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 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.

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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