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 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.

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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