5 | 2 | 4
TP53 WILD-TYPE | 2 | 20 | 48 | 8

Figure S5. Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5.91e-12 (Chi-square test), Q value = 1.2e-09

Table S6. Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 44 | 32 | 31 | 54 | 7
TP53 MUTATED | 42 | 12 | 3 | 27 | 3
TP53 WILD-TYPE | 2 | 20 | 28 | 27 | 4

Figure S6. Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.65e-10 (Fisher's exact test), Q value = 3.3e-08

Table S7. Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 88 | 51
TP53 MUTATED | 1 | 62 | 24
TP53 WILD-TYPE | 28 | 26 | 27

Figure S7. Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.46e-05 (Fisher's exact test), Q value = 0.0046

Table S8. Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 40 | 38 | 27 | 65
TP53 MUTATED | 26 | 28 | 5 | 29
TP53 WILD-TYPE | 14 | 10 | 22 | 36

Figure S8. Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000481 (Fisher's exact test), Q value = 0.087

Table S9. Gene #4: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 40 | 63
PIK3CA MUTATED | 0 | 4 | 11
PIK3CA WILD-TYPE | 66 | 36 | 52

Figure S9. Get High-res Image Gene #4: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 8.12e-05 (Fisher's exact test), Q value = 0.015

Table S10. Gene #4: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 79 | 25 | 50 | 12
PIK3CA MUTATED | 0 | 4 | 10 | 1
PIK3CA WILD-TYPE | 79 | 21 | 40 | 11

Figure S10. Get High-res Image Gene #4: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 1.44e-10 (Fisher's exact test), Q value = 2.9e-08

Table S11. Gene #5: 'ATRX MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 40 | 63
ATRX MUTATED | 48 | 15 | 10
ATRX WILD-TYPE | 18 | 25 | 53

Figure S11. Get High-res Image Gene #5: 'ATRX MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.03e-23 (Fisher's exact test), Q value = 8.4e-21

Table S12. Gene #5: 'ATRX MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 79 | 25 | 50 | 12
ATRX MUTATED | 65 | 3 | 2 | 3
ATRX WILD-TYPE | 14 | 22 | 48 | 9

Figure S12. Get High-res Image Gene #5: 'ATRX MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.76e-12 (Chi-square test), Q value = 3.6e-10

Table S13. Gene #5: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 44 | 32 | 31 | 54 | 7
ATRX MUTATED | 39 | 8 | 2 | 22 | 1
ATRX WILD-TYPE | 5 | 24 | 29 | 32 | 6

Figure S13. Get High-res Image Gene #5: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.04e-07 (Fisher's exact test), Q value = 9.7e-05

Table S14. Gene #5: 'ATRX MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 88 | 51
ATRX MUTATED | 1 | 49 | 22
ATRX WILD-TYPE | 28 | 39 | 29

Figure S14. Get High-res Image Gene #5: 'ATRX MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.0025

Table S15. Gene #5: 'ATRX MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 40 | 38 | 27 | 65
ATRX MUTATED | 18 | 27 | 3 | 25
ATRX WILD-TYPE | 22 | 11 | 24 | 40

Figure S15. Get High-res Image Gene #5: 'ATRX MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'CIC MUTATION STATUS' versus 'CN_CNMF'

P value = 6.08e-15 (Fisher's exact test), Q value = 1.2e-12

Table S16. Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 40 | 63
CIC MUTATED | 1 | 1 | 33
CIC WILD-TYPE | 65 | 39 | 30

Figure S16. Get High-res Image Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'CIC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.46e-18 (Fisher's exact test), Q value = 1.3e-15

Table S17. Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 79 | 25 | 50 | 12
CIC MUTATED | 0 | 1 | 31 | 2
CIC WILD-TYPE | 79 | 24 | 19 | 10

Figure S17. Get High-res Image Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'CIC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.68e-10 (Chi-square test), Q value = 9.2e-08

Table S18. Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 44 | 32 | 31 | 54 | 7
CIC MUTATED | 0 | 1 | 19 | 14 | 1
CIC WILD-TYPE | 44 | 31 | 12 | 40 | 6

Figure S18. Get High-res Image Gene #6: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'CIC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.81e-12 (Fisher's exact test), Q value = 1.2e-09

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 88 | 51
CIC MUTATED | 19 | 3 | 13
CIC WILD-TYPE | 10 | 85 | 38

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

'CIC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.72e-07 (Fisher's exact test), Q value = 5.3e-05

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 40 | 38 | 27 | 65
CIC MUTATED | 4 | 1 | 16 | 14
CIC WILD-TYPE | 36 | 37 | 11 | 51

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

'FUBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 3.3e-08 (Fisher's exact test), Q value = 6.5e-06

Table S21. Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 40 | 63
FUBP1 MUTATED | 0 | 1 | 18
FUBP1 WILD-TYPE | 66 | 39 | 45

Figure S21. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'FUBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.6e-07 (Fisher's exact test), Q value = 3.1e-05

Table S22. Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 79 | 25 | 50 | 12
FUBP1 MUTATED | 0 | 1 | 15 | 0
FUBP1 WILD-TYPE | 79 | 24 | 35 | 12

Figure S22. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.36e-05 (Chi-square test), Q value = 0.0062

Table S23. Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 44 | 32 | 31 | 54 | 7
FUBP1 MUTATED | 0 | 1 | 11 | 6 | 1
FUBP1 WILD-TYPE | 44 | 31 | 20 | 48 | 6

Figure S23. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.003

Table S24. Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 88 | 51
FUBP1 MUTATED | 11 | 3 | 5
FUBP1 WILD-TYPE | 18 | 85 | 46

Figure S24. Get High-res Image Gene #7: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000268 (Fisher's exact test), Q value = 0.049

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 40 | 38 | 27 | 65
FUBP1 MUTATED | 2 | 1 | 10 | 6
FUBP1 WILD-TYPE | 38 | 37 | 17 | 59

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

'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000671 (Fisher's exact test), Q value = 0.12

Table S26. Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 40 | 63
NOTCH1 MUTATED | 1 | 2 | 13
NOTCH1 WILD-TYPE | 65 | 38 | 50

Figure S26. Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.1

Table S27. Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 79 | 25 | 50 | 12
NOTCH1 MUTATED | 2 | 1 | 12 | 0
NOTCH1 WILD-TYPE | 77 | 24 | 38 | 12

Figure S27. Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.11

Table S28. Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 88 | 51
NOTCH1 MUTATED | 7 | 2 | 7
NOTCH1 WILD-TYPE | 22 | 86 | 44

Figure S28. Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 5.51e-06 (Fisher's exact test), Q value = 0.001

Table S29. Gene #12: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 40 | 63
PTEN MUTATED | 0 | 8 | 0
PTEN WILD-TYPE | 66 | 32 | 63

Figure S29. Get High-res Image Gene #12: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.42e-06 (Fisher's exact test), Q value = 0.00027

Table S30. Gene #12: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 79 | 25 | 50 | 12
PTEN MUTATED | 0 | 7 | 0 | 0
PTEN WILD-TYPE | 79 | 18 | 50 | 12

Figure S30. Get High-res Image Gene #12: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.34e-07 (Chi-square test), Q value = 6.4e-05

Table S31. Gene #12: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 44 | 32 | 31 | 54 | 7
PTEN MUTATED | 0 | 8 | 0 | 0 | 0
PTEN WILD-TYPE | 44 | 24 | 31 | 54 | 7

Figure S31. Get High-res Image Gene #12: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000742 (Fisher's exact test), Q value = 0.13

Table S32. Gene #17: 'NF1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 79 | 25 | 50 | 12
NF1 MUTATED | 1 | 5 | 0 | 1
NF1 WILD-TYPE | 78 | 20 | 50 | 11

Figure S32. Get High-res Image Gene #17: 'NF1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00123 (Chi-square test), Q value = 0.22

Table S33. Gene #17: 'NF1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 44 | 32 | 31 | 54 | 7
NF1 MUTATED | 0 | 7 | 2 | 1 | 1
NF1 WILD-TYPE | 44 | 25 | 29 | 53 | 6

Figure S33. Get High-res Image Gene #17: 'NF1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 5.51e-06 (Fisher's exact test), Q value = 0.001

Table S34. Gene #20: 'EGFR MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 66 | 40 | 63
EGFR MUTATED | 0 | 8 | 0
EGFR WILD-TYPE | 66 | 32 | 63

Figure S34. Get High-res Image Gene #20: 'EGFR MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.63e-06 (Fisher's exact test), Q value = 0.00031

Table S35. Gene #20: 'EGFR MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 79 | 25 | 50 | 12
EGFR MUTATED | 0 | 7 | 0 | 1
EGFR WILD-TYPE | 79 | 18 | 50 | 11

Figure S35. Get High-res Image Gene #20: 'EGFR MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00121 (Chi-square test), Q value = 0.21

Table S36. Gene #20: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 44 | 32 | 31 | 54 | 7
EGFR MUTATED | 0 | 6 | 0 | 2 | 0
EGFR WILD-TYPE | 44 | 26 | 31 | 52 | 7

Figure S36. Get High-res Image Gene #20: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

Methods & Data
Input

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

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

- Number of patients = 170

- Number of significantly mutated genes = 33

- Number of Molecular subtypes = 8

- 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- 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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