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 6 genes and 8 molecular subtypes across 66 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

No gene mutations related to molecuar subtypes.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 6 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, no significant finding detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	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	Chi-square test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test
MUC2	8 (12%)	58	1 (1.00)	0.276 (1.00)	0.745 (1.00)	0.71 (1.00)	0.572 (1.00)	0.586 (1.00)	0.49 (1.00)	0.481 (1.00)
MUC6	21 (32%)	45	0.178 (1.00)	0.634 (1.00)	0.253 (1.00)	0.174 (1.00)	0.306 (1.00)	0.252 (1.00)	0.205 (1.00)	0.267 (1.00)
TP53	22 (33%)	44	0.615 (1.00)	0.0856 (1.00)	0.0665 (1.00)	0.0593 (1.00)	0.655 (1.00)	0.706 (1.00)	0.76 (1.00)	0.86 (1.00)
PTEN	6 (9%)	60	0.0988 (1.00)	0.321 (1.00)	0.351 (1.00)	0.13 (1.00)	0.354 (1.00)	0.585 (1.00)	0.00617 (0.296)	0.0812 (1.00)
PRSS3	7 (11%)	59	0.386 (1.00)	0.668 (1.00)	0.0182 (0.855)	0.252 (1.00)	0.0815 (1.00)	0.581 (1.00)	0.61 (1.00)	0.159 (1.00)
HLA-C	7 (11%)	59	0.49 (1.00)	0.574 (1.00)	0.714 (1.00)	0.569 (1.00)	0.158 (1.00)	0.581 (1.00)	0.401 (1.00)	0.561 (1.00)

'MUC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	47	14
MUC2 MUTATED	0	6	2
MUC2 WILD-TYPE	5	41	12

'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
MUC2 MUTATED	2	6	0
MUC2 WILD-TYPE	16	29	13

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
MUC2 MUTATED	3	3	2	0
MUC2 WILD-TYPE	16	19	13	10

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.71 (Chi-square test), Q value = 1

Table S4. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
MUC2 MUTATED	1	0	2	1	4
MUC2 WILD-TYPE	9	10	15	5	19

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	24	22
MUC2 MUTATED	1	4	3
MUC2 WILD-TYPE	19	20	19

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	9	57
MUC2 MUTATED	0	8
MUC2 WILD-TYPE	9	49

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.49 (Chi-square test), Q value = 1

Table S7. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	16	16	10	14
MUC2 MUTATED	1	1	4	1	1
MUC2 WILD-TYPE	9	15	12	9	13

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	8	25	21
MUC2 MUTATED	0	1	3	4
MUC2 WILD-TYPE	12	7	22	17

'MUC6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 1

Table S9. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	47	14
MUC6 MUTATED	2	12	7
MUC6 WILD-TYPE	3	35	7

'MUC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S10. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
MUC6 MUTATED	7	11	3
MUC6 WILD-TYPE	11	24	10

'MUC6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.253 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
MUC6 MUTATED	6	10	4	1
MUC6 WILD-TYPE	13	12	11	9

'MUC6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.174 (Chi-square test), Q value = 1

Table S12. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
MUC6 MUTATED	2	1	9	2	7
MUC6 WILD-TYPE	8	9	8	4	16

'MUC6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	24	22
MUC6 MUTATED	4	10	7
MUC6 WILD-TYPE	16	14	15

'MUC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	9	57
MUC6 MUTATED	1	20
MUC6 WILD-TYPE	8	37

'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.205 (Chi-square test), Q value = 1

Table S15. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	16	16	10	14
MUC6 MUTATED	6	5	3	4	3
MUC6 WILD-TYPE	4	11	13	6	11

'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.267 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	8	25	21
MUC6 MUTATED	1	3	9	8
MUC6 WILD-TYPE	11	5	16	13

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 1

Table S17. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	47	14
TP53 MUTATED	2	14	6
TP53 WILD-TYPE	3	33	8

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0856 (Fisher's exact test), Q value = 1

Table S18. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
TP53 MUTATED	3	16	3
TP53 WILD-TYPE	15	19	10

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0665 (Fisher's exact test), Q value = 1

Table S19. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
TP53 MUTATED	6	6	9	1
TP53 WILD-TYPE	13	16	6	9

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0593 (Chi-square test), Q value = 1

Table S20. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
TP53 MUTATED	7	1	6	2	6
TP53 WILD-TYPE	3	9	11	4	17

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S21. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	24	22
TP53 MUTATED	5	9	8
TP53 WILD-TYPE	15	15	14

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.706 (Fisher's exact test), Q value = 1

Table S22. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	9	57
TP53 MUTATED	2	20
TP53 WILD-TYPE	7	37

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.76 (Chi-square test), Q value = 1

Table S23. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	16	16	10	14
TP53 MUTATED	5	5	4	3	5
TP53 WILD-TYPE	5	11	12	7	9

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	8	25	21
TP53 MUTATED	3	3	8	8
TP53 WILD-TYPE	9	5	17	13

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0988 (Fisher's exact test), Q value = 1

Table S25. Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	47	14
PTEN MUTATED	2	3	1
PTEN WILD-TYPE	3	44	13

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 1

Table S26. Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
PTEN MUTATED	3	3	0
PTEN WILD-TYPE	15	32	13

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.351 (Fisher's exact test), Q value = 1

Table S27. Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
PTEN MUTATED	2	1	3	0
PTEN WILD-TYPE	17	21	12	10

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.13 (Chi-square test), Q value = 1

Table S28. Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
PTEN MUTATED	3	0	1	0	2
PTEN WILD-TYPE	7	10	16	6	21

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 1

Table S29. Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	24	22
PTEN MUTATED	1	4	1
PTEN WILD-TYPE	19	20	21

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S30. Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	9	57
PTEN MUTATED	0	6
PTEN WILD-TYPE	9	51

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00617 (Chi-square test), Q value = 0.3

Table S31. Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	16	16	10	14
PTEN MUTATED	4	0	1	0	1
PTEN WILD-TYPE	6	16	15	10	13

Figure S1. Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0812 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	8	25	21
PTEN MUTATED	0	0	1	5
PTEN WILD-TYPE	12	8	24	16

'PRSS3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S33. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	47	14
PRSS3 MUTATED	0	4	3
PRSS3 WILD-TYPE	5	43	11

'PRSS3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S34. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
PRSS3 MUTATED	1	4	2
PRSS3 WILD-TYPE	17	31	11

'PRSS3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.86

Table S35. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
PRSS3 MUTATED	0	6	1	0
PRSS3 WILD-TYPE	19	16	14	10

Figure S2. Get High-res Image Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PRSS3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.252 (Chi-square test), Q value = 1

Table S36. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
PRSS3 MUTATED	1	0	4	1	1
PRSS3 WILD-TYPE	9	10	13	5	22

'PRSS3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0815 (Fisher's exact test), Q value = 1

Table S37. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	24	22
PRSS3 MUTATED	3	0	4
PRSS3 WILD-TYPE	17	24	18

'PRSS3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S38. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	9	57
PRSS3 MUTATED	0	7
PRSS3 WILD-TYPE	9	50

'PRSS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.61 (Chi-square test), Q value = 1

Table S39. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	16	16	10	14
PRSS3 MUTATED	0	2	1	2	2
PRSS3 WILD-TYPE	10	14	15	8	12

'PRSS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 1

Table S40. Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	8	25	21
PRSS3 MUTATED	2	1	4	0
PRSS3 WILD-TYPE	10	7	21	21

'HLA-C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S41. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	47	14
HLA-C MUTATED	1	4	2
HLA-C WILD-TYPE	4	43	12

'HLA-C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S42. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	18	35	13
HLA-C MUTATED	3	3	1
HLA-C WILD-TYPE	15	32	12

'HLA-C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S43. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
HLA-C MUTATED	3	3	1	0
HLA-C WILD-TYPE	16	19	14	10

'HLA-C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.569 (Chi-square test), Q value = 1

Table S44. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	10	17	6	23
HLA-C MUTATED	1	0	3	0	3
HLA-C WILD-TYPE	9	10	14	6	20

'HLA-C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 1

Table S45. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	24	22
HLA-C MUTATED	0	3	4
HLA-C WILD-TYPE	20	21	18

'HLA-C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S46. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	9	57
HLA-C MUTATED	0	7
HLA-C WILD-TYPE	9	50

'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.401 (Chi-square test), Q value = 1

Table S47. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	10	16	16	10	14
HLA-C MUTATED	1	1	3	2	0
HLA-C WILD-TYPE	9	15	13	8	14

'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S48. Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	8	25	21
HLA-C MUTATED	0	1	4	2
HLA-C WILD-TYPE	12	7	21	19

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = KICH-TP.transferedmergedcluster.txt
Number of patients = 66
Number of significantly mutated genes = 6
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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