Correlation between gene mutation status and molecular subtypes

Brain Lower Grade Glioma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C12805T8

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)	1.8e-32 (3.78e-30)	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)	1.97e-21 (4.1e-19)	1.76e-12 (3.58e-10)	5.04e-07 (9.73e-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)	2.65e-18 (5.47e-16)	4.68e-10 (9.23e-08)	5.81e-12 (1.17e-09)	2.72e-07 (5.31e-05)	0.15 (1.00)
FUBP1	19 (11%)	151	0.0862 (1.00)	0.0919 (1.00)	3.3e-08 (6.47e-06)	3.75e-06 (0.000717)	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)	2.28e-26 (4.77e-24)	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)	0.000265 (0.0485)	0.0188 (1.00)	0.00063 (0.112)	0.00675 (1.00)	0.043 (1.00)
PTEN	8 (5%)	162			5.51e-06 (0.00105)	7.94e-06 (0.00149)	3.34e-07 (6.47e-05)	0.0227 (1.00)	0.00448 (0.78)	0.235 (1.00)
EGFR	8 (5%)	162			5.51e-06 (0.00105)	8.8e-07 (0.000169)	0.00121 (0.213)	0.382 (1.00)	0.0688 (1.00)	1 (1.00)
PIK3CA	15 (9%)	155			0.000481 (0.0866)	0.000482 (0.0866)	0.0362 (1.00)	0.215 (1.00)	0.573 (1.00)	0.305 (1.00)
NF1	11 (6%)	159			0.0489 (1.00)	0.000388 (0.0703)	0.00123 (0.216)	0.306 (1.00)	0.29 (1.00)	0.763 (1.00)
IDH2	6 (4%)	164			0.24 (1.00)	0.281 (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)	0.378 (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)	0.838 (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)	0.106 (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)	0.68 (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)	0.0547 (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)	0.201 (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)	0.504 (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)	0.247 (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)	1 (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)	0.232 (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)	0.231 (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)	0.821 (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)	0.436 (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)	0.0445 (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)	1 (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)	0.362 (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)	0.838 (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)	0.0703 (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)	0.062 (1.00)	0.369 (1.00)	0.388 (1.00)	1 (1.00)	1 (1.00)
C3ORF35	3 (2%)	167			1 (1.00)	0.845 (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)	0.0988 (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)	1 (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 = 2.28e-26 (Fisher's exact test), Q value = 4.8e-24

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	30	18	48
IDH1 MUTATED	68	0	16	44
IDH1 WILD-TYPE	2	30	2	4

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 = 1.8e-32 (Fisher's exact test), Q value = 3.8e-30

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	30	18	48
TP53 MUTATED	69	6	11	2
TP53 WILD-TYPE	1	24	7	46

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 = 0.000482 (Fisher's exact test), Q value = 0.087

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	30	18	48
PIK3CA MUTATED	0	4	2	9
PIK3CA WILD-TYPE	70	26	16	39

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 = 1.97e-21 (Fisher's exact test), Q value = 4.1e-19

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	30	18	48
ATRX MUTATED	58	4	9	2
ATRX WILD-TYPE	12	26	9	46

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 = 2.65e-18 (Fisher's exact test), Q value = 5.5e-16

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	30	18	48
CIC MUTATED	0	1	2	31
CIC WILD-TYPE	70	29	16	17

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 = 3.75e-06 (Fisher's exact test), Q value = 0.00072

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	30	18	48
FUBP1 MUTATED	0	1	2	13
FUBP1 WILD-TYPE	70	29	16	35

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 = 0.000265 (Fisher's exact test), Q value = 0.048

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	30	18	48
NOTCH1 MUTATED	2	1	0	12
NOTCH1 WILD-TYPE	68	29	18	36

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 = 7.94e-06 (Fisher's exact test), Q value = 0.0015

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	30	18	48
PTEN MUTATED	0	7	0	0
PTEN WILD-TYPE	70	23	18	48

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 = 6.5e-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 = 0.000388 (Fisher's exact test), Q value = 0.07

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	30	18	48
NF1 MUTATED	1	6	0	0
NF1 WILD-TYPE	69	24	18	48

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 = 8.8e-07 (Fisher's exact test), Q value = 0.00017

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	70	30	18	48
EGFR MUTATED	0	8	0	0
EGFR WILD-TYPE	70	22	18	48

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.

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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