Correlation between gene mutation status and molecular subtypes
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.

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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