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 3 genes and 9 molecular subtypes across 83 patients, 15 significant findings detected with P value < 0.05 and Q value < 0.25.

  • NRAS mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • BRAF mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • HRAS mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 3 genes and 9 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 15 significant findings detected.

Clinical
Features 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Chi-square 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 Fisher's exact test
BRAF 13 (16%) 70 1.67e-06
(4.17e-05) 		1
(1.00) 		0.698
(1.00) 		1.35e-07
(3.52e-06) 		4.3e-09
(1.16e-07) 		1.46e-05
(0.00032) 		1.73e-06
(4.17e-05) 		0.000763
(0.013) 		7.85e-05
(0.00157)
NRAS 19 (23%) 64 9.1e-06
(0.000209) 		0.585
(1.00) 		0.247
(1.00) 		0.00155
(0.0248) 		2.5e-05
(0.000525) 		0.498
(1.00) 		0.00909
(0.132) 		0.142
(1.00) 		1
(1.00)
HRAS 8 (10%) 75 0.000225
(0.00404) 		0.0645
(0.71) 		0.399
(1.00) 		0.0109
(0.142) 		0.000139
(0.00264) 		0.0296
(0.356) 		1
(1.00) 		0.131
(1.00) 		0.00878
(0.132)
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9.1e-06 (Chi-square test), Q value = 0.00021

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 7 18 16 1 10 8 17 6
NRAS MUTATED 3 0 8 1 1 0 1 5
NRAS WILD-TYPE 4 18 8 0 9 8 16 1

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

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.025

Table S2.  Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 17 22 23
NRAS MUTATED 11 2 1 5
NRAS WILD-TYPE 10 15 21 18

Figure S2.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.5e-05 (Fisher's exact test), Q value = 0.00053

Table S3.  Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 18 25 25
NRAS MUTATED 0 0 6 13
NRAS WILD-TYPE 15 18 19 12

Figure S3.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00909 (Fisher's exact test), Q value = 0.13

Table S4.  Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 17 66
NRAS MUTATED 0 19
NRAS WILD-TYPE 17 47

Figure S4.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.67e-06 (Chi-square test), Q value = 4.2e-05

Table S5.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #1: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 7 18 16 1 10 8 17 6
BRAF MUTATED 0 1 1 0 0 0 11 0
BRAF WILD-TYPE 7 17 15 1 10 8 6 6

Figure S5.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #1: 'METHLYATION_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.35e-07 (Fisher's exact test), Q value = 3.5e-06

Table S6.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 17 22 23
BRAF MUTATED 1 0 12 0
BRAF WILD-TYPE 20 17 10 23

Figure S6.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.3e-09 (Fisher's exact test), Q value = 1.2e-07

Table S7.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 18 25 25
BRAF MUTATED 0 12 0 1
BRAF WILD-TYPE 15 6 25 24

Figure S7.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.00032

Table S8.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 25 20
BRAF MUTATED 0 4 9
BRAF WILD-TYPE 38 21 11

Figure S8.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MIRSEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.73e-06 (Fisher's exact test), Q value = 4.2e-05

Table S9.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 17 66
BRAF MUTATED 10 3
BRAF WILD-TYPE 7 63

Figure S9.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000763 (Fisher's exact test), Q value = 0.013

Table S10.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 18 25 17
BRAF MUTATED 1 3 1 8
BRAF WILD-TYPE 22 15 24 9

Figure S10.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_MATURE_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.85e-05 (Fisher's exact test), Q value = 0.0016

Table S11.  Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 48 35
BRAF MUTATED 1 12
BRAF WILD-TYPE 47 23

Figure S11.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000225 (Chi-square test), Q value = 0.004

Table S12.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 7 18 16 1 10 8 17 6
HRAS MUTATED 1 0 7 0 0 0 0 0
HRAS WILD-TYPE 6 18 9 1 10 8 17 6

Figure S12.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.14

Table S13.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 17 22 23
HRAS MUTATED 6 0 1 1
HRAS WILD-TYPE 15 17 21 22

Figure S13.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000139 (Fisher's exact test), Q value = 0.0026

Table S14.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 18 25 25
HRAS MUTATED 0 0 0 8
HRAS WILD-TYPE 15 18 25 17

Figure S14.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00878 (Fisher's exact test), Q value = 0.13

Table S15.  Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 48 35
HRAS MUTATED 1 7
HRAS WILD-TYPE 47 28

Figure S15.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = THCA-HistologicalType_Follicular.mutsig.cluster.txt

  • Molecular subtypes file = THCA-HistologicalType_Follicular.transferedmergedcluster.txt

  • Number of patients = 83

  • Number of significantly mutated genes = 3

  • Number of Molecular subtypes = 9

  • Exclude genes that fewer than K tumors have mutations, K = 3

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[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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