Correlation between gene mutation status and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1QV3JHP
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Brain Lower Grade Glioma (Primary solid tumor cohort) - 21 April 2013: Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1QV3JHP
Overview
Introduction

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

Summary

Testing the association between mutation status of 37 genes and 8 molecular subtypes across 217 patients, 37 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', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • NOTCH1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • PTEN mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_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 37 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, 37 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 113 (52%) 104 0.113
(1.00) 		0.157
(1.00) 		2.78e-23
(6.47e-21) 		6.42e-42
(1.52e-39) 		9.59e-16
(2.19e-13) 		5.01e-12
(1.12e-09) 		0.000891
(0.18) 		0.0181
(1.00)
CIC 41 (19%) 176 0.0502
(1.00) 		0.0625
(1.00) 		6.22e-19
(1.43e-16) 		1.53e-22
(3.55e-20) 		4.98e-13
(1.12e-10) 		5.58e-15
(1.26e-12) 		1.43e-06
(0.000304) 		0.00468
(0.913)
NOTCH1 19 (9%) 198 0.615
(1.00) 		0.458
(1.00) 		1.01e-05
(0.00212) 		6.03e-06
(0.00127) 		0.000143
(0.0297) 		2.65e-05
(0.00552) 		0.00323
(0.632) 		0.000941
(0.189)
ATRX 93 (43%) 124 0.0256
(1.00) 		0.022
(1.00) 		3.04e-15
(6.9e-13) 		3.48e-29
(8.14e-27) 		1.17e-16
(2.67e-14) 		1.15e-08
(2.49e-06) 		0.00191
(0.378) 		0.0485
(1.00)
FUBP1 22 (10%) 195 0.0231
(1.00) 		0.0459
(1.00) 		1.06e-09
(2.31e-07) 		8.13e-10
(1.79e-07) 		1.98e-08
(4.27e-06) 		2e-07
(4.31e-05) 		0.0194
(1.00) 		0.222
(1.00)
PTEN 12 (6%) 205 6.19e-09
(1.35e-06) 		4.63e-10
(1.02e-07) 		2.43e-11
(5.39e-09) 		0.00194
(0.382) 		0.000294
(0.0602) 		0.0174
(1.00)
IDH1 165 (76%) 52 0.225
(1.00) 		0.329
(1.00) 		1.02e-12
(2.28e-10) 		1.4e-32
(3.3e-30) 		1.8e-19
(4.15e-17) 		0.0595
(1.00) 		0.0684
(1.00) 		0.106
(1.00)
EGFR 10 (5%) 207 7.43e-06
(0.00156) 		3.01e-07
(6.45e-05) 		0.000501
(0.102) 		0.45
(1.00) 		0.162
(1.00) 		0.835
(1.00)
PIK3CA 19 (9%) 198 0.000509
(0.103) 		0.000193
(0.0398) 		0.0642
(1.00) 		0.345
(1.00) 		0.4
(1.00) 		0.246
(1.00)
NF1 16 (7%) 201 0.0451
(1.00) 		1.94e-06
(0.000412) 		0.00101
(0.202) 		0.774
(1.00) 		0.426
(1.00) 		0.551
(1.00)
IDH2 9 (4%) 208 0.103
(1.00) 		0.075
(1.00) 		0.0501
(1.00) 		0.00158
(0.314) 		0.0207
(1.00) 		0.509
(1.00)
IL32 6 (3%) 211 0.0609
(1.00) 		0.0214
(1.00) 		0.33
(1.00) 		0.304
(1.00) 		0.357
(1.00) 		0.28
(1.00)
PIK3R1 14 (6%) 203 0.615
(1.00) 		0.594
(1.00) 		0.00526
(1.00) 		0.0921
(1.00) 		0.5
(1.00) 		0.451
(1.00) 		0.875
(1.00) 		1
(1.00)
ZNF844 6 (3%) 211 1
(1.00) 		0.534
(1.00) 		0.442
(1.00) 		0.628
(1.00) 		0.185
(1.00) 		1
(1.00)
TCF12 9 (4%) 208 0.907
(1.00) 		0.703
(1.00) 		0.571
(1.00) 		0.193
(1.00) 		0.39
(1.00) 		0.812
(1.00)
ZBTB20 10 (5%) 207 0.415
(1.00) 		0.339
(1.00) 		0.562
(1.00) 		0.908
(1.00) 		0.911
(1.00) 		0.45
(1.00)
TIMD4 6 (3%) 211 0.577
(1.00) 		0.871
(1.00) 		0.711
(1.00) 		0.858
(1.00) 		0.554
(1.00) 		0.754
(1.00)
CREBZF 4 (2%) 213 0.161
(1.00) 		0.248
(1.00) 		0.356
(1.00) 		0.0581
(1.00) 		0.343
(1.00) 		0.0769
(1.00)
ZNF57 6 (3%) 211 0.131
(1.00) 		0.218
(1.00) 		0.0976
(1.00) 		0.085
(1.00) 		0.0274
(1.00) 		0.382
(1.00)
ARID1A 13 (6%) 204 0.866
(1.00) 		0.651
(1.00) 		0.381
(1.00) 		0.277
(1.00) 		0.339
(1.00) 		0.745
(1.00)
EMG1 4 (2%) 213 0.683
(1.00) 		0.681
(1.00) 		0.97
(1.00) 		0.642
(1.00) 		0.226
(1.00) 		0.68
(1.00)
PRAMEF11 6 (3%) 211 1
(1.00) 		0.328
(1.00) 		0.213
(1.00) 		0.242
(1.00) 		0.222
(1.00) 		0.0269
(1.00)
PRDM9 6 (3%) 211 0.659
(1.00) 		0.218
(1.00) 		0.305
(1.00) 		0.858
(1.00) 		0.437
(1.00) 		1
(1.00)
NOX4 5 (2%) 212 0.102
(1.00) 		0.916
(1.00) 		0.594
(1.00) 		0.238
(1.00) 		0.865
(1.00) 		0.323
(1.00)
ANKRD30A 8 (4%) 209 0.529
(1.00) 		0.409
(1.00) 		0.841
(1.00) 		1
(1.00) 		0.503
(1.00) 		0.302
(1.00)
MUC7 5 (2%) 212 0.24
(1.00) 		0.256
(1.00) 		0.401
(1.00) 		0.57
(1.00) 		0.805
(1.00) 		0.72
(1.00)
PAX4 5 (2%) 212 0.453
(1.00) 		0.916
(1.00) 		0.757
(1.00) 		0.705
(1.00) 		0.473
(1.00) 		0.72
(1.00)
ZNF845 6 (3%) 211 0.278
(1.00) 		0.929
(1.00) 		0.711
(1.00) 		0.628
(1.00) 		0.839
(1.00) 		0.535
(1.00)
C15ORF2 8 (4%) 209 0.239
(1.00) 		0.339
(1.00) 		0.0132
(1.00) 		0.318
(1.00) 		0.69
(1.00) 		0.302
(1.00)
SPDYE5 4 (2%) 213 0.0526
(1.00) 		0.0338
(1.00) 		0.0565
(1.00) 		0.286
(1.00) 		0.0712
(1.00) 		0.25
(1.00)
SCAF1 4 (2%) 213 1
(1.00) 		1
(1.00) 		0.424
(1.00) 		0.373
(1.00) 		0.0853
(1.00) 		1
(1.00)
FSTL5 6 (3%) 211 0.0609
(1.00) 		0.304
(1.00) 		0.118
(1.00) 		0.0256
(1.00) 		0.0875
(1.00) 		0.382
(1.00)
C9ORF79 8 (4%) 209 1
(1.00) 		0.467
(1.00) 		0.657
(1.00) 		0.779
(1.00) 		0.792
(1.00) 		0.801
(1.00)
ZCCHC12 3 (1%) 214 0.0543
(1.00) 		0.0816
(1.00) 		0.546
(1.00) 		0.144
(1.00) 		0.434
(1.00) 		0.191
(1.00)
SMARCA4 13 (6%) 204 0.714
(1.00) 		0.612
(1.00) 		0.5
(1.00) 		0.676
(1.00) 		0.35
(1.00) 		0.412
(1.00)
MYH4 5 (2%) 212 0.453
(1.00) 		0.916
(1.00) 		0.418
(1.00) 		0.107
(1.00) 		0.00846
(1.00) 		0.72
(1.00)
TRDN 4 (2%) 213 0.448
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.642
(1.00) 		1
(1.00) 		0.427
(1.00)
'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.02e-12 (Fisher's exact test), Q value = 2.3e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 49 76
IDH1 MUTATED 78 17 69
IDH1 WILD-TYPE 12 32 7

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 = 1.4e-32 (Fisher's exact test), Q value = 3.3e-30

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 32 59 23
IDH1 MUTATED 96 0 54 11
IDH1 WILD-TYPE 2 32 5 12

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 = 1.8e-19 (Chi-square test), Q value = 4.1e-17

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 58 40 36 71 10
IDH1 MUTATED 58 8 33 56 9
IDH1 WILD-TYPE 0 32 3 15 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 = 2.78e-23 (Fisher's exact test), Q value = 6.5e-21

Table S4.  Gene #4: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 49 76
TP53 MUTATED 80 22 11
TP53 WILD-TYPE 10 27 65

Figure S4.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.42e-42 (Fisher's exact test), Q value = 1.5e-39

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 32 59 23
TP53 MUTATED 96 6 3 7
TP53 WILD-TYPE 2 26 56 16

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9.59e-16 (Chi-square test), Q value = 2.2e-13

Table S6.  Gene #4: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 40 36 71 10
TP53 MUTATED 56 14 4 32 6
TP53 WILD-TYPE 2 26 32 39 4

Figure S6.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.01e-12 (Fisher's exact test), Q value = 1.1e-09

Table S7.  Gene #4: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 112 70
TP53 MUTATED 2 80 30
TP53 WILD-TYPE 31 32 40

Figure S7.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000891 (Fisher's exact test), Q value = 0.18

Table S8.  Gene #4: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 33 82 46
TP53 MUTATED 35 12 33 32
TP53 WILD-TYPE 20 21 49 14

Figure S8.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000509 (Fisher's exact test), Q value = 0.1

Table S9.  Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 49 76
PIK3CA MUTATED 1 5 13
PIK3CA WILD-TYPE 89 44 63

Figure S9.  Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.04

Table S10.  Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 32 59 23
PIK3CA MUTATED 1 5 11 2
PIK3CA WILD-TYPE 97 27 48 21

Figure S10.  Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 3.04e-15 (Fisher's exact test), Q value = 6.9e-13

Table S11.  Gene #7: 'ATRX MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 49 76
ATRX MUTATED 66 17 10
ATRX WILD-TYPE 24 32 66

Figure S11.  Get High-res Image Gene #7: 'ATRX MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.48e-29 (Fisher's exact test), Q value = 8.1e-27

Table S12.  Gene #7: 'ATRX MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 32 59 23
ATRX MUTATED 81 4 2 5
ATRX WILD-TYPE 17 28 57 18

Figure S12.  Get High-res Image Gene #7: 'ATRX MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.17e-16 (Chi-square test), Q value = 2.7e-14

Table S13.  Gene #7: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 40 36 71 10
ATRX MUTATED 52 10 2 26 2
ATRX WILD-TYPE 6 30 34 45 8

Figure S13.  Get High-res Image Gene #7: 'ATRX MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.15e-08 (Fisher's exact test), Q value = 2.5e-06

Table S14.  Gene #7: 'ATRX MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 112 70
ATRX MUTATED 1 64 27
ATRX WILD-TYPE 32 48 43

Figure S14.  Get High-res Image Gene #7: 'ATRX MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.06e-09 (Fisher's exact test), Q value = 2.3e-07

Table S15.  Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 49 76
FUBP1 MUTATED 0 1 21
FUBP1 WILD-TYPE 90 48 55

Figure S15.  Get High-res Image Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'FUBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 8.13e-10 (Fisher's exact test), Q value = 1.8e-07

Table S16.  Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 32 59 23
FUBP1 MUTATED 0 1 18 0
FUBP1 WILD-TYPE 98 31 41 23

Figure S16.  Get High-res Image Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.98e-08 (Chi-square test), Q value = 4.3e-06

Table S17.  Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 40 36 71 10
FUBP1 MUTATED 0 1 14 6 1
FUBP1 WILD-TYPE 58 39 22 65 9

Figure S17.  Get High-res Image Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-07 (Fisher's exact test), Q value = 4.3e-05

Table S18.  Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 112 70
FUBP1 MUTATED 13 3 6
FUBP1 WILD-TYPE 20 109 64

Figure S18.  Get High-res Image Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'CN_CNMF'

P value = 6.22e-19 (Fisher's exact test), Q value = 1.4e-16

Table S19.  Gene #9: 'CIC MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 49 76
CIC MUTATED 1 1 39
CIC WILD-TYPE 89 48 37

Figure S19.  Get High-res Image Gene #9: 'CIC MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'CIC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.53e-22 (Fisher's exact test), Q value = 3.6e-20

Table S20.  Gene #9: 'CIC MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 32 59 23
CIC MUTATED 0 1 37 2
CIC WILD-TYPE 98 31 22 21

Figure S20.  Get High-res Image Gene #9: 'CIC MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'CIC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.98e-13 (Chi-square test), Q value = 1.1e-10

Table S21.  Gene #9: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 40 36 71 10
CIC MUTATED 0 1 22 17 1
CIC WILD-TYPE 58 39 14 54 9

Figure S21.  Get High-res Image Gene #9: 'CIC MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'CIC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.58e-15 (Fisher's exact test), Q value = 1.3e-12

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 112 70
CIC MUTATED 22 3 16
CIC WILD-TYPE 11 109 54

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

'CIC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.43e-06 (Fisher's exact test), Q value = 3e-04

Table S23.  Gene #9: 'CIC MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 33 82 46
CIC MUTATED 6 16 18 1
CIC WILD-TYPE 49 17 64 45

Figure S23.  Get High-res Image Gene #9: 'CIC MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0021

Table S24.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 49 76
NOTCH1 MUTATED 1 2 16
NOTCH1 WILD-TYPE 89 47 60

Figure S24.  Get High-res Image Gene #10: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.03e-06 (Fisher's exact test), Q value = 0.0013

Table S25.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 32 59 23
NOTCH1 MUTATED 2 1 15 0
NOTCH1 WILD-TYPE 96 31 44 23

Figure S25.  Get High-res Image Gene #10: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000143 (Chi-square test), Q value = 0.03

Table S26.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 40 36 71 10
NOTCH1 MUTATED 1 1 10 7 0
NOTCH1 WILD-TYPE 57 39 26 64 10

Figure S26.  Get High-res Image Gene #10: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.65e-05 (Fisher's exact test), Q value = 0.0055

Table S27.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 112 70
NOTCH1 MUTATED 9 2 8
NOTCH1 WILD-TYPE 24 110 62

Figure S27.  Get High-res Image Gene #10: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000941 (Fisher's exact test), Q value = 0.19

Table S28.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 95 113
NOTCH1 MUTATED 0 16 3
NOTCH1 WILD-TYPE 8 79 110

Figure S28.  Get High-res Image Gene #10: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 6.19e-09 (Fisher's exact test), Q value = 1.3e-06

Table S29.  Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 49 76
PTEN MUTATED 0 12 0
PTEN WILD-TYPE 90 37 76

Figure S29.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.63e-10 (Fisher's exact test), Q value = 1e-07

Table S30.  Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 32 59 23
PTEN MUTATED 0 11 0 0
PTEN WILD-TYPE 98 21 59 23

Figure S30.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.43e-11 (Chi-square test), Q value = 5.4e-09

Table S31.  Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 40 36 71 10
PTEN MUTATED 0 12 0 0 0
PTEN WILD-TYPE 58 28 36 71 10

Figure S31.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.06

Table S32.  Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 33 82 46
PTEN MUTATED 8 0 0 4
PTEN WILD-TYPE 47 33 82 42

Figure S32.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.94e-06 (Fisher's exact test), Q value = 0.00041

Table S33.  Gene #12: 'NF1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 32 59 23
NF1 MUTATED 1 8 0 3
NF1 WILD-TYPE 97 24 59 20

Figure S33.  Get High-res Image Gene #12: 'NF1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00101 (Chi-square test), Q value = 0.2

Table S34.  Gene #12: 'NF1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 40 36 71 10
NF1 MUTATED 0 9 2 4 1
NF1 WILD-TYPE 58 31 34 67 9

Figure S34.  Get High-res Image Gene #12: 'NF1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 7.43e-06 (Fisher's exact test), Q value = 0.0016

Table S35.  Gene #20: 'EGFR MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 49 76
EGFR MUTATED 1 9 0
EGFR WILD-TYPE 89 40 76

Figure S35.  Get High-res Image Gene #20: 'EGFR MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.01e-07 (Fisher's exact test), Q value = 6.4e-05

Table S36.  Gene #20: 'EGFR MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 32 59 23
EGFR MUTATED 0 8 0 2
EGFR WILD-TYPE 98 24 59 21

Figure S36.  Get High-res Image Gene #20: 'EGFR MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000501 (Chi-square test), Q value = 0.1

Table S37.  Gene #20: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 40 36 71 10
EGFR MUTATED 0 7 0 3 0
EGFR WILD-TYPE 58 33 36 68 10

Figure S37.  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 = 217

  • Number of significantly mutated genes = 37

  • 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.

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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