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 41 genes and 8 molecular subtypes across 323 patients, 20 significant findings detected with P value < 0.05 and Q value < 0.25.

BRAF mutation correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
HRAS mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
NRAS mutation correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 41 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, 20 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	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	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
BRAF	183 (57%)	140	0.00338 (0.874)	1.08e-37 (2.98e-35)	3.6e-07 (9.6e-05)	3.71e-13 (1.01e-10)	4.03e-46 (1.12e-43)	1.56e-39 (4.29e-37)	1.34e-43 (3.7e-41)	2.16e-45 (6e-43)
HRAS	12 (4%)	311	0.000107 (0.0279)	2.48e-06 (0.000658)	0.000224 (0.0582)	0.00349 (0.9)	1.37e-05 (0.00361)	6.79e-06 (0.00179)	1.49e-06 (0.000397)	3.38e-07 (9.06e-05)
NRAS	26 (8%)	297	0.0098 (1.00)	6.63e-14 (1.82e-11)	1 (1.00)	0.000209 (0.0545)	4.7e-11 (1.26e-08)	4.03e-11 (1.09e-08)	1.64e-12 (4.43e-10)	1.76e-13 (4.8e-11)
EMG1	6 (2%)	317	0.557 (1.00)	0.862 (1.00)	0.267 (1.00)	0.147 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.166 (1.00)
PTTG1IP	4 (1%)	319	1 (1.00)	1 (1.00)			0.242 (1.00)	0.252 (1.00)	0.471 (1.00)	0.0379 (1.00)
RPTN	8 (2%)	315	1 (1.00)	0.688 (1.00)	0.327 (1.00)	0.485 (1.00)	0.0249 (1.00)	0.415 (1.00)	0.741 (1.00)	1 (1.00)
EIF1AX	5 (2%)	318	1 (1.00)	0.028 (1.00)	0.444 (1.00)	0.115 (1.00)	0.0621 (1.00)	0.0109 (1.00)	0.0616 (1.00)	0.234 (1.00)
CCDC15	5 (2%)	318	1 (1.00)	0.17 (1.00)	1 (1.00)	0.778 (1.00)	0.132 (1.00)	0.136 (1.00)	0.628 (1.00)	0.527 (1.00)
ZNF845	6 (2%)	317	0.557 (1.00)	0.615 (1.00)	0.64 (1.00)	0.35 (1.00)	0.943 (1.00)	0.166 (1.00)	0.38 (1.00)	0.327 (1.00)
ZNF878	4 (1%)	319	1 (1.00)	0.456 (1.00)			0.0454 (1.00)	0.833 (1.00)	0.694 (1.00)	1 (1.00)
TG	16 (5%)	307	1 (1.00)	0.0255 (1.00)	0.286 (1.00)	0.273 (1.00)	0.406 (1.00)	0.293 (1.00)	0.0426 (1.00)	0.0244 (1.00)
PRB2	6 (2%)	317	1 (1.00)	0.615 (1.00)	0.0809 (1.00)	1 (1.00)	0.474 (1.00)	0.723 (1.00)	0.525 (1.00)	0.594 (1.00)
R3HDM2	4 (1%)	319	0.0134 (1.00)	0.0495 (1.00)			0.0699 (1.00)	0.0388 (1.00)	0.0202 (1.00)	0.00788 (1.00)
IL32	3 (1%)	320	1 (1.00)	0.39 (1.00)			1 (1.00)	0.78 (1.00)	0.206 (1.00)	0.641 (1.00)
TMCO2	3 (1%)	320	1 (1.00)	0.545 (1.00)	0.778 (1.00)	0.185 (1.00)	0.492 (1.00)	0.303 (1.00)	0.413 (1.00)	0.779 (1.00)
PPTC7	3 (1%)	320	0.079 (1.00)	0.0835 (1.00)			0.172 (1.00)	0.0916 (1.00)	0.306 (1.00)	0.395 (1.00)
MUC7	5 (2%)	318	1 (1.00)	0.274 (1.00)	0.684 (1.00)	0.778 (1.00)	0.805 (1.00)	0.848 (1.00)	0.453 (1.00)	0.632 (1.00)
LYPD3	3 (1%)	320	0.55 (1.00)	0.545 (1.00)			0.492 (1.00)	0.303 (1.00)	0.65 (1.00)	0.779 (1.00)
TMEM90B	3 (1%)	320	0.136 (1.00)	1 (1.00)			1 (1.00)	0.78 (1.00)	1 (1.00)	1 (1.00)
ZNF799	5 (2%)	318	0.473 (1.00)	0.834 (1.00)	0.51 (1.00)	1 (1.00)	0.592 (1.00)	0.848 (1.00)	0.453 (1.00)	1 (1.00)
PPM1D	5 (2%)	318	1 (1.00)	1 (1.00)	0.778 (1.00)	0.35 (1.00)	0.693 (1.00)	0.848 (1.00)	0.868 (1.00)	0.281 (1.00)
MAP3K3	4 (1%)	319	0.381 (1.00)	0.276 (1.00)	0.393 (1.00)	0.147 (1.00)	0.274 (1.00)	0.184 (1.00)	0.471 (1.00)	0.391 (1.00)
TROAP	3 (1%)	320	1 (1.00)	0.39 (1.00)	0.778 (1.00)	1 (1.00)	0.746 (1.00)	1 (1.00)	0.306 (1.00)	0.395 (1.00)
SYNPO2L	3 (1%)	320	0.55 (1.00)	1 (1.00)			1 (1.00)	0.78 (1.00)	1 (1.00)	1 (1.00)
ATAD2	4 (1%)	319	1 (1.00)	0.612 (1.00)			0.808 (1.00)	1 (1.00)	0.694 (1.00)	1 (1.00)
KRAS	3 (1%)	320	1 (1.00)	0.0835 (1.00)			0.172 (1.00)	0.0916 (1.00)	0.0642 (1.00)	0.0267 (1.00)
SLC5A11	3 (1%)	320	0.55 (1.00)	0.716 (1.00)					0.306 (1.00)	0.395 (1.00)
PRG4	4 (1%)	319	0.232 (1.00)	0.362 (1.00)			0.0128 (1.00)	0.142 (1.00)	0.471 (1.00)	0.558 (1.00)
SCUBE2	3 (1%)	320		0.246 (1.00)			0.314 (1.00)	0.303 (1.00)	0.65 (1.00)	0.511 (1.00)
ZNF479	3 (1%)	320	1 (1.00)	0.39 (1.00)			1 (1.00)	0.78 (1.00)	1 (1.00)	1 (1.00)
SREBF2	3 (1%)	320	1 (1.00)	0.39 (1.00)			0.568 (1.00)	1 (1.00)	0.413 (1.00)	0.779 (1.00)
SLC26A11	3 (1%)	320	0.079 (1.00)	1 (1.00)			0.368 (1.00)	0.78 (1.00)	0.777 (1.00)	0.292 (1.00)
TSC22D1	3 (1%)	320	1 (1.00)	1 (1.00)			0.746 (1.00)	1 (1.00)	1 (1.00)	0.641 (1.00)
ANKRD30A	5 (2%)	318	1 (1.00)	0.43 (1.00)			0.749 (1.00)	0.507 (1.00)	0.742 (1.00)	0.865 (1.00)
FAM155A	4 (1%)	319	0.144 (1.00)	0.612 (1.00)	0.778 (1.00)	1 (1.00)			0.332 (1.00)	0.832 (1.00)
SLA	3 (1%)	320	0.55 (1.00)	0.0835 (1.00)	0.29 (1.00)	0.35 (1.00)	0.172 (1.00)	0.0916 (1.00)	0.0642 (1.00)	0.0267 (1.00)
ZFHX3	10 (3%)	313	0.178 (1.00)	0.737 (1.00)	0.483 (1.00)	0.533 (1.00)	0.794 (1.00)	0.437 (1.00)	0.615 (1.00)	0.727 (1.00)
ARMCX3	3 (1%)	320	0.55 (1.00)	0.39 (1.00)			0.646 (1.00)	0.213 (1.00)	0.528 (1.00)	0.199 (1.00)
SLC25A45	3 (1%)	320	0.136 (1.00)	1 (1.00)					0.206 (1.00)	0.641 (1.00)
COL5A3	6 (2%)	317	0.758 (1.00)	1 (1.00)	0.778 (1.00)	1 (1.00)	0.044 (1.00)	0.753 (1.00)	0.876 (1.00)	0.519 (1.00)
CDC27	3 (1%)	320	1 (1.00)	1 (1.00)			0.368 (1.00)	0.0446 (1.00)	0.777 (1.00)	1 (1.00)

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.08e-37 (Fisher's exact test), Q value = 3e-35

Table S1. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	44	174
BRAF MUTATED	10	25	148
BRAF WILD-TYPE	95	19	26

Figure S1. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 3.6e-07 (Fisher's exact test), Q value = 9.6e-05

Table S2. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	75	79
BRAF MUTATED	19	57	42
BRAF WILD-TYPE	44	18	37

Figure S2. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 3.71e-13 (Fisher's exact test), Q value = 1e-10

Table S3. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	95	95
BRAF MUTATED	11	78	29
BRAF WILD-TYPE	16	17	66

Figure S3. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.03e-46 (Fisher's exact test), Q value = 1.1e-43

Table S4. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	102	36	70	95
BRAF MUTATED	6	20	57	90
BRAF WILD-TYPE	96	16	13	5

Figure S4. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.56e-39 (Fisher's exact test), Q value = 4.3e-37

Table S5. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	136	57
BRAF MUTATED	11	120	42
BRAF WILD-TYPE	99	16	15

Figure S5. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.34e-43 (Fisher's exact test), Q value = 3.7e-41

Table S6. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	116	101
BRAF MUTATED	5	101	76
BRAF WILD-TYPE	100	15	25

Figure S6. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.16e-45 (Fisher's exact test), Q value = 6e-43

Table S7. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	122	103
BRAF MUTATED	1	97	84
BRAF WILD-TYPE	96	25	19

Figure S7. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.028

Table S8. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	244	48
HRAS MUTATED	0	4	8
HRAS WILD-TYPE	26	240	40

Figure S8. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.48e-06 (Fisher's exact test), Q value = 0.00066

Table S9. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	44	174
HRAS MUTATED	12	0	0
HRAS WILD-TYPE	93	44	174

Figure S9. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.058

Table S10. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	75	79
HRAS MUTATED	9	2	0
HRAS WILD-TYPE	54	73	79

Figure S10. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.0036

Table S11. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	102	36	70	95
HRAS MUTATED	12	0	0	0
HRAS WILD-TYPE	90	36	70	95

Figure S11. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.79e-06 (Fisher's exact test), Q value = 0.0018

Table S12. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	136	57
HRAS MUTATED	12	0	0
HRAS WILD-TYPE	98	136	57

Figure S12. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 4e-04

Table S13. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	116	101
HRAS MUTATED	12	0	0
HRAS WILD-TYPE	93	116	101

Figure S13. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.38e-07 (Fisher's exact test), Q value = 9.1e-05

Table S14. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	122	103
HRAS MUTATED	12	0	0
HRAS WILD-TYPE	85	122	103

Figure S14. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.63e-14 (Fisher's exact test), Q value = 1.8e-11

Table S15. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	44	174
NRAS MUTATED	26	0	0
NRAS WILD-TYPE	79	44	174

Figure S15. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.000209 (Fisher's exact test), Q value = 0.054

Table S16. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	95	95
NRAS MUTATED	5	0	9
NRAS WILD-TYPE	22	95	86

Figure S16. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.7e-11 (Fisher's exact test), Q value = 1.3e-08

Table S17. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	102	36	70	95
NRAS MUTATED	23	0	0	0
NRAS WILD-TYPE	79	36	70	95

Figure S17. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.03e-11 (Fisher's exact test), Q value = 1.1e-08

Table S18. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	136	57
NRAS MUTATED	23	0	0
NRAS WILD-TYPE	87	136	57

Figure S18. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.64e-12 (Fisher's exact test), Q value = 4.4e-10

Table S19. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	116	101
NRAS MUTATED	25	0	1
NRAS WILD-TYPE	80	116	100

Figure S19. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.76e-13 (Fisher's exact test), Q value = 4.8e-11

Table S20. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	122	103
NRAS MUTATED	25	1	0
NRAS WILD-TYPE	72	121	103

Figure S20. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Mutation data file = THCA-TP.mutsig.cluster.txt
Molecular subtypes file = THCA-TP.transferedmergedcluster.txt
Number of patients = 323
Number of significantly mutated genes = 41
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

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] 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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